Spectrally selective fluorescence imaging of Chlorobaculum tepidum reaction centers conjugated to chelator-modified silver nanowires.

PubMed

Kowalska, Dorota; Szalkowski, Marcin; Ashraf, Khuram; Grzelak, Justyna; Lokstein, Heiko; Niedziolka-Jonsson, Joanna; Cogdell, Richard; Mackowski, Sebastian

2018-03-01

A polyhistidine tag (His-tag) present on Chlorobaculum tepidum reaction centers (RCs) was used to immobilize photosynthetic complexes on a silver nanowire (AgNW) modified with nickel-chelating nitrilo-triacetic acid (Ni-NTA). The optical properties of conjugated nanostructures were studied using wide-field and confocal fluorescence microscopy. Plasmonic enhancement of RCs conjugated to AgNWs was observed as their fluorescence intensity dependence on the excitation wavelength does not follow the excitation spectrum of RC complexes in solution. The strongest effect of plasmonic interactions on the emission intensity of RCs coincides with the absorption spectrum of AgNWs and is observed for excitation into the carotenoid absorption. From the absence of fluorescence decay shortening, we attribute the emission enhancement to increase of absorption in RC complexes.

Waste Information Management System-2012 - 12114

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

Upadhyay, H.; Quintero, W.; Shoffner, P.

2012-07-01

The Waste Information Management System (WIMS) -2012 was updated to support the Department of Energy (DOE) accelerated cleanup program. The schedule compression required close coordination and a comprehensive review and prioritization of the barriers that impeded treatment and disposition of the waste streams at each site. Many issues related to waste treatment and disposal were potential critical path issues under the accelerated schedule. In order to facilitate accelerated cleanup initiatives, waste managers at DOE field sites and at DOE Headquarters in Washington, D.C., needed timely waste forecast and transportation information regarding the volumes and types of radioactive waste that wouldmore » be generated by DOE sites over the next 40 years. Each local DOE site historically collected, organized, and displayed waste forecast information in separate and unique systems. In order for interested parties to understand and view the complete DOE complex-wide picture, the radioactive waste and shipment information of each DOE site needed to be entered into a common application. The WIMS application was therefore created to serve as a common application to improve stakeholder comprehension and improve DOE radioactive waste treatment and disposal planning and scheduling. WIMS allows identification of total forecasted waste volumes, material classes, disposition sites, choke points, technological or regulatory barriers to treatment and disposal, along with forecasted waste transportation information by rail, truck and inter-modal shipments. The Applied Research Center (ARC) at Florida International University (FIU) in Miami, Florida, developed and deployed the web-based forecast and transportation system and is responsible for updating the radioactive waste forecast and transportation data on a regular basis to ensure the long-term viability and value of this system. WIMS continues to successfully accomplish the goals and objectives set forth by DOE for this project. It has replaced the historic process of each DOE site gathering, organizing, and reporting their waste forecast information utilizing different databases and display technologies. In addition, WIMS meets DOE's objective to have the complex-wide waste forecast and transportation information available to all stakeholders and the public in one easy-to-navigate system. The enhancements to WIMS made since its initial deployment include the addition of new DOE sites and facilities, an updated waste and transportation information, and the ability to easily display and print customized waste forecast, the disposition maps, GIS maps and transportation information. The system also allows users to customize and generate reports over the web. These reports can be exported to various formats, such as Adobe{sup R} PDF, Microsoft Excel{sup R}, and Microsoft Word{sup R} and downloaded to the user's computer. Future enhancements will include database/application migration to the next level. A new data import interface will be developed to integrate 2012-13 forecast waste streams. In addition, the application is updated on a continuous basis based on DOE feedback. (authors)« less

A New Low Complexity Angle of Arrival Algorithm for 1D and 2D Direction Estimation in MIMO Smart Antenna Systems

PubMed Central

Al-Sadoon, Mohammed A. G.; Zuid, Abdulkareim; Jones, Stephen M. R.; Noras, James M.

2017-01-01

This paper proposes a new low complexity angle of arrival (AOA) method for signal direction estimation in multi-element smart wireless communication systems. The new method estimates the AOAs of the received signals directly from the received signals with significantly reduced complexity since it does not need to construct the correlation matrix, invert the matrix or apply eigen-decomposition, which are computationally expensive. A mathematical model of the proposed method is illustrated and then verified using extensive computer simulations. Both linear and circular sensors arrays are studied using various numerical examples. The method is systematically compared with other common and recently introduced AOA methods over a wide range of scenarios. The simulated results show that the new method has several advantages in terms of reduced complexity and improved accuracy under the assumptions of correlated signals and limited numbers of snapshots. PMID:29140313

A New Low Complexity Angle of Arrival Algorithm for 1D and 2D Direction Estimation in MIMO Smart Antenna Systems.

PubMed

Al-Sadoon, Mohammed A G; Ali, Nazar T; Dama, Yousf; Zuid, Abdulkareim; Jones, Stephen M R; Abd-Alhameed, Raed A; Noras, James M

2017-11-15

This paper proposes a new low complexity angle of arrival (AOA) method for signal direction estimation in multi-element smart wireless communication systems. The new method estimates the AOAs of the received signals directly from the received signals with significantly reduced complexity since it does not need to construct the correlation matrix, invert the matrix or apply eigen-decomposition, which are computationally expensive. A mathematical model of the proposed method is illustrated and then verified using extensive computer simulations. Both linear and circular sensors arrays are studied using various numerical examples. The method is systematically compared with other common and recently introduced AOA methods over a wide range of scenarios. The simulated results show that the new method has several advantages in terms of reduced complexity and improved accuracy under the assumptions of correlated signals and limited numbers of snapshots.

Atrial flutter with 1:1 conduction in undiagnosed Wolff-Parkinson-White syndrome.

PubMed

Nelson, Jessie G; Zhu, Dennis W

2014-05-01

Atrial flutter with 1:1 atrioventricular conduction via an accessory pathway is an uncommon presentation of Wolff-Parkinson-White syndrome not previously reported in the emergency medicine literature. Wolff-Parkinson-White syndrome, a form of ventricular preexcitation sometimes initially seen and diagnosed in the emergency department (ED), can present with varied tachydysrhythmias for which certain treatments are contraindicated. For instance, atrial fibrillation with preexcited conduction needs specific consideration of medication choice to avoid potential degeneration into ventricular fibrillation. We describe an adult female presenting with a very rapid, regular wide complex tachycardia successfully cardioverted in the ED followed by a normal electrocardiogram (ECG). Electrophysiology study confirmed atrial flutter with 1:1 conduction and revealed an accessory pathway consistent with Wolff-Parkinson-White syndrome, despite lack of ECG findings of preexcitation during sinus rhythm. Why should an emergency physician be aware of this? Ventricular tachycardia must be the first consideration in patients with regular wide complex tachycardia. However, clinicians should consider atrial flutter with 1:1 conduction related to an accessory pathway when treating patients with the triad of very rapid rate (>250 beats/min), wide QRS complex, and regular rhythm, especially when considering pharmacologic treatment. Emergency physicians also should be aware of electrocardiographically concealed accessory pathways, and that lack of delta waves does not rule out preexcitation syndromes such as Wolff-Parkinson-White syndrome. Copyright © 2014 Elsevier Inc. All rights reserved.

Actin filament curvature biases branching direction

NASA Astrophysics Data System (ADS)

Wang, Evan; Risca, Viviana; Chaudhuri, Ovijit; Chia, Jia-Jun; Geissler, Phillip; Fletcher, Daniel

2012-02-01

Actin filaments are key components of the cellular machinery, vital for a wide range of processes ranging from cell motility to endocytosis. Actin filaments can branch, and essential in this process is a protein complex known as the Arp2/3 complex, which nucleate new ``daughter'' filaments from pre-existing ``mother'' filaments by attaching itself to the mother filament. Though much progress has been made in understanding the Arp2/3-actin junction, some very interesting questions remain. In particular, F-actin is a dynamic polymer that undergoes a wide range of fluctuations. Prior studies of the Arp2/3-actin junction provides a very static notion of Arp2/3 binding. The question we ask is how differently does the Arp2/3 complex interact with a straight filament compared to a bent filament? In this study, we used Monte Carlo simulations of a surface-tethered worm-like chain to explore possible mechanisms underlying the experimental observation that there exists preferential branch formation by the Arp2/3 complex on the convex face of a curved filament. We show that a fluctuation gating model in which Arp2/3 binding to the actin filament is dependent upon a rare high-local-curvature shape fluctuation of the filament is consistent with the experimental data.

Analysis of time-of-flight spectra

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

Gibson, E.M.; Foxon, C.T.; Zhang, J.

1990-07-01

A simplified method of data analysis for time of flight measurements of the velocity of molecular beams sources is described. This method does not require the complex data fitting previously used in such studies. The method is applied to the study of Pb molecular beams from a true Knudsen source and has been used to show that a VG Quadrupoles SXP300H mass spectrometer, when fitted with an open cross-beam ionizer, acts as an ideal density detector over a wide range of operating conditions.

Waste information management system: a web-based system for DOE waste forecasting

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

Geisler, T.J.; Shoffner, P.A.; Upadhyay, U.

2007-07-01

The implementation of the Department of Energy (DOE) mandated accelerated cleanup program has created significant potential technical impediments that must be overcome. The schedule compression will require close coordination and a comprehensive review and prioritization of the barriers that may impede treatment and disposition of the waste streams at each site. Many issues related to site waste treatment and disposal have now become potential critical path issues under the accelerated schedules. In order to facilitate accelerated cleanup initiatives, waste managers at DOE field sites and at DOE headquarters in Washington, D.C., need timely waste forecast information regarding the volumes andmore » types of waste that will be generated by DOE sites over the next 25 years. Each local DOE site has historically collected, organized, and displayed site waste forecast information in separate and unique systems. However, waste information from all sites needs a common application to allow interested parties to understand and view the complete complex-wide picture. A common application would allow identification of total waste volumes, material classes, disposition sites, choke points, and technological or regulatory barriers to treatment and disposal. The Applied Research Center (ARC) at Florida International University (FIU) in Miami, Florida, has completed the development of this web-based forecast system. (authors)« less

Waste Information Management System: One Year After Web Deployment

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

Shoffner, P.A.; Geisler, T.J.; Upadhyay, H.

2008-07-01

The implementation of the Department of Energy (DOE) mandated accelerated cleanup program created significant potential technical impediments. The schedule compression required close coordination and a comprehensive review and prioritization of the barriers that impeded treatment and disposition of the waste streams at each site. Many issues related to site waste treatment and disposal were potential critical path issues under the accelerated schedules. In order to facilitate accelerated cleanup initiatives, waste managers at DOE field sites and at DOE Headquarters in Washington, D.C., needed timely waste forecast information regarding the volumes and types of waste that would be generated by DOEmore » sites over the next 30 years. Each local DOE site has historically collected, organized, and displayed site waste forecast information in separate and unique systems. However, waste information from all sites needed a common application to allow interested parties to understand and view the complete complex-wide picture. A common application allows identification of total waste volumes, material classes, disposition sites, choke points, and technological or regulatory barriers to treatment and disposal. The Applied Research Center (ARC) at Florida International University (FIU) in Miami, Florida, has completed the deployment of this fully operational, web-based forecast system. New functional modules and annual waste forecast data updates have been added to ensure the long-term viability and value of this system. In conclusion: WIMS continues to successfully accomplish the goals and objectives set forth by DOE for this project. WIMS has replaced the historic process of each DOE site gathering, organizing, and reporting their waste forecast information utilizing different database and display technologies. In addition, WIMS meets DOE's objective to have the complex-wide waste forecast information available to all stakeholders and the public in one easy-to-navigate system. The enhancements to WIMS made over the year since its web deployment include the addition of new DOE sites, an updated data set, and the ability to easily print the forecast data tables, the disposition maps, and the GIS maps. Future enhancements will include a high-level waste summary, a display of waste forecast by mode of transportation, and a user help module. The waste summary display module will provide a high-level summary view of the waste forecast data based on the selection of sites, facilities, material types, and forecast years. The waste summary report module will allow users to build custom filtered reports in a variety of formats, such as MS Excel, MS Word, and PDF. The user help module will provide a step-by-step explanation of various modules, using screen shots and general tutorials. The help module will also provide instructions for printing and margin/layout settings to assist users in using their local printers to print maps and reports. (authors)« less

Modeling the IR spectra of aqueous metal carboxylate complexes: correlation between bonding geometry and stretching mode wavenumber shifts.

PubMed

Sutton, Catherine C R; da Silva, Gabriel; Franks, George V

2015-04-27

A widely used principle is that shifts in the wavenumber of carboxylate stretching modes upon bonding with a metal center can be used to infer if the geometry of the bonding is monodentate or bidentate. We have tested this principle with ab initio modeling for aqueous metal carboxylate complexes and have shown that it does indeed hold. Modeling of the bonding of acetate and formate in aqueous solution to a range of cations was used to predict the infrared spectra of the metal-carboxylate complexes, and the wavenumbers of the symmetric and antisymmetric vibrational modes are reported. Furthermore, we have shown that these shifts in wavenumber occur primarily due to how bonding with the metal changes the carboxylate C-O bond lengths and O-C-O angle. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Virality Prediction and Community Structure in Social Networks

NASA Astrophysics Data System (ADS)

Weng, Lilian; Menczer, Filippo; Ahn, Yong-Yeol

2013-08-01

How does network structure affect diffusion? Recent studies suggest that the answer depends on the type of contagion. Complex contagions, unlike infectious diseases (simple contagions), are affected by social reinforcement and homophily. Hence, the spread within highly clustered communities is enhanced, while diffusion across communities is hampered. A common hypothesis is that memes and behaviors are complex contagions. We show that, while most memes indeed spread like complex contagions, a few viral memes spread across many communities, like diseases. We demonstrate that the future popularity of a meme can be predicted by quantifying its early spreading pattern in terms of community concentration. The more communities a meme permeates, the more viral it is. We present a practical method to translate data about community structure into predictive knowledge about what information will spread widely. This connection contributes to our understanding in computational social science, social media analytics, and marketing applications.

Virality Prediction and Community Structure in Social Networks

PubMed Central

Weng, Lilian; Menczer, Filippo; Ahn, Yong-Yeol

2013-01-01

How does network structure affect diffusion? Recent studies suggest that the answer depends on the type of contagion. Complex contagions, unlike infectious diseases (simple contagions), are affected by social reinforcement and homophily. Hence, the spread within highly clustered communities is enhanced, while diffusion across communities is hampered. A common hypothesis is that memes and behaviors are complex contagions. We show that, while most memes indeed spread like complex contagions, a few viral memes spread across many communities, like diseases. We demonstrate that the future popularity of a meme can be predicted by quantifying its early spreading pattern in terms of community concentration. The more communities a meme permeates, the more viral it is. We present a practical method to translate data about community structure into predictive knowledge about what information will spread widely. This connection contributes to our understanding in computational social science, social media analytics, and marketing applications. PMID:23982106

Virality prediction and community structure in social networks.

PubMed

Weng, Lilian; Menczer, Filippo; Ahn, Yong-Yeol

2013-01-01

How does network structure affect diffusion? Recent studies suggest that the answer depends on the type of contagion. Complex contagions, unlike infectious diseases (simple contagions), are affected by social reinforcement and homophily. Hence, the spread within highly clustered communities is enhanced, while diffusion across communities is hampered. A common hypothesis is that memes and behaviors are complex contagions. We show that, while most memes indeed spread like complex contagions, a few viral memes spread across many communities, like diseases. We demonstrate that the future popularity of a meme can be predicted by quantifying its early spreading pattern in terms of community concentration. The more communities a meme permeates, the more viral it is. We present a practical method to translate data about community structure into predictive knowledge about what information will spread widely. This connection contributes to our understanding in computational social science, social media analytics, and marketing applications.

Detecting UV-lesions in the genome: The modular CRL4 ubiquitin ligase does it best!

PubMed

Scrima, Andrea; Fischer, Eric S; Lingaraju, Gondichatnahalli M; Böhm, Kerstin; Cavadini, Simone; Thomä, Nicolas H

2011-09-16

The DDB1-DDB2-CUL4-RBX1 complex serves as the primary detection device for UV-induced lesions in the genome. It simultaneously functions as a CUL4 type E3 ubiquitin ligase. We review the current understanding of this dual function ubiquitin ligase and damage detection complex. The DDB2 damage binding module is merely one of a large family of possible DDB1-CUL4 associated factors (DCAF), most of which are substrate receptors for other DDB1-CUL4 complexes. DDB2 and the Cockayne-syndrome A protein (CSA) function in nucleotide excision repair, whereas the remaining receptors operate in a wide range of other biological pathways. We will examine the modular architecture of DDB1-CUL4 in complex with DDB2, CSA and CDT2 focusing on shared architectural, targeting and regulatory principles. Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Behavioural ecology: transient sexual mimicry leads to fertilization.

PubMed

Hanlon, Roger T; Naud, Marié-Jose; Shaw, Paul W; Havenhand, Jon N

2005-01-20

Sexual mimicry among animals is widespread, but does it impart a fertilization advantage in the widely accepted 'sneak-guard' model of sperm competition? Here we describe field results in which a dramatic facultative switch in sexual phenotype by sneaker-male cuttlefish leads to immediate fertilization success, even in the presence of the consort male. These results are surprising, given the high rate at which females reject copulation attempts by males, the strong mate-guarding behaviour of consort males, and the high level of sperm competition in this complex mating system.

Monitoring of protease catalyzed reactions by quantitative MALDI MS using metal labeling.

PubMed

Gregorius, Barbara; Jakoby, Thomas; Schaumlöffel, Dirk; Tholey, Andreas

2013-05-21

Quantitative mass spectrometry is a powerful tool for the determination of enzyme activities as it does not require labeled substrates and simultaneously allows for the identification of reaction products. However, major restrictions are the limited number of samples which can be measured in parallel due to the need for isotope labeled internal standards. Here we describe the use of metal labeling of peptides for the setup of multiplexed enzyme activity assays. After proteolytic reaction, using the protease trypsin, remaining substrates and peptide products formed in the reaction were labeled with metal chelators complexing rare earth metal ions. Labeled peptides were quantified with high accuracy and over a wide dynamic range (at least 2 orders of magnitude) using MALDI MS in case of simple peptide mixtures or by LC-MALDI MS for complex substrate mixtures and used for the monitoring of time-dependent product formation and substrate consumption. Due to multiplexing capabilities and accuracy, the presented approach will be useful for the determination of enzyme activities with a wide range of biochemical and biotechnological applications.

12 CFR 502.27 - How does OTS determine the risk/complexity component for a savings and loan holding company?

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false How does OTS determine the risk/complexity...-Calculation of Assessments § 502.27 How does OTS determine the risk/complexity component for a savings and loan holding company? (a) OTS computes the risk/complexity component for responsible savings and loan...

Web-Based Geographic Information System Tool for Accessing Hanford Site Environmental Data

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

Triplett, Mark B.; Seiple, Timothy E.; Watson, David J.

Data volume, complexity, and access issues pose severe challenges for analysts, regulators and stakeholders attempting to efficiently use legacy data to support decision making at the U.S. Department of Energy’s (DOE) Hanford Site. DOE has partnered with the Pacific Northwest National Laboratory (PNNL) on the PHOENIX (PNNL-Hanford Online Environmental Information System) project, which seeks to address data access, transparency, and integration challenges at Hanford to provide effective decision support. PHOENIX is a family of spatially-enabled web applications providing quick access to decades of valuable scientific data and insight through intuitive query, visualization, and analysis tools. PHOENIX realizes broad, public accessibilitymore » by relying only on ubiquitous web-browsers, eliminating the need for specialized software. It accommodates a wide range of users with intuitive user interfaces that require little or no training to quickly obtain and visualize data. Currently, PHOENIX is actively hosting three applications focused on groundwater monitoring, groundwater clean-up performance reporting, and in-tank monitoring. PHOENIX-based applications are being used to streamline investigative and analytical processes at Hanford, saving time and money. But more importantly, by integrating previously isolated datasets and developing relevant visualization and analysis tools, PHOENIX applications are enabling DOE to discover new correlations hidden in legacy data, allowing them to more effectively address complex issues at Hanford.« less

EXTENDING THE USEFUL LIFE OF OLDER MASS SPECTROMETERS

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

Johnson, S.; Cordaro, J.; Holland, M.

2010-06-17

Thermal ionization and gas mass spectrometers are widely used across the Department of Energy (DOE) Complex and contractor laboratories. These instruments support critical missions, where high reliability and low measurement uncertainty are essential. A growing number of these mass spectrometers are significantly older than their original design life. The reality is that manufacturers have declared many of the instrument models obsolete, with direct replacement parts and service no longer available. Some of these obsolete models do not have a next generation, commercially available replacement. Today's budget conscious economy demands for the use of creative funds management. Therefore, the ability tomore » refurbish (or upgrade) these valuable analytical tools and extending their useful life is a cost effective option. The Savannah River Site (SRS) has the proven expertise to breathe new life into older mass spectrometers, at a significant cost savings compared to the purchase and installation of new instruments. A twenty-seven year old Finnigan MAT-261{trademark} Thermal Ionization Mass Spectrometer (TIMS), located at the SRS F/H Area Production Support Laboratory, has been successfully refurbished. Engineers from the Savannah River National Laboratory (SRNL) fabricated and installed the new electronics. These engineers also provide continued instrument maintenance services. With electronic component drawings being DOE Property, other DOE Complex laboratories have the option to extend the life of their aged Mass Spectrometers.« less

Crystal structure of plant light-harvesting complex shows the active, energy-transmitting state

PubMed Central

Barros, Tiago; Royant, Antoine; Standfuss, Jörg; Dreuw, Andreas; Kühlbrandt, Werner

2009-01-01

Plants dissipate excess excitation energy as heat by non-photochemical quenching (NPQ). NPQ has been thought to resemble in vitro aggregation quenching of the major antenna complex, light harvesting complex of photosystem II (LHC-II). Both processes are widely believed to involve a conformational change that creates a quenching centre of two neighbouring pigments within the complex. Using recombinant LHC-II lacking the pigments implicated in quenching, we show that they have no particular role. Single crystals of LHC-II emit strong, orientation-dependent fluorescence with an emission maximum at 680 nm. The average lifetime of the main 680 nm crystal emission at 100 K is 1.31 ns, but only 0.39 ns for LHC-II aggregates under identical conditions. The strong emission and comparatively long fluorescence lifetimes of single LHC-II crystals indicate that the complex is unquenched, and that therefore the crystal structure shows the active, energy-transmitting state of LHC-II. We conclude that quenching of excitation energy in the light-harvesting antenna is due to the molecular interaction with external pigments in vitro or other pigment–protein complexes such as PsbS in vivo, and does not require a conformational change within the complex. PMID:19131972

36 CFR 1202.8 - How does NARA handle records that are in Government-wide Privacy Act systems?

Code of Federal Regulations, 2011 CFR

2011-07-01

... that are in Government-wide Privacy Act systems? 1202.8 Section 1202.8 Parks, Forests, and Public... ACT OF 1974 General Information About the Privacy Act § 1202.8 How does NARA handle records that are in Government-wide Privacy Act systems? Records in the custody of NARA in a Government-wide Privacy...

36 CFR 1202.8 - How does NARA handle records that are in Government-wide Privacy Act systems?

Code of Federal Regulations, 2010 CFR

2010-07-01

... that are in Government-wide Privacy Act systems? 1202.8 Section 1202.8 Parks, Forests, and Public... ACT OF 1974 General Information About the Privacy Act § 1202.8 How does NARA handle records that are in Government-wide Privacy Act systems? Records in the custody of NARA in a Government-wide Privacy...

Multislice does it all—calculating the performance of nanofocusing X-ray optics

DOE PAGES

Li, Kenan; Wojcik, Michael; Jacobsen, Chris

2017-01-23

Here, we describe an approach to calculating the optical performance of a wide range of nanofocusing X-ray optics using multislice scalar wave propagation with a complex X-ray refractive index. This approach produces results indistinguishable from methods such as coupled wave theory, and it allows one to reproduce other X-ray optical phenomena such as grazing incidence reflectivity where the direction of energy flow is changed significantly. Just as finite element analysis methods allow engineers to compute the thermal and mechanical responses of arbitrary structures too complex to model by analytical approaches, multislice propagation can be used to understand the properties ofmore » the real-world optics of finite extent and with local imperfections, allowing one to better understand the limits to nanoscale X-ray imaging.« less

Content of system design descriptions

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

NONE

A System Design Description (SDD) describes the requirements and features of a system. This standard provides guidance on the expected technical content of SDDs. The need for such a standard was recognized during efforts to develop SDDs for safety systems at DOE Hazard Category 2 nonreactor nuclear facilities. Existing guidance related to the corresponding documents in other industries is generally not suitable to meet the needs of DOE nuclear facilities. Across the DOE complex, different contractors have guidance documents, but they vary widely from site to site. While such guidance documents are valuable, no single guidance document has all themore » attributes that DOE considers important, including a reasonable degree of consistency or standardization. This standard is a consolidation of the best of the existing guidance. This standard has been developed with a technical content and level of detail intended to be most applicable to safety systems at DOE Hazard Category 2 nonreactor nuclear facilities. Notwithstanding that primary intent, this standard is recommended for other systems at such facilities, especially those that are important to achieving the programmatic mission of the facility. In addition, application of this standard should be considered for systems at other facilities, including non-nuclear facilities, on the basis that SDDs may be beneficial and cost-effective.« less

Wide-range stiffness gradient PVA/HA hydrogel to investigate stem cell differentiation behavior.

PubMed

Oh, Se Heang; An, Dan Bi; Kim, Tae Ho; Lee, Jin Ho

2016-04-15

Although stiffness-controllable substrates have been developed to investigate the effect of stiffness on cell behavior and function, the use of separate substrates with different degrees of stiffness, substrates with a narrow range stiffness gradient, toxicity of residues, different surface composition, complex fabrication procedures/devices, and low cell adhesion are still considered as hurdles of conventional techniques. In this study, a cylindrical polyvinyl alcohol (PVA)/hyaluronic acid (HA) hydrogel with a wide-range stiffness gradient (between ∼20kPa and ∼200kPa) and cell adhesiveness was prepared by a liquid nitrogen (LN2)-contacting gradual freezing-thawing method that does not use any additives or specific devices to produce the stiffness gradient hydrogel. From an in vitro cell culture using the stiffness gradient PVA/HA hydrogel, it was observed that human bone marrow mesenchymal stem cells have favorable stiffness ranges for induction of differentiation into specific cell types (∼20kPa for nerve cell, ∼40kPa for muscle cell, ∼80kPa for chondrocyte, and ∼190kPa for osteoblast). The PVA/HA hydrogel with a wide range of stiffness spectrum can be a useful tool for basic studies related with the stem cell differentiation, cell reprogramming, cell migration, and tissue regeneration in terms of substrate stiffness. It is postulated that the stiffness of the extracellular matrix influences cell behavior. To prove this concept, various techniques to prepare substrates with a stiffness gradient have been developed. However, the narrow ranges of stiffness gradient and complex fabrication procedures/devices are still remained as limitations. Herein, we develop a substrate (hydrogel) with a wide-range stiffness gradient using a gradual freezing-thawing method which does not need specific devices to produce a stiffness gradient hydrogel. From cell culture experiments using the hydrogel, it is observed that human bone marrow mesenchymal stem cells have favorable stiffness ranges for induction of differentiation into specific cell types (∼20kPa for nerve, ∼40kPa for muscle, ∼80kPa for cartilage, and ∼190kPa for bone in our hydrogel system). Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

1996 DOE technical standards program workshop: Proceedings

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

NONE

1996-07-01

The workshop theme is `The Strategic Standardization Initiative - A Technology Exchange and Global Competitiveness Challenge for DOE.` The workshop goal is to inform the DOE technical standards community of strategic standardization activities taking place in the Department, other Government agencies, standards developing organizations, and industry. Individuals working on technical standards will be challenged to improve cooperation and communications with the involved organizations in response to the initiative. Workshop sessions include presentations by representatives from various Government agencies that focus on coordination among and participation of Government personnel in the voluntary standards process; reports by standards organizations, industry, and DOEmore » representatives on current technology exchange programs; and how the road ahead appears for `information superhighway` standardization. Another session highlights successful standardization case studies selected from several sites across the DOE complex. The workshop concludes with a panel discussion on the goals and objectives of the DOE Technical Standards Program as envisioned by senior DOE management. The annual workshop on technical standards has proven to be an effective medium for communicating information related to standards throughout the DOE community. Technical standards are used to transfer technology and standardize work processes to produce consistent, acceptable results. They provide a practical solution to the Department`s challenge to protect the environment and the health and safety of the public and workers during all facility operations. Through standards, the technologies of industries and governments worldwide are available to DOE. The DOE Technical Standards Program, a Department-wide effort that crosscuts all organizations and disciplines, links the Department to those technologies.« less

U.S. DOE Progress Towards Developing Low-Cost, High Performance, Durable Polymer Electrolyte Membranes for Fuel Cell Applications.

PubMed

Houchins, Cassidy; Kleen, Greg J; Spendelow, Jacob S; Kopasz, John; Peterson, David; Garland, Nancy L; Ho, Donna Lee; Marcinkoski, Jason; Martin, Kathi Epping; Tyler, Reginald; Papageorgopoulos, Dimitrios C

2012-12-18

Low cost, durable, and selective membranes with high ionic conductivity are a priority need for wide-spread adoption of polymer electrolyte membrane fuel cells (PEMFCs) and direct methanol fuel cells (DMFCs). Electrolyte membranes are a major cost component of PEMFC stacks at low production volumes. PEMFC membranes also impose limitations on fuel cell system operating conditions that add system complexity and cost. Reactant gas and fuel permeation through the membrane leads to decreased fuel cell performance, loss of efficiency, and reduced durability in both PEMFCs and DMFCs. To address these challenges, the U.S. Department of Energy (DOE) Fuel Cell Technologies Program, in the Office of Energy Efficiency and Renewable Energy, supports research and development aimed at improving ion exchange membranes for fuel cells. For PEMFCs, efforts are primarily focused on developing materials for higher temperature operation (up to 120 °C) in automotive applications. For DMFCs, efforts are focused on developing membranes with reduced methanol permeability. In this paper, the recently revised DOE membrane targets, strategies, and highlights of DOE-funded projects to develop new, inexpensive membranes that have good performance in hot and dry conditions (PEMFC) and that reduce methanol crossover (DMFC) will be discussed.

Characterization of Early Partial Seizure Onset: Frequency, Complexity and Entropy

PubMed Central

Jouny, Christophe C.; Bergey, Gregory K.

2011-01-01

Objective A clear classification of partial seizures onset features is not yet established. Complexity and entropy have been very widely used to describe dynamical systems, but a systematic evaluation of these measures to characterize partial seizures has never been performed. Methods Eighteen different measures including power in frequency bands up to 300Hz, Gabor atom density (GAD), Higuchi fractal dimension (HFD), Lempel-Ziv complexity, Shannon entropy, sample entropy, and permutation entropy, were selected to test sensitivity to partial seizure onset. Intracranial recordings from forty-five patients with mesial temporal, neocortical temporal and neocortical extratemporal seizure foci were included (331 partial seizures). Results GAD, Lempel-Ziv complexity, HFD, high frequency activity, and sample entropy were the most reliable measures to assess early seizure onset. Conclusions Increases in complexity and occurrence of high-frequency components appear to be commonly associated with early stages of partial seizure evolution from all regions. The type of measure (frequency-based, complexity or entropy) does not predict the efficiency of the method to detect seizure onset. Significance Differences between measures such as GAD and HFD highlight the multimodal nature of partial seizure onsets. Improved methods for early seizure detection may be achieved from a better understanding of these underlying dynamics. PMID:21872526

A Wearable Textile 2D Touchpad Sensor Based on Screen-Printing Technology.

PubMed

Ferri, Josue; Lidón-Roger, Jose Vicente; Moreno, Jorge; Martinez, Gabriel; Garcia-Breijo, Eduardo

2017-12-20

Among many of the designs used in the detection of 2D gestures for portable technology, the touchpad is one of the most complex and with more functions to implement. Its development has undergone a great push due to its use in displays, but it is not widely used with other technologies. Its application on textiles could allow a wide range of applications in the field of medicine, sports, etc. Obtaining a flexible, robust touchpad with good response and low cost is one of the objectives of this work. A textile touchpad based on a diamond pattern design using screen printing technology has been developed. This technology is widely used in the textile industry and therefore does not require heavy investments. The developed prototypes were analyzed using a particular controller for projected capacitive technologies (pro-cap), which is the most used in gesture detection. Two different designs were used to obtain the best configuration, obtaining a good result in both cases.

A Wearable Textile 2D Touchpad Sensor Based on Screen-Printing Technology

PubMed Central

Ferri, Josue; Moreno, Jorge; Martinez, Gabriel

2017-01-01

Among many of the designs used in the detection of 2D gestures for portable technology, the touchpad is one of the most complex and with more functions to implement. Its development has undergone a great push due to its use in displays, but it is not widely used with other technologies. Its application on textiles could allow a wide range of applications in the field of medicine, sports, etc. Obtaining a flexible, robust touchpad with good response and low cost is one of the objectives of this work. A textile touchpad based on a diamond pattern design using screen printing technology has been developed. This technology is widely used in the textile industry and therefore does not require heavy investments. The developed prototypes were analyzed using a particular controller for projected capacitive technologies (pro-cap), which is the most used in gesture detection. Two different designs were used to obtain the best configuration, obtaining a good result in both cases. PMID:29261167

Does linear separability really matter? Complex visual search is explained by simple search

PubMed Central

Vighneshvel, T.; Arun, S. P.

2013-01-01

Visual search in real life involves complex displays with a target among multiple types of distracters, but in the laboratory, it is often tested using simple displays with identical distracters. Can complex search be understood in terms of simple searches? This link may not be straightforward if complex search has emergent properties. One such property is linear separability, whereby search is hard when a target cannot be separated from its distracters using a single linear boundary. However, evidence in favor of linear separability is based on testing stimulus configurations in an external parametric space that need not be related to their true perceptual representation. We therefore set out to assess whether linear separability influences complex search at all. Our null hypothesis was that complex search performance depends only on classical factors such as target-distracter similarity and distracter homogeneity, which we measured using simple searches. Across three experiments involving a variety of artificial and natural objects, differences between linearly separable and nonseparable searches were explained using target-distracter similarity and distracter heterogeneity. Further, simple searches accurately predicted complex search regardless of linear separability (r = 0.91). Our results show that complex search is explained by simple search, refuting the widely held belief that linear separability influences visual search. PMID:24029822

X-ray atlas of rheumatic diseases

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

Dihlmann, W.

1986-01-01

This atlas comprises instructive X-rays of the various inflammatory rheumatic joint diseases in all stages at the extremities and the spinal column. In addition, the complex pattern of the wide range of arthroses, also known as degenerative rheumatic disease is included. Besides the instructive pointers to X-ray diagnosis, the book is also a guide to differential diagnosis. Hence, this book is actually an X-ray atlas of joint diseases in general. Selected Contents: Introduction: What Does ''Rheumatism'' Actually Mean./Radiographic Methodology in Rheumatic Diseases of the Locomotor System/The Mosaic of Arthritis/Adult Rheumatoid Arthritis/Seronegative Spondylarthritis/Classic Collagen Diseases/Enthesiopathies/Gout-Pseudogout

Abstract Linguistic Structure Correlates with Temporal Activity during Naturalistic Comprehension

PubMed Central

Brennan, Jonathan R.; Stabler, Edward P.; Van Wagenen, Sarah E.; Luh, Wen-Ming; Hale, John T.

2016-01-01

Neurolinguistic accounts of sentence comprehension identify a network of relevant brain regions, but do not detail the information flowing through them. We investigate syntactic information. Does brain activity implicate a computation over hierarchical grammars or does it simply reflect linear order, as in a Markov chain? To address this question, we quantify the cognitive states implied by alternative parsing models. We compare processing-complexity predictions from these states against fMRI timecourses from regions that have been implicated in sentence comprehension. We find that hierarchical grammars independently predict timecourses from left anterior and posterior temporal lobe. Markov models are predictive in these regions and across a broader network that includes the inferior frontal gyrus. These results suggest that while linear effects are wide-spread across the language network, certain areas in the left temporal lobe deal with abstract, hierarchical syntactic representations. PMID:27208858

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer

PubMed Central

Li, Jinyu; Rossetti, Giulia; Dreyer, Jens; Raugei, Simone; Ippoliti, Emiliano; Lüscher, Bernhard; Carloni, Paolo

2014-01-01

Protein electrospray ionization (ESI) mass spectrometry (MS)-based techniques are widely used to provide insight into structural proteomics under the assumption that non-covalent protein complexes being transferred into the gas phase preserve basically the same intermolecular interactions as in solution. Here we investigate the applicability of this assumption by extending our previous structural prediction protocol for single proteins in ESI-MS to protein complexes. We apply our protocol to the human insulin dimer (hIns2) as a test case. Our calculations reproduce the main charge and the collision cross section (CCS) measured in ESI-MS experiments. Molecular dynamics simulations for 0.075 ms show that the complex maximizes intermolecular non-bonded interactions relative to the structure in water, without affecting the cross section. The overall gas-phase structure of hIns2 does exhibit differences with the one in aqueous solution, not inferable from a comparison with calculated CCS. Hence, care should be exerted when interpreting ESI-MS proteomics data based solely on NMR and/or X-ray structural information. PMID:25210764

Finding equilibrium in the spatiotemporal chaos of the complex Ginzburg-Landau equation

NASA Astrophysics Data System (ADS)

Ballard, Christopher C.; Esty, C. Clark; Egolf, David A.

2016-11-01

Equilibrium statistical mechanics allows the prediction of collective behaviors of large numbers of interacting objects from just a few system-wide properties; however, a similar theory does not exist for far-from-equilibrium systems exhibiting complex spatial and temporal behavior. We propose a method for predicting behaviors in a broad class of such systems and apply these ideas to an archetypal example, the spatiotemporal chaotic 1D complex Ginzburg-Landau equation in the defect chaos regime. Building on the ideas of Ruelle and of Cross and Hohenberg that a spatiotemporal chaotic system can be considered a collection of weakly interacting dynamical units of a characteristic size, the chaotic length scale, we identify underlying, mesoscale, chaotic units and effective interaction potentials between them. We find that the resulting equilibrium Takahashi model accurately predicts distributions of particle numbers. These results suggest the intriguing possibility that a class of far-from-equilibrium systems may be well described at coarse-grained scales by the well-established theory of equilibrium statistical mechanics.

Finding equilibrium in the spatiotemporal chaos of the complex Ginzburg-Landau equation.

PubMed

Ballard, Christopher C; Esty, C Clark; Egolf, David A

2016-11-01

Equilibrium statistical mechanics allows the prediction of collective behaviors of large numbers of interacting objects from just a few system-wide properties; however, a similar theory does not exist for far-from-equilibrium systems exhibiting complex spatial and temporal behavior. We propose a method for predicting behaviors in a broad class of such systems and apply these ideas to an archetypal example, the spatiotemporal chaotic 1D complex Ginzburg-Landau equation in the defect chaos regime. Building on the ideas of Ruelle and of Cross and Hohenberg that a spatiotemporal chaotic system can be considered a collection of weakly interacting dynamical units of a characteristic size, the chaotic length scale, we identify underlying, mesoscale, chaotic units and effective interaction potentials between them. We find that the resulting equilibrium Takahashi model accurately predicts distributions of particle numbers. These results suggest the intriguing possibility that a class of far-from-equilibrium systems may be well described at coarse-grained scales by the well-established theory of equilibrium statistical mechanics.

Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes

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

Lambert, B.; Jacques, V.; Shivanyuk, A.

The lanthanide and Th{sup 4+} complexes with calix[4]arene ligands substituted either on the narrow or at the wide rim by four coordinating groups behave totally differently as shown by an NMR investigation of the dia- and paramagnetic complexes. Solutions of complexes were prepared by reacting anhydrous metal perchlorate salts with the ligands in dry acetonitrile (CAUTION). Relaxation time T{sub 1} titrations of acetonitrile solutions of Gd{sup 3+} by calixarenes indicate that ligands substituted on the narrow rim form stable 1:1 complexes whether they feature four amide groups (1) or four phosphine oxide functions. In contrast, a ligand substituted by fourmore » (carbamoylmethyl)-diphenylphosphine oxide moieties on the wide rim (3) and its derivatives form polymeric species even at a 1:1 ligand/metal concentration ratio. Nuclear magnetic relaxation dispersion (NMRD) curves (relaxation rates 1/T{sub 1} vs magnetic field strength) of Gd{sup 3+}, Gd{sup 3+}{center_dot}1 and Gd{sup 3+}{center_dot}3 perchlorates in acetonitrile are analyzed by an extended version of the Solomon-Bloembergen-Morgan equations. A comparison of the calculated rotational correlation times {tau}{sub r} shows that ligand 3 forms oligomeric Gd{sup 3+} species. The chelates of ligand 1 are axially symmetric (C{sub 4} symmetry), and the paramagnetic shifts induced by the Yb{sup 3+} ion are accounted for quantitatively. The addition of water or of nitrate ions does not modify the geometry of the complex. The metal chelates of 3 and its derivatives adopt a C{sub 2} symmetry, and the paramagnetic shifts are interpreted on a semiquantitative basis only. Water and NO{sub 3}{sup {minus}} ions completely labilize the complexes of the heavy lanthanides. The very high selectivity of ligand 3 through the lanthanide series stems from a complex interplay of factors.« less

Report of Official Foreign Travel to Germany, May 16-June 1, 2001

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

J. D. Mason

2001-06-18

The Department of Energy (DOE) and associated agencies have moved rapidly toward electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Like most government agencies, DOE has expressed a preference for openly developed standards over proprietary designs promoted as ''standards'' by vendors. In particular, there is a preference for standards developed by organizations such as the International Organization for Standardizationmore » (ISO) and the American National Standards Institute (ANSI) that use open, public processes to develop their standards. Among the most widely adopted international standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), to which DOE long ago made a commitment. Besides the official commitment, which has resulted in several specialized projects, DOE makes heavy use of coding derived from SGML: Most documents on the WWW are coded in HTML (Hypertext Markup Language), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Adobe, IBM, Microsoft, Netscape, Oracle, and Sun, is promoting XML (eXtensible Markup Language), a class of SGML applications, for the future of the WWW and the basis for EC. In support of DOE's use of these standards, I have served since 1985 as Chairman of the international committee responsible for SGML and related standards, ISO/IEC JTC1/SC34 (SC34) and its predecessor organizations. During my May 2001 trip, I chaired the spring 2001 meeting of SC34 in Berlin, Germany. I also attended XML Europe 2001, a major conference on the use of SGML and XML sponsored by the Graphic Communications Association (GCA), and chaired a meeting of the International SGML/XML Users' Group (ISUG). In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there have been several past and present SGML- and XML-based projects at the Y-12 National Security Complex (Y-12). Our local project team has done SGML and XML development at Y-12 and Oak Ridge National Laboratory (ORNL) since the late 1980s. SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at Y-12 and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). The ''Ferret'' system for automated classification analysis uses XML to structure its knowledge base. The Ferret team also provides XML consulting to OSTI and DOE Headquarters, particularly the National Nuclear Security Administration (NNSA). Supporting standards development allows DOE and Y-12 the opportunity both to provide input into the process and to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML, XML, and related topics.« less

Effective electromagnetic properties of microheterogeneous materials with surface phenomena

NASA Astrophysics Data System (ADS)

Levin, Valery; Markov, Mikhail; Mousatov, Aleksandr; Kazatchenko, Elena; Pervago, Evgeny

2017-10-01

In this paper, we present an approach to calculate the complex dielectric permittivity of a micro-heterogeneous medium composed of non-conductive solid inclusions embedded into the conductive liquid continuous host. To take into account the surface effects, we approximate the inclusion by a layered ellipsoid consisting of a dielectric core and an infinitesimally thin outer shell corresponding to an electrical double layer (EDL). To predict the effective complex dielectric permittivity of materials with a high concentration of inclusions, we have modified the Effective Field Method (EFM) for the layered ellipsoidal particles with complex electrical properties. We present the results of complex permittivity calculations for the composites with randomly and parallel oriented ellipsoidal inclusions. To analyze the influence of surface polarization, we have accomplished modeling in a wide frequency range for different existing physic-chemical models of double electrical layer. The results obtained show that the tensor of effective complex permittivity of a micro-heterogeneous medium with surface effects has complicate dependences on the component electrical properties, spatial material texture, and the inclusion shape (ellipsoid aspect ratio) and size. The dispersion of dielectric permittivity corresponds to the frequency dependence for individual inclusion of given size, and does not depend on the inclusion concentration.

Proceedings from the Workshop on Phytoremediation of Inorganic Contaminants

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

J. T. Brown; G. Matthern; A. Glenn

The Metals and Radionuclides Product Line of the US Department of Energy (DOE) Subsurface Contaminants Focus Area (SCFA) is responsible for the development of technologies and systems that reduce the risk and cost of remediation of radionuclide and hazardous metal contamination in soils and groundwater. The rapid and efficient remediation of these sites and the areas surrounding them represents a technological challenge. Phytoremediation, the use of living plants to cleanup contaminated soils, sediments, surface water and groundwater, is an emerging technology that may be applicable to the problem. The use of phytoremediation to cleanup organic contamination is widely accepted andmore » is being implemented at numerous sites. This workshop was held to initiate a discussion in the scientific community about whether phytoremediation is applicable to inorganic contaminants, such as metals and radionuclides, across the DOE complex. The Workshop on Phytoremediation of Inorganic Contaminants was held at Argonne National Laboratory from November 30 through December 2, 1999. The purpose of the workshop was to provide SCFA and the DOE Environmental Restoration Program with an understanding of the status of phytoremediation as a potential remediation technology for DOE sites. The workshop was expected to identify data gaps, technologies ready for demonstration and deployment, and to provide a set of recommendations for the further development of these technologies.« less

U.S. DOE Progress Towards Developing Low-Cost, High Performance, Durable Polymer Electrolyte Membranes for Fuel Cell Applications

PubMed Central

Houchins, Cassidy; Kleen, Greg J.; Spendelow, Jacob S.; Kopasz, John; Peterson, David; Garland, Nancy L.; Ho, Donna Lee; Marcinkoski, Jason; Martin, Kathi Epping; Tyler, Reginald; Papageorgopoulos, Dimitrios C.

2012-01-01

Low cost, durable, and selective membranes with high ionic conductivity are a priority need for wide-spread adoption of polymer electrolyte membrane fuel cells (PEMFCs) and direct methanol fuel cells (DMFCs). Electrolyte membranes are a major cost component of PEMFC stacks at low production volumes. PEMFC membranes also impose limitations on fuel cell system operating conditions that add system complexity and cost. Reactant gas and fuel permeation through the membrane leads to decreased fuel cell performance, loss of efficiency, and reduced durability in both PEMFCs and DMFCs. To address these challenges, the U.S. Department of Energy (DOE) Fuel Cell Technologies Program, in the Office of Energy Efficiency and Renewable Energy, supports research and development aimed at improving ion exchange membranes for fuel cells. For PEMFCs, efforts are primarily focused on developing materials for higher temperature operation (up to 120 °C) in automotive applications. For DMFCs, efforts are focused on developing membranes with reduced methanol permeability. In this paper, the recently revised DOE membrane targets, strategies, and highlights of DOE-funded projects to develop new, inexpensive membranes that have good performance in hot and dry conditions (PEMFC) and that reduce methanol crossover (DMFC) will be discussed. PMID:24958432

Polycation-sodium lauryl ether sulfate-type surfactant complexes: influence of ethylene oxide length.

PubMed

Vleugels, Leo F W; Pollet, Jennifer; Tuinier, Remco

2015-05-21

Polyelectrolyte-surfactant complexes (PESC) are a class of materials which form spontaneously by self-assembly driven by electrostatic and hydrophobic interactions. PESC containing sodium lauryl ether sulfates (SLES) have found wide application in hair care products like shampoo. Typically, SLES with only one or two ethylene oxide (EO) groups are used for this application. We have studied the influence of the size of the EO block (ranging from 0 to 30 EO groups) on complexation with two model polycations: linear polyDADMAC and branched PEI. PESC size and electrostatic properties were determined during stepwise titration of buffered polycation solutions. The critical aggregation concentration (CAC) of PESC was determined by surface tension measurements and fluorescence spectroscopy. For polyDADMAC, there is no influence of the size of the EO block on the complexation behavior; the stiff polycation governs the structure formation. For PEI, it was seen that the EO block size does affect the structure of the complexes. The CAC value of the investigated complexes turns out to be rather independent of the EO block size; however, the CMC/CAC ratio decreases with increasing size of the EO block. This latter observation explains why the Lochhead-Goddard effect is most effective for small EO blocks.

Waste Information Management System with 2012-13 Waste Streams - 13095

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

Upadhyay, H.; Quintero, W.; Lagos, L.

2013-07-01

The Waste Information Management System (WIMS) 2012-13 was updated to support the Department of Energy (DOE) accelerated cleanup program. The schedule compression required close coordination and a comprehensive review and prioritization of the barriers that impeded treatment and disposition of the waste streams at each site. Many issues related to waste treatment and disposal were potential critical path issues under the accelerated schedule. In order to facilitate accelerated cleanup initiatives, waste managers at DOE field sites and at DOE Headquarters in Washington, D.C., needed timely waste forecast and transportation information regarding the volumes and types of radioactive waste that wouldmore » be generated by DOE sites over the next 40 years. Each local DOE site historically collected, organized, and displayed waste forecast information in separate and unique systems. In order for interested parties to understand and view the complete DOE complex-wide picture, the radioactive waste and shipment information of each DOE site needed to be entered into a common application. The WIMS application was therefore created to serve as a common application to improve stakeholder comprehension and improve DOE radioactive waste treatment and disposal planning and scheduling. WIMS allows identification of total forecasted waste volumes, material classes, disposition sites, choke points, technological or regulatory barriers to treatment and disposal, along with forecasted waste transportation information by rail, truck and inter-modal shipments. The Applied Research Center (ARC) at Florida International University (FIU) in Miami, Florida, developed and deployed the web-based forecast and transportation system and is responsible for updating the radioactive waste forecast and transportation data on a regular basis to ensure the long-term viability and value of this system. (authors)« less

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

Hayes, Timothy; Nelson, Roger

The Department of Energy (DOE) and the National Nuclear Security Administration (NNSA) manages defense nuclear material that has been determined to be excess to programmatic needs and declared waste. When these wastes contain plutonium, they almost always meet the definition of defense transuranic (TRU) waste and are thus eligible for disposal at the Waste Isolation Pilot Plant (WIPP). The DOE operates the WIPP in a manner that physical protections for attractiveness level D or higher special nuclear material (SNM) are not the normal operating condition. Therefore, there is currently a requirement to terminate safeguards before disposal of these wastes atmore » the WIPP. Presented are the processes used to terminate safeguards, lessons learned during the termination process, and how these approaches might be useful for future defense TRU waste needing safeguards termination prior to shipment and disposal at the WIPP. Also described is a new criticality control container, which will increase the amount of fissile material that can be loaded per container, and how it will save significant taxpayer dollars. Retrieval, compliant packaging and shipment of retrievably stored legacy TRU waste has dominated disposal operations at WIPP since it began operations 12 years ago. But because most of this legacy waste has successfully been emplaced in WIPP, the TRU waste clean-up focus is turning to newly-generated TRU materials. A major component will be transuranic SNM, currently managed in safeguards-protected vaults around the weapons complex. As DOE and NNSA continue to consolidate and shrink the weapons complex footprint, it is expected that significant quantities of transuranic SNM will be declared surplus to the nation's needs. Safeguards termination of SNM varies due to the wide range of attractiveness level of the potential material that may be directly discarded as waste. To enhance the efficiency of shipping waste with high TRU fissile content to WIPP, DOE designed an over-pack container, similar to the pipe component, called the criticality control over-pack, which will significantly enhance the efficiency of disposal. Hundreds of shipments of transuranic SNM, suitably packaged to meet WIPP waste acceptance criteria and with safeguards terminated have been successfully emplaced at WIPP (primarily from the Rocky Flats site clean-up) since WIPP opened. DOE expects that thousands more may eventually result from SNM consolidation efforts throughout the weapons complex. (authors)« less

Design of experiments (DOE) - history, concepts, and relevance to in vitro culture

USDA-ARS?s Scientific Manuscript database

Design of experiments (DOE) is a large and well-developed field for understanding and improving the performance of complex systems. Because in vitro culture systems are complex, but easily manipulated in controlled conditions, they are particularly well-suited for the application of DOE principle...

A Novel Image Encryption Algorithm Based on DNA Subsequence Operation

PubMed Central

Zhang, Qiang; Xue, Xianglian; Wei, Xiaopeng

2012-01-01

We present a novel image encryption algorithm based on DNA subsequence operation. Different from the traditional DNA encryption methods, our algorithm does not use complex biological operation but just uses the idea of DNA subsequence operations (such as elongation operation, truncation operation, deletion operation, etc.) combining with the logistic chaotic map to scramble the location and the value of pixel points from the image. The experimental results and security analysis show that the proposed algorithm is easy to be implemented, can get good encryption effect, has a wide secret key's space, strong sensitivity to secret key, and has the abilities of resisting exhaustive attack and statistic attack. PMID:23093912

Potential implementation of reservoir computing models based on magnetic skyrmions

NASA Astrophysics Data System (ADS)

Bourianoff, George; Pinna, Daniele; Sitte, Matthias; Everschor-Sitte, Karin

2018-05-01

Reservoir Computing is a type of recursive neural network commonly used for recognizing and predicting spatio-temporal events relying on a complex hierarchy of nested feedback loops to generate a memory functionality. The Reservoir Computing paradigm does not require any knowledge of the reservoir topology or node weights for training purposes and can therefore utilize naturally existing networks formed by a wide variety of physical processes. Most efforts to implement reservoir computing prior to this have focused on utilizing memristor techniques to implement recursive neural networks. This paper examines the potential of magnetic skyrmion fabrics and the complex current patterns which form in them as an attractive physical instantiation for Reservoir Computing. We argue that their nonlinear dynamical interplay resulting from anisotropic magnetoresistance and spin-torque effects allows for an effective and energy efficient nonlinear processing of spatial temporal events with the aim of event recognition and prediction.

Groundwater Protection Program Management Plan For The U.S. Department Of Energy Y-12 National Security Complex, Oak Ridge, Tennessee

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

Elvado Environmental, LLC

2009-09-01

This document presents the Groundwater Protection Program (GWPP) management plan for the U.S. Department of Energy (DOE) Y-12 National Security Complex (hereafter referenced as Y-12). The Y-12 GWPP functions as the primary point-of-contact for groundwater-related issues at Y-12, provides stewardship of the extensive network of groundwater monitoring wells at Y-12, and serves as a resource for technical expertise, support, and historical data for groundwater-related activities at Y-12. These organizational functions each serve the primary programmatic purpose of the GWPP, which is to ensure that groundwater monitoring activities within areas under Y-12 administrative control provide representative data in compliance with themore » multiple purposes of applicable state and federal regulations, DOE orders, and the corporate policies of Babcock & Wilcox Technical Services Y-12 LLC (hereafter referenced as B&W Y-12), the Y-12 management and operations (M&O) contractor for DOE. B&W Y-12 is a new corporate name, assumed in January 2007, for the company formerly known as BWXT Y-12, L.L.C., hereafter referenced as BWXT. This GWPP management plan addresses the requirements of DOE Order 450.1A Environmental Protection Program (hereafter referenced as DOE O 450.1A), which emphasize a site-wide approach for groundwater protection at each DOE facility through implementation of groundwater surveillance monitoring. Additionally, this plan addresses the relevant and applicable GWPP elements and goals described in the DOE O 450.1A technical guidance documents issued in June 2004 (DOE 2004) and May 2005 (DOE 2005). This GWPP management plan is a 'living' document that is reviewed annually, revised and reissued every three years, and is formatted to provide for updating individual sections independent of the rest of the document. Section 2 includes a short description of the groundwater system at Y-12, the history of groundwater monitoring at Y-12 and the corresponding evolution of the GWPP, and an overview of ongoing Y-12 groundwater monitoring activities. Section 3 describes the key elements of the GWPP management strategy. Organizational roles and responsibilities of GWPP personnel are outlined in Section 4. Section 5 presents an overview of the GWPP project plans for applicable programmatic elements. Section 6 lists the reports, plans, and documents that are referenced for technical and administrative details.« less

Multichromosomal median and halving problems under different genomic distances

PubMed Central

Tannier, Eric; Zheng, Chunfang; Sankoff, David

2009-01-01

Background Genome median and genome halving are combinatorial optimization problems that aim at reconstructing ancestral genomes as well as the evolutionary events leading from the ancestor to extant species. Exploring complexity issues is a first step towards devising efficient algorithms. The complexity of the median problem for unichromosomal genomes (permutations) has been settled for both the breakpoint distance and the reversal distance. Although the multichromosomal case has often been assumed to be a simple generalization of the unichromosomal case, it is also a relaxation so that complexity in this context does not follow from existing results, and is open for all distances. Results We settle here the complexity of several genome median and halving problems, including a surprising polynomial result for the breakpoint median and guided halving problems in genomes with circular and linear chromosomes, showing that the multichromosomal problem is actually easier than the unichromosomal problem. Still other variants of these problems are NP-complete, including the DCJ double distance problem, previously mentioned as an open question. We list the remaining open problems. Conclusion This theoretical study clears up a wide swathe of the algorithmical study of genome rearrangements with multiple multichromosomal genomes. PMID:19386099

Fast and accurate detection of spread source in large complex networks.

PubMed

Paluch, Robert; Lu, Xiaoyan; Suchecki, Krzysztof; Szymański, Bolesław K; Hołyst, Janusz A

2018-02-06

Spread over complex networks is a ubiquitous process with increasingly wide applications. Locating spread sources is often important, e.g. finding the patient one in epidemics, or source of rumor spreading in social network. Pinto, Thiran and Vetterli introduced an algorithm (PTVA) to solve the important case of this problem in which a limited set of nodes act as observers and report times at which the spread reached them. PTVA uses all observers to find a solution. Here we propose a new approach in which observers with low quality information (i.e. with large spread encounter times) are ignored and potential sources are selected based on the likelihood gradient from high quality observers. The original complexity of PTVA is O(N α ), where α ∈ (3,4) depends on the network topology and number of observers (N denotes the number of nodes in the network). Our Gradient Maximum Likelihood Algorithm (GMLA) reduces this complexity to O (N 2 log (N)). Extensive numerical tests performed on synthetic networks and real Gnutella network with limitation that id's of spreaders are unknown to observers demonstrate that for scale-free networks with such limitation GMLA yields higher quality localization results than PTVA does.

The Effect of Social Trust on Citizens’ Health Risk Perception in the Context of a Petrochemical Industrial Complex

PubMed Central

López-Navarro, Miguel Ángel; Llorens-Monzonís, Jaume; Tortosa-Edo, Vicente

2013-01-01

Perceived risk of environmental threats often translates into psychological stress with a wide range of effects on health and well-being. Petrochemical industrial complexes constitute one of the sites that can cause considerable pollution and health problems. The uncertainty around emissions results in a perception of risk for citizens residing in neighboring areas, which translates into anxiety and physiological stress. In this context, social trust is a key factor in managing the perceived risk. In the case of industrial risks, it is essential to distinguish between trust in the companies that make up the industry, and trust in public institutions. In the context of a petrochemical industrial complex located in the port of Castellón (Spain), this paper primarily discusses how trust—both in the companies located in the petrochemical complex and in the public institutions—affects citizens’ health risk perception. The research findings confirm that while the trust in companies negatively affects citizens’ health risk perception, trust in public institutions does not exert a direct and significant effect. Analysis also revealed that trust in public institutions and health risk perception are essentially linked indirectly (through trust in companies). PMID:23337129

Synthesis and characterization of glucosyl-curcuminoids as Fe3+ suppliers in the treatment of iron deficiency.

PubMed

Ferrari, Erika; Arezzini, Beatrice; Ferrali, Marco; Lazzari, Sandra; Pignedoli, Francesca; Spagnolo, Ferdinando; Saladini, Monica

2009-10-01

The Fe(3+) chelating ability of some curcumin glucosyl derivatives (Glc-H; Glc-OH; Glc-OCH(3)) is tested by means of UV and NMR study. The pK(a) values of the ligands and the overall stability constants of Fe(3+) and Ga(3+) complexes are evaluated from UV spectra. The only metal binding site of the ligand is the beta-diketo moiety in the keto-enolic form; the glucosyl moiety does not interact with metal ion but it contributes to the stability of metal/ligand 1:2 complexes by means of hydrophilic interactions. These glucosyl derivatives are able to bind Fe(3+) in a wide pH rage, forming complex species thermodynamically more stable than those of other ligands commonly used in the treatment of iron deficiency. In addition they demonstrate to have a poor affinity for competitive biological metal ions such as Ca(2+). All ligands and their iron complexes have a good lypophilicity (log P > -0.7) suggesting an efficient gastrointestinal absorption in view of their possible use as iron supplements in oral therapy. The ligand molecules are also tested for their antioxidant properties in "ex vivo" biological system.

Protein-Linked Glycan Degradation in Infants Fed Human Milk

PubMed Central

Dallas, David C.; Sela, David; Underwood, Mark A.; German, J. Bruce; Lebrilla, Carlito

2014-01-01

Many human milk proteins are glycosylated. Glycosylation is important in protecting bioactive proteins and peptide fragments from digestion. Protein-linked glycans have a variety of functions; however, there is a paucity of information on protein-linked glycan degradation in either the infant or the adult digestive system. Human digestive enzymes can break down dietary disaccharides and starches, but most of the digestive enzymes required for complex protein-linked glycan degradation are absent from both human digestive secretions and the external brush border membrane of the intestinal lining. Indeed, complex carbohydrates remain intact throughout their transit through the stomach and small intestine, and are undegraded by in vitro incubation with either adult pancreatic secretions or intact intestinal brush border membranes. Human gastrointestinal bacteria, however, produce a wide variety of glycosidases with regio- and anomeric specificities matching those of protein-linked glycan structures. These bacteria degrade a wide array of complex carbohydrates including various protein-linked glycans. That bacteria possess glycan degradation capabilities, whereas the human digestive system, perse, does not, suggests that most dietary protein-linked glycan breakdown will be of bacterial origin. In addition to providing a food source for specific bacteria in the colon, protein-linked glycans from human milk may act as decoys for pathogenic bacteria to prevent invasion and infection of the host. The composition of the intestinal microbiome may be particularly important in the most vulnerable humans-the elderly, the immunocompromised, and infants (particularly premature infants). PMID:24533224

Architectural Framework for Addressing Legacy Waste from the Cold War - 13611

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

Love, Gregory A.; Glazner, Christopher G.; Steckley, Sam

We present an architectural framework for the use of a hybrid simulation model of enterprise-wide operations used to develop system-level insight into the U.S. Department of Energy's (DOE) environmental cleanup of legacy nuclear waste at the Savannah River Site. We use this framework for quickly exploring policy and architectural options, analyzing plans, addressing management challenges and developing mitigation strategies for DOE Office of Environmental Management (EM). The socio-technical complexity of EM's mission compels the use of a qualitative approach to complement a more a quantitative discrete event modeling effort. We use this model-based analysis to pinpoint pressure and leverage pointsmore » and develop a shared conceptual understanding of the problem space and platform for communication among stakeholders across the enterprise in a timely manner. This approach affords the opportunity to discuss problems using a unified conceptual perspective and is also general enough that it applies to a broad range of capital investment/production operations problems. (authors)« less

10 CFR 1021.330 - Programmatic (including site-wide) NEPA documents.

Code of Federal Regulations, 2010 CFR

2010-01-01

... prepare a programmatic EIS or EA (40 CFR 1502.4). DOE may also prepare a programmatic EIS or EA at any... Analysis, DOE shall determine whether the existing EIS remains adequate or whether to prepare a new site-wide EIS or supplement the existing EIS, as appropriate. The determination and supporting analysis...

Fire hazard analysis for Plutonium Finishing Plant complex

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

MCKINNIS, D.L.

1999-02-23

A fire hazards analysis (FHA) was performed for the Plutonium Finishing Plant (PFP) Complex at the Department of Energy (DOE) Hanford site. The scope of the FHA focuses on the nuclear facilities/structures in the Complex. The analysis was conducted in accordance with RLID 5480.7, [DOE Directive RLID 5480.7, 1/17/94] and DOE Order 5480.7A, ''Fire Protection'' [DOE Order 5480.7A, 2/17/93] and addresses each of the sixteen principle elements outlined in paragraph 9.a(3) of the Order. The elements are addressed in terms of the fire protection objectives stated in paragraph 4 of DOE 5480.7A. In addition, the FHA also complies with WHC-CM-4-41,more » Fire Protection Program Manual, Section 3.4 [1994] and WHC-SD-GN-FHA-30001, Rev. 0 [WHC, 1994]. Objectives of the FHA are to determine: (1) the fire hazards that expose the PFP facilities, or that are inherent in the building operations, (2) the adequacy of the fire safety features currently located in the PFP Complex, and (3) the degree of compliance of the facility with specific fire safety provisions in DOE orders, related engineering codes, and standards.« less

The Glyphosate-Based Herbicide Roundup Does not Elevate Genome-Wide Mutagenesis of Escherichia coli.

PubMed

Tincher, Clayton; Long, Hongan; Behringer, Megan; Walker, Noah; Lynch, Michael

2017-10-05

Mutations induced by pollutants may promote pathogen evolution, for example by accelerating mutations conferring antibiotic resistance. Generally, evaluating the genome-wide mutagenic effects of long-term sublethal pollutant exposure at single-nucleotide resolution is extremely difficult. To overcome this technical barrier, we use the mutation accumulation/whole-genome sequencing (MA/WGS) method as a mutagenicity test, to quantitatively evaluate genome-wide mutagenesis of Escherichia coli after long-term exposure to a wide gradient of the glyphosate-based herbicide (GBH) Roundup Concentrate Plus. The genome-wide mutation rate decreases as GBH concentration increases, suggesting that even long-term GBH exposure does not compromise the genome stability of bacteria. Copyright © 2017 Tincher et al.

Drug Modulation of Water–Heme Interactions in Low-Spin P450 Complexes of CYP2C9d and CYP125A1

PubMed Central

Conner, Kip P.; Cruce, Alex A.; Krzyaniak, Matthew D.; Schimpf, Alina M.; Frank, Daniel J.; de Montellano, Paul Ortiz; Atkins, William M.; Bowman, Michael K.

2015-01-01

Azoles and pyridines are commonly incorporated into small molecule inhibitor scaffolds that target cytochromes P450 (CYPs) as a strategy to increase drug binding affinity, impart isoform-dependent selectivity, and improve metabolic stability. Optical absorbance spectra of the CYP–inhibitor complex are widely used to infer whether these inhibitors are ligated directly to the heme iron as catalytically inert, low-spin (type II) complexes. Here, we show that the low-spin complex between a drug-metabolizing CYP2C9 variant and 4-(3-phenyl-propyl)-1H-1,2,3-triazole (PPT) retains an axial water ligand despite exhibiting elements of “classic” type II optical behavior. Hydrogens of the axial water ligand are observed by pulsed electron paramagnetic resonance (EPR) spectroscopy for both inhibitor-free and inhibitor-bound species and show that inhibitor binding does not displace the axial water. A 15N label incorporated into PPT is 0.444 nm from the heme iron, showing that PPT is also in the active site. The reverse type I inhibitor, LP10, of CYP125A1 from Mycobacterium tuberculosis, known from X-ray crystal structures to form a low-spin water-bridged complex, is found by EPR and by visible and near-infrared magnetic circular dichroism spectroscopy to retain the axial water ligand in the complex in solution. PMID:25591012

Organizational crisis management: the human factor.

PubMed

Lewis, Gerald

2005-01-01

While many professionals are quite competent when dealing with operational aspects of organizational continuity, often the "human factor" does not receive adequate attention. This article provides a brief overview of a soon to be published book by the same title. It provides a comprehensive understanding of the ubiquitous yet complex reactions of the workforce to a wide array of organizational disruptions. It goes beyond the short term intervention of debriefings to describe the more extensive pre and post incident strategies required to mitigate the impact of crises on the workforce. It is important to remember: "An organization can get its phone lines back up and have its computers backed up...but its workers may still be messed up."

Does the Hertz solution estimate pressures correctly in diamond indentor experiments?

NASA Astrophysics Data System (ADS)

Bruno, M. S.; Dunn, K. J.

1986-05-01

The Hertz solution has been widely used to estimate pressures in a spherical indentor against flat matrix type high pressure experiments. It is usually assumed that the pressure generated when compressing a sample between the indentor and substrate is the same as that generated when compressing an indentor against a flat surface with no sample present. A non-linear finite element analysis of this problem has shown that the situation is far more complex. The actual peak pressure in the sample is highly dependent on plastic deformation and the change in material properties due to hydrostatic pressure. An analysis with two material models is presented and compared with the Hertz solution.

Development studies of a novel wet oxidation process

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

Rogers, T.W.; Dhooge, P.M.

1995-12-01

Many DOE waste streams and remediates contain complex and variable mixtures of organic compounds, toxic metals, and radionuclides. These materials are often dispersed in organic or inorganic matrices, such as personal protective equipment, various sludges, soils, and water. Incineration and similar combustive processes do not appear to be viable options for treatment of these waste streams due to various considerations. There is a need for non-combustion processes with a wide application range to treat the large majority of these waste forms. The non-combustion process should also be safe, effective, cost-competitive, permit-able, and preferrably mobile. This paper describes the DETOX processmore » of organic waste oxidation.« less

Solving Navier-Stokes Equations with Advanced Turbulence Models on Three-Dimensional Unstructured Grids

NASA Technical Reports Server (NTRS)

Wang, Qun-Zhen; Massey, Steven J.; Abdol-Hamid, Khaled S.; Frink, Neal T.

1999-01-01

USM3D is a widely-used unstructured flow solver for simulating inviscid and viscous flows over complex geometries. The current version (version 5.0) of USM3D, however, does not have advanced turbulence models to accurately simulate complicated flows. We have implemented two modified versions of the original Jones and Launder k-epsilon two-equation turbulence model and the Girimaji algebraic Reynolds stress model in USM3D. Tests have been conducted for two flat plate boundary layer cases, a RAE2822 airfoil and an ONERA M6 wing. The results are compared with those of empirical formulae, theoretical results and the existing Spalart-Allmaras one-equation model.

Physiological time-series analysis: what does regularity quantify?

NASA Technical Reports Server (NTRS)

Pincus, S. M.; Goldberger, A. L.

1994-01-01

Approximate entropy (ApEn) is a recently developed statistic quantifying regularity and complexity that appears to have potential application to a wide variety of physiological and clinical time-series data. The focus here is to provide a better understanding of ApEn to facilitate its proper utilization, application, and interpretation. After giving the formal mathematical description of ApEn, we provide a multistep description of the algorithm as applied to two contrasting clinical heart rate data sets. We discuss algorithm implementation and interpretation and introduce a general mathematical hypothesis of the dynamics of a wide class of diseases, indicating the utility of ApEn to test this hypothesis. We indicate the relationship of ApEn to variability measures, the Fourier spectrum, and algorithms motivated by study of chaotic dynamics. We discuss further mathematical properties of ApEn, including the choice of input parameters, statistical issues, and modeling considerations, and we conclude with a section on caveats to ensure correct ApEn utilization.

Haltere mechanosensory influence on tethered flight behavior in Drosophila.

PubMed

Mureli, Shwetha; Fox, Jessica L

2015-08-01

In flies, mechanosensory information from modified hindwings known as halteres is combined with visual information for wing-steering behavior. Haltere input is necessary for free flight, making it difficult to study the effects of haltere ablation under natural flight conditions. We thus used tethered Drosophila melanogaster flies to examine the relationship between halteres and the visual system, using wide-field motion or moving figures as visual stimuli. Haltere input was altered by surgically decreasing its mass, or by removing it entirely. Haltere removal does not affect the flies' ability to flap or steer their wings, but it does increase the temporal frequency at which they modify their wingbeat amplitude. Reducing the haltere mass decreases the optomotor reflex response to wide-field motion, and removing the haltere entirely does not further decrease the response. Decreasing the mass does not attenuate the response to figure motion, but removing the entire haltere does attenuate the response. When flies are allowed to control a visual stimulus in closed-loop conditions, haltereless flies fixate figures with the same acuity as intact flies, but cannot stabilize a wide-field stimulus as accurately as intact flies can. These manipulations suggest that the haltere mass is influential in wide-field stabilization, but less so in figure tracking. In both figure and wide-field experiments, we observe responses to visual motion with and without halteres, indicating that during tethered flight, intact halteres are not strictly necessary for visually guided wing-steering responses. However, the haltere feedback loop may operate in a context-dependent way to modulate responses to visual motion. © 2015. Published by The Company of Biologists Ltd.

Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.

PubMed

Low, Siew-Kee; Chung, Suyoun; Takahashi, Atsushi; Zembutsu, Hitoshi; Mushiroda, Taisei; Kubo, Michiaki; Nakamura, Yusuke

2013-08-01

Chemotherapeutic agents are notoriously known to have a narrow therapeutic range that often results in life-threatening toxicity. Hence, it is clinically important to identify the patients who are at high risk for severe toxicity to certain chemotherapy through a pharmacogenomics approach. In this study, we carried out multiple genome-wide association studies (GWAS) of 13 122 cancer patients who received different chemotherapy regimens, including cyclophosphamide- and platinum-based (cisplatin and carboplatin), anthracycline-based (doxorubicin and epirubicin), and antimetabolite-based (5-fluorouracil and gemcitabine) treatment, antimicrotubule agents (paclitaxel and docetaxel), and topoisomerase inhibitors (camptothecin and etoposide), as well as combination therapy with paclitaxel and carboplatin, to identify genetic variants that are associated with the risk of severe neutropenia/leucopenia in the Japanese population. In addition, we used a weighted genetic risk scoring system to evaluate the cumulative effects of the suggestive genetic variants identified from GWAS in order to predict the risk levels of individuals who carry multiple risk alleles. Although we failed to identify genetic variants that surpassed the genome-wide significance level (P < 5.0 × 10(-8) ) through GWAS, probably due to insufficient statistical power and complex clinical features, we were able to shortlist some of the suggestive associated loci. The current study is at the relatively preliminary stage, but does highlight the complexity and problematic issues associated with retrospective pharmacogenomics studies. However, we hope that verification of these genetic variants through local and international collaborations could improve the clinical outcome for cancer patients. © 2013 Japanese Cancer Association.

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework.

PubMed

Zhang, Kunlin; Chang, Suhua; Cui, Sijia; Guo, Liyuan; Zhang, Liuyan; Wang, Jing

2011-07-01

Genome-wide association study (GWAS) is widely utilized to identify genes involved in human complex disease or some other trait. One key challenge for GWAS data interpretation is to identify causal SNPs and provide profound evidence on how they affect the trait. Currently, researches are focusing on identification of candidate causal variants from the most significant SNPs of GWAS, while there is lack of support on biological mechanisms as represented by pathways. Although pathway-based analysis (PBA) has been designed to identify disease-related pathways by analyzing the full list of SNPs from GWAS, it does not emphasize on interpreting causal SNPs. To our knowledge, so far there is no web server available to solve the challenge for GWAS data interpretation within one analytical framework. ICSNPathway is developed to identify candidate causal SNPs and their corresponding candidate causal pathways from GWAS by integrating linkage disequilibrium (LD) analysis, functional SNP annotation and PBA. ICSNPathway provides a feasible solution to bridge the gap between GWAS and disease mechanism study by generating hypothesis of SNP → gene → pathway(s). The ICSNPathway server is freely available at http://icsnpathway.psych.ac.cn/.

Does Supporting Multiple Student Strategies Lead to Greater Learning and Motivation? Investigating a Source of Complexity in the Architecture of Intelligent Tutoring Systems

ERIC Educational Resources Information Center

Waalkens, Maaike; Aleven, Vincent; Taatgen, Niels

2013-01-01

Intelligent tutoring systems (ITS) support students in learning a complex problem-solving skill. One feature that makes an ITS architecturally complex, and hard to build, is support for strategy freedom, that is, the ability to let students pursue multiple solution strategies within a given problem. But does greater freedom mean that students…

Network structure exploration in networks with node attributes

NASA Astrophysics Data System (ADS)

Chen, Yi; Wang, Xiaolong; Bu, Junzhao; Tang, Buzhou; Xiang, Xin

2016-05-01

Complex networks provide a powerful way to represent complex systems and have been widely studied during the past several years. One of the most important tasks of network analysis is to detect structures (also called structural regularities) embedded in networks by determining group number and group partition. Most of network structure exploration models only consider network links. However, in real world networks, nodes may have attributes that are useful for network structure exploration. In this paper, we propose a novel Bayesian nonparametric (BNP) model to explore structural regularities in networks with node attributes, called Bayesian nonparametric attribute (BNPA) model. This model does not only take full advantage of both links between nodes and node attributes for group partition via shared hidden variables, but also determine group number automatically via the Bayesian nonparametric theory. Experiments conducted on a number of real and synthetic networks show that our BNPA model is able to automatically explore structural regularities in networks with node attributes and is competitive with other state-of-the-art models.

Analytical Methods for Biomass Characterization during Pretreatment and Bioconversion

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

Pu, Yunqiao; Meng, Xianzhi; Yoo, Chang Geun

2016-01-01

Lignocellulosic biomass has been introduced as a promising resource for alternative fuels and chemicals because of its abundance and complement for petroleum resources. Biomass is a complex biopolymer and its compositional and structural characteristics largely vary depending on its species as well as growth environments. Because of complexity and variety of biomass, understanding its physicochemical characteristics is a key for effective biomass utilization. Characterization of biomass does not only provide critical information of biomass during pretreatment and bioconversion, but also give valuable insights on how to utilize the biomass. For better understanding biomass characteristics, good grasp and proper selection ofmore » analytical methods are necessary. This chapter introduces existing analytical approaches that are widely employed for biomass characterization during biomass pretreatment and conversion process. Diverse analytical methods using Fourier transform infrared (FTIR) spectroscopy, gel permeation chromatography (GPC), and nuclear magnetic resonance (NMR) spectroscopy for biomass characterization are reviewed. In addition, biomass accessibility methods by analyzing surface properties of biomass are also summarized in this chapter.« less

What drives the formation of massive stars and clusters?

NASA Astrophysics Data System (ADS)

Ochsendorf, Bram; Meixner, Margaret; Roman-Duval, Julia; Evans, Neal J., II; Rahman, Mubdi; Zinnecker, Hans; Nayak, Omnarayani; Bally, John; Jones, Olivia C.; Indebetouw, Remy

2018-01-01

Galaxy-wide surveys allow to study star formation in unprecedented ways. In this talk, I will discuss our analysis of the Large Magellanic Cloud (LMC) and the Milky Way, and illustrate how studying both the large and small scale structure of galaxies are critical in addressing the question: what drives the formation of massive stars and clusters?I will show that ‘turbulence-regulated’ star formation models do not reproduce massive star formation properties of GMCs in the LMC and Milky Way: this suggests that theory currently does not capture the full complexity of star formation on small scales. I will also report on the discovery of a massive star forming complex in the LMC, which in many ways manifests itself as an embedded twin of 30 Doradus: this may shed light on the formation of R136 and 'Super Star Clusters' in general. Finally, I will highlight what we can expect in the next years in the field of star formation with large-scale sky surveys, ALMA, and our JWST-GTO program.

Loss tangent and complex modulus estimated by acoustic radiation force creep and shear wave dispersion

PubMed Central

Amador, Carolina; Urban, Matthew W; Chen, Shigao; Greenleaf, James F

2012-01-01

Elasticity imaging methods have been used to study tissue mechanical properties and have demonstrated that tissue elasticity changes with disease state. In current shear wave elasticity imaging methods typically only shear wave speed is measured and rheological models, e.g., Kelvin-Voigt, Maxwell and Standard Linear Solid, are used to solve for tissue mechanical properties such as the shear viscoelastic complex modulus. This paper presents a method to quantify viscoelastic material properties in a model-independent way by estimating the complex shear elastic modulus over a wide frequency range using time-dependent creep response induced by acoustic radiation force. This radiation force induced creep (RFIC) method uses a conversion formula that is the analytic solution of a constitutive equation. The proposed method in combination with Shearwave Dispersion Ultrasound Vibrometry (SDUV) is used to measure the complex modulus so that knowledge of the applied radiation force magnitude is not necessary. The conversion formula is shown to be sensitive to sampling frequency and the first reliable measure in time according to numerical simulations using the Kelvin-Voigt model creep strain and compliance. Representative model-free shear complex moduli from homogeneous tissue mimicking phantoms and one excised swine kidney were obtained. This work proposes a novel model-free ultrasound-based elasticity method that does not require a rheological model with associated fitting requirements. PMID:22345425

Loss tangent and complex modulus estimated by acoustic radiation force creep and shear wave dispersion.

PubMed

Amador, Carolina; Urban, Matthew W; Chen, Shigao; Greenleaf, James F

2012-03-07

Elasticity imaging methods have been used to study tissue mechanical properties and have demonstrated that tissue elasticity changes with disease state. In current shear wave elasticity imaging methods typically only shear wave speed is measured and rheological models, e.g. Kelvin-Voigt, Maxwell and Standard Linear Solid, are used to solve for tissue mechanical properties such as the shear viscoelastic complex modulus. This paper presents a method to quantify viscoelastic material properties in a model-independent way by estimating the complex shear elastic modulus over a wide frequency range using time-dependent creep response induced by acoustic radiation force. This radiation force induced creep method uses a conversion formula that is the analytic solution of a constitutive equation. The proposed method in combination with shearwave dispersion ultrasound vibrometry is used to measure the complex modulus so that knowledge of the applied radiation force magnitude is not necessary. The conversion formula is shown to be sensitive to sampling frequency and the first reliable measure in time according to numerical simulations using the Kelvin-Voigt model creep strain and compliance. Representative model-free shear complex moduli from homogeneous tissue mimicking phantoms and one excised swine kidney were obtained. This work proposes a novel model-free ultrasound-based elasticity method that does not require a rheological model with associated fitting requirements.

Modeling of protein binary complexes using structural mass spectrometry data

PubMed Central

Kamal, J.K. Amisha; Chance, Mark R.

2008-01-01

In this article, we describe a general approach to modeling the structure of binary protein complexes using structural mass spectrometry data combined with molecular docking. In the first step, hydroxyl radical mediated oxidative protein footprinting is used to identify residues that experience conformational reorganization due to binding or participate in the binding interface. In the second step, a three-dimensional atomic structure of the complex is derived by computational modeling. Homology modeling approaches are used to define the structures of the individual proteins if footprinting detects significant conformational reorganization as a function of complex formation. A three-dimensional model of the complex is constructed from these binary partners using the ClusPro program, which is composed of docking, energy filtering, and clustering steps. Footprinting data are used to incorporate constraints—positive and/or negative—in the docking step and are also used to decide the type of energy filter—electrostatics or desolvation—in the successive energy-filtering step. By using this approach, we examine the structure of a number of binary complexes of monomeric actin and compare the results to crystallographic data. Based on docking alone, a number of competing models with widely varying structures are observed, one of which is likely to agree with crystallographic data. When the docking steps are guided by footprinting data, accurate models emerge as top scoring. We demonstrate this method with the actin/gelsolin segment-1 complex. We also provide a structural model for the actin/cofilin complex using this approach which does not have a crystal or NMR structure. PMID:18042684

Assessment of antibody library diversity through next generation sequencing and technical error compensation

PubMed Central

Lisi, Simonetta; Chirichella, Michele; Arisi, Ivan; Goracci, Martina; Cremisi, Federico; Cattaneo, Antonino

2017-01-01

Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error. PMID:28505201

Assessment of antibody library diversity through next generation sequencing and technical error compensation.

PubMed

Fantini, Marco; Pandolfini, Luca; Lisi, Simonetta; Chirichella, Michele; Arisi, Ivan; Terrigno, Marco; Goracci, Martina; Cremisi, Federico; Cattaneo, Antonino

2017-01-01

Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error.

Sec66-Dependent Regulation of Yeast Spindle-Pole Body Duplication Through Pom152

PubMed Central

Katta, Santharam S.; Chen, Jingjing; Gardner, Jennifer M.; Friederichs, Jennifer M.; Smith, Sarah E.; Gogol, Madelaine; Unruh, Jay R.; Slaughter, Brian D.; Jaspersen, Sue L.

2015-01-01

In closed mitotic systems such as Saccharomyces cerevisiae, the nuclear envelope (NE) does not break down during mitosis, so microtubule-organizing centers such as the spindle-pole body (SPB) must be inserted into the NE to facilitate bipolar spindle formation and chromosome segregation. The mechanism of SPB insertion has been linked to NE insertion of nuclear pore complexes (NPCs) through a series of genetic and physical interactions between NPCs and SPB components. To identify new genes involved in SPB duplication and NE insertion, we carried out genome-wide screens for suppressors of deletion alleles of SPB components, including Mps3 and Mps2. In addition to the nucleoporins POM152 and POM34, we found that elimination of SEC66/SEC71/KAR7 suppressed lethality of cells lacking MPS2 or MPS3. Sec66 is a nonessential subunit of the Sec63 complex that functions together with the Sec61 complex in import of proteins into the endoplasmic reticulum (ER). Cells lacking Sec66 have reduced levels of Pom152 protein but not Pom34 or Ndc1, a shared component of the NPC and SPB. The fact that Sec66 but not other subunits of the ER translocon bypass deletion mutants in SPB genes suggests a specific role for Sec66 in the control of Pom152 levels. Based on the observation that sec66∆ does not affect the distribution of Ndc1 on the NE or Ndc1 binding to the SPB, we propose that Sec66-mediated regulation of Pom152 plays an NPC-independent role in the control of SPB duplication. PMID:26510791

Effects of Display Complexity on Location and Feature Inhibition

PubMed Central

K.Hu, Frank; Fan, Zhiwei; Samuel, Arthur G.; He, ShuChang

2013-01-01

Inhibition of return (IOR) refers to the slowing of reaction times to a target when a preceding stimulus has occupied the same location in space. Recently, we observed a robust inhibitory effect for color and shape in moderately complex displays: It is more difficult to detect a target with a particular nonspatial attribute if a stimulus with the same attribute was recently the focus of attention. Such nonspatial inhibitory effects have not generally been found in simpler displays. In the present study, we test how location-based and nonspatial inhibitory effects vary as a function of display complexity (8, 6, 4 and 2 locations). The results demonstrated that: (1) location based inhibition effects were much stronger in more complex displays, whereas the nonspatial inhibition was only slightly stronger in more complex displays; (2) Nonspatial inhibitory effects emerged at longer SOAs than location-based effects; and (3) Nonspatial inhibition only appeared when cues and targets occurred in the same locations, confirming that pure feature repetition does not produce a cost. Taken together, the results are consistent with perceptual processes based on object files that are organized by spatial location. Using somewhat more complex displays than are most commonly employed provides a more sensitive method to observe the role of inhibitory processes in facilitating visual search. In addition, using a relatively wide set of cue-target timing relationships is necessary in order to clearly see how inhibitory effects operate. PMID:23907617

3D cancer cell migration in a confined matrix

NASA Astrophysics Data System (ADS)

Alobaidi, Amani; Sun, Bo

Cancer cell migration is widely studied in 2D motion, which does not mimic the invasion processes in vivo. More recently, 3D cell migration studies have been performed. The ability of cancer cells to migrate within the extracellular matrix depends on the physical and biochemical features of the extracellular matrix. We present a model of cell motility in confined matrix geometry. The aim of the study is to study cancer migration in collagen matrix, as a soft tissue, to investigate their motility within the confined and surrounding collagen environment. Different collagen concentrations have been used to show the ability of these cancer cells to move through such a complex structure by measuring Cancer cell migration velocity as well as the displacement. Graduate student physics department.

Non-Destructive Techniques Based on Eddy Current Testing

PubMed Central

García-Martín, Javier; Gómez-Gil, Jaime; Vázquez-Sánchez, Ernesto

2011-01-01

Non-destructive techniques are used widely in the metal industry in order to control the quality of materials. Eddy current testing is one of the most extensively used non-destructive techniques for inspecting electrically conductive materials at very high speeds that does not require any contact between the test piece and the sensor. This paper includes an overview of the fundamentals and main variables of eddy current testing. It also describes the state-of-the-art sensors and modern techniques such as multi-frequency and pulsed systems. Recent advances in complex models towards solving crack-sensor interaction, developments in instrumentation due to advances in electronic devices, and the evolution of data processing suggest that eddy current testing systems will be increasingly used in the future. PMID:22163754

Implementation of Advanced Two Equation Turbulence Models in the USM3D Unstructured Flow Solver

NASA Technical Reports Server (NTRS)

Wang, Qun-Zhen; Massey, Steven J.; Abdol-Hamid, Khaled S.

2000-01-01

USM3D is a widely-used unstructured flow solver for simulating inviscid and viscous flows over complex geometries. The current version (version 5.0) of USM3D, however, does not have advanced turbulence models to accurately simulate complicated flow. We have implemented two modified versions of the original Jones and Launder k-epsilon "two-equation" turbulence model and the Girimaji algebraic Reynolds stress model in USM3D. Tests have been conducted for three flat plate boundary layer cases, a RAE2822 airfoil and an ONERA M6 wing. The results are compared with those from direct numerical simulation, empirical formulae, theoretical results, and the existing Spalart-Allmaras one-equation model.

Non-destructive techniques based on eddy current testing.

PubMed

García-Martín, Javier; Gómez-Gil, Jaime; Vázquez-Sánchez, Ernesto

2011-01-01

Non-destructive techniques are used widely in the metal industry in order to control the quality of materials. Eddy current testing is one of the most extensively used non-destructive techniques for inspecting electrically conductive materials at very high speeds that does not require any contact between the test piece and the sensor. This paper includes an overview of the fundamentals and main variables of eddy current testing. It also describes the state-of-the-art sensors and modern techniques such as multi-frequency and pulsed systems. Recent advances in complex models towards solving crack-sensor interaction, developments in instrumentation due to advances in electronic devices, and the evolution of data processing suggest that eddy current testing systems will be increasingly used in the future.

Environmental Enrichments for a Group of Captive Macaws: Low Interaction Does Not Mean Low Behavioral Changes.

PubMed

Reimer, Jéssica; Maia, Caroline Marques; Santos, Eliana Ferraz

2016-01-01

Environmental enrichment has been widely used to improve conditions for nonhuman animals in captivity. However, there is no consensus about the best way to evaluate the success of enrichments. This study evaluated whether the proportion of time spent interacting with enrichments indicated the proportion of overall behavioral changes. Six environmental enrichments were introduced in succession to 16 captive macaws, and interaction of the animals with them as well as the behaviors of the group were recorded before and during the enrichments. All of the enrichments affected the proportions of time spent in different behaviors. Macaws interacted more with certain items (hibiscus and food tree) than with others (a toy or swings and stairs), but introduction of the enrichments that invoked the least interaction caused as many behavioral changes as those that invoked the most. Moreover, feeding behavior was only affected by the enrichment that invoked the least interaction, a change not detected by a general analysis of enrichment effects. In conclusion, little interaction with enrichment does not mean little change in behavior, and the effects of enrichments are more complex than previously considered.

A novel recursive Fourier transform for nonuniform sampled signals: application to heart rate variability spectrum estimation.

PubMed

Holland, Alexander; Aboy, Mateo

2009-07-01

We present a novel method to iteratively calculate discrete Fourier transforms for discrete time signals with sample time intervals that may be widely nonuniform. The proposed recursive Fourier transform (RFT) does not require interpolation of the samples to uniform time intervals, and each iterative transform update of N frequencies has computational order N. Because of the inherent non-uniformity in the time between successive heart beats, an application particularly well suited for this transform is power spectral density (PSD) estimation for heart rate variability. We compare RFT based spectrum estimation with Lomb-Scargle Transform (LST) based estimation. PSD estimation based on the LST also does not require uniform time samples, but the LST has a computational order greater than Nlog(N). We conducted an assessment study involving the analysis of quasi-stationary signals with various levels of randomly missing heart beats. Our results indicate that the RFT leads to comparable estimation performance to the LST with significantly less computational overhead and complexity for applications requiring iterative spectrum estimations.

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

PubMed Central

2011-01-01

Background Many plants have large and complex genomes with an abundance of repeated sequences. Many plants are also polyploid. Both of these attributes typify the genome architecture in the tribe Triticeae, whose members include economically important wheat, rye and barley. Large genome sizes, an abundance of repeated sequences, and polyploidy present challenges to genome-wide SNP discovery using next-generation sequencing (NGS) of total genomic DNA by making alignment and clustering of short reads generated by the NGS platforms difficult, particularly in the absence of a reference genome sequence. Results An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions from repetitive sequences and sequences shared by paralogous genes. Multiple genome equivalents of shotgun reads of another genotype generated with SOLiD or Solexa are then mapped to the annotated Roche 454 reads to identify putative SNPs. A pipeline program package, AGSNP, was developed and used for genome-wide SNP discovery in Aegilops tauschii-the diploid source of the wheat D genome, and with a genome size of 4.02 Gb, of which 90% is repetitive sequences. Genomic DNA of Ae. tauschii accession AL8/78 was sequenced with the Roche 454 NGS platform. Genomic DNA and cDNA of Ae. tauschii accession AS75 was sequenced primarily with SOLiD, although some Solexa and Roche 454 genomic sequences were also generated. A total of 195,631 putative SNPs were discovered in gene sequences, 155,580 putative SNPs were discovered in uncharacterized single-copy regions, and another 145,907 putative SNPs were discovered in repeat junctions. These SNPs were dispersed across the entire Ae. tauschii genome. To assess the false positive SNP discovery rate, DNA containing putative SNPs was amplified by PCR from AL8/78 and AS75 and resequenced with the ABI 3730 xl. In a sample of 302 randomly selected putative SNPs, 84.0% in gene regions, 88.0% in repeat junctions, and 81.3% in uncharacterized regions were validated. Conclusion An annotation-based genome-wide SNP discovery pipeline for NGS platforms was developed. The pipeline is suitable for SNP discovery in genomic libraries of complex genomes and does not require a reference genome sequence. The pipeline is applicable to all current NGS platforms, provided that at least one such platform generates relatively long reads. The pipeline package, AGSNP, and the discovered 497,118 Ae. tauschii SNPs can be accessed at (http://avena.pw.usda.gov/wheatD/agsnp.shtml). PMID:21266061

Genetic reduction of mitochondrial complex I function does not lead to loss of dopamine neurons in vivo.

PubMed

Kim, Hyung-Wook; Choi, Won-Seok; Sorscher, Noah; Park, Hyung Joon; Tronche, François; Palmiter, Richard D; Xia, Zhengui

2015-09-01

Inhibition of mitochondrial complex I activity is hypothesized to be one of the major mechanisms responsible for dopaminergic neuron death in Parkinson's disease. However, loss of complex I activity by systemic deletion of the Ndufs4 gene, one of the subunits comprising complex I, does not cause dopaminergic neuron death in culture. Here, we generated mice with conditional Ndufs4 knockout in dopaminergic neurons (Ndufs4 conditional knockout mice [cKO]) to examine the effect of complex I inhibition on dopaminergic neuron function and survival during aging and on 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) treatment in vivo. Ndufs4 cKO mice did not show enhanced dopaminergic neuron loss in the substantia nigra pars compacta or dopamine-dependent motor deficits over the 24-month life span. These mice were just as susceptible to MPTP as control mice. However, compared with control mice, Ndufs4 cKO mice exhibited an age-dependent reduction of dopamine in the striatum and increased α-synuclein phosphorylation in dopaminergic neurons of the substantia nigra pars compacta. We also used an inducible Ndufs4 knockout mouse strain (Ndufs4 inducible knockout) in which Ndufs4 is conditionally deleted in all cells in adult to examine the effect of adult onset, complex I inhibition on MPTP sensitivity of dopaminergic neurons. The Ndufs4 inducible knockout mice exhibited similar sensitivity to MPTP as control littermates. These data suggest that mitochondrial complex I inhibition in dopaminergic neurons does contribute to dopamine loss and the development of α-synuclein pathology. However, it is not sufficient to cause cell-autonomous dopaminergic neuron death during the normal life span of mice. Furthermore, mitochondrial complex I inhibition does not underlie MPTP toxicity in vivo in either cell autonomous or nonautonomous manner. These results provide strong evidence that inhibition of mitochondrial complex I activity is not sufficient to cause dopaminergic neuron death during aging nor does it contribute to dopamine neuron toxicity in the MPTP model of Parkinson's disease. These findings suggest the existence of alternative mechanisms of dopaminergic neuron death independent of mitochondrial complex I inhibition. Copyright © 2015 Elsevier Inc. All rights reserved.

Patterns and Variation in Benthic Biodiversity in a Large Marine Ecosystem.

PubMed

Piacenza, Susan E; Barner, Allison K; Benkwitt, Cassandra E; Boersma, Kate S; Cerny-Chipman, Elizabeth B; Ingeman, Kurt E; Kindinger, Tye L; Lee, Jonathan D; Lindsley, Amy J; Reimer, Jessica N; Rowe, Jennifer C; Shen, Chenchen; Thompson, Kevin A; Thurman, Lindsey L; Heppell, Selina S

2015-01-01

While there is a persistent inverse relationship between latitude and species diversity across many taxa and ecosystems, deviations from this norm offer an opportunity to understand the conditions that contribute to large-scale diversity patterns. Marine systems, in particular, provide such an opportunity, as marine diversity does not always follow a strict latitudinal gradient, perhaps because several hypothesized drivers of the latitudinal diversity gradient are uncorrelated in marine systems. We used a large scale public monitoring dataset collected over an eight year period to examine benthic marine faunal biodiversity patterns for the continental shelf (55-183 m depth) and slope habitats (184-1280 m depth) off the US West Coast (47°20'N-32°40'N). We specifically asked whether marine biodiversity followed a strict latitudinal gradient, and if these latitudinal patterns varied across depth, in different benthic substrates, and over ecological time scales. Further, we subdivided our study area into three smaller regions to test whether coast-wide patterns of biodiversity held at regional scales, where local oceanographic processes tend to influence community structure and function. Overall, we found complex patterns of biodiversity on both the coast-wide and regional scales that differed by taxonomic group. Importantly, marine biodiversity was not always highest at low latitudes. We found that latitude, depth, substrate, and year were all important descriptors of fish and invertebrate diversity. Invertebrate richness and taxonomic diversity were highest at high latitudes and in deeper waters. Fish richness also increased with latitude, but exhibited a hump-shaped relationship with depth, increasing with depth up to the continental shelf break, ~200 m depth, and then decreasing in deeper waters. We found relationships between fish taxonomic and functional diversity and latitude, depth, substrate, and time at the regional scale, but not at the coast-wide scale, suggesting that coast-wide patterns can obscure important correlates at smaller scales. Our study provides insight into complex diversity patterns of the deep water soft substrate benthic ecosystems off the US West Coast.

Savannah River Site Eastern Transportation Hub: A Concept For a DOE Eastern Packaging, Staging and Maintenance Center - 13143

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

England, Jeffery L.; Adams, Karen; Maxted, Maxcine

2013-07-01

The Department of Energy (DOE) is working to de-inventory sites and consolidate hazardous materials for processing and disposal. The DOE administers a wide range of certified shipping packages for the transport of hazardous materials to include Special Nuclear Material (SNM), radioactive materials, sealed sources and radioactive wastes. A critical element to successful and safe transportation of these materials is the availability of certified shipping packages. There are over seven thousand certified packagings (i.e., Type B/Type AF) utilized within the DOE for current missions. The synergistic effects of consolidated maintenance, refurbishment, testing, certification, and costing of these services would allow formore » efficient management of the packagings inventory and to support anticipated future in-commerce shipping needs. The Savannah River Site (SRS) receives and ships radioactive materials (including SNM) and waste on a regular basis for critical missions such as consolidated storage, stabilization, purification, or disposition using H-Canyon and HB-Line. The Savannah River National Laboratory (SRNL) has the technical capability and equipment for all aspects of packaging management. SRS has the only active material processing facility in the DOE complex and is one of the sites of choice for nuclear material consolidation. SRS is a logical location to perform maintenance and periodic testing of the DOE fleet of certified packagings. This initiative envisions a DOE Eastern Packaging Staging and Maintenance Center (PSMC) at the SRS and a western hub at the Nevada National Security Site (NNSS), an active DOE Regional Disposal Site. The PSMC's would be the first place DOE would go to meet their radioactive packaging needs and the primary locations projects would go to disposition excess packaging for beneficial reuse. These two hubs would provide the centralized management of a packaging fleet rather than the current approach to design, procure, maintain and dispose of packagings on a project-by-project basis. This initiative provides significant savings in packaging costs and acceleration of project schedules. In addition to certified packaging, the PSMC would be well suited for select designs of 7A Type A packaging and Industrial Packaging. (authors)« less

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

Elvado Environmental LLC; Environmental Compliance Department Environment, Safety, and Health Division Y-12 National Security Complex

This document presents the Groundwater Protection Program (GWPP) management plan for the U.S. Department of Energy (DOE) Y-12 National Security Complex (hereafter referenced as Y-12). The Y-12 GWPP functions as the primary point-of-contact for groundwater-related issues at Y-12, provides stewardship of the extensive network of groundwater monitoring wells at Y-12, and serves as a resource for technical expertise, support, and historical data for groundwater-related activities at Y-12. These organizational functions each serve the primary programmatic purpose of the GWPP, which is to ensure that groundwater monitoring activities within areas under Y-12 administrative control provide representative data in compliance with themore » multiple purposes of applicable state and federal regulations, DOE orders, and the corporate policies of BWXT Y-12, L.L.C. (hereafter referenced as BWXT), the Y-12 management and operations (M&O) contractor for DOE. This GWPP management plan addresses the requirements of DOE Order 450.1 (BWXT Y12 S/RID) regarding the implementation of a site-wide approach for groundwater protection at each DOE facility. Additionally, this plan is a ''living'' document that is reviewed annually, revised and reissued every three years, and is formatted to provide for updating individual sections independent of the rest of the document. Section 2 includes a short description of the groundwater system at Y-12, the history of groundwater monitoring at Y-12 and the corresponding evolution of the GWPP, and an overview of ongoing Y-12 groundwater monitoring activities. Section 3 describes the key elements of the GWPP management strategy. Organizational roles and responsibilities of GWPP personnel are outlined in Section 4. Section 5 presents an overview of the GWPP project plans for applicable programmatic elements. Section 6 lists the reports, plans, and documents that are referenced for technical and administrative details.« less

Bipartite recognition of target RNAs activates DNA cleavage by the Type III-B CRISPR–Cas system

PubMed Central

Elmore, Joshua R.; Sheppard, Nolan F.; Ramia, Nancy; Deighan, Trace; Li, Hong; Terns, Rebecca M.; Terns, Michael P.

2016-01-01

CRISPR–Cas systems eliminate nucleic acid invaders in bacteria and archaea. The effector complex of the Type III-B Cmr system cleaves invader RNAs recognized by the CRISPR RNA (crRNA ) of the complex. Here we show that invader RNAs also activate the Cmr complex to cleave DNA. As has been observed for other Type III systems, Cmr eliminates plasmid invaders in Pyrococcus furiosus by a mechanism that depends on transcription of the crRNA target sequence within the plasmid. Notably, we found that the target RNA per se induces DNA cleavage by the Cmr complex in vitro. DNA cleavage activity does not depend on cleavage of the target RNA but notably does require the presence of a short sequence adjacent to the target sequence within the activating target RNA (rPAM [RNA protospacer-adjacent motif]). The activated complex does not require a target sequence (or a PAM) in the DNA substrate. Plasmid elimination by the P. furiosus Cmr system also does not require the Csx1 (CRISPR-associated Rossman fold [CARF] superfamily) protein. Plasmid silencing depends on the HD nuclease and Palm domains of the Cmr2 (Cas10 superfamily) protein. The results establish the Cmr complex as a novel DNA nuclease activated by invader RNAs containing a crRNA target sequence and a rPAM. PMID:26848045

When does alcohol hurt? A driving simulator study.

PubMed

Vollrath, Mark; Fischer, Josefine

2017-12-01

World-wide, alcohol is still a major cause of traffic accidents. The dose-related accident risk function has been found in a large number of risk studies. A plethora of laboratory studies has examined the effect of alcohol with regard to different information processing capabilities of drivers. Summarizing the results, alcohol effects occur at lower blood alcohol concentrations (BAC) the more complex the tasks get. However, in contrast, typical alcohol-related crashes are frequently single vehicle crashes but not so often crashes in complex situations like at intersections. It may be that the subjective assessment of the traffic situation and the adaptation of behavior under the influence of alcohol plays a major role in accident causation. In order to examine this hypothesis, two driving simulator studies were conducted at a target BAC of 0.5g/l comparing two (alcohol vs. placebo; n=48, Experiment 1) and three (sober, placebo and alcohol; n=63, Experiment 2) groups of subjects in two critical scenarios. The first scenario was a seemingly easy traffic situation and was supposed to lead to a relaxed driving behavior under alcohol. The second scenario involved a complex intersection situation where especially drivers under the influence of alcohol should try to concentrate and compensate their experienced alcohol effects. In all scenarios, a critical object appeared suddenly and the driver had to react fast in order to prevent a (simulated) accident. Overall, the results support the hypothesis. Accidents were more frequent for alcohol drivers as compared to placebo/sober drivers in the easy scenario, but not the complex one. The initial speed of the driver when entering the scenario seems to play a major role in the accident causation. Drivers under the influence of alcohol seem to lower their speed in complex scenarios, possibly to thus counteract alcohol effects. In seemingly easy scenarios this does not seem necessary for them and the arousing effect of alcohol may contribute to driving faster. The results are summarized in a model of alcohol-related crashes. Further in-depth analyses of real crashes would be an interesting next step to further corroborate this model. Copyright © 2017 Elsevier Ltd. All rights reserved.

Assessing the Readability of Medical Documents: A Ranking Approach.

PubMed

Zheng, Jiaping; Yu, Hong

2018-03-23

The use of electronic health record (EHR) systems with patient engagement capabilities, including viewing, downloading, and transmitting health information, has recently grown tremendously. However, using these resources to engage patients in managing their own health remains challenging due to the complex and technical nature of the EHR narratives. Our objective was to develop a machine learning-based system to assess readability levels of complex documents such as EHR notes. We collected difficulty ratings of EHR notes and Wikipedia articles using crowdsourcing from 90 readers. We built a supervised model to assess readability based on relative orders of text difficulty using both surface text features and word embeddings. We evaluated system performance using the Kendall coefficient of concordance against human ratings. Our system achieved significantly higher concordance (.734) with human annotators than did a baseline using the Flesch-Kincaid Grade Level, a widely adopted readability formula (.531). The improvement was also consistent across different disease topics. This method's concordance with an individual human user's ratings was also higher than the concordance between different human annotators (.658). We explored methods to automatically assess the readability levels of clinical narratives. Our ranking-based system using simple textual features and easy-to-learn word embeddings outperformed a widely used readability formula. Our ranking-based method can predict relative difficulties of medical documents. It is not constrained to a predefined set of readability levels, a common design in many machine learning-based systems. Furthermore, the feature set does not rely on complex processing of the documents. One potential application of our readability ranking is personalization, allowing patients to better accommodate their own background knowledge. ©Jiaping Zheng, Hong Yu. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 23.03.2018.

Verification of Space Station Secondary Power System Stability Using Design of Experiment

NASA Technical Reports Server (NTRS)

Karimi, Kamiar J.; Booker, Andrew J.; Mong, Alvin C.; Manners, Bruce

1998-01-01

This paper describes analytical methods used in verification of large DC power systems with applications to the International Space Station (ISS). Large DC power systems contain many switching power converters with negative resistor characteristics. The ISS power system presents numerous challenges with respect to system stability such as complex sources and undefined loads. The Space Station program has developed impedance specifications for sources and loads. The overall approach to system stability consists of specific hardware requirements coupled with extensive system analysis and testing. Testing of large complex distributed power systems is not practical due to size and complexity of the system. Computer modeling has been extensively used to develop hardware specifications as well as to identify system configurations for lab testing. The statistical method of Design of Experiments (DoE) is used as an analysis tool for verification of these large systems. DOE reduces the number of computer runs which are necessary to analyze the performance of a complex power system consisting of hundreds of DC/DC converters. DoE also provides valuable information about the effect of changes in system parameters on the performance of the system. DoE provides information about various operating scenarios and identification of the ones with potential for instability. In this paper we will describe how we have used computer modeling to analyze a large DC power system. A brief description of DoE is given. Examples using applications of DoE to analysis and verification of the ISS power system are provided.

Source Recertification, Refurbishment, and Transfer Logistics

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

Gastelum, Zoe N.; Duckworth, Leesa L.; Greenfield, Bryce A.

2013-09-01

The 2012 Gap Analysis of Department of Energy Radiological Sealed Sources, Standards, and Materials for Safeguards Technology Development [1] report, and the subsequent Reconciliation of Source Needs and Surpluses across the U.S. Department of Energy National Laboratory Complex [2] report, resulted in the identification of 33 requests for nuclear or radiological sealed sources for which there was potentially available, suitable material from within the U.S. Department of Energy (DOE) complex to fill the source need. Available, suitable material was defined by DOE laboratories as material slated for excess, or that required recertification or refurbishment before being used for safeguards technologymore » development. This report begins by outlining the logistical considerations required for the shipment of nuclear and radiological materials between DOE laboratories. Then, because of the limited need for transfer of matching sources, the report also offers considerations for an alternative approach – the shipment of safeguards equipment between DOE laboratories or technology testing centers. Finally, this report addresses repackaging needs for the two source requests for which there was available, suitable material within the DOE complex.« less

Soft Functionals for Hard Matter

NASA Astrophysics Data System (ADS)

Cooper, Valentino R.; Yuk, Simuck F.; Krogel, Jaron T.

Theory and computation are critical to the materials discovery process. While density functional theory (DFT) has become the standard for predicting materials properties, it is often plagued by inaccuracies in the underlying exchange-correlation functionals. Using high-throughput DFT calculations we explore the accuracy of various exchange-correlation functionals for modeling the structural and thermodynamic properties of a wide range of complex oxides. In particular, we examine the feasibility of using the nonlocal van der Waals density correlation functional with C09 exchange (C09x), which was designed for sparsely packed soft matter, for investigating the properties of hard matter like bulk oxides. Preliminary results show unprecedented performance for some prototypical bulk ferroelectrics, which can be correlated with similarities between C09x and PBEsol. This effort lays the groundwork for understanding how these soft functionals can be employed as general purpose functionals for studying a wide range of materials where strong internal bonds and nonlocal interactions coexist. Research was sponsored by the US DOE, Office of Science, BES, MSED and Early Career Research Programs and used resources at NERSC.

A New MI-Based Visualization Aided Validation Index for Mining Big Longitudinal Web Trial Data

PubMed Central

Zhang, Zhaoyang; Fang, Hua; Wang, Honggang

2016-01-01

Web-delivered clinical trials generate big complex data. To help untangle the heterogeneity of treatment effects, unsupervised learning methods have been widely applied. However, identifying valid patterns is a priority but challenging issue for these methods. This paper, built upon our previous research on multiple imputation (MI)-based fuzzy clustering and validation, proposes a new MI-based Visualization-aided validation index (MIVOOS) to determine the optimal number of clusters for big incomplete longitudinal Web-trial data with inflated zeros. Different from a recently developed fuzzy clustering validation index, MIVOOS uses a more suitable overlap and separation measures for Web-trial data but does not depend on the choice of fuzzifiers as the widely used Xie and Beni (XB) index. Through optimizing the view angles of 3-D projections using Sammon mapping, the optimal 2-D projection-guided MIVOOS is obtained to better visualize and verify the patterns in conjunction with trajectory patterns. Compared with XB and VOS, our newly proposed MIVOOS shows its robustness in validating big Web-trial data under different missing data mechanisms using real and simulated Web-trial data. PMID:27482473

Remote Sensing of Suspended Sediments and Shallow Coastal Waters

NASA Technical Reports Server (NTRS)

Li, Rong-Rong; Kaufman, Yoram J.; Gao, Bo-Cai; Davis, Curtiss O.

2002-01-01

Ocean color sensors were designed mainly for remote sensing of chlorophyll concentrations over the clear open oceanic areas (case 1 water) using channels between 0.4 and 0.86 micrometers. The Moderate Resolution Imaging Spectroradiometer (MODIS) launched on the NASA Terra and Aqua Spacecrafts is equipped with narrow channels located within a wider wavelength range between 0.4 and 2.5 micrometers for a variety of remote sensing applications. The wide spectral range can provide improved capabilities for remote sensing of the more complex and turbid coastal waters (case 2 water) and for improved atmospheric corrections for Ocean scenes. In this article, we describe an empirical algorithm that uses this wide spectral range to identifying areas with suspended sediments in turbid waters and shallow waters with bottom reflections. The algorithm takes advantage of the strong water absorption at wavelengths longer than 1 micrometer that does not allow illumination of sediments in the water or a shallow ocean floor. MODIS data acquired over the east coast of China, west coast of Africa, Arabian Sea, Mississippi Delta, and west coast of Florida are used in this study.

An Evaluation of the Effectiveness of Local Site-Specific Advisory Boards for US Department of Energy Environmental Restoration Programs

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

Bradbury, J.A.; Branch, K.M.

1999-03-12

In the early 1990s, the US Department of Energy (DOE) undertook a major new effort to involve community stakeholders in decisions that would affect them and their communities and interests. An important component of this effort was the establishment of local Site-Specific Advisory Boards (SSABs) at 12 DOE environmental remediation sites. These boards were a formal representation of a change in the way DOE conducts its missions, adding consideration of community concerns and values to the Department's decision-making processes. DOE's purpose in creating the SSAB Initiative was to obtain broadly based, independent, consensus advice and recommendations on issues that havemore » the potential to affect communities surrounding DOE sites, so that it could formulate policies that could be implemented with community consent. Because the boards represented a significant commitment by DOE to change its relationships with community stakeholders, the Department has conducted several assessments of the boards. In 1996 and 1997 a survey was administered to board members and others involved in the work of the boards (DOE/EM 0311, 1996; DOE/EM, 1997). As part of the first survey, DOE and the boards established a set of performance criteria. The surveys provided data that revealed wide variations in board performance and significant change over time. To gain a better understanding of the factors affecting board performance, DOE initiated a more in-depth, qualitative study of nine of the boards across the complex. This study focused on identifying and analyzing the factors affecting board performance and presenting that information in a format that helped the boards and DOE gain insight into their strengths and weaknesses and learn from one another. This report presents the results of this in-depth study. It begins with an overview report that identifies and discusses the six factors that were found to affect board performance. The overview report provides the framework and rationale for the information presented in the nine individual site reports, which follow in alphabetical order. The individual site reports describe each of the boards in terms of the six factors affecting board performance, beginning with a brief summary of the history and setting for the local SSAB. They end with a list of issues raised by members and the researchers' assessment of the key accomplishments and challenges facing the board.« less

28 CFR 83.105 - Does this part apply to me?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 28 Judicial Administration 2 2011-07-01 2011-07-01 false Does this part apply to me? 83.105 Section 83.105 Judicial Administration DEPARTMENT OF JUSTICE (CONTINUED) GOVERNMENT-WIDE REQUIREMENTS FOR DRUG-FREE WORKPLACE (GRANTS) Purpose and Coverage § 83.105 Does this part apply to me? (a) Portions of...

28 CFR 83.105 - Does this part apply to me?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Does this part apply to me? 83.105 Section 83.105 Judicial Administration DEPARTMENT OF JUSTICE (CONTINUED) GOVERNMENT-WIDE REQUIREMENTS FOR DRUG-FREE WORKPLACE (GRANTS) Purpose and Coverage § 83.105 Does this part apply to me? (a) Portions of...

28 CFR 83.105 - Does this part apply to me?

Code of Federal Regulations, 2013 CFR

2013-07-01

... 28 Judicial Administration 2 2013-07-01 2013-07-01 false Does this part apply to me? 83.105 Section 83.105 Judicial Administration DEPARTMENT OF JUSTICE (CONTINUED) GOVERNMENT-WIDE REQUIREMENTS FOR DRUG-FREE WORKPLACE (GRANTS) Purpose and Coverage § 83.105 Does this part apply to me? (a) Portions of...

28 CFR 83.105 - Does this part apply to me?

Code of Federal Regulations, 2012 CFR

2012-07-01

... 28 Judicial Administration 2 2012-07-01 2012-07-01 false Does this part apply to me? 83.105 Section 83.105 Judicial Administration DEPARTMENT OF JUSTICE (CONTINUED) GOVERNMENT-WIDE REQUIREMENTS FOR DRUG-FREE WORKPLACE (GRANTS) Purpose and Coverage § 83.105 Does this part apply to me? (a) Portions of...

Protein-Protein Docking in Drug Design and Discovery.

PubMed

Kaczor, Agnieszka A; Bartuzi, Damian; Stępniewski, Tomasz Maciej; Matosiuk, Dariusz; Selent, Jana

2018-01-01

Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

Common occupational classification system - revision 3

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

Stahlman, E.J.; Lewis, R.E.

1996-05-01

Workforce planning has become an increasing concern within the DOE community as the Office of Environmental Restoration and Waste Management (ER/WM or EM) seeks to consolidate and refocus its activities and the Office of Defense Programs (DP) closes production sites. Attempts to manage the growth and skills mix of the EM workforce while retaining the critical skills of the DP workforce have been difficult due to the lack of a consistent set of occupational titles and definitions across the complex. Two reasons for this difficulty may be cited. First, classification systems commonly used in industry often fail to cover inmore » sufficient depth the unique demands of DOE`s nuclear energy and research community. Second, the government practice of contracting the operation of government facilities to the private sector has introduced numerous contractor-specific classification schemes to the DOE complex. As a result, sites/contractors report their workforce needs using unique classification systems. It becomes difficult, therefore, to roll these data up to the national level necessary to support strategic planning and analysis. The Common Occupational Classification System (COCS) is designed to overcome these workforce planning barriers. The COCS is based on earlier workforce planning activities and the input of technical, workforce planning, and human resource managers from across the DOE complex. It provides a set of mutually-exclusive occupation titles and definitions that cover the broad range of activities present in the DOE complex. The COCS is not a required record-keeping or data management guide. Neither is it intended to replace contractor/DOE-specific classification systems. Instead, the system provides a consistent, high- level, functional structure of occupations to which contractors can crosswalk (map) their job titles.« less

De Novo Centromere Formation and Centromeric Sequence Expansion in Wheat and its Wide Hybrids.

PubMed

Guo, Xiang; Su, Handong; Shi, Qinghua; Fu, Shulan; Wang, Jing; Zhang, Xiangqi; Hu, Zanmin; Han, Fangpu

2016-04-01

Centromeres typically contain tandem repeat sequences, but centromere function does not necessarily depend on these sequences. We identified functional centromeres with significant quantitative changes in the centromeric retrotransposons of wheat (CRW) contents in wheat aneuploids (Triticum aestivum) and the offspring of wheat wide hybrids. The CRW signals were strongly reduced or essentially lost in some wheat ditelosomic lines and in the addition lines from the wide hybrids. The total loss of the CRW sequences but the presence of CENH3 in these lines suggests that the centromeres were formed de novo. In wheat and its wide hybrids, which carry large complex genomes or no sequenced genome, we performed CENH3-ChIP-dot-blot methods alone or in combination with CENH3-ChIP-seq and identified the ectopic genomic sequences present at the new centromeres. In adcdition, the transcription of the identified DNA sequences was remarkably increased at the new centromere, suggesting that the transcription of the corresponding sequences may be associated with de novo centromere formation. Stable alien chromosomes with two and three regions containing CRW sequences induced by centromere breakage were observed in the wheat-Th. elongatum hybrid derivatives, but only one was a functional centromere. In wheat-rye (Secale cereale) hybrids, the rye centromere-specific sequences spread along the chromosome arms and may have caused centromere expansion. Frequent and significant quantitative alterations in the centromere sequence via chromosomal rearrangement have been systematically described in wheat wide hybridizations, which may affect the retention or loss of the alien chromosomes in the hybrids. Thus, the centromere behavior in wide crosses likely has an important impact on the generation of biodiversity, which ultimately has implications for speciation.

De Novo Centromere Formation and Centromeric Sequence Expansion in Wheat and its Wide Hybrids

PubMed Central

Fu, Shulan; Wang, Jing; Zhang, Xiangqi; Hu, Zanmin; Han, Fangpu

2016-01-01

Centromeres typically contain tandem repeat sequences, but centromere function does not necessarily depend on these sequences. We identified functional centromeres with significant quantitative changes in the centromeric retrotransposons of wheat (CRW) contents in wheat aneuploids (Triticum aestivum) and the offspring of wheat wide hybrids. The CRW signals were strongly reduced or essentially lost in some wheat ditelosomic lines and in the addition lines from the wide hybrids. The total loss of the CRW sequences but the presence of CENH3 in these lines suggests that the centromeres were formed de novo. In wheat and its wide hybrids, which carry large complex genomes or no sequenced genome, we performed CENH3-ChIP-dot-blot methods alone or in combination with CENH3-ChIP-seq and identified the ectopic genomic sequences present at the new centromeres. In adcdition, the transcription of the identified DNA sequences was remarkably increased at the new centromere, suggesting that the transcription of the corresponding sequences may be associated with de novo centromere formation. Stable alien chromosomes with two and three regions containing CRW sequences induced by centromere breakage were observed in the wheat-Th. elongatum hybrid derivatives, but only one was a functional centromere. In wheat-rye (Secale cereale) hybrids, the rye centromere-specific sequences spread along the chromosome arms and may have caused centromere expansion. Frequent and significant quantitative alterations in the centromere sequence via chromosomal rearrangement have been systematically described in wheat wide hybridizations, which may affect the retention or loss of the alien chromosomes in the hybrids. Thus, the centromere behavior in wide crosses likely has an important impact on the generation of biodiversity, which ultimately has implications for speciation. PMID:27110907

The value of electrocardiography for differential diagnosis in wide QRS complex tachycardia.

PubMed

Sousa, Pedro A; Pereira, Salomé; Candeias, Rui; de Jesus, Ilídio

2014-03-01

Correct diagnosis in wide QRS complex tachycardia remains a challenge. Differential diagnosis between ventricular and supraventricular tachycardia has important therapeutic and prognostic implications, and although data from clinical history and physical examination may suggest a particular origin, it is the 12-lead surface electrocardiogram that usually enables this differentiation. Since 1978, various electrocardiographic criteria have been proposed for the differential diagnosis of wide complex tachycardias, particularly the presence of atrioventricular dissociation, and the axis, duration and morphology of QRS complexes. Despite the wide variety of criteria, diagnosis is still often difficult, and errors can have serious consequences. To reduce such errors, several differential diagnosis algorithms have been proposed since 1991. However, in a small percentage of wide QRS tachycardias the diagnosis remains uncertain and in these the wisest decision is to treat them as ventricular tachycardias. The authors' objective was to review the main electrocardiographic criteria and differential diagnosis algorithms of wide QRS tachycardia. Copyright © 2012 Sociedade Portuguesa de Cardiologia. Published by Elsevier España. All rights reserved.

The future of image-guided radiotherapy-is image everything?

PubMed

Noble, David J; Burnet, Neil G

2018-05-17

MR-based image-guided (IG) radiotherapy via all-in-one MR treatment units (MR-linacs) is one of the hottest topics in contemporary radiotherapy research. From ingenious engineering solutions to complex physical problems, researchers have developed machines with the promise of superior image quality, and all the advantages this may confer. Benefits include better tumour visualisation, online adaptation and the potential for image biomarker-based personalised RT. However, it is important to remember that the technical challenges are real. In many instances, they are skillfully managed rather than abolished, a point illustrated by the wide variety of MR-linac designs. The proposed benefits also deserve careful inspection. Better visibility of the primary tumour on an IG scan cannot be bad, but does not automatically equate to better IG, which often depends on a more generalised match to daily anatomy. MR-linac will undoubtedly be a rich milieu to search for IMBs, but these will need to be carefully validated, and similar work with CT-based biomarkers using existing, cheaper, and more widely available hardware is currently ongoing. Online adaptation is an attractive concept, but practicalities are complex, and more work is required to understand which patients will benefit from plan adaptation, and when. Finally, the issue of cost cannot be overlooked, nor can the research community's responsibilities to global healthcare inequalities. MR-linac is an exciting and ingenious technology, which merits both investment and research. It may not, however, have the future to itself.

Nanotechnology for sustainability: what does nanotechnology offer to address complex sustainability problems?

NASA Astrophysics Data System (ADS)

Wiek, Arnim; Foley, Rider W.; Guston, David H.

2012-09-01

Nanotechnology is widely associated with the promise of positively contributing to sustainability. However, this view often focuses on end-of-pipe applications, for instance, for water purification or energy efficiency, and relies on a narrow concept of sustainability. Approaching sustainability problems and solution options from a comprehensive and systemic perspective instead may yield quite different conclusions about the contribution of nanotechnology to sustainability. This study conceptualizes sustainability problems as complex constellations with several potential intervention points and amenable to different solution options. The study presents results from interdisciplinary workshops and literature reviews that appraise the contribution of the selected nanotechnologies to mitigate such problems. The study focuses exemplarily on the urban context to make the appraisals tangible and relevant. The solution potential of nanotechnology is explored not only for well-known urban sustainability problems such as water contamination and energy use but also for less obvious ones such as childhood obesity. Results indicate not only potentials but also limitations of nanotechnology's contribution to sustainability and can inform anticipatory governance of nanotechnology in general, and in the urban context in particular.

An underwater robo-leader for collective motion studies

NASA Astrophysics Data System (ADS)

Sanchez, Yair; Wilhelmus, Monica M.

2016-11-01

A wide range of aquatic species, from bacteria to large tuna, exhibits collective behavior. It has long been hypothesized that the formation of complex configurations brings an energetic advantage to the members of a group as well as protection against larger predators or harmful agents. Lately, however, laboratory experiments have suggested that both the physics and the behavioral aspects of collective motion yield more complexity than previously attributed. With the goal to understand the fluid mechanical implications behind collective motion in a laboratory setting, we have developed a new device to induce this behavior on demand. Following recent studies of lab-induced vertical migration of Artemia salina, we have designed and constructed a remotely controlled underwater robotic swimmer that acts as a leader for groups of phototactic organisms. Preliminary quantitative flow visualizations done during vertical migration of brine shrimp show that this new instrument does induce collective motion in the laboratory. With this setup, we can address the hydrodynamic effect of having different swarm configurations, a variable that so far has been challenging to study in a controllable and reproducible manner.

On the accuracy of the LSC-IVR approach for excitation energy transfer in molecular aggregates

NASA Astrophysics Data System (ADS)

Teh, Hung-Hsuan; Cheng, Yuan-Chung

2017-04-01

We investigate the applicability of the linearized semiclassical initial value representation (LSC-IVR) method to excitation energy transfer (EET) problems in molecular aggregates by simulating the EET dynamics of a dimer model in a wide range of parameter regime and comparing the results to those obtained from a numerically exact method. It is found that the LSC-IVR approach yields accurate population relaxation rates and decoherence rates in a broad parameter regime. However, the classical approximation imposed by the LSC-IVR method does not satisfy the detailed balance condition, generally leading to incorrect equilibrium populations. Based on this observation, we propose a post-processing algorithm to solve the long time equilibrium problem and demonstrate that this long-time correction method successfully removed the deviations from exact results for the LSC-IVR method in all of the regimes studied in this work. Finally, we apply the LSC-IVR method to simulate EET dynamics in the photosynthetic Fenna-Matthews-Olson complex system, demonstrating that the LSC-IVR method with long-time correction provides excellent description of coherent EET dynamics in this typical photosynthetic pigment-protein complex.

The NGA-DOE grant to examine critical issues related to radioactive waste and materials disposition involving DOE facilities. Quarterly report, October 1--December 31, 1997

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

Beauchesne, A.M.

1997-12-31

Topics explored through this project include: decisions involving disposal of mixed, low-level, and transuranic (TRU) waste and disposition of nuclear materials; decisions involving DOE budget requests and their effect on environmental cleanup and compliance at DOE facilities; strategies to treat mixed, low-level, and transuranic (TRU) waste and their effect on individual sites in the complex; changes to the FFCA site treatment plans as a result of proposals in the EM 2006 cleanup plans and contractor integration analysis; interstate waste and materials shipments; and reforms to existing RCRA and CERCLA regulations/guidance to address regulatory overlap and risks posed by DOE wastes.more » The work accomplished by the NGA project team during the past four months can be categorized as follows: maintained open communication with DOE on a variety of activities and issues within the DOE environmental management complex; and maintained communication with NGA Federal Facilities Compliance Task Force members regarding DOE efforts to formulate a configuration for mixed low-level waste and low-level treatment and disposal, DOE activities in the area of the Hazardous Waste Identification Rule, and DOE`s proposed National Dialogue.« less

Across-cohort QC analyses of GWAS summary statistics from complex traits.

PubMed

Chen, Guo-Bo; Lee, Sang Hong; Robinson, Matthew R; Trzaskowski, Maciej; Zhu, Zhi-Xiang; Winkler, Thomas W; Day, Felix R; Croteau-Chonka, Damien C; Wood, Andrew R; Locke, Adam E; Kutalik, Zoltán; Loos, Ruth J F; Frayling, Timothy M; Hirschhorn, Joel N; Yang, Jian; Wray, Naomi R; Visscher, Peter M

2016-01-01

Genome-wide association studies (GWASs) have been successful in discovering SNP trait associations for many quantitative traits and common diseases. Typically, the effect sizes of SNP alleles are very small and this requires large genome-wide association meta-analyses (GWAMAs) to maximize statistical power. A trend towards ever-larger GWAMA is likely to continue, yet dealing with summary statistics from hundreds of cohorts increases logistical and quality control problems, including unknown sample overlap, and these can lead to both false positive and false negative findings. In this study, we propose four metrics and visualization tools for GWAMA, using summary statistics from cohort-level GWASs. We propose methods to examine the concordance between demographic information, and summary statistics and methods to investigate sample overlap. (I) We use the population genetics F st statistic to verify the genetic origin of each cohort and their geographic location, and demonstrate using GWAMA data from the GIANT Consortium that geographic locations of cohorts can be recovered and outlier cohorts can be detected. (II) We conduct principal component analysis based on reported allele frequencies, and are able to recover the ancestral information for each cohort. (III) We propose a new statistic that uses the reported allelic effect sizes and their standard errors to identify significant sample overlap or heterogeneity between pairs of cohorts. (IV) To quantify unknown sample overlap across all pairs of cohorts, we propose a method that uses randomly generated genetic predictors that does not require the sharing of individual-level genotype data and does not breach individual privacy.

Across-cohort QC analyses of GWAS summary statistics from complex traits

PubMed Central

Chen, Guo-Bo; Lee, Sang Hong; Robinson, Matthew R; Trzaskowski, Maciej; Zhu, Zhi-Xiang; Winkler, Thomas W; Day, Felix R; Croteau-Chonka, Damien C; Wood, Andrew R; Locke, Adam E; Kutalik, Zoltán; Loos, Ruth J F; Frayling, Timothy M; Hirschhorn, Joel N; Yang, Jian; Wray, Naomi R; Visscher, Peter M

2017-01-01

Genome-wide association studies (GWASs) have been successful in discovering SNP trait associations for many quantitative traits and common diseases. Typically, the effect sizes of SNP alleles are very small and this requires large genome-wide association meta-analyses (GWAMAs) to maximize statistical power. A trend towards ever-larger GWAMA is likely to continue, yet dealing with summary statistics from hundreds of cohorts increases logistical and quality control problems, including unknown sample overlap, and these can lead to both false positive and false negative findings. In this study, we propose four metrics and visualization tools for GWAMA, using summary statistics from cohort-level GWASs. We propose methods to examine the concordance between demographic information, and summary statistics and methods to investigate sample overlap. (I) We use the population genetics Fst statistic to verify the genetic origin of each cohort and their geographic location, and demonstrate using GWAMA data from the GIANT Consortium that geographic locations of cohorts can be recovered and outlier cohorts can be detected. (II) We conduct principal component analysis based on reported allele frequencies, and are able to recover the ancestral information for each cohort. (III) We propose a new statistic that uses the reported allelic effect sizes and their standard errors to identify significant sample overlap or heterogeneity between pairs of cohorts. (IV) To quantify unknown sample overlap across all pairs of cohorts, we propose a method that uses randomly generated genetic predictors that does not require the sharing of individual-level genotype data and does not breach individual privacy. PMID:27552965

Performance characterization of complex fuel port geometries for hybrid rocket fuel grains

NASA Astrophysics Data System (ADS)

Bath, Andrew

This research investigated the 3D printing and burning of fuel grains with complex geometry and the development of software capable of modeling and predicting the regression of a cross-section of these complex fuel grains. The software developed did predict the geometry to a fair degree of accuracy, especially when enhanced corner rounding was turned on. The model does have some drawbacks, notably being relatively slow, and does not perfectly predict the regression. If corner rounding is turned off, however, the model does become much faster; although less accurate, this method does still predict a relatively accurate resulting burn geometry, and is fast enough to be used for performance-tuning or genetic algorithms. In addition to the modeling method, preliminary investigations into the burning behavior of fuel grains with a helical flow path were performed. The helix fuel grains have a regression rate of nearly 3 times that of any other fuel grain geometry, primarily due to the enhancement of the friction coefficient between the flow and flow path.

Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein–DNA Complex

PubMed Central

2016-01-01

Metal ion cofactors can alter the energetics and specificity of sequence specific protein–DNA interactions, but it is unknown if the underlying effects on structure and dynamics are local or dispersed throughout the protein–DNA complex. This work uses EcoRV endonuclease as a model, and catalytically inactive lanthanide ions, which replace the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations indicate that four Lu3+ or two La3+ cations bind, and two new crystal structures confirm that Lu3+ binding is confined to the active sites. NMR spectra show that the metal-free EcoRV complex with cognate (GATATC) DNA is structurally distinct from the nonspecific complex, and that metal ion binding sites are not assembled in the nonspecific complex. NMR chemical shift perturbations were determined for 1H–15N amide resonances, for 1H–13C Ile-δ-CH3 resonances, and for stereospecifically assigned Leu-δ-CH3 and Val-γ-CH3 resonances. Many chemical shifts throughout the cognate complex are unperturbed, so metal binding does not induce major conformational changes. However, some large perturbations of amide and side chain methyl resonances occur as far as 34 Å from the metal ions. Concerted changes in specific residues imply that local effects of metal binding are propagated via a β-sheet and an α-helix. Both amide and methyl resonance perturbations indicate changes in the interface between subunits of the EcoRV homodimer. Bound metal ions also affect amide hydrogen exchange rates for distant residues, including a distant subdomain that contacts DNA phosphates and promotes DNA bending, showing that metal ions in the active sites, which relieve electrostatic repulsion between protein and DNA, cause changes in slow dynamics throughout the complex. PMID:27786446

An ASM/ADM model interface for dynamic plant-wide simulation.

PubMed

Nopens, Ingmar; Batstone, Damien J; Copp, John B; Jeppsson, Ulf; Volcke, Eveline; Alex, Jens; Vanrolleghem, Peter A

2009-04-01

Mathematical modelling has proven to be very useful in process design, operation and optimisation. A recent trend in WWTP modelling is to include the different subunits in so-called plant-wide models rather than focusing on parts of the entire process. One example of a typical plant-wide model is the coupling of an upstream activated sludge plant (including primary settler, and secondary clarifier) to an anaerobic digester for sludge digestion. One of the key challenges when coupling these processes has been the definition of an interface between the well accepted activated sludge model (ASM1) and anaerobic digestion model (ADM1). Current characterisation and interface models have key limitations, the most critical of which is the over-use of X(c) (or lumped complex) variable as a main input to the ADM1. Over-use of X(c) does not allow for variation of degradability, carbon oxidation state or nitrogen content. In addition, achieving a target influent pH through the proper definition of the ionic system can be difficult. In this paper, we define an interface and characterisation model that maps degradable components directly to carbohydrates, proteins and lipids (and their soluble analogues), as well as organic acids, rather than using X(c). While this interface has been designed for use with the Benchmark Simulation Model No. 2 (BSM2), it is widely applicable to ADM1 input characterisation in general. We have demonstrated the model both hypothetically (BSM2), and practically on a full-scale anaerobic digester treating sewage sludge.

Mask fabrication and its applications to extreme ultra-violet diffractive optics

NASA Astrophysics Data System (ADS)

Cheng, Yang-Chun

Short-wavelength radiation around 13nm of wavelength (Extreme Ultra-Violet, EUV) is being considered for patterning microcircuits, and other electronic chips with dimensions in the nanometer range. Interferometric Lithography (IL) uses two beams of radiation to form high-resolution interference fringes, as small as half the wavelength of the radiation used. As a preliminary step toward manufacturing technology, IL can be used to study the imaging properties of materials in a wide spectral range and at nanoscale dimensions. A simple implementation of IL uses two transmission diffraction gratings to form the interference pattern. More complex interference patterns can be created by using different types of transmission gratings. In this thesis, I describe the development of a EUV lithography system that uses diffractive optical elements (DOEs), from simple gratings to holographic structures. The exposure system is setup on a EUV undulator beamline at the Synchrotron Radiation Center, in the Center for NanoTechnology clean room. The setup of the EUV exposure system is relatively simple, while the design and fabrication of the DOE "mask" is complex, and relies on advanced nanofabrication techniques. The EUV interferometric lithography provides reliable EUV exposures of line/space patterns and is ideal for the development of EUV resist technology. In this thesis I explore the fabrication of these DOE for the EUV range, and discuss the processes I have developed for the fabrication of ultra-thin membranes. In addition, I discuss EUV holographic lithography and generalized Talbot imaging techniques to extend the capability of our EUV-IL system to pattern arbitrary shapes, using more coherent sources than the undulator. In a series of experiments, we have demonstrated the use of a soft X-ray (EUV) laser as effective source for EUV lithography. EUV-IL, as implemented at CNTech, is being used by several companies and research organizations to characterize photoresist materials.

Reliable Wide-Area Wavelength Division Multiplexing Passive Optical Network Accommodating Gigabit Ethernet and 10-Gb Ethernet Services

NASA Astrophysics Data System (ADS)

Nakamura, Hirotaka; Suzuki, Hiro; Kani, Jun-Ichi; Iwatsuki, Katsumi

2006-05-01

This paper proposes and demonstrates a reliable wide-area wavelength-division-multiplexing passive optical network (WDM-PON) with a wavelength-shifted protection scheme. This protection scheme utilizes the cyclic property of 2 × N athermal arrayed-waveguide grating and two kinds of wavelength allocations, each of which is assigned for working and protection, respectively. Compared with conventional protection schemes, this scheme does not need a 3-dB optical coupler, thus leading to ensure the large loss budget that is suited for wide-area WDM-PONs. It also features a passive access node and does not have a protection function in the optical network unit (ONU). The feasibility of the proposed scheme is experimentally confirmed by the carrier-distributed WDM-PON with gigabit Ethernet interface (GbE-IF) and 10-GbE-IF, in which the ONU does not employ a light source, and all wavelengths for upstream signals are centralized and distributed from the central office.

An Efficient Image Compressor for Charge Coupled Devices Camera

PubMed Central

Li, Jin; Xing, Fei; You, Zheng

2014-01-01

Recently, the discrete wavelet transforms- (DWT-) based compressor, such as JPEG2000 and CCSDS-IDC, is widely seen as the state of the art compression scheme for charge coupled devices (CCD) camera. However, CCD images project on the DWT basis to produce a large number of large amplitude high-frequency coefficients because these images have a large number of complex texture and contour information, which are disadvantage for the later coding. In this paper, we proposed a low-complexity posttransform coupled with compressing sensing (PT-CS) compression approach for remote sensing image. First, the DWT is applied to the remote sensing image. Then, a pair base posttransform is applied to the DWT coefficients. The pair base are DCT base and Hadamard base, which can be used on the high and low bit-rate, respectively. The best posttransform is selected by the l p-norm-based approach. The posttransform is considered as the sparse representation stage of CS. The posttransform coefficients are resampled by sensing measurement matrix. Experimental results on on-board CCD camera images show that the proposed approach significantly outperforms the CCSDS-IDC-based coder, and its performance is comparable to that of the JPEG2000 at low bit rate and it does not have the high excessive implementation complexity of JPEG2000. PMID:25114977

Air monitoring for volatile organic compounds at the Pilot Plant Complex, Aberdeen Proving Ground, Maryland

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

Schneider, J.F.; O`Neill, H.J.; Raphaelian, L.A.

1995-03-01

The US Army`s Aberdeen Proving Ground has been a test site for a variety of munitions, including chemical warfare agents (CWA). The Pilot Plant Complex (PPC) at Aberdeen was the site of development, manufacture, storage, and disposal of CWA. Deterioration of the buildings and violations of environmental laws led to closure of the complex in 1986. Since that time, all equipment, piping, and conduit in the buildings have been removed. The buildings have been declared free of surface CWA contamination as a result of air sampling using the military system. However, no air sampling has been done to determine ifmore » other hazardous volatile organic compounds are present in the PPC, although a wide range of toxic and/or hazardous materials other than CWA was used in the PPC. The assumption has been that the air in the PPC is not hazardous. The purpose of this air-monitoring study was to screen the indoor air in the PPC to confirm the assumption that the air does not contain volatile organic contaminants at levels that would endanger persons in the buildings. A secondary purpose was to identify any potential sources of volatile organic contaminants that need to be monitored in subsequent sampling efforts.« less

Dynamic Uncertain Causality Graph for Knowledge Representation and Probabilistic Reasoning: Directed Cyclic Graph and Joint Probability Distribution.

PubMed

Zhang, Qin

2015-07-01

Probabilistic graphical models (PGMs) such as Bayesian network (BN) have been widely applied in uncertain causality representation and probabilistic reasoning. Dynamic uncertain causality graph (DUCG) is a newly presented model of PGMs, which can be applied to fault diagnosis of large and complex industrial systems, disease diagnosis, and so on. The basic methodology of DUCG has been previously presented, in which only the directed acyclic graph (DAG) was addressed. However, the mathematical meaning of DUCG was not discussed. In this paper, the DUCG with directed cyclic graphs (DCGs) is addressed. In contrast, BN does not allow DCGs, as otherwise the conditional independence will not be satisfied. The inference algorithm for the DUCG with DCGs is presented, which not only extends the capabilities of DUCG from DAGs to DCGs but also enables users to decompose a large and complex DUCG into a set of small, simple sub-DUCGs, so that a large and complex knowledge base can be easily constructed, understood, and maintained. The basic mathematical definition of a complete DUCG with or without DCGs is proved to be a joint probability distribution (JPD) over a set of random variables. The incomplete DUCG as a part of a complete DUCG may represent a part of JPD. Examples are provided to illustrate the methodology.

Thermo-mechanical performance of precision C/SiC mounts

NASA Astrophysics Data System (ADS)

Goodman, William A.; Mueller, Claus E.; Jacoby, Marc T.; Wells, Jim D.

2001-12-01

For complex shaped, lightweight, high precision opto- mechanical structures that must operate in adverse environments and over wide ranges of temperature, we consider IABG's optical grade silicon carbide composite ceramic (C/SiC) as the material of choice. C/SiC employs conventional NC machining/milling equipment to rapidly fabricate near-net shape parts, providing substantial schedule, cost, and risk savings for high precision components. Unlike powder based SiC ceramics, C/SiC does not experience significant shrinkage during processing, nor does it suffer from incomplete densification. If required, e.g. for large-size components, a fully-monolithic ceramic joining technique can be applied. Generally, the thermal and mechanical properties of C/SiC are tunable in certain ranges by modifying certain process steps. This paper focuses on the thermo-mechanical performance of new, high precision mounts designed by Schafer Corporation and manufactured by IABG. The mounts were manufactured using standard optical grade C/SiC (formulation internally called A-3). The A-3 formulation has a near-perfect CTE match with silicon, making it the ideal material to athermally support Schafer produced Silicon Lightweight Mirrors (SLMs) that will operate in a cryogenic environment. Corresponding thermo- mechanical testing and analysis is presented in this manuscript.

Nuclear waste transportation: case studies of identifying stakeholder risk information needs.

PubMed Central

Drew, Christina H; Grace, Deirdre A; Silbernagel, Susan M; Hemmings, Erin S; Smith, Alan; Griffith, William C; Takaro, Timothy K; Faustman, Elaine M

2003-01-01

The U.S. Department of Energy (DOE) is responsible for the cleanup of our nation's nuclear legacy, involving complex decisions about how and where to dispose of nuclear waste and how to transport it to its ultimate disposal site. It is widely recognized that a broad range of stakeholders and tribes should be involved in this kind of decision. All too frequently, however, stakeholders and tribes are only invited to participate by commenting on processes and activities that are near completion; they are not included in the problem formulation stages. Moreover, it is often assumed that high levels of complexity and uncertainty prevent meaningful participation by these groups. Considering the types of information that stakeholders and tribes need to be able to participate in the full life cycle of decision making is critical for improving participation and transparency of decision making. Toward this objective, the Consortium for Risk Evaluation with Stakeholder Participation (CRESP) participated in three public processes relating to nuclear waste transportation and disposal in 1997-1998. First, CRESP organized focus groups to identify concerns about nuclear waste transportation. Second, CRESP conducted exit surveys at regional public workshops held by DOE to get input from stakeholders on intersite waste transfer issues. Third, CRESP developed visual tools to synthesize technical information and allow stakeholders and tribes with varying levels of knowledge about nuclear waste to participate in meaningful discussion. In this article we share the results of the CRESP findings, discuss common themes arising from these interactions, and comment on special considerations needed to facilitate stakeholder and tribal participation in similar decision-making processes. PMID:12611653

Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence.

PubMed

Pereira, Ricardo J; Monahan, William B; Wake, David B

2011-07-06

Reproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ring species complex Ensatina eschscholtzii in order to assess the relative contribution of genetic and ecological divergence for the development of RI. By augmenting previous genetic datasets and adding new ecological data, we quantify levels of genetic and ecological divergence between populations and test how they correlate with a restriction of genetic admixture upon secondary contact. Our results indicate that the isolated effect of ecological divergence between parental populations does not result in reproductively isolated taxa, even when genetic transitions between parental taxa are narrow. Instead, processes associated with overall genetic divergence are the best predictors of reproductive isolation, and when parental taxa diverge in nuclear markers we observe a complete cessation of hybridization, even to sympatric occurrence of distinct evolutionary lineages. Although every parental population has diverged in mitochondrial DNA, its degree of divergence does not predict the extent of RI. These results show that in Ensatina, the evolutionary outcomes of ecological divergence differ from those of genetic divergence. While evident properties of taxa may emerge via ecological divergence, such as adaptation to local environment, RI is likely to be a byproduct of processes that contribute to overall genetic divergence, such as time in geographic isolation, rather than being a direct outcome of local adaptation.

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

Crolley, R.; Thompson, M.

There has been a need for a faster and cheaper deployment model for information technology (IT) solutions to address waste management needs at US Department of Energy (DOE) complex sites for years. Budget constraints, challenges in deploying new technologies, frequent travel, and increased job demands for existing employees have prevented IT organizations from staying abreast of new technologies or deploying them quickly. Despite such challenges, IT organizations have added significant value to waste management handling through better worker safety, tracking, characterization, and disposition at DOE complex sites. Systems developed for site-specific missions have broad applicability to waste management challenges andmore » in many cases have been expanded to meet other waste missions. Radio frequency identification (RFID) and global positioning satellite (GPS)-enabled solutions have reduced the risk of radiation exposure and safety risks. New web-based and mobile applications have enabled precision characterization and control of nuclear materials. These solutions have also improved operational efficiencies and shortened schedules, reduced cost, and improved regulatory compliance. Collaboration between US Department of Energy (DOE) complex sites is improving time to delivery and cost efficiencies for waste management missions with new information technologies (IT) such as wireless computing, global positioning satellite (GPS), and radio frequency identification (RFID). Integrated solutions developed at separate DOE complex sites by new technology Centers of Excellence (CoE) have increased material control and accountability, worker safety, and environmental sustainability. CoEs offer other DOE sister sites significant cost and time savings by leveraging their technology expertise in project scoping, implementation, and ongoing operations.« less

76 FR 50212 - Site-Wide Environmental Impact Statement for Sandia National Laboratories, New Mexico (SNL/NM)

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-12

... other DOE operations on and around Kirtland Air Force Base (KAFB). NNSA issued a Record of Decision (ROD... Transportation, NNSA Kirtland Operations, the NNSA Aviation Facility, and the DOE National Training Center). The...

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

Verbanis, E.; Martin, A.; Rosset, D.

Imperfections in experimental measurement schemes can lead to falsely identifying, or over estimating, entanglement in a quantum system. A recent solution to this is to define schemes that are robust to measurement imperfections—measurement-device-independent entanglement witness (MDI-EW). This approach can be adapted to witness all entangled qubit states for a wide range of physical systems and does not depend on detection efficiencies or classical communication between devices. In this paper, we extend the theory to remove the necessity of prior knowledge about the two-qubit states to be witnessed. Moreover, we tested this model via a novel experimental implementation for MDI-EW thatmore » significantly reduces the experimental complexity. Finally, by applying it to a bipartite Werner state, we demonstrate the robustness of this approach against noise by witnessing entanglement down to an entangled state fraction close to 0.4.« less

Controllability of Surface Water Networks

NASA Astrophysics Data System (ADS)

Riasi, M. Sadegh; Yeghiazarian, Lilit

2017-12-01

To sustainably manage water resources, we must understand how to control complex networked systems. In this paper, we study surface water networks from the perspective of structural controllability, a concept that integrates classical control theory with graph-theoretic formalism. We present structural controllability theory and compute four metrics: full and target controllability, control centrality and control profile (FTCP) that collectively determine the structural boundaries of the system's control space. We use these metrics to answer the following questions: How does the structure of a surface water network affect its controllability? How to efficiently control a preselected subset of the network? Which nodes have the highest control power? What types of topological structures dominate controllability? Finally, we demonstrate the structural controllability theory in the analysis of a wide range of surface water networks, such as tributary, deltaic, and braided river systems.

Differentially Methylated Region-Representational Difference Analysis (DMR-RDA): A Powerful Method to Identify DMRs in Uncharacterized Genomes.

PubMed

Sasheva, Pavlina; Grossniklaus, Ueli

2017-01-01

Over the last years, it has become increasingly clear that environmental influences can affect the epigenomic landscape and that some epigenetic variants can have heritable, phenotypic effects. While there are a variety of methods to perform genome-wide analyses of DNA methylation in model organisms, this is still a challenging task for non-model organisms without a reference genome. Differentially methylated region-representational difference analysis (DMR-RDA) is a sensitive and powerful PCR-based technique that isolates DNA fragments that are differentially methylated between two otherwise identical genomes. The technique does not require special equipment and is independent of prior knowledge about the genome. It is even applicable to genomes that have high complexity and a large size, being the method of choice for the analysis of plant non-model systems.

Complex wave fields in the interacting one-dimensional Bose gas

NASA Astrophysics Data System (ADS)

Pietraszewicz, J.; Deuar, P.

2018-05-01

We study the temperature regimes of the one-dimensional interacting gas to determine when the matter wave (c-field) theory is, in fact, correct and usable. The judgment is made by investigating the level of discrepancy in many observables at once in comparison to the exact Yang-Yang theory. We also determine what cutoff maximizes the accuracy of such an approach. Results are given in terms of a bound on accuracy, as well as an optimal cutoff prescription. For a wide range of temperatures the optimal cutoff is independent of density or interaction strength and so its temperature-dependent form is suitable for many cloud shapes and, possibly, basis choices. However, this best global choice is higher in energy than most prior determinations. The high value is needed to obtain the correct kinetic energy, but does not detrimentally affect other observables.

Introduction: Sustainability: Multi-Disciplinary Perspectives

EPA Science Inventory

WHAT DOES SUSTAINABILITY MEAN? The word sustainability has over the past two or three decades become widely used in both professional and public speech. But what does it actually mean? As again mentioned in Chapter 9, according to one standard reference of the English languag...

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

Pruski, Marek; Sadow, Aaron D.; Slowing, Igor I.

Here the catalysis research at the U.S. Department of Energy's (DOE's) National Laboratories covers a wide range of research topics in heterogeneous catalysis, homogeneous/molecular catalysis, biocatalysis, electrocatalysis, and surface science. Since much of the work at National Laboratories is funded by DOE, the research is largely focused on addressing DOE's mission to ensure America's security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions.

Observation-Driven Configuration of Complex Software Systems

NASA Astrophysics Data System (ADS)

Sage, Aled

2010-06-01

The ever-increasing complexity of software systems makes them hard to comprehend, predict and tune due to emergent properties and non-deterministic behaviour. Complexity arises from the size of software systems and the wide variety of possible operating environments: the increasing choice of platforms and communication policies leads to ever more complex performance characteristics. In addition, software systems exhibit different behaviour under different workloads. Many software systems are designed to be configurable so that policies can be chosen to meet the needs of various stakeholders. For complex software systems it can be difficult to accurately predict the effects of a change and to know which configuration is most appropriate. This thesis demonstrates that it is useful to run automated experiments that measure a selection of system configurations. Experiments can find configurations that meet the stakeholders' needs, find interesting behavioural characteristics, and help produce predictive models of the system's behaviour. The design and use of ACT (Automated Configuration Tool) for running such experiments is described, in combination a number of search strategies for deciding on the configurations to measure. Design Of Experiments (DOE) is discussed, with emphasis on Taguchi Methods. These statistical methods have been used extensively in manufacturing, but have not previously been used for configuring software systems. The novel contribution here is an industrial case study, applying the combination of ACT and Taguchi Methods to DC-Directory, a product from Data Connection Ltd (DCL). The case study investigated the applicability of Taguchi Methods for configuring complex software systems. Taguchi Methods were found to be useful for modelling and configuring DC- Directory, making them a valuable addition to the techniques available to system administrators and developers.

Proceedings from the Workshop on Phytoremediation of Inorganic Contaminants

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

Brown, Jay Thatcher; Matthern, Gretchen Elise; Glenn, Anne Williams

The Metals and Radionuclides Product Line of the U.S. Department of Energy (DOE) Subsurface Contaminants Focus Area (SCFA) is responsible for the development of technologies and systems that reduce the risk and cost of remediation of radionuclide and hazardous metal contamination in soils and groundwater. The rapid and efficient remediation of these sites and the areas surrounding them represents a technological challenge. Phytoremediation, the use of living plants to cleanup contaminated soils, sediments, surface water and groundwater, is an emerging technology that may be applicable to the problem. The use of phytoremediation to cleanup organic contamination is widely accepted andmore » is being implemented at numerous sites. This workshop was held to initiate a discussion in the scientific community about whether phytoremediation is applicable to inorganic contaminants, such as metals and radionuclides, across the DOE complex. The Workshop on Phytoremediation of Inorganic Contaminants was held at Argonne National Laboratory from November 30 through December 2, 1999. The purpose of the workshop was to provide SCFA and the DOE Environmental Restoration Program with an understanding of the status of phytoremediation as a potential remediation technology for DOE sites. The workshop was expected to identify data gaps, technologies ready for demonstration and deployment, and to provide a set of recommendations for the further development of these technologies. More specifically, the objectives of the workshop were to: · Determine the status of the existing baseline, including technological maturation, · Identify areas for future potential research, · Identify the key issues and recommendations for issue resolution, · Recommend a strategy for maturing key aspects of phytoremediation, · Improve communication and collaboration among organizations currently involved in phytoremediation research, and · Identify technical barriers to making phytoremediation commercially successful in more areas.« less

The Practical Obstacles of Data Transfer: Why researchers still love scp

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

Nam, Hai Ah; Hill, Jason J; Parete-Koon, Suzanne T

The importance of computing facilities is heralded every six months with the announcement of the new Top500 list, showcasing the world s fastest supercomputers. Unfortu- nately, with great computing capability does not come great long-term data storage capacity, which often means users must move their data to their local site archive, to remote sites where they may be doing future computation or anal- ysis, or back to their home institution, else face the dreaded data purge that most HPC centers employ to keep utiliza- tion of large parallel filesystems low to manage performance and capacity. At HPC centers, data transfermore » is crucial to the scientific workflow and will increase in importance as computing systems grow in size. The Energy Sciences Net- work (ESnet) recently launched its fifth generation network, a 100 Gbps high-performance, unclassified national network connecting more than 40 DOE research sites to support scientific research and collaboration. Despite the tenfold increase in bandwidth to DOE research sites amenable to multiple data transfer streams and high throughput, in prac- tice, researchers often under-utilize the network and resort to painfully-slow single stream transfer methods such as scp to avoid the complexity of using multiple stream tools such as GridFTP and bbcp, and contend with frustration from the lack of consistency of available tools between sites. In this study we survey and assess the data transfer methods pro- vided at several DOE supported computing facilities, includ- ing both leadership-computing facilities, connected through ESnet. We present observed transfer rates, suggested opti- mizations, and discuss the obstacles the tools must overcome to receive wide-spread adoption over scp.« less

Spinal cord dysmyelination caused by an anti-PLP IgM antibody: implications for the mechanism of CNS myelin formation

PubMed Central

Rosenbluth, J.; Schiff, R.

2008-01-01

Antiglycolipid IgM antibodies are known to induce formation of ‘wide-spaced’ or ‘expanded’ myelin, a distinctive form of dysmylination characterized by a repeat period ~2X or 3X normal, seen also in diseases including multiple sclerosis. To determine whether an antibody directed against a myelin protein would cause equivalent pathology, we implanted O10 hybridoma cells into the spinal cord of adult or juvenile rats. O10 produces an IgM directed against PLP, the major protein of CNS myelin. Subsequent examination of the cords showed focal demyelination and remyelination. In addition, however, some juvenile cords, but none of the adults, displayed wide-spaced myelin with lamellae separated by an extracellular material comprised of elements consistent with IgM molecules in appearance. Wide spacing tended to involve the outer layers of the sheath and in some cases alternated with normally spaced lamellae. A feature not seen previously consists of multiple expanded myelin lamellae in one sector of a sheath continuous with normally spaced lamellae in another, resulting in variation in sheath thickness around the axonal circumference. This uneven distribution of wide-spaced lamellae is most simply explained based on incorporation of IgM molecules into immature sheaths during myelin formation and implies a model of CNS myelinogenesis more complex than simple spiraling. The periaxonal space never displays widening of this kind, but the interface with adjacent myelin sheaths or oligodendrocytes may. Thus, wide spacing appears to require that IgM molecules bridge between two PLP-containing membranes and does not reflect the mere presence of immunoglobulin within the extracellular space. PMID:18951490

Interaction between macrocyclic nickel complexes and the nucleotides GMP, AMP and ApG.

PubMed

Liu, Yangzhong; Sletten, Einar

2003-01-15

Reactions between the nucleotides GMP, AMP and ApG and the complexes Ni(tren), Ni(cyclam) and NiCR in aqueous solution have been monitored by (1)H, (15)N NMR and UV spectroscopy. The three nickel complexes display different properties in reactions with nucleotides. Ni(tren) which has a pseudo-octahedral coordination geometry was shown to bind to all three nucleotides. Ni(cyclam) and NiCR, both with four nitrogen atoms in a square planar arrangement are not able to bind to nucleotides efficiently because of steric hindrance. Oxidation of Ni(cyclam) by KHSO(5) to produce trivalent Ni(III)(cyclam) improves the coordination capacity, while oxidation of NiCR does not produce a similar effect. The nucleotides interact with trivalent nickel complexes to different extent. Ni(III)CR is seen to oxidize GMP gradually but does not affect AMP significantly. Ni(III)(cyclam), on the other hand, does not oxidize either GMP or AMP at the 1:1 concentration of oxidant used. This result is probably due to the lower redox potential of Ni(cyclam). ApG binds less efficiently to the Ni complexes but is easier oxidized than the mononucleotides.

New solutions to realize complex optical systems by a combination of diffractive and refractive optical components

NASA Astrophysics Data System (ADS)

Brunner, Robert; Steiner, Reinhard; Dobschal, Hans-Juergen; Martin, Dietrich; Burkhardt, Matthias; Helgert, Michael

2003-11-01

Diffractive optical elements (DOEs) have a great potential in the complete or partial substitution of refractive or reflective optical elements in imaging systems. The greater design flexibility compared to an all-refractive/reflective solution allows a more convenient realization of the optical systems and additionally opens up new possibilities for optimizing the performance or compactness. To demonstrate the opportunities of the hybrid optical concept we discuss different imaging systems for various applications. We present the lens design of a hybrid microscope objective which is especially applicable for wafer inspection technologies. Meeting the requirements for such a system used in the deep-UV regime (248 nm) is very challenging. The short wavelength limits the material selection and demands cement free optical groups. The additional requirement of an autofocus system, working at a wavelength in the near infrared region, is fulfilled by the special combination of two selected and adjusted DOEs. Furthermore, we discuss the opportunities of the hybrid concept c of a slit lamp used for ophthalmologic examinations. The DOEs are the basic elements of this hybrid concept. We demonstrate that holographic lithography is an appropriate technology to realize a wide variety of elements with different profile geometries. We address in particular the additional possibilities of an UV-laser system as an exposure tool. Additionally to the high spatial frequencies, the 266 nm exposure wavelength allows the use of novel photo resists with advantageous development behavior.

Method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation in conjunction with mass spectrometric analysis

DOEpatents

Laskin, Julia [Richland, WA; Futrell, Jean H [Richland, WA

2008-04-29

The invention relates to a method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation (SID) in conjunction with mass spectrometric analysis. Results demonstrate formation of a wide distribution of structure-specific fragments having wide sequence coverage useful for sequencing and identifying the complex molecules.

Hanford science and technology needs statements, 2000

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

BERLIN, G.T.

In the aftermath of the Cold War, the United States has begun addressing the environmental consequences of five decades of nuclear weapons production. In November 1989, DOE established the Office of Environmental Restoration and Waste Management (EM) as the central authority for cleaning up the DOE weapons complex legacy of pollution, for preventing further environmental contamination, and for instituting responsible environmental management. While performing its tasks, EM found that many aspects of its large and complex mission could not be achieved using existing science and technology or without incurring unreasonable costs, risks, or schedule impacts. Consequently, a process was developedmore » to solicit needs from around the DOE complex and focus the science and technology resources of EM-50, the National Laboratories, private industry, and colleges and universities on those needs. This document describes those needs that the Hanford Site has identified as requiring additional science or technology to complete.« less

Hanford science and technology needs statements, 1999

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

Berlin, G.T.

In the aftermath of the Cold War, the US has begun addressing the environmental consequences of five decades of nuclear weapons production. In November 1989, DOE established the Office of Environmental Restoration and Waste Management (EM) as the central authority for cleaning up the DOE weapons complex legacy of pollution, for preventing further environmental contamination, and for instituting responsible environmental management. While performing its tasks, EM found that many aspects of its large and complex decisions could not be achieved using existing science and technology or without incurring unreasonable costs, risks, or schedule impacts. Consequently, a process was developed tomore » solicit needs from around the DOE complex and focus the science and technology resources of EM-50, the National Laboratories, private industry, and collages and universities on those needs. This document describes those needs which the Hanford Site has identified as requiring additional science or technology to complete.« less

Patterns and Variation in Benthic Biodiversity in a Large Marine Ecosystem

PubMed Central

Lee, Jonathan D.

2015-01-01

While there is a persistent inverse relationship between latitude and species diversity across many taxa and ecosystems, deviations from this norm offer an opportunity to understand the conditions that contribute to large-scale diversity patterns. Marine systems, in particular, provide such an opportunity, as marine diversity does not always follow a strict latitudinal gradient, perhaps because several hypothesized drivers of the latitudinal diversity gradient are uncorrelated in marine systems. We used a large scale public monitoring dataset collected over an eight year period to examine benthic marine faunal biodiversity patterns for the continental shelf (55–183 m depth) and slope habitats (184–1280 m depth) off the US West Coast (47°20′N—32°40′N). We specifically asked whether marine biodiversity followed a strict latitudinal gradient, and if these latitudinal patterns varied across depth, in different benthic substrates, and over ecological time scales. Further, we subdivided our study area into three smaller regions to test whether coast-wide patterns of biodiversity held at regional scales, where local oceanographic processes tend to influence community structure and function. Overall, we found complex patterns of biodiversity on both the coast-wide and regional scales that differed by taxonomic group. Importantly, marine biodiversity was not always highest at low latitudes. We found that latitude, depth, substrate, and year were all important descriptors of fish and invertebrate diversity. Invertebrate richness and taxonomic diversity were highest at high latitudes and in deeper waters. Fish richness also increased with latitude, but exhibited a hump-shaped relationship with depth, increasing with depth up to the continental shelf break, ~200 m depth, and then decreasing in deeper waters. We found relationships between fish taxonomic and functional diversity and latitude, depth, substrate, and time at the regional scale, but not at the coast-wide scale, suggesting that coast-wide patterns can obscure important correlates at smaller scales. Our study provides insight into complex diversity patterns of the deep water soft substrate benthic ecosystems off the US West Coast. PMID:26308521

A new method for detecting signal regions in ordered sequences of real numbers, and application to viral genomic data.

PubMed

Gog, Julia R; Lever, Andrew M L; Skittrall, Jordan P

2018-01-01

We present a fast, robust and parsimonious approach to detecting signals in an ordered sequence of numbers. Our motivation is in seeking a suitable method to take a sequence of scores corresponding to properties of positions in virus genomes, and find outlying regions of low scores. Suitable statistical methods without using complex models or making many assumptions are surprisingly lacking. We resolve this by developing a method that detects regions of low score within sequences of real numbers. The method makes no assumptions a priori about the length of such a region; it gives the explicit location of the region and scores it statistically. It does not use detailed mechanistic models so the method is fast and will be useful in a wide range of applications. We present our approach in detail, and test it on simulated sequences. We show that it is robust to a wide range of signal morphologies, and that it is able to capture multiple signals in the same sequence. Finally we apply it to viral genomic data to identify regions of evolutionary conservation within influenza and rotavirus.

The Relationship between Relative Humidity and the Dewpoint Temperature in Moist Air: A Simple Conversion and Applications.

NASA Astrophysics Data System (ADS)

Lawrence, Mark G.

2005-02-01

The relative humidity (RH) and the dewpoint temperature (td) are two widely used indicators of the amount of moisture in air. The exact conversion from RH to td, as well as highly accurate approximations, are too complex to be done easily without the help of a calculator or computer. However, there is a very simple rule of thumb that can be very useful for approximating the conversion for moist air (RH > 50%) which does not appear to be widely known by the meteorological community: td decreases by about 1°C for every 5% decrease in RH (starting at td = t, the dry bulb temperature, when RH = 100%). This article examines the mathematical basis and accuracy of this and other relationships between the dewpoint and relative humidity. Several useful applications of the simple conversion are presented, in particular the computation of the cumulus cloud-base level (or lifting condensation level) as zLCL (20 + t/5) (100 - RH), where zLCL is in meters when t is in degrees Celcius and RH in percent. Finally, a historical perspective is given with anecdotes about some of the early work in this field.

Studies of Inviscid Flux Schemes for Acoustics and Turbulence Problems

NASA Technical Reports Server (NTRS)

Morris, C. I.

2013-01-01

The last two decades have witnessed tremendous growth in computational power, the development of computational fluid dynamics (CFD) codes which scale well over thousands of processors, and the refinement of unstructured grid-generation tools which facilitate rapid surface and volume gridding of complex geometries. Thus, engineering calculations of 10(exp 7) - 10(exp 8) finite-volume cells have become routine for some types of problems. Although the Reynolds Averaged Navier Stokes (RANS) approach to modeling turbulence is still in extensive and wide use, increasingly large-eddy simulation (LES) and hybrid RANS-LES approaches are being applied to resolve the largest scales of turbulence in many engineering problems. However, it has also become evident that LES places different requirements on the numerical approaches for both the spatial and temporal discretization of the Navier Stokes equations than does RANS. In particular, LES requires high time accuracy and minimal intrinsic numerical dispersion and dissipation over a wide spectral range. In this paper, the performance of both central-difference and upwind-biased spatial discretizations is examined for a one-dimensional acoustic standing wave problem, the Taylor-Green vortex problem, and the turbulent channel fl ow problem.

Studies of Inviscid Flux Schemes for Acoustics and Turbulence Problems

NASA Technical Reports Server (NTRS)

Morris, Christopher I.

2013-01-01

The last two decades have witnessed tremendous growth in computational power, the development of computational fluid dynamics (CFD) codes which scale well over thousands of processors, and the refinement of unstructured grid-generation tools which facilitate rapid surface and volume gridding of complex geometries. Thus, engineering calculations of 10(exp 7) - 10(exp 8) finite-volume cells have become routine for some types of problems. Although the Reynolds Averaged Navier Stokes (RANS) approach to modeling turbulence is still in extensive and wide use, increasingly large-eddy simulation (LES) and hybrid RANS-LES approaches are being applied to resolve the largest scales of turbulence in many engineering problems. However, it has also become evident that LES places different requirements on the numerical approaches for both the spatial and temporal discretization of the Navier Stokes equations than does RANS. In particular, LES requires high time accuracy and minimal intrinsic numerical dispersion and dissipation over a wide spectral range. In this paper, the performance of both central-difference and upwind-biased spatial discretizations is examined for a one-dimensional acoustic standing wave problem, the Taylor-Green vortex problem, and the turbulent channel ow problem.

Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells.

PubMed

Tan, Chris Soon Heng; Go, Ka Diam; Bisteau, Xavier; Dai, Lingyun; Yong, Chern Han; Prabhu, Nayana; Ozturk, Mert Burak; Lim, Yan Ting; Sreekumar, Lekshmy; Lengqvist, Johan; Tergaonkar, Vinay; Kaldis, Philipp; Sobota, Radoslaw M; Nordlund, Pär

2018-03-09

Proteins differentially interact with each other across cellular states and conditions, but an efficient proteome-wide strategy to monitor them is lacking. We report the application of thermal proximity coaggregation (TPCA) for high-throughput intracellular monitoring of protein complex dynamics. Significant TPCA signatures observed among well-validated protein-protein interactions correlate positively with interaction stoichiometry and are statistically observable in more than 350 annotated human protein complexes. Using TPCA, we identified many complexes without detectable differential protein expression, including chromatin-associated complexes, modulated in S phase of the cell cycle. Comparison of six cell lines by TPCA revealed cell-specific interactions even in fundamental cellular processes. TPCA constitutes an approach for system-wide studies of protein complexes in nonengineered cells and tissues and might be used to identify protein complexes that are modulated in diseases. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Some research perspectives in galloping phenomena: critical conditions and post-critical behavior

NASA Astrophysics Data System (ADS)

Piccardo, Giuseppe; Pagnini, Luisa Carlotta; Tubino, Federica

2015-01-01

This paper gives an overview of wind-induced galloping phenomena, describing its manifold features and the many advances that have taken place in this field. Starting from a quasi-steady model of aeroelastic forces exerted by the wind on a rigid cylinder with three degree-of-freedom, two translations and a rotation in the plane of the model cross section, the fluid-structure interaction forces are described in simple terms, yet suitable with complexity of mechanical systems, both in the linear and in the nonlinear field, thus allowing investigation of a wide range of structural typologies and their dynamic behavior. The paper is driven by some key concerns. A great effort is made in underlying strengths and weaknesses of the classic quasi-steady theory as well as of the simplistic assumptions that are introduced in order to investigate such complex phenomena through simple engineering models. A second aspect, which is crucial to the authors' approach, is to take into account and harmonize the engineering, physical and mathematical perspectives in an interdisciplinary way—something which does not happen often. The authors underline that the quasi-steady approach is an irreplaceable tool, tough approximate and simple, for performing engineering analyses; at the same time, the study of this phenomenon gives origin to numerous problems that make the application of high-level mathematical solutions particularly attractive. Finally, the paper discusses a wide range of features of the galloping theory and its practical use which deserve further attention and refinements, pointing to the great potential represented by new fields of application and advanced analysis tools.

Nesting Behavior is Associated with VIP Expression and VIP-Fos Colocalization in a Network-Wide Manner

PubMed Central

Kingsbury, Marcy A.; Jan, Namratha; Klatt, James D.; Goodson, James L.

2015-01-01

Many species, including humans, engage in a series of behaviors that are preparatory to the arrival of offspring. Such "nesting behaviors" are of obvious importance, but relevant neuroendocrine mechanisms remain little studied. We here focus on the potential roles of vasoactive intestinal polypeptide (VIP) in the performance of appetitive and consummatory nesting behaviors in male and female zebra finches (Taeniopygia guttata). Using combined immunocytochemistry for Fos and in situ hybridization for VIP, we now show that many VIP cell groups show increased transcriptional activity in response to nest building in male and female zebra finches. Particularly strong data come from the preoptic area (medial preoptic area and medial preoptic nucleus), where VIP-Fos co-expression correlates positively with three different measures of nesting behavior, as does the number of VIP-expressing cells. Remarkably, we find that VIP mRNA and/or VIP-Fos co-expression is correlated with nesting behavior in virtually every brain area that we examined, including the medial amygdala (anterior and posterior), medial bed nucleus of the stria terminalis, medial preoptic area, medial preoptic nucleus, anterior hypothalamus, ventromedial hypothalamus, periaqueductal gray complex (central gray and nucleus intercollicularis), and ventral tegmental area. Near-significant effects are also obtained in the tuberoinfundibular hypothalamus. Although most correlations are positive, negative correlations are observed for the VIP cell group of the anterior hypothalamus, a population that selectively promotes aggression, and also the periaqueductal gray complex. These data demonstrate a network-wide relationship between peptide production and social behavior that is, to our knowledge, unparalleled by other peptidergic modulators. PMID:25573700

GAO’s Views on DOE’s 1991 Budget for Addressing Problems at the Nuclear Weapons Complex

DTIC Science & Technology

1990-03-02

management, and efforts by DOE to make its contractors more accountable. Also, the Defense Nuclear Facilities Safety Board mandated by the Congress became...and safety matters. 6 Finally, the Defense Nuclear Facilities Safety Board was established. Although not a DOE action, its establishment, nevertheless

Tanks focus area multiyear program plan FY97-FY99

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

NONE

1996-08-01

The U.S. Department of Energy (DOE) continues to face a major tank remediation problem with approximately 332 tanks storing over 378,000 ml of high-level waste (HLW) and transuranic (TRU) waste across the DOE complex. Most of the tanks have significantly exceeded their life spans. Approximately 90 tanks across the DOE complex are known or assumed to have leaked. Some of the tank contents are potentially explosive. These tanks must be remediated and made safe. How- ever, regulatory drivers are more ambitious than baseline technologies and budgets will support. Therefore, the Tanks Focus Area (TFA) began operation in October 1994. Themore » focus area manages, coordinates, and leverages technology development to provide integrated solutions to remediate problems that will accelerate safe and cost-effective cleanup and closure of DOE`s national tank system. The TFA is responsible for technology development to support DOE`s four major tank sites: Hanford Site (Washington), INEL (Idaho), Oak Ridge Reservation (ORR) (Tennessee), and Savannah River Site (SRS) (South Carolina). Its technical scope covers the major functions that comprise a complete tank remediation system: safety, characterization, retrieval, pretreatment, immobilization, and closure.« less

Congress targets DOE plants

NASA Astrophysics Data System (ADS)

Maggs, William Ward

Calling the Department of Energy's management of the nation's crippled nuclear weapons production complex “a 35-year secret chemical war waged against people living near DOE's sites,” Representative Thomas Luken (D-OH) opened a congressional hearing on February 23 with an appeal to DOE Secretary-designate James Watkins to release secret health records of workers at the plants. In testimony that followed, Comptroller General Charles Bowsher told a subcommittee of the House Energy and Commerce Committee that President Bush's new budget does not go far enough on the long and costly road of cleaning up and modernizing the contaminated and aging facilities. The renovation is expected to cost up to $155 billion.By next month, 11 of the 17 installations that make up the DOE complex will be on the EPA's Superfund list of the nation's most contaminated waste sites. Some o f the DOE facilities, including the Rocky Flats plant in Denver, Colo., the Hanford Reservation in eastern Washington, and the Savannah River plant in South Carolina, are among the most polluted sites ever identified by EPA. The principal function of the facilities, the production of tritium and plutonium for nuclear weapons, has stopped, creating what DOE has characterized as a looming national security crisis.

Development and Execution of a Large-scale DDT Tube Test for IHE Material Qualification

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

Parker, Gary Robert; Broilo, Robert M.; Lopez-Pulliam, Ian Daniel

Insensitive High Explosive (IHE) Materials are defined in Chapter IX of the DOE Explosive Safety Standard (DOE-STD-1212-2012) as being materials that are massdetonable explosives that are so insensitive that the probability of accidental initiation or transition from burning to detonation is negligible1. There are currently a number of tests included in the standard that are required to qualify a material as IHE, however, none of the tests directly evaluate for the transition from burning to detonation (aka deflagration-to-detonation transition, DDT). Currently, there is a DOE complex-wide effort to revisit the IHE definition in DOE-STD-1212-2012 and change the qualification requirements. Themore » proposal lays out a new approach, requiring fewer, but more appropriate tests, for IHE Material qualification. One of these new tests is the Deflagration-to-Detonation Test. According to the redefinition proposal, the purpose of the new deflagration-todetonation test is “to demonstrate that an IHE material will not undergo deflagration-to-detonation under stockpile relevant conditions of scale, confinement, and material condition. Inherent in this test design is the assumption that ignition does occur, with onset of deflagration. The test design will incorporate large margins and replicates to account for the stochastic nature of DDT events.” In short, the philosophy behind this approach is that if a material fails to undergo DDT in a significant over-test, then it is extremely unlikely to do so in realistic conditions. This effort will be valuable for the B61 LEP to satisfy their need qualify the new production lots of PBX 9502. The work described in this report is intended as a preliminary investigation to support the proposed design of an overly conservative, easily fielded DDT test for updated IHE Material Qualification standard. Specifically, we evaluated the aspects of confinement, geometry, material morphology and temperature. We also developed and tested a thermally robust igniter system.« less

Metal adsorption onto bacterial surfaces: development of a predictive approach

NASA Astrophysics Data System (ADS)

Fein, Jeremy B.; Martin, Aaron M.; Wightman, Peter G.

2001-12-01

Aqueous metal cation adsorption onto bacterial surfaces can be successfully modeled by means of a surface complexation approach. However, relatively few stability constants for metal-bacterial surface complexes have been measured. In order to determine the bacterial adsorption behavior of cations that have not been studied in the laboratory, predictive techniques are required that enable estimation of the stability constants of bacterial surface complexes. In this study, we use a linear free-energy approach to compare previously measured stability constants for Bacillus subtilis metal-carboxyl surface complexes with aqueous metal-organic acid anion stability constants. The organic acids that we consider are acetic, oxalic, citric, and tiron. We add to this limited data set by conducting metal adsorption experiments onto Bacillus subtilis, determining bacterial surface stability constants for Co, Nd, Ni, Sr, and Zn. The adsorption behavior of each of the metals studied here was described well by considering metal-carboxyl bacterial surface complexation only, except for the Zn adsorption behavior, which required carboxyl and phosphoryl complexation to obtain a suitable fit to the data. The best correlation between bacterial carboxyl surface complexes and aqueous organic acid anion stability constants was obtained by means of metal-acetate aqueous complexes, with a linear correlation coefficient of 0.97. This correlation applies only to unhydrolyzed aqueous cations and only to carboxyl binding of those cations, and it does not predict the binding behavior under conditions where metal binding to other bacterial surface site types occurs. However, the relationship derived in this study permits estimation of the carboxyl site adsorption behavior of a wide range of aqueous metal cations for which there is an absence of experimental data. This technique, coupled with the observation of similar adsorption behaviors across bacterial species (Yee and Fein, 2001), enables estimation of the effects of bacterial adsorption on metal mobilities for a large number of environmental and geologic applications.

Does Aggregate School-Wide Achievement Mediate Fifth Grade Outcomes for Former Early Childhood Education Participants?

ERIC Educational Resources Information Center

Curenton, Stephanie M.; Dong, Nianbo; Shen, Xiangjin

2015-01-01

This study used a multilevel mediation model to test the theory that former early childhood education (ECE) attendees' 5th grade achievement is mediated by the aggregate school-wide achievement of their elementary school. Aggregate school-wide achievement was defined as the percentage of 5th graders in a school who were at/above academic…

RESULTS OF THE ENVIRONMENTAL MANAGEMENT (EM) CORPORATE PROJECT TEAM DISPOSING WASTE & REDUCING RISK

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

SHRADER, T.A.; KNERR, R.

2005-01-31

In 2002, the US Department of Energy's (DOE) Office of Environmental Management (EM) released the Top-To-Bottom Review of cognizant clean-up activities around the DOE Complex. The review contained a number of recommendations for changing the way EM operates in order to reduce environmental risk by significantly accelerating clean-up at the DOE-EM sites. In order to develop and implement these recommendations, a number of corporate project teams were formed to identify, evaluate, and initiate implementation of alternatives for the different aspects of clean-up. In August 2002, a corporate team was formed to review all aspects of the management, treatment, and disposalmore » of low level radioactive waste (LLW), mixed low level radioactive waste (MLLW), transuranic waste (TRU), and hazardous waste (HW). Over the next 21 months, the Corporate Project Team: Disposing Waste, Reducing Risk, developed a number of alternatives for implementing the recommendations of the Top-To-Bottom Review based on information developed during numerous site visits and interviews with complex and industry personnel. With input from over a dozen EM sites at various stages of clean-up, the team identified the barriers to the treatment and disposal of low level waste, mixed low level waste, and transuranic waste. Once identified, preliminary design alternatives were developed and presented to the Acquisition Authority (for this project, the Assistant Secretary for Environmental Management) for review and approval. Once the preliminary design was approved, the team down selected to seven key alternatives which were subsequently fully developed in the Project Execution Plan. The seven most viable alternatives were: (1) creation of an Executive Waste Disposal Board; (2) projectizing the disposal of low level waste and mixed low level waste; (3) creation of a National Consolidation and Acceleration Facility for waste; (4) improvements to the Broad Spectrum contract; (5) improvements to the Toxic Substance Control Act (TSCA) Incinerator contract and operations; (6) development of a policy for load management of waste shipments to the Waste Isolation Pilot Plant (WIPP); and (7) development of a complex-wide fee incentive for transuranic waste disposal. The alternatives were further refined and a plan developed for institutionalizing the alternatives in various site contracts. In order to focus the team's efforts, all team activities were conducted per the principles of DOE Order 413.3, Program and Project Management for the Acquisition of Capital Assets. Although the Order was developed for construction projects, the principles were adapted for use on this ''soft'' project in which the deliverables were alternatives for the way work was performed. The results of the team's investigation and the steps taken during the project are presented along with lessons learned.« less

Human Mars Mission Design - The Ultimate Systems Challenge

NASA Technical Reports Server (NTRS)

Connolly, John F.; Joosten, B. Kent; Drake, Bret; Hoffman, Steve; Polsgrove, Tara; Rucker, Michelle; Andrews, Alida; Williams, Nehemiah

2017-01-01

A human mission to Mars will occur at some time in the coming decades. When it does, it will be the end result of a complex network of interconnected design choices, systems analyses, technical optimizations, and non-technical compromises. This mission will extend the technologies, engineering design, and systems analyses to new limits, and may very well be the most complex undertaking in human history. It can be illustrated as a large menu, or as a large decision tree. Whatever the visualization tool, there are numerous design decisions required to assemble a human Mars mission, and many of these interconnect with one another. This paper examines these many decisions and further details a number of choices that are highly interwoven throughout the mission design. The large quantity of variables and their interconnectedness results in a highly complex systems challenge, and the paper illustrates how a change in one variable results in ripples (sometimes unintended) throughout many other facets of the design. The paper concludes with a discussion of some mission design variables that can be addressed first, and those that have already been addressed as a result of ongoing National Aeronautics and Space Administration (NASA) developments, or as a result of decisions outside the technical arena. It advocates the need for a 'reference design' that can be used as a point of comparison, and to illustrate the system-wide impacts as design variables change.

Reliability, return periods, and risk under nonstationarity

NASA Astrophysics Data System (ADS)

Read, Laura K.; Vogel, Richard M.

2015-08-01

Water resources design has widely used the average return period as a concept to inform management and communication of the risk of experiencing an exceedance event within a planning horizon. Even though nonstationarity is often apparent, in practice hydrologic design often mistakenly assumes that the probability of exceedance, p, is constant from year to year which leads to an average return period To equal to 1/p; this expression is far more complex under nonstationarity. Even for stationary processes, the common application of an average return period is problematic: it does not account for planning horizon, is an average value that may not be representative of the time to the next flood, and is generally not applied in other areas of water planning. We combine existing theoretical and empirical results from the literature to provide the first general, comprehensive description of the probabilistic behavior of the return period and reliability under nonstationarity. We show that under nonstationarity, the underlying distribution of the return period exhibits a more complex shape than the exponential distribution under stationary conditions. Using a nonstationary lognormal model, we document the increased complexity and challenges associated with planning for future flood events over a planning horizon. We compare application of the average return period with the more common concept of reliability and recommend replacing the average return period with reliability as a more practical way to communicate event likelihood in both stationary and nonstationary contexts.

An endosomal syntaxin and the AP-3 complex are required for formation and maturation of candidate lysosome-related secretory organelles (mucocysts) in Tetrahymena thermophila

PubMed Central

Kaur, Harsimran; Sparvoli, Daniela; Osakada, Hiroko; Iwamoto, Masaaki; Haraguchi, Tokuko; Turkewitz, Aaron P.

2017-01-01

The ciliate Tetrahymena thermophila synthesizes large secretory vesicles called mucocysts. Mucocyst biosynthesis shares features with dense core granules (DCGs) in animal cells, including proteolytic processing of cargo proteins during maturation. However, other molecular features have suggested relatedness to lysosome-related organelles (LROs). LROs, which include diverse organelles in animals, are formed via convergence of secretory and endocytic trafficking. Here we analyzed Tetrahymena syntaxin 7-like 1 (Stx7l1p), a Qa-SNARE whose homologues in other lineages are linked with vacuoles/LROs. Stx7l1p is targeted to both immature and mature mucocysts and is essential in mucocyst formation. In STX7L1-knockout cells, the two major classes of mucocyst cargo proteins localize independently, accumulating in largely nonoverlapping vesicles. Thus initial formation of immature mucocysts involves heterotypic fusion, in which a subset of mucocyst proteins is delivered via an endolysosomal compartment. Further, we show that subsequent maturation requires AP-3, a complex widely implicated in LRO formation. Knockout of the µ-subunit gene does not impede delivery of any known mucocyst cargo but nonetheless arrests mucocyst maturation. Our data argue that secretory organelles in ciliates may represent a new class of LROs and reveal key roles of an endosomal syntaxin and AP-3 in the assembly of this complex compartment. PMID:28381425

`You caught me off guard': Probing the futures of complex engineered nanomaterials

NASA Astrophysics Data System (ADS)

Sadowski, Jathan; Guston, David H.

2016-07-01

This paper applies principles and methods from the framework of anticipatory governance to the case of what the National Research Council calls "complex engineered nanomaterials" (CENM). This framework does not aim to generate crystal ball visions or definitive answers, but rather provides guidance for uncovering, understanding, and addressing social, ethical, environmental, and policy issues that stem from emerging technologies. Thus, in anticipation of increased CENM research, CENM products, and their different governance challenges, we aim to lay the groundwork for the anticipatory governance of CENMs by mapping out what—according to the engineers and scientists, we interviewed who are working at the research level of these CENMs—will be the main issues and themes that we need to pay attention to in the near future. The structured interviews focused on three groups of questions: (1) potential and/or actual applications and/or products from the participant's research; (2) environmental health and safety issues pertaining to both the participant's research and CENMs generally; and (3) the future of CENMs. Without a foundational understanding to build on, social scientists, policymakers, and regulatory agencies will be at a loss about how to govern CENMs before they are widely implemented in society.

Native Mass Spectrometry: What is in the Name?

NASA Astrophysics Data System (ADS)

Leney, Aneika C.; Heck, Albert J. R.

2017-01-01

Electrospray ionization mass spectrometry (ESI-MS) is nowadays one of the cornerstones of biomolecular mass spectrometry and proteomics. Advances in sample preparation and mass analyzers have enabled researchers to extract much more information from biological samples than just the molecular weight. In particular, relevant for structural biology, noncovalent protein-protein and protein-ligand complexes can now also be analyzed by MS. For these types of analyses, assemblies need to be retained in their native quaternary state in the gas phase. This initial small niche of biomolecular mass spectrometry, nowadays often referred to as "native MS," has come to maturation over the last two decades, with dozens of laboratories using it to study mostly protein assemblies, but also DNA and RNA-protein assemblies, with the goal to define structure-function relationships. In this perspective, we describe the origins of and (re)define the term native MS, portraying in detail what we meant by "native MS," when the term was coined and also describing what it does (according to us) not entail. Additionally, we describe a few examples highlighting what native MS is, showing its successes to date while illustrating the wide scope this technology has in solving complex biological questions.

A generalized linear integrate-and-fire neural model produces diverse spiking behaviors.

PubMed

Mihalaş, Stefan; Niebur, Ernst

2009-03-01

For simulations of neural networks, there is a trade-off between the size of the network that can be simulated and the complexity of the model used for individual neurons. In this study, we describe a generalization of the leaky integrate-and-fire model that produces a wide variety of spiking behaviors while still being analytically solvable between firings. For different parameter values, the model produces spiking or bursting, tonic, phasic or adapting responses, depolarizing or hyperpolarizing after potentials and so forth. The model consists of a diagonalizable set of linear differential equations describing the time evolution of membrane potential, a variable threshold, and an arbitrary number of firing-induced currents. Each of these variables is modified by an update rule when the potential reaches threshold. The variables used are intuitive and have biological significance. The model's rich behavior does not come from the differential equations, which are linear, but rather from complex update rules. This single-neuron model can be implemented using algorithms similar to the standard integrate-and-fire model. It is a natural match with event-driven algorithms for which the firing times are obtained as a solution of a polynomial equation.

Agent-based modeling of the immune system: NetLogo, a promising framework.

PubMed

Chiacchio, Ferdinando; Pennisi, Marzio; Russo, Giulia; Motta, Santo; Pappalardo, Francesco

2014-01-01

Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents. This behavior is unpredictable, as it does not follow linear rules. There are a lot of works that investigates the immune system with agent-based modeling and cellular automata. They have shown the ability to see clearly and intuitively into the nature of immunological processes. NetLogo is a multiagent programming language and modeling environment for simulating complex phenomena. It is designed for both research and education and is used across a wide range of disciplines and education levels. In this paper, we summarize NetLogo applications to immunology and, particularly, how this framework can help in the development and formulation of hypotheses that might drive further experimental investigations of disease mechanisms.

Biologic surveys for the Sandia National Laboratories, Coyote Canyon Test Complex, Kirtland Air Force Base, Albuquerque, New Mexico

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

Sullivan, R.M.; Knight, P.J.

This report provides results of a comprehensive biologic survey performed in Coyote Canyon Test Complex (CCTC), Sandia National Laboratories (SNL), Bernalillo County, New Mexico, which was conducted during the spring and summer of 1992 and 1993. CCTC is sited on land owned by the Department of Energy (DOE) and Kirtland Air Force Base and managed by SNL. The survey covered 3,760 acres of land, most of which is rarely disturbed by CCTC operations. Absence of grazing by livestock and possibly native ungulates, and relative to the general condition of private range lands throughout New Mexico, and relative to other grazingmore » lands in central New Mexico. Widely dispersed, low intensity use by SNL as well as prohibition of grazing has probably contributed to abundance of special status species such as grama grass cactus within the CCTC area. This report evaluates threatened and endangered species found in the area, as well as comprehensive assessment of biologic habitats. Included are analyses of potential impacts and mitigative measures designed to reduce or eliminate potential impacts. Included is a summary of CCTC program and testing activities.« less

The Multi-Scale Network Landscape of Collaboration.

PubMed

Bae, Arram; Park, Doheum; Ahn, Yong-Yeol; Park, Juyong

2016-01-01

Propelled by the increasing availability of large-scale high-quality data, advanced data modeling and analysis techniques are enabling many novel and significant scientific understanding of a wide range of complex social, natural, and technological systems. These developments also provide opportunities for studying cultural systems and phenomena--which can be said to refer to all products of human creativity and way of life. An important characteristic of a cultural product is that it does not exist in isolation from others, but forms an intricate web of connections on many levels. In the creation and dissemination of cultural products and artworks in particular, collaboration and communication of ideas play an essential role, which can be captured in the heterogeneous network of the creators and practitioners of art. In this paper we propose novel methods to analyze and uncover meaningful patterns from such a network using the network of western classical musicians constructed from a large-scale comprehensive Compact Disc recordings data. We characterize the complex patterns in the network landscape of collaboration between musicians across multiple scales ranging from the macroscopic to the mesoscopic and microscopic that represent the diversity of cultural styles and the individuality of the artists.

LIN9, a Subunit of the DREAM Complex, Regulates Mitotic Gene Expression and Proliferation of Embryonic Stem Cells

PubMed Central

Esterlechner, Jasmina; Reichert, Nina; Iltzsche, Fabian; Krause, Michael; Finkernagel, Florian; Gaubatz, Stefan

2013-01-01

The DREAM complex plays an important role in regulation of gene expression during the cell cycle. We have previously shown that the DREAM subunit LIN9 is required for early embryonic development and for the maintenance of the inner cell mass in vitro. In this study we examined the effect of knocking down LIN9 on ESCs. We demonstrate that depletion of LIN9 alters the cell cycle distribution of ESCs and results in an accumulation of cells in G2 and M and in an increase of polyploid cells. Genome-wide expression studies showed that the depletion of LIN9 results in downregulation of mitotic genes and in upregulation of differentiation-specific genes. ChIP-on chip experiments showed that mitotic genes are direct targets of LIN9 while lineage specific markers are regulated indirectly. Importantly, depletion of LIN9 does not alter the expression of pluripotency markers SOX2, OCT4 and Nanog and LIN9 depleted ESCs retain alkaline phosphatase activity. We conclude that LIN9 is essential for proliferation and genome stability of ESCs by activating genes with important functions in mitosis and cytokinesis. PMID:23667535

A Generalized Linear Integrate-and-Fire Neural Model Produces Diverse Spiking Behaviors

PubMed Central

Mihalaş, Ştefan; Niebur, Ernst

2010-01-01

For simulations of neural networks, there is a trade-off between the size of the network that can be simulated and the complexity of the model used for individual neurons. In this study, we describe a generalization of the leaky integrate-and-fire model that produces a wide variety of spiking behaviors while still being analytically solvable between firings. For different parameter values, the model produces spiking or bursting, tonic, phasic or adapting responses, depolarizing or hyperpolarizing after potentials and so forth. The model consists of a diagonalizable set of linear differential equations describing the time evolution of membrane potential, a variable threshold, and an arbitrary number of firing-induced currents. Each of these variables is modified by an update rule when the potential reaches threshold. The variables used are intuitive and have biological significance. The model’s rich behavior does not come from the differential equations, which are linear, but rather from complex update rules. This single-neuron model can be implemented using algorithms similar to the standard integrate-and-fire model. It is a natural match with event-driven algorithms for which the firing times are obtained as a solution of a polynomial equation. PMID:18928368

HIV+ women's narratives of non-disclosure: resisting the label of immorality.

PubMed

Groves, Allison Kjellman; Maman, Suzanne; Moodley, Dhayendre

2012-01-01

Increasing partner disclosure rates among HIV+ individuals is widely seen as an important public health strategy to reduce HIV transmission. One approach for encouraging disclosure is to emphasise individuals' moral responsibility to disclose their status to their partners. We use South Africa as a case study to draw attention to two problems with labelling non-disclosure as immoral. First, we argue that because women are tested for HIV at much higher rates than men, any approach that involves blaming HIV+ individuals for not disclosing their status will disproportionately burden women. Second, through the narratives of six HIV+ women, we highlight how a focus on morality undervalues the complexity of sexual partnerships. Specifically, women describe how their perceived obligation to disclose their status is directly influenced by communication with their sexual partners. Women also discuss how the onset of different life events might alter the meaning of HIV and change obligations regarding disclosure within the partnership. The differences in testing rates across gender combined with the complexity of sexual partnerships leads us to suggest that labelling non-disclosure as immoral does little to advance HIV prevention. There is an urgent need to identify alternative interventions that support women through the disclosure process.

Flexible DNA Path in the MCM Double Hexamer Loaded on DNA.

PubMed

Hizume, Kohji; Kominami, Hiroaki; Kobayashi, Kei; Yamada, Hirofumi; Araki, Hiroyuki

2017-05-16

The formation of the pre-replicative complex (pre-RC) during the G1 phase, which is also called the licensing of DNA replication, is the initial and essential step of faithful DNA replication during the subsequent S phase. It is widely accepted that in the pre-RC, double-stranded DNA passes through the holes of two ring-shaped minichromosome maintenance (MCM) 2-7 hexamers; however, the spatial organization of the DNA and proteins involved in pre-RC formation is unclear. Here we reconstituted the pre-RC from purified DNA and proteins and visualized the complex using atomic force microscopy (AFM). AFM revealed that the MCM double hexamers formed elliptical particles on DNA. Analysis of the angle of binding of DNA to the MCM double hexamer suggests that the DNA does not completely pass through both holes of the MCM hexamers, possibly because the DNA exited from the gap between Mcm2 and Mcm5. A DNA loop fastened by the MCM double hexamer was detected in pre-RC samples reconstituted from purified proteins as well as those purified from yeast cells, suggesting a higher-order architecture of the loaded MCM hexamers and DNA strands.

The Multi-Scale Network Landscape of Collaboration

PubMed Central

Ahn, Yong-Yeol; Park, Juyong

2016-01-01

Propelled by the increasing availability of large-scale high-quality data, advanced data modeling and analysis techniques are enabling many novel and significant scientific understanding of a wide range of complex social, natural, and technological systems. These developments also provide opportunities for studying cultural systems and phenomena—which can be said to refer to all products of human creativity and way of life. An important characteristic of a cultural product is that it does not exist in isolation from others, but forms an intricate web of connections on many levels. In the creation and dissemination of cultural products and artworks in particular, collaboration and communication of ideas play an essential role, which can be captured in the heterogeneous network of the creators and practitioners of art. In this paper we propose novel methods to analyze and uncover meaningful patterns from such a network using the network of western classical musicians constructed from a large-scale comprehensive Compact Disc recordings data. We characterize the complex patterns in the network landscape of collaboration between musicians across multiple scales ranging from the macroscopic to the mesoscopic and microscopic that represent the diversity of cultural styles and the individuality of the artists. PMID:26990088

High-resolution seismic profiling reveals faulting associated with the 1934 Ms 6.6 Hansel Valley earthquake (Utah, USA)

USGS Publications Warehouse

Bruno, Pier Paolo G.; Duross, Christopher; Kokkalas, Sotirios

2017-01-01

The 1934 Ms 6.6 Hansel Valley, Utah, earthquake produced an 8-km-long by 3-km-wide zone of north-south−trending surface deformation in an extensional basin within the easternmost Basin and Range Province. Less than 0.5 m of purely vertical displacement was measured at the surface, although seismologic data suggest mostly strike-slip faulting at depth. Characterization of the origin and kinematics of faulting in the Hansel Valley earthquake is important to understand how complex fault ruptures accommodate regions of continental extension and transtension. Here, we address three questions: (1) How does the 1934 surface rupture compare with faults in the subsurface? (2) Are the 1934 fault scarps tectonic or secondary features? (3) Did the 1934 earthquake have components of both strike-slip and dip-slip motion? To address these questions, we acquired a 6.6-km-long, high-resolution seismic profile across Hansel Valley, including the 1934 ruptures. We observed numerous east- and west-dipping normal faults that dip 40°−70° and offset late Quaternary strata from within a few tens of meters of the surface down to a depth of ∼1 km. Spatial correspondence between the 1934 surface ruptures and subsurface faults suggests that ruptures associated with the earthquake are of tectonic origin. Our data clearly show complex basin faulting that is most consistent with transtensional tectonics. Although the kinematics of the 1934 earthquake remain underconstrained, we interpret the disagreement between surface (normal) and subsurface (strike-slip) kinematics as due to slip partitioning during fault propagation and to the effect of preexisting structural complexities. We infer that the 1934 earthquake occurred along an ∼3-km wide, off-fault damage zone characterized by distributed deformation along small-displacement faults that may be alternatively activated during different earthquake episodes.

DOE’s Management and Oversight of the Nuclear Weapons Complex

DTIC Science & Technology

1990-03-22

and Economic Development Division Before the Department of Energy Defense Nuclear Facilities Panel Committee on Armed Services House of Representatives...and newly created DOE offices. The Defense Nuclear Facilities Safety Board, whose board members were appointed this past year, was created to provide 6...mandated Defense Nuclear Facilities Safety Board. Continuing dialogue between DOE and the Board can also serve to enhance DOE’s ability to respond more

A Multifaceted Mathematical Approach for Complex Systems

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

Alexander, F.; Anitescu, M.; Bell, J.

2012-03-07

Applied mathematics has an important role to play in developing the tools needed for the analysis, simulation, and optimization of complex problems. These efforts require the development of the mathematical foundations for scientific discovery, engineering design, and risk analysis based on a sound integrated approach for the understanding of complex systems. However, maximizing the impact of applied mathematics on these challenges requires a novel perspective on approaching the mathematical enterprise. Previous reports that have surveyed the DOE's research needs in applied mathematics have played a key role in defining research directions with the community. Although these reports have had significantmore » impact, accurately assessing current research needs requires an evaluation of today's challenges against the backdrop of recent advances in applied mathematics and computing. To address these needs, the DOE Applied Mathematics Program sponsored a Workshop for Mathematics for the Analysis, Simulation and Optimization of Complex Systems on September 13-14, 2011. The workshop had approximately 50 participants from both the national labs and academia. The goal of the workshop was to identify new research areas in applied mathematics that will complement and enhance the existing DOE ASCR Applied Mathematics Program efforts that are needed to address problems associated with complex systems. This report describes recommendations from the workshop and subsequent analysis of the workshop findings by the organizing committee.« less

THE NGA-DOE GRANT TO EXAMINE CRITICAL ISSUES RELATED TO RADIOACTIVE WASTE AND MATERIALS DISPOSITION INVOLVING DOE FACILITIES

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

NONE

1998-01-01

Through the National Governors' Association (NGA) project ''Critical Issues Related to Radioactive Waste and Materials Disposition Involving DOE Facilities'' NGA brings together Governors' policy advisors, state regulators, and DOE officials to examine critical issues related to the cleanup and operation of DOE nuclear weapons and research facilities. Topics explored through this project include: Decisions involving disposal of mixed, low-level, and transuranic (TRU) waste and disposition of nuclear materials. Decisions involving DOE budget requests and their effect on environmental cleanup and compliance at DOE facilities. Strategies to treat mixed, low-level, and transuranic (TRU) waste and their effect on individual sites inmore » the complex. Changes to the FFCA site treatment plans as a result of proposals in the EM 2006 cleanup plans and contractor integration analysis. Interstate waste and materials shipments. Reforms to existing RCRA and CERCLA regulations/guidance to address regulatory overlap and risks posed by DOE wastes. The overarching theme of this project is to help the Department improve coordination of its major program decisions with Governors' offices and state regulators and to ensure such decisions reflect input from these key state officials and stakeholders. This report summarizes activities conducted during the quarter from October 1, 1997 through December 31, 1997, under the NGA project. The work accomplished by the NGA project team during the past four months can be categorized as follows: maintained open communication with DOE on a variety of activities and issues within the DOE environmental management complex; and maintained communication with NGA Federal Facilities Compliance Task Force members regarding DOE efforts to formulate a configuration for mixed low-level waste and low-level treatment and disposal, DOE activities in the area of the Hazardous Waste Identification Rule, and DOE's proposed National Dialogue.« less

Lessons Learned from the 200 West Pump and Treatment Facility Construction Project at the US DOE Hanford Site - A Leadership for Energy and Environmental Design (LEED) Gold-Certified Facility - 13113

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

Dorr, Kent A.; Freeman-Pollard, Jhivaun R.; Ostrom, Michael J.

CH2M Hill Plateau Remediation Company (CHPRC) designed, constructed, commissioned, and began operation of the largest groundwater pump and treatment facility in the U.S. Department of Energy's (DOE) nationwide complex. This one-of-a-kind groundwater pump and treatment facility, located at the Hanford Nuclear Reservation Site (Hanford Site) in Washington State, was built to an accelerated schedule with American Recovery and Reinvestment Act (ARRA) funds. There were many contractual, technical, configuration management, quality, safety, and Leadership in Energy and Environmental Design (LEED) challenges associated with the design, procurement, construction, and commissioning of this $95 million, 52,000 ft groundwater pump and treatment facility tomore » meet DOE's mission objective of treating contaminated groundwater at the Hanford Site with a new facility by June 28, 2012. The project team's successful integration of the project's core values and green energy technology throughout design, procurement, construction, and start-up of this complex, first-of-its-kind Bio Process facility resulted in successful achievement of DOE's mission objective, as well as attainment of LEED GOLD certification (Figure 1), which makes this Bio Process facility the first non-administrative building in the DOE Office of Environmental Management complex to earn such an award. (authors)« less

Designing HIGH-COST medicine: hospital surveys, health planning, and the paradox of progressive reform.

PubMed

Perkins, Barbara Bridgman

2010-02-01

Inspired by social medicine, some progressive US health reforms have paradoxically reinforced a business model of high-cost medical delivery that does not match social needs. In analyzing the financial status of their areas' hospitals, for example, city-wide hospital surveys of the 1910s through 1930s sought to direct capital investments and, in so doing, control competition and markets. The 2 national health planning programs that ran from the mid-1960s to the mid-1980s continued similar strategies of economic organization and management, as did the so-called market reforms that followed. Consequently, these reforms promoted large, extremely specialized, capital-intensive institutions and systems at the expense of less complex (and less costly) primary and chronic care. The current capital crisis may expose the lack of sustainability of such a model and open up new ideas and new ways to build health care designed to meet people's health needs.

Quantum realization of the bilinear interpolation method for NEQR.

PubMed

Zhou, Ri-Gui; Hu, Wenwen; Fan, Ping; Ian, Hou

2017-05-31

In recent years, quantum image processing is one of the most active fields in quantum computation and quantum information. Image scaling as a kind of image geometric transformation has been widely studied and applied in the classical image processing, however, the quantum version of which does not exist. This paper is concerned with the feasibility of the classical bilinear interpolation based on novel enhanced quantum image representation (NEQR). Firstly, the feasibility of the bilinear interpolation for NEQR is proven. Then the concrete quantum circuits of the bilinear interpolation including scaling up and scaling down for NEQR are given by using the multiply Control-Not operation, special adding one operation, the reverse parallel adder, parallel subtractor, multiplier and division operations. Finally, the complexity analysis of the quantum network circuit based on the basic quantum gates is deduced. Simulation result shows that the scaled-up image using bilinear interpolation is clearer and less distorted than nearest interpolation.

DFT Performance Prediction in FFTW

NASA Astrophysics Data System (ADS)

Gu, Liang; Li, Xiaoming

Fastest Fourier Transform in the West (FFTW) is an adaptive FFT library that generates highly efficient Discrete Fourier Transform (DFT) implementations. It is one of the fastest FFT libraries available and it outperforms many adaptive or hand-tuned DFT libraries. Its success largely relies on the huge search space spanned by several FFT algorithms and a set of compiler generated C code (called codelets) for small size DFTs. FFTW empirically finds the best algorithm by measuring the performance of different algorithm combinations. Although the empirical search works very well for FFTW, the search process does not explain why the best plan found performs best, and the search overhead grows polynomially as the DFT size increases. The opposite of empirical search is model-driven optimization. However, it is widely believed that model-driven optimization is inferior to empirical search and is particularly powerless to solve problems as complex as the optimization of DFT.

Dynamic heterogeneity and non-Gaussian statistics for acetylcholine receptors on live cell membrane

NASA Astrophysics Data System (ADS)

He, W.; Song, H.; Su, Y.; Geng, L.; Ackerson, B. J.; Peng, H. B.; Tong, P.

2016-05-01

The Brownian motion of molecules at thermal equilibrium usually has a finite correlation time and will eventually be randomized after a long delay time, so that their displacement follows the Gaussian statistics. This is true even when the molecules have experienced a complex environment with a finite correlation time. Here, we report that the lateral motion of the acetylcholine receptors on live muscle cell membranes does not follow the Gaussian statistics for normal Brownian diffusion. From a careful analysis of a large volume of the protein trajectories obtained over a wide range of sampling rates and long durations, we find that the normalized histogram of the protein displacements shows an exponential tail, which is robust and universal for cells under different conditions. The experiment indicates that the observed non-Gaussian statistics and dynamic heterogeneity are inherently linked to the slow-active remodelling of the underlying cortical actin network.

Ion exchange of several radionuclides on the hydrous crystalline silicotitanate, UOP IONSIV IE-911

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

Huckman, M.E.; Latheef, I.M.; Anthony, R.G.

1999-04-01

The crystalline silicotitanate, UOP IONSIV IE-911, is a proven material for removing radionuclides from a wide variety of waste streams. It is superior for removing several radionuclides from the highly alkaline solutions typical of DOE wastes. This laboratory previously developed an equilibrium model applicable to complex solutions for IE-910 (the power form of the granular IE-911), and more recently, the authors have developed several single component ion-exchange kinetic models for predicting column breakthrough curves and batch reactor concentration histories. In this paper, the authors model ion-exchange column performance using effective diffusivities determined from batch kinetic experiments. This technique is preferablemore » because the batch experiments are easier, faster, and cheaper to perform than column experiments. They also extend these ideas to multicomponent systems. Finally, they evaluate the ability of the equilibrium model to predict data for IE-911.« less

Effect of Pore Size and Pore Connectivity on Unidirectional Capillary Penetration Kinetics in 3-D Porous Media using Direct Numerical Simulation

NASA Astrophysics Data System (ADS)

Fu, An; Palakurthi, Nikhil; Konangi, Santosh; Comer, Ken; Jog, Milind

2017-11-01

The physics of capillary flow is used widely in multiple fields. Lucas-Washburn equation is developed by using a single pore-sized capillary tube with continuous pore connection. Although this equation has been extended to describe the penetration kinetics into porous medium, multiple studies have indicated L-W does not accurately predict flow patterns in real porous media. In this study, the penetration kinetics including the effect of pore size and pore connectivity will be closely examined since they are expected to be the key factors effecting the penetration process. The Liquid wicking process is studied from a converging and diverging capillary tube to the complex virtual 3-D porous structures with Direct Numerical Simulation (DNS) using the Volume-Of-Fluid (VOF) method within the OpenFOAM CFD Solver. Additionally Porous Medium properties such as Permeability (k) , Tortuosity (τ) will be also analyzed.

Spatial-dependence recurrence sample entropy

NASA Astrophysics Data System (ADS)

Pham, Tuan D.; Yan, Hong

2018-03-01

Measuring complexity in terms of the predictability of time series is a major area of research in science and engineering, and its applications are spreading throughout many scientific disciplines, where the analysis of physiological signals is perhaps the most widely reported in literature. Sample entropy is a popular measure for quantifying signal irregularity. However, the sample entropy does not take sequential information, which is inherently useful, into its calculation of sample similarity. Here, we develop a method that is based on the mathematical principle of the sample entropy and enables the capture of sequential information of a time series in the context of spatial dependence provided by the binary-level co-occurrence matrix of a recurrence plot. Experimental results on time-series data of the Lorenz system, physiological signals of gait maturation in healthy children, and gait dynamics in Huntington's disease show the potential of the proposed method.

Survivability of Deterministic Dynamical Systems

PubMed Central

Hellmann, Frank; Schultz, Paul; Grabow, Carsten; Heitzig, Jobst; Kurths, Jürgen

2016-01-01

The notion of a part of phase space containing desired (or allowed) states of a dynamical system is important in a wide range of complex systems research. It has been called the safe operating space, the viability kernel or the sunny region. In this paper we define the notion of survivability: Given a random initial condition, what is the likelihood that the transient behaviour of a deterministic system does not leave a region of desirable states. We demonstrate the utility of this novel stability measure by considering models from climate science, neuronal networks and power grids. We also show that a semi-analytic lower bound for the survivability of linear systems allows a numerically very efficient survivability analysis in realistic models of power grids. Our numerical and semi-analytic work underlines that the type of stability measured by survivability is not captured by common asymptotic stability measures. PMID:27405955

Resource-Efficient Measurement-Device-Independent Entanglement Witness

DOE PAGES

Verbanis, E.; Martin, A.; Rosset, D.; ...

2016-05-09

Imperfections in experimental measurement schemes can lead to falsely identifying, or over estimating, entanglement in a quantum system. A recent solution to this is to define schemes that are robust to measurement imperfections—measurement-device-independent entanglement witness (MDI-EW). This approach can be adapted to witness all entangled qubit states for a wide range of physical systems and does not depend on detection efficiencies or classical communication between devices. In this paper, we extend the theory to remove the necessity of prior knowledge about the two-qubit states to be witnessed. Moreover, we tested this model via a novel experimental implementation for MDI-EW thatmore » significantly reduces the experimental complexity. Finally, by applying it to a bipartite Werner state, we demonstrate the robustness of this approach against noise by witnessing entanglement down to an entangled state fraction close to 0.4.« less

High Temperature Joining and Characterization of Joint Properties in Silicon Carbide-Based Composite Materials

NASA Technical Reports Server (NTRS)

Halbig, Michael C.; Singh, Mrityunjay

2015-01-01

Advanced silicon carbide-based ceramics and composites are being developed for a wide variety of high temperature extreme environment applications. Robust high temperature joining and integration technologies are enabling for the fabrication and manufacturing of large and complex shaped components. The development of a new joining approach called SET (Single-step Elevated Temperature) joining will be described along with the overview of previously developed joining approaches including high temperature brazing, ARCJoinT (Affordable, Robust Ceramic Joining Technology), diffusion bonding, and REABOND (Refractory Eutectic Assisted Bonding). Unlike other approaches, SET joining does not have any lower temperature phases and will therefore have a use temperature above 1315C. Optimization of the composition for full conversion to silicon carbide will be discussed. The goal is to find a composition with no remaining carbon or free silicon. Green tape interlayers were developed for joining. Microstructural analysis and preliminary mechanical tests of the joints will be presented.

2 CFR 901.950 - Federal agency (Department of Energy supplement to government-wide definition at 2 CFR 180.950).

Code of Federal Regulations, 2011 CFR

2011-01-01

... 2 Grants and Agreements 1 2011-01-01 2011-01-01 false Federal agency (Department of Energy supplement to government-wide definition at 2 CFR 180.950). 901.950 Section 901.950 Grants and Agreements...-wide definition at 2 CFR 180.950). DOE means the U.S. Department of Energy, including the NNSA. NNSA...

Competing spreading processes on multiplex networks: awareness and epidemics.

PubMed

Granell, Clara; Gómez, Sergio; Arenas, Alex

2014-07-01

Epidemiclike spreading processes on top of multilayered interconnected complex networks reveal a rich phase diagram of intertwined competition effects. A recent study by the authors [C. Granell et al., Phys. Rev. Lett. 111, 128701 (2013).] presented an analysis of the interrelation between two processes accounting for the spreading of an epidemic, and the spreading of information awareness to prevent infection, on top of multiplex networks. The results in the case in which awareness implies total immunization to the disease revealed the existence of a metacritical point at which the critical onset of the epidemics starts, depending on completion of the awareness process. Here we present a full analysis of these critical properties in the more general scenario where the awareness spreading does not imply total immunization, and where infection does not imply immediate awareness of it. We find the critical relation between the two competing processes for a wide spectrum of parameters representing the interaction between them. We also analyze the consequences of a massive broadcast of awareness (mass media) on the final outcome of the epidemic incidence. Importantly enough, the mass media make the metacritical point disappear. The results reveal that the main finding, i.e., existence of a metacritical point, is rooted in the competition principle and holds for a large set of scenarios.

Association of intraventricular mechanical dyssynchrony with response to cardiac resynchronization therapy in heart failure patients with a narrow QRS complex

PubMed Central

van Bommel, Rutger J.; Tanaka, Hidekazu; Delgado, Victoria; Bertini, Matteo; Borleffs, Carel Jan Willem; Ajmone Marsan, Nina; Holzmeister, Johannes; Ruschitzka, Frank; Schalij, Martin J.; Bax, Jeroen J.; Gorcsan, John

2010-01-01

Aims Current criteria for cardiac resynchronization therapy (CRT) are restricted to patients with a wide QRS complex (>120 ms). Overall, only 30% of heart failure patients demonstrate a wide QRS complex, leaving the majority of heart failure patients without this treatment option. However, patients with a narrow QRS complex exhibit left ventricular (LV) mechanical dyssynchrony, as assessed with echocardiography. To further elucidate the possible beneficial effect of CRT in heart failure patients with a narrow QRS complex, this two-centre, non-randomized observational study focused on different echocardiographic parameters of LV mechanical dyssynchrony reflecting atrioventricular, interventricular and intraventricular dyssynchrony, and the response to CRT in these patients. Methods and results A total of 123 consecutive heart failure patients with a narrow QRS complex (<120 ms) undergoing CRT was included at two centres. Several widely accepted measures of mechanical dyssynchrony were evaluated: LV filling ratio (LVFT/RR), LV pre-ejection time (LPEI), interventricular mechanical dyssynchrony (IVMD), opposing wall delay (OWD), and anteroseptal posterior wall delay with speckle tracking (ASPWD). Response to CRT was defined as a reduction ≥15% in left ventricular end-systolic volume at 6 months follow-up. Measures of dyssynchrony can frequently be observed in patients with a narrow QRS complex. Nonetheless, for LVFT/RR, LPEI, and IVMD, presence of predefined significant dyssynchrony is <20%. Significant intraventricular dyssynchrony is more widely observed in these patients. With receiver operator characteristic curve analyses, both OWD and ASPWD demonstrated usefulness in predicting response to CRT in narrow QRS patients with a cut-off value of 75 and 107 ms, respectively. Conclusion Mechanical dyssynchrony can be widely observed in heart failure patients with a narrow QRS complex. In particular, intraventricular measures of mechanical dyssynchrony may be useful in predicting LV reverse remodelling at 6 months follow-up in heart failure patients with a narrow QRS complex, but with more stringent cut-off values than currently used in ‘wide’ QRS patients. PMID:20864484

Visual Short-Term Memory Capacity for Simple and Complex Objects

ERIC Educational Resources Information Center

Luria, Roy; Sessa, Paola; Gotler, Alex; Jolicoeur, Pierre; Dell'Acqua, Roberto

2010-01-01

Does the capacity of visual short-term memory (VSTM) depend on the complexity of the objects represented in memory? Although some previous findings indicated lower capacity for more complex stimuli, other results suggest that complexity effects arise during retrieval (due to errors in the comparison process with what is in memory) that is not…

THE NGA-DOE GRANT TO EXAMINE CRITICAL ISSUES RELATED TO RADIOACTIVE WASTE AND MATERIALS DISPOSITION INVOLVING DOE FACILITIES

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

NONE

1998-04-01

Through the National Governors' Association (NGA) project ''Critical Issues Related to Radioactive Waste and Materials Disposition Involving DOE Facilities'' NGA brings together Governors' policy advisors, state regulators, and DOE officials to examine critical issues related to the cleanup and operation of DOE nuclear weapons and research facilities. Topics explored through this project include: Decisions involving disposal of mixed, low-level, and transuranic (TRU) waste and disposition of nuclear materials. Decisions involving DOE budget requests and their effect on environmental cleanup and compliance at DOE facilities. Strategies to treat mixed, low-level, and transuranic (TRU) waste and their effect on individual sites inmore » the complex. Changes to the FFCA site treatment plans as a result of proposals in DOE's Accelerating Cleanup: Paths to Closure strategy and contractor integration analysis. Interstate waste and materials shipments. Reforms to existing RCRA and CERCLA regulations/guidance to address regulatory overlap and risks posed by DOE wastes. The overarching theme of this project is to help the Department improve coordination of its major program decisions with Governors' offices and state regulators and to ensure such decisions reflect input from these key state officials and stakeholders. This report summarizes activities conducted during the quarter from December 31, 1997 through April 30, 1998 under the NGA project. The work accomplished by the NGA project team during the past four months can be categorized as follows: maintained open communication with DOE on a variety of activities and issues within the DOE environmental management complex; and provided ongoing support to state-DOE interactions in preparation for the March 30-31, 1998 NGA Federal Facilities Compliance Task Force Meeting with DOE. maintained communication with NGA Federal Facilities Compliance Task Force members regarding DOE efforts to formulate a configuration for mixed low-level waste and low-level treatment and disposal, DOE's Environmental Management Budget, and DOE's proposed Intersite Discussions.« less

Virtual special issue on catalysis at the U.S. Department of Energy's National Laboratories

DOE PAGES

Pruski, Marek; Sadow, Aaron D.; Slowing, Igor I.; ...

2016-04-21

Here the catalysis research at the U.S. Department of Energy's (DOE's) National Laboratories covers a wide range of research topics in heterogeneous catalysis, homogeneous/molecular catalysis, biocatalysis, electrocatalysis, and surface science. Since much of the work at National Laboratories is funded by DOE, the research is largely focused on addressing DOE's mission to ensure America's security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions.

Analytical Chemistry and Measurement Science: (What Has DOE Done for Analytical Chemistry?)

DOE R&D Accomplishments Database

Shults, W. D.

1989-04-01

Over the past forty years, analytical scientists within the DOE complex have had a tremendous impact on the field of analytical chemistry. This paper suggests six "high impact" research/development areas that either originated within or were brought to maturity within the DOE laboratories. "High impact" means they lead to new subdisciplines or to new ways of doing business.

Disclaimer | NOAA Gulf Spill Restoration

Science.gov Websites

other information resources available on the World Wide Web, and NOAA does not control and cannot , reliability, or completeness of furnished data. Non-federal sites are identified on this site with this icon Linking to a non-federal government web site. This link does not imply endorsement. . The icon appears

76 FR 40352 - National Nuclear Security Administration; Amended Record of Decision: Site-Wide Environmental...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-08

... similar to those estimated for transportation of radioactive material in other DOE NEPA documents. The air... radiological materials located at civilian sites worldwide. Part of the GTRI mission is implemented through... specific actions analyzed in DOE/EIS-0380-SA-02 include packaging the sealed sources (sometimes with a part...

Actinomycetal complex of light sierozem on the Kopet-Dag piedmont plain

NASA Astrophysics Data System (ADS)

Zenova, G. M.; Zvyagintsev, D. G.; Manucharova, N. A.; Stepanova, O. A.; Chernov, I. Yu.

2016-10-01

The population density of actinomycetes in the samples of light sierozem from the Kopet Dag piedmont plain (75 km from Ashkhabad, Turkmenistan) reaches hundreds of thousand CFU/g soil. The actinomycetal complex is represented by two genera: Streptomyces and Micromonospora. Representatives of the Streptomyces genus predominate and comprise 73 to 87% of the actinomycetal complex. In one sample, representatives of the Micromonospora genus predominated in the complex (75%). The Streptomyces genus in the studied soil samples is represented by the species from several sections and series: the species of section Helvolo-Flavus series Helvolus represent the dominant component of the streptomycetal complex; their portion is up to 77% of all isolated actinomycetes. The species of other sections and series are much less abundant. Thus, the percentage of the Cinereus Achromogenes section in the actinomycetal complex does not exceed 28%; representatives of the Albus section Albus series, Roseus section Lavendulae-Roseus series, and Imperfectus section belong to rare species; they have been isolated not from all the studied samples of light sierozem, and their portion does not exceed 10% of the actinomycetal complex.

Hoisting and Rigging (Formerly Hoisting and Rigging Manual)

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

NONE

1995-06-01

This standard is intended as a reference document to be used by supervisors, line managers, safety personnel, equipment operators, and any other personnel responsible for safety of hoisting and rigging operations at DOE sites. It quotes or paraphrases the US OSHA and ANSI requirements. It also encompasses, under one cover,hoisting and rigging requirements, codes, standards, and regulations, eliminating the need to maintain extensive (and often incomplete) libraries of hoisting and rigging standards throughout DOE. The standard occasionally goes beyond the minimum general industry standards established by OSHA and ANSI, and also delineates the more stringent requirements necessary to accomplish themore » complex, diversified, critical, and often hazardous hoisting and rigging work found with the DOE complex.« less

MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation

PubMed Central

Stojanova, Angelina; Tu, William B.; Ponzielli, Romina; Kotlyar, Max; Chan, Pak-Kei; Boutros, Paul C.; Khosravi, Fereshteh; Jurisica, Igor; Raught, Brian; Penn, Linda Z.

2016-01-01

ABSTRACT MYC is a key driver of cellular transformation and is deregulated in most human cancers. Studies of MYC and its interactors have provided mechanistic insight into its role as a regulator of gene transcription. MYC has been previously linked to chromatin regulation through its interaction with INI1 (SMARCB1/hSNF5/BAF47), a core member of the SWI/SNF chromatin remodeling complex. INI1 is a potent tumor suppressor that is inactivated in several types of cancers, most prominently as the hallmark alteration in pediatric malignant rhabdoid tumors. However, the molecular and functional interaction of MYC and INI1 remains unclear. Here, we characterize the MYC-INI1 interaction in mammalian cells, mapping their minimal binding domains to functionally significant regions of MYC (leucine zipper) and INI1 (repeat motifs), and demonstrating that the interaction does not interfere with MYC-MAX interaction. Protein-protein interaction network analysis expands the MYC-INI1 interaction to the SWI/SNF complex and a larger network of chromatin regulatory complexes. Genome-wide analysis reveals that the DNA-binding regions and target genes of INI1 significantly overlap with those of MYC. In an INI1-deficient rhabdoid tumor system, we observe that with re-expression of INI1, MYC and INI1 bind to common target genes and have opposing effects on gene expression. Functionally, INI1 re-expression suppresses cell proliferation and MYC-potentiated transformation. Our findings thus establish the antagonistic roles of the INI1 and MYC transcriptional regulators in mediating cellular and oncogenic functions. PMID:27267444

Enhancing genomic prediction with genome-wide association studies in multiparental maize populations

USDA-ARS?s Scientific Manuscript database

Genome-wide association mapping using dense marker sets has identified some nucleotide variants affecting complex traits which have been validated with fine-mapping and functional analysis. Many sequence variants associated with complex traits in maize have small effects and low repeatability, howev...

Wide QRS tachycardia: what is the rhythm?

PubMed

Rosman, Jonathan; Tawil, Joseph; Hanon, Sam; Schweitzer, Paul

2006-10-01

We report a case of an elderly man who presented to the emergency room complaining of palpitations. Electrocardiogram revealed wide QRS tachycardia with a narrow beat within the tachycardia. Most commonly, a narrow complex beat during a wide complex tachycardia suggests a capture or fusion beat in the setting of ventricular tachycardia. However, there are situations where supraventricular tachycardia can also manifest this way. In our patient a pacemaker interrogation clarified the diagnosis.

TEAM: efficient two-locus epistasis tests in human genome-wide association study.

PubMed

Zhang, Xiang; Huang, Shunping; Zou, Fei; Wang, Wei

2010-06-15

As a promising tool for identifying genetic markers underlying phenotypic differences, genome-wide association study (GWAS) has been extensively investigated in recent years. In GWAS, detecting epistasis (or gene-gene interaction) is preferable over single locus study since many diseases are known to be complex traits. A brute force search is infeasible for epistasis detection in the genome-wide scale because of the intensive computational burden. Existing epistasis detection algorithms are designed for dataset consisting of homozygous markers and small sample size. In human study, however, the genotype may be heterozygous, and number of individuals can be up to thousands. Thus, existing methods are not readily applicable to human datasets. In this article, we propose an efficient algorithm, TEAM, which significantly speeds up epistasis detection for human GWAS. Our algorithm is exhaustive, i.e. it does not ignore any epistatic interaction. Utilizing the minimum spanning tree structure, the algorithm incrementally updates the contingency tables for epistatic tests without scanning all individuals. Our algorithm has broader applicability and is more efficient than existing methods for large sample study. It supports any statistical test that is based on contingency tables, and enables both family-wise error rate and false discovery rate controlling. Extensive experiments show that our algorithm only needs to examine a small portion of the individuals to update the contingency tables, and it achieves at least an order of magnitude speed up over the brute force approach.

Composition of complex numbers: Delineating the computational role of the left anterior temporal lobe.

PubMed

Blanco-Elorrieta, Esti; Pylkkänen, Liina

2016-01-01

What is the neurobiological basis of our ability to create complex messages with language? Results from multiple methodologies have converged on a set of brain regions as relevant for this general process, but the computational details of these areas remain to be characterized. The left anterior temporal lobe (LATL) has been a consistent node within this network, with results suggesting that although it rather systematically shows increased activation for semantically complex structured stimuli, this effect does not extend to number phrases such as 'three books.' In the present work we used magnetoencephalography to investigate whether numbers in general are an invalid input to the combinatory operations housed in the LATL or whether the lack of LATL engagement for stimuli such as 'three books' is due to the quantificational nature of such phrases. As a relevant test case, we employed complex number terms such as 'twenty-three', where one number term is not a quantifier of the other but rather, the two terms form a type of complex concept. In a number naming paradigm, participants viewed rows of numbers and depending on task instruction, named them as complex number terms ('twenty-three'), numerical quantifications ('two threes'), adjectival modifications ('blue threes') or non-combinatory lists (e.g., 'two, three'). While quantificational phrases failed to engage the LATL as compared to non-combinatory controls, both complex number terms and adjectival modifications elicited a reliable activity increase in the LATL. Our results show that while the LATL does not participate in the enumeration of tokens within a set, exemplified by the quantificational phrases, it does support conceptual combination, including the composition of complex number concepts. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Wide-band array signal processing via spectral smoothing

NASA Technical Reports Server (NTRS)

Xu, Guanghan; Kailath, Thomas

1989-01-01

A novel algorithm for the estimation of direction-of-arrivals (DOA) of multiple wide-band sources via spectral smoothing is presented. The proposed algorithm does not require an initial DOA estimate or a specific signal model. The advantages of replacing the MUSIC search with an ESPRIT search are discussed.

THE NGA-DOE GRANT TO EXAMINE CRITICAL ISSUES RELATED TO RADIOACTIVE WASTE AND MATERIALS DISPOSITION INVOLVING DOE FACILITIES

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

NONE

1998-07-01

Through the National Governors' Association (NGA) project ''Critical Issues Related to Radioactive Waste and Materials Disposition Involving DOE Facilities'' NGA brings together Governors' policy advisors, state regulators, and DOE officials to examine critical issues related to the cleanup and operation of DOE nuclear weapons and research facilities. Topics explored through this project include: Decisions involving disposal of mixed, low-level, and transuranic (TRU) waste and disposition of nuclear materials. Decisions involving DOE budget requests and their effect on environmental cleanup and compliance at DOE facilities. Strategies to treat mixed, low-level, and transuranic (TRU) waste and their effect on individual sites inmore » the complex. Changes to the FFCA site treatment plans as a result of proposals in DOE's Accelerating Cleanup: Paths to Closure strategy and contractor integration analysis. Interstate waste and materials shipments. Reforms to existing RCRA and CERCLA regulations/guidance to address regulatory overlap and risks posed by DOE wastes. The overarching theme of this project is to help the Department improve coordination of its major program decisions with Governors' offices and state regulators and to ensure such decisions reflect input from these key state officials and stakeholders. This report summarizes activities conducted during the quarter from April 30, 1998 through June 30, 1998 under the NGA project. The work accomplished by the NGA project team during the past four months can be categorized as follows: maintained open communication with DOE on a variety of activities and issues within the DOE environmental management complex; and provided ongoing support to state-DOE interactions. maintained communication with NGA Federal Facilities Compliance Task Force members regarding DOE efforts to formulate a configuration for mixed low-level waste and low-level treatment and disposal, DOE's Environmental Management Budget, and DOE's proposed Intersite Discussions.« less

Enabling Advanced Wind-Tunnel Research Methods Using the NASA Langley 12-Foot Low Speed Tunnel

NASA Technical Reports Server (NTRS)

Busan, Ronald C.; Rothhaar, Paul M.; Croom, Mark A.; Murphy, Patrick C.; Grafton, Sue B.; O-Neal, Anthony W.

2014-01-01

Design of Experiment (DOE) testing methods were used to gather wind tunnel data characterizing the aerodynamic and propulsion forces and moments acting on a complex vehicle configuration with 10 motor-driven propellers, 9 control surfaces, a tilt wing, and a tilt tail. This paper describes the potential benefits and practical implications of using DOE methods for wind tunnel testing - with an emphasis on describing how it can affect model hardware, facility hardware, and software for control and data acquisition. With up to 23 independent variables (19 model and 2 tunnel) for some vehicle configurations, this recent test also provides an excellent example of using DOE methods to assess critical coupling effects in a reasonable timeframe for complex vehicle configurations. Results for an exploratory test using conventional angle of attack sweeps to assess aerodynamic hysteresis is summarized, and DOE results are presented for an exploratory test used to set the data sampling time for the overall test. DOE results are also shown for one production test characterizing normal force in the Cruise mode for the vehicle.

Genome-wide characterization of Mediator recruitment, function, and regulation.

PubMed

Grünberg, Sebastian; Zentner, Gabriel E

2017-05-27

Mediator is a conserved and essential coactivator complex broadly required for RNA polymerase II (RNAPII) transcription. Recent genome-wide studies of Mediator binding in budding yeast have revealed new insights into the functions of this critical complex and raised new questions about its role in the regulation of gene expression.

Clades of Photosynthetic Bacteria Belonging to the Genus Rhodopseudomonas Show Marked Diversity in Light-Harvesting Antenna Complex Gene Composition and Expression

DOE PAGES

Fixen, Kathryn R.; Oda, Yasuhiro; Harwood, Caroline S.; ...

2015-12-22

Many photosynthetic bacteria have peripheral light-harvesting (LH) antenna complexes that increase the efficiency of light energy capture. The purple nonsulfur photosynthetic bacteriumRhodopseudomonas palustrisproduces different types of LH complexes under high light intensities (LH2 complex) and low light intensities (LH3 and LH4 complexes). There are multiplepucBAoperons that encode the α and β peptides that make up these complexes. But, low-resolution structures, amino acid similarities between the complexes, and a lack of transcription analysis have made it difficult to determine the contributions of differentpucBAoperons to the composition and function of different LH complexes. It was also unclear how much diversity of LHmore » complexes exists inR. palustrisand affiliated strains. To address this, we undertook an integrative genomics approach using 20 sequenced strains. Gene content analysis revealed that even closely related strains have differences in theirpucBAgene content. Transcriptome analyses of the strains grown under high light and low light revealed that the patterns of expression of thepucBAoperons varied among strains grown under the same conditions. We also found that one set of LH2 complex proteins compensated for the lack of an LH4 complex under low light intensities but not under extremely low light intensities, indicating that there is functional redundancy between some of the LH complexes under certain light intensities. The variation observed in LH gene composition and expression inRhodopseudomonasstrains likely reflects how they have evolved to adapt to light conditions in specific soil and water microenvironments. ImportanceRhodopseudomonas palustrisis a phototrophic purple nonsulfur bacterium that adapts its photosystem to allow growth at a range of light intensities. It does this by adjusting the amount and composition of peripheral light-harvesting (LH) antenna complexes that it synthesizes.Rhodopseudomonasstrains are notable for containing numerous sets of light-harvesting genes. We determined the diversity of LH complexes and their transcript levels during growth under high and low light intensities in 20 sequenced genomes of strains related to the speciesRhodopseudomonas palustris. Finally, the data obtained are a resource for investigators with interests as wide-ranging as the biophysics of photosynthesis, the ecology of phototrophic bacteria, and the use of photosynthetic bacteria for biotechnology applications.« less

Clades of Photosynthetic Bacteria Belonging to the Genus Rhodopseudomonas Show Marked Diversity in Light-Harvesting Antenna Complex Gene Composition and Expression

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

Fixen, Kathryn R.; Oda, Yasuhiro; Harwood, Caroline S.

Many photosynthetic bacteria have peripheral light-harvesting (LH) antenna complexes that increase the efficiency of light energy capture. The purple nonsulfur photosynthetic bacteriumRhodopseudomonas palustrisproduces different types of LH complexes under high light intensities (LH2 complex) and low light intensities (LH3 and LH4 complexes). There are multiplepucBAoperons that encode the α and β peptides that make up these complexes. But, low-resolution structures, amino acid similarities between the complexes, and a lack of transcription analysis have made it difficult to determine the contributions of differentpucBAoperons to the composition and function of different LH complexes. It was also unclear how much diversity of LHmore » complexes exists inR. palustrisand affiliated strains. To address this, we undertook an integrative genomics approach using 20 sequenced strains. Gene content analysis revealed that even closely related strains have differences in theirpucBAgene content. Transcriptome analyses of the strains grown under high light and low light revealed that the patterns of expression of thepucBAoperons varied among strains grown under the same conditions. We also found that one set of LH2 complex proteins compensated for the lack of an LH4 complex under low light intensities but not under extremely low light intensities, indicating that there is functional redundancy between some of the LH complexes under certain light intensities. The variation observed in LH gene composition and expression inRhodopseudomonasstrains likely reflects how they have evolved to adapt to light conditions in specific soil and water microenvironments. ImportanceRhodopseudomonas palustrisis a phototrophic purple nonsulfur bacterium that adapts its photosystem to allow growth at a range of light intensities. It does this by adjusting the amount and composition of peripheral light-harvesting (LH) antenna complexes that it synthesizes.Rhodopseudomonasstrains are notable for containing numerous sets of light-harvesting genes. We determined the diversity of LH complexes and their transcript levels during growth under high and low light intensities in 20 sequenced genomes of strains related to the speciesRhodopseudomonas palustris. Finally, the data obtained are a resource for investigators with interests as wide-ranging as the biophysics of photosynthesis, the ecology of phototrophic bacteria, and the use of photosynthetic bacteria for biotechnology applications.« less

How and when Does Complex Reasoning Occur? Empirically Driven Development of a Learning Progression Focused on Complex Reasoning about Biodiversity

ERIC Educational Resources Information Center

Songer, Nancy Butler; Kelcey, Ben; Gotwals, Amelia Wenk

2009-01-01

In order to compete in a global economy, students are going to need resources and curricula focusing on critical thinking and reasoning in science. Despite awareness for the need for complex reasoning, American students perform poorly relative to peers on international standardized tests measuring complex thinking in science. Research focusing on…

Combined genome-wide linkage and targeted association analysis of head circumference in autism spectrum disorder families.

PubMed

Woodbury-Smith, M; Bilder, D A; Morgan, J; Jerominski, L; Darlington, T; Dyer, T; Paterson, A D; Coon, H

2017-01-01

It has long been recognized that there is an association between enlarged head circumference (HC) and autism spectrum disorder (ASD), but the genetics of HC in ASD is not well understood. In order to investigate the genetic underpinning of HC in ASD, we undertook a genome-wide linkage study of HC followed by linkage signal targeted association among a sample of 67 extended pedigrees with ASD. HC measurements on members of 67 multiplex ASD extended pedigrees were used as a quantitative trait in a genome-wide linkage analysis. The Illumina 6K SNP linkage panel was used, and analyses were carried out using the SOLAR implemented variance components model. Loci identified in this way formed the target for subsequent association analysis using the Illumina OmniExpress chip and imputed genotypes. A modification of the qTDT was used as implemented in SOLAR. We identified a linkage signal spanning 6p21.31 to 6p22.2 (maximum LOD = 3.4). Although targeted association did not find evidence of association with any SNP overall, in one family with the strongest evidence of linkage, there was evidence for association (rs17586672, p  = 1.72E-07). Although this region does not overlap with ASD linkage signals in these same samples, it has been associated with other psychiatric risk, including ADHD, developmental dyslexia, schizophrenia, specific language impairment, and juvenile bipolar disorder. The genome-wide significant linkage signal represents the first reported observation of a potential quantitative trait locus for HC in ASD and may be relevant in the context of complex multivariate risk likely leading to ASD.

Cognitive Agility Measurement in a Complex Environment

DTIC Science & Technology

2017-04-01

correlate with their corresponding historical psychology tests? EEA3.1: Does the variable for Make Goal cognitive flexibility correlate with the...Stroop Test cognitive flexibility variable? EEA3.2: Does the variable for Make Goal cognitive openness correlate with the AUT cognitive openness...variable? EEA3.3: Does the variable for Make Goal focused attention correlate with the Go, No Go Paradigm focused attention variable? 1.6

Positive correlation between ADAR expression and its targets suggests a complex regulation mediated by RNA editing in the human brain

PubMed Central

Liscovitch, Noa; Bazak, Lily; Levanon, Erez Y; Chechik, Gal

2014-01-01

A-to-I RNA editing by adenosine deaminases acting on RNA is a post-transcriptional modification that is crucial for normal life and development in vertebrates. RNA editing has been shown to be very abundant in the human transcriptome, specifically at the primate-specific Alu elements. The functional role of this wide-spread effect is still not clear; it is believed that editing of transcripts is a mechanism for their down-regulation via processes such as nuclear retention or RNA degradation. Here we combine 2 neural gene expression datasets with genome-level editing information to examine the relation between the expression of ADAR genes with the expression of their target genes. Specifically, we computed the spatial correlation across structures of post-mortem human brains between ADAR and a large set of targets that were found to be edited in their Alu repeats. Surprisingly, we found that a large fraction of the edited genes are positively correlated with ADAR, opposing the assumption that editing would reduce expression. When considering the correlations between ADAR and its targets over development, 2 gene subsets emerge, positively correlated and negatively correlated with ADAR expression. Specifically, in embryonic time points, ADAR is positively correlated with many genes related to RNA processing and regulation of gene expression. These findings imply that the suggested mechanism of regulation of expression by editing is probably not a global one; ADAR expression does not have a genome wide effect reducing the expression of editing targets. It is possible, however, that RNA editing by ADAR in non-coding regions of the gene might be a part of a more complex expression regulation mechanism. PMID:25692240

Positive correlation between ADAR expression and its targets suggests a complex regulation mediated by RNA editing in the human brain.

PubMed

Liscovitch, Noa; Bazak, Lily; Levanon, Erez Y; Chechik, Gal

2014-01-01

A-to-I RNA editing by adenosine deaminases acting on RNA is a post-transcriptional modification that is crucial for normal life and development in vertebrates. RNA editing has been shown to be very abundant in the human transcriptome, specifically at the primate-specific Alu elements. The functional role of this wide-spread effect is still not clear; it is believed that editing of transcripts is a mechanism for their down-regulation via processes such as nuclear retention or RNA degradation. Here we combine 2 neural gene expression datasets with genome-level editing information to examine the relation between the expression of ADAR genes with the expression of their target genes. Specifically, we computed the spatial correlation across structures of post-mortem human brains between ADAR and a large set of targets that were found to be edited in their Alu repeats. Surprisingly, we found that a large fraction of the edited genes are positively correlated with ADAR, opposing the assumption that editing would reduce expression. When considering the correlations between ADAR and its targets over development, 2 gene subsets emerge, positively correlated and negatively correlated with ADAR expression. Specifically, in embryonic time points, ADAR is positively correlated with many genes related to RNA processing and regulation of gene expression. These findings imply that the suggested mechanism of regulation of expression by editing is probably not a global one; ADAR expression does not have a genome wide effect reducing the expression of editing targets. It is possible, however, that RNA editing by ADAR in non-coding regions of the gene might be a part of a more complex expression regulation mechanism.

Selective Limbic Blood–Brain Barrier Breakdown in a Feline Model of Limbic Encephalitis with LGI1 Antibodies

PubMed Central

Tröscher, Anna R.; Klang, Andrea; French, Maria; Quemada-Garrido, Lucía; Kneissl, Sibylle Maria; Bien, Christian G.; Pákozdy, Ákos; Bauer, Jan

2017-01-01

Human leucine-rich glioma-inactivated protein 1 encephalitis (LGI1) is an autoimmune limbic encephalitis in which serum and cerebrospinal fluid contain antibodies targeting LGI1, a protein of the voltage gated potassium channel (VGKC) complex. Recently, we showed that a feline model of limbic encephalitis with LGI1 antibodies, called feline complex partial seizures with orofacial involvement (FEPSO), is highly comparable to human LGI1 encephalitis. In human LGI1 encephalitis, neuropathological investigations are difficult because very little material is available. Taking advantage of this natural animal model to study pathological mechanisms will, therefore, contribute to a better understanding of its human counterpart. Here, we present a brain-wide histopathological analysis of FEPSO. We discovered that blood–brain barrier (BBB) leakage was present not only in all regions of the hippocampus but also in other limbic structures such as the subiculum, amygdale, and piriform lobe. However, in other regions, such as the cerebellum, no leakage was observed. In addition, this brain-region-specific immunoglobulin leakage was associated with the breakdown of endothelial tight junctions. Brain areas affected by BBB dysfunction also revealed immunoglobulin and complement deposition as well as neuronal cell death. These neuropathological findings were supported by magnetic resonance imaging showing signal and volume increase in the amygdala and the piriform lobe. Importantly, we could show that BBB disturbance in LGI1 encephalitis does not depend on T cell infiltrates, which were present brain-wide. This finding points toward another, so far unknown, mechanism of opening the BBB. The limbic predilection sites of immunoglobulin antibody leakage into the brain may explain why most patients with LGI1 antibodies have a limbic phenotype even though LGI1, the target protein, is ubiquitously distributed across the central nervous system. PMID:29093718

Selective Limbic Blood-Brain Barrier Breakdown in a Feline Model of Limbic Encephalitis with LGI1 Antibodies.

PubMed

Tröscher, Anna R; Klang, Andrea; French, Maria; Quemada-Garrido, Lucía; Kneissl, Sibylle Maria; Bien, Christian G; Pákozdy, Ákos; Bauer, Jan

2017-01-01

Human leucine-rich glioma-inactivated protein 1 encephalitis (LGI1) is an autoimmune limbic encephalitis in which serum and cerebrospinal fluid contain antibodies targeting LGI1, a protein of the voltage gated potassium channel (VGKC) complex. Recently, we showed that a feline model of limbic encephalitis with LGI1 antibodies, called feline complex partial seizures with orofacial involvement (FEPSO), is highly comparable to human LGI1 encephalitis. In human LGI1 encephalitis, neuropathological investigations are difficult because very little material is available. Taking advantage of this natural animal model to study pathological mechanisms will, therefore, contribute to a better understanding of its human counterpart. Here, we present a brain-wide histopathological analysis of FEPSO. We discovered that blood-brain barrier (BBB) leakage was present not only in all regions of the hippocampus but also in other limbic structures such as the subiculum, amygdale, and piriform lobe. However, in other regions, such as the cerebellum, no leakage was observed. In addition, this brain-region-specific immunoglobulin leakage was associated with the breakdown of endothelial tight junctions. Brain areas affected by BBB dysfunction also revealed immunoglobulin and complement deposition as well as neuronal cell death. These neuropathological findings were supported by magnetic resonance imaging showing signal and volume increase in the amygdala and the piriform lobe. Importantly, we could show that BBB disturbance in LGI1 encephalitis does not depend on T cell infiltrates, which were present brain-wide. This finding points toward another, so far unknown, mechanism of opening the BBB. The limbic predilection sites of immunoglobulin antibody leakage into the brain may explain why most patients with LGI1 antibodies have a limbic phenotype even though LGI1, the target protein, is ubiquitously distributed across the central nervous system.

T Cell Receptor-Major Histocompatibility Complex Interaction Strength Defines Trafficking and CD103+ Memory Status of CD8 T Cells in the Brain.

PubMed

Sanecka, Anna; Yoshida, Nagisa; Kolawole, Elizabeth Motunrayo; Patel, Harshil; Evavold, Brian D; Frickel, Eva-Maria

2018-01-01

T cell receptor-major histocompatibility complex (TCR-MHC) affinities span a wide range in a polyclonal T cell response, yet it is undefined how affinity shapes long-term properties of CD8 T cells during chronic infection with persistent antigen. Here, we investigate how the affinity of the TCR-MHC interaction shapes the phenotype of memory CD8 T cells in the chronically Toxoplasma gondii- infected brain. We employed CD8 T cells from three lines of transnuclear (TN) mice that harbor in their endogenous loci different T cell receptors specific for the same Toxoplasma antigenic epitope ROP7. The three TN CD8 T cell clones span a wide range of affinities to MHCI-ROP7. These three CD8 T cell clones have a distinct and fixed hierarchy in terms of effector function in response to the antigen measured as proliferation capacity, trafficking, T cell maintenance, and memory formation. In particular, the T cell clone of lowest affinity does not home to the brain. The two higher affinity T cell clones show differences in establishing resident-like memory populations (CD103 + ) in the brain with the higher affinity clone persisting longer in the host during chronic infection. Transcriptional profiling of naïve and activated ROP7-specific CD8 T cells revealed that Klf2 encoding a transcription factor that is known to be a negative marker for T cell trafficking is upregulated in the activated lowest affinity ROP7 clone. Our data thus suggest that TCR-MHC affinity dictates memory CD8 T cell fate at the site of infection.

The Girls and Boys Town Book on Patriotism.

ERIC Educational Resources Information Center

Peter, Val J.; Dowd, Tom

The word "patriotism" summons up a wide range of images, but true patriotism goes beyond special occasions and special people. Do young people know what living as a patriot means? What obligations does a citizen owe to the United States? What opportunities does the country give to him or her? The lessons in this booklet can help students…

75 FR 73128 - Certain Printing and Imaging Devices and Components Thereof; Notice of Commission Determination...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-29

...'' include any line extending parallel to the central axis of the roller? Or, does this refer to the central... ``a longitudinal direction'' can include any line extending parallel to the central axis of the roller...) The finding that the Taylor reference (``A Telerobot on the World Wide Web'') (RX-281) does not...

Macroencapsulation Equivalency Guidance for Classified Weapon Components and NNSSWAC Compliance

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

Poling, J.

2012-05-15

The U.S. Department of Energy (DOE) complex has a surplus of classified legacy weapon components generated over the years with no direct path for disposal. The majority of the components have been held for uncertainty of future use or no identified method of sanitization or disposal. As more weapons are retired, there is an increasing need to reduce the amount of components currently in storage or on hold. A process is currently underway to disposition and dispose of the legacy/retired weapons components across the DOE complex.

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

Pruski, Marek; Sadow, Aaron D.; Slowing, Igor I.

Catalysis research at the U.S. Department of Energy's (DOE's) National Laboratories covers a wide range of research topics in heterogeneous catalysis, homogeneous/molecular catalysis, biocatalysis, electrocatalysis, and surface science. Since much of the work at National Laboratories is funded by DOE, the research is largely focused on addressing DOE's mission to ensure America's security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. The catalysis research carried out at the DOE National Laboratories ranges from very fundamental catalysis science, funded by DOE's Office of Basic Energy Sciences (BES), to applied research and development (R&D)more » in areas such as biomass conversion to fuels and chemicals, fuel cells, and vehicle emission control with primary funding from DOE's Office of Energy Efficiency and Renewable Energy.« less

Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding

PubMed Central

Tajima, Satohiro; Yanagawa, Toru; Fujii, Naotaka; Toyoizumi, Taro

2015-01-01

Brain-wide interactions generating complex neural dynamics are considered crucial for emergent cognitive functions. However, the irreducible nature of nonlinear and high-dimensional dynamical interactions challenges conventional reductionist approaches. We introduce a model-free method, based on embedding theorems in nonlinear state-space reconstruction, that permits a simultaneous characterization of complexity in local dynamics, directed interactions between brain areas, and how the complexity is produced by the interactions. We demonstrate this method in large-scale electrophysiological recordings from awake and anesthetized monkeys. The cross-embedding method captures structured interaction underlying cortex-wide dynamics that may be missed by conventional correlation-based analysis, demonstrating a critical role of time-series analysis in characterizing brain state. The method reveals a consciousness-related hierarchy of cortical areas, where dynamical complexity increases along with cross-area information flow. These findings demonstrate the advantages of the cross-embedding method in deciphering large-scale and heterogeneous neuronal systems, suggesting a crucial contribution by sensory-frontoparietal interactions to the emergence of complex brain dynamics during consciousness. PMID:26584045

Knowledge representation in metabolic pathway databases.

PubMed

Stobbe, Miranda D; Jansen, Gerbert A; Moerland, Perry D; van Kampen, Antoine H C

2014-05-01

The accurate representation of all aspects of a metabolic network in a structured format, such that it can be used for a wide variety of computational analyses, is a challenge faced by a growing number of researchers. Analysis of five major metabolic pathway databases reveals that each database has made widely different choices to address this challenge, including how to deal with knowledge that is uncertain or missing. In concise overviews, we show how concepts such as compartments, enzymatic complexes and the direction of reactions are represented in each database. Importantly, also concepts which a database does not represent are described. Which aspects of the metabolic network need to be available in a structured format and to what detail differs per application. For example, for in silico phenotype prediction, a detailed representation of gene-protein-reaction relations and the compartmentalization of the network is essential. Our analysis also shows that current databases are still limited in capturing all details of the biology of the metabolic network, further illustrated with a detailed analysis of three metabolic processes. Finally, we conclude that the conceptual differences between the databases, which make knowledge exchange and integration a challenge, have not been resolved, so far, by the exchange formats in which knowledge representation is standardized.

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.

PubMed

Burroughs, A Maxwell; Ando, Yoshinari; de Hoon, Michiel J L; Tomaru, Yasuhiro; Nishibu, Takahiro; Ukekawa, Ryo; Funakoshi, Taku; Kurokawa, Tsutomu; Suzuki, Harukazu; Hayashizaki, Yoshihide; Daub, Carsten O

2010-10-01

Animal microRNA sequences are subject to 3' nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3' adenylation function, we deep-sequenced RNA after knockdown of nucleotidyltransferase enzymes. The PAPD4 nucleotidyltransferase adenylates a wide range of miRNA loci, but adenylation does not appear to affect miRNA stability on a genome-wide scale. Adenine addition appears to reduce effectiveness of miRNA targeting of mRNA transcripts while deep-sequencing of RNA bound to immunoprecipitated Argonaute (AGO) subfamily proteins EIF2C1-EIF2C3 revealed substantial reduction of adenine addition in miRNA associated with EIF2C2 and EIF2C3. Our findings show 3' addition events are widespread and conserved across animals, PAPD4 is a primary miRNA adenylating enzyme, and suggest a role for 3' adenine addition in modulating miRNA effectiveness, possibly through interfering with incorporation into the RNA-induced silencing complex (RISC), a regulatory role that would complement the role of miRNA uridylation in blocking DICER1 uptake.

26 CFR 1.190-2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... individual's major life activities, such as performing manual tasks, walking, speaking, breathing, learning... least 5 feet deep and 5 feet wide. If a door does not swing onto the platform or toward the walk, such platform shall be at least 3 feet deep and 5 feet wide. A platform shall extend at least 1 foot beyond the...

26 CFR 1.190-2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... individual's major life activities, such as performing manual tasks, walking, speaking, breathing, learning... least 5 feet deep and 5 feet wide. If a door does not swing onto the platform or toward the walk, such platform shall be at least 3 feet deep and 5 feet wide. A platform shall extend at least 1 foot beyond the...

26 CFR 1.190-2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... individual's major life activities, such as performing manual tasks, walking, speaking, breathing, learning... least 5 feet deep and 5 feet wide. If a door does not swing onto the platform or toward the walk, such platform shall be at least 3 feet deep and 5 feet wide. A platform shall extend at least 1 foot beyond the...

26 CFR 1.190-2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... individual's major life activities, such as performing manual tasks, walking, speaking, breathing, learning... least 5 feet deep and 5 feet wide. If a door does not swing onto the platform or toward the walk, such platform shall be at least 3 feet deep and 5 feet wide. A platform shall extend at least 1 foot beyond the...

10 CFR 50.65 - Requirements for monitoring the effectiveness of maintenance at nuclear power plants.

Code of Federal Regulations, 2010 CFR

2010-01-01

... with safety and, where practical, take into account industry-wide operating experience. When the...) of this section is not required where it has been demonstrated that the performance or condition of a... evaluations does not exceed 24 months. The evaluations shall take into account, where practical, industry-wide...

47 CFR 64.1002 - International settlements policy.

Code of Federal Regulations, 2012 CFR

2012-10-01

... foreign carrier that does not qualify for the presumption that it lacks market power on the foreign end of... the requirements of this paragraph. This list is available on the International Bureau's World Wide.... This list is available on the International Bureau's World Wide Web site at http://www.fcc.gov/ib. (c...

Does Accreditation Matter for Art & Design Schools in Canada?

ERIC Educational Resources Information Center

Shimizu, Reiko (Leiko)

2013-01-01

Studio-based degrees in fine arts and design are not often written about in higher education literature. Ten years ago, urban theorist Richard Florida coined the term the "creative class" as individuals who "do a wide variety of work in a wide variety of industries -- from technology to entertainment, journalism to finance, highend…

13 CFR 101.404 - How does the Administrator receive comments?

Code of Federal Regulations, 2010 CFR

2010-01-01

... of contact is not obligated to transmit comments from state, area-wide, regional, or local officials... transmitted by a single point of contact, all comments from state, area-wide, regional, and local officials... single point of contact between a state process and all Federal agencies; and (2) That office or official...

Does Extensive Reading Promote Reading Speed?

ERIC Educational Resources Information Center

He, Mu

2014-01-01

Research has shown a wide range of learning benefits accruing from extensive reading. Not only is there improvement in reading, but also in a wide range of language uses and areas of language knowledge. However, few research studies have examined reading speed. The existing literature on reading speed focused on students' reading speed without…

Genome-wide characterization of Mediator recruitment, function, and regulation

PubMed Central

2017-01-01

ABSTRACT Mediator is a conserved and essential coactivator complex broadly required for RNA polymerase II (RNAPII) transcription. Recent genome-wide studies of Mediator binding in budding yeast have revealed new insights into the functions of this critical complex and raised new questions about its role in the regulation of gene expression. PMID:28301289

What Difference Does It Make? Implicit, Explicit and Complex Social Cognition in Autism Spectrum Disorders

ERIC Educational Resources Information Center

Schaller, Ulrich M.; Rauh, Reinhold

2017-01-01

We tested social cognition abilities of adolescents with autism spectrum disorders (ASD) and neurotypically developed peers (NTD). A multi-faceted test-battery including facial emotion categorization (FEC), classical false belief tasks (FBT), and complex social cognition (SC), yielded significantly lower accuracy rates for FEC and complex SC tasks…

Micro-Macro Compatibility: When Does a Complex Systems Approach Strongly Benefit Science Learning?

ERIC Educational Resources Information Center

Samon, Sigal; Levy, Sharona T.

2017-01-01

The study explores how a complexity approach empowers science learning. A complexity approach represents systems as many interacting entities. The construct of micro-macro compatibility is introduced, the degree of similarity between behaviors at the micro- and macro-levels of the system. Seventh-grade students' learning about gases was studied…

Classrooms as Complex Adaptive Systems: A Relational Model

ERIC Educational Resources Information Center

Burns, Anne; Knox, John S.

2011-01-01

In this article, we describe and model the language classroom as a complex adaptive system (see Logan & Schumann, 2005). We argue that linear, categorical descriptions of classroom processes and interactions do not sufficiently explain the complex nature of classrooms, and cannot account for how classroom change occurs (or does not occur), over…

Web life: ComplexityBlog.com

NASA Astrophysics Data System (ADS)

2010-02-01

The site's homepage calls it "a repository of ideas and perspectives regarding the science, engineering and philosophy of complexity", and it pretty much does what it says on the tin. Part blog, part links archive, part library of modelling tips and tricks, the site is chock full of information that comes under the general heading of "complexity".

Graduate Social Work Education and Cognitive Complexity: Does Prior Experience Really Matter?

ERIC Educational Resources Information Center

Simmons, Chris

2014-01-01

This study examined the extent to which age, education, and practice experience among social work graduate students (N = 184) predicted cognitive complexity, an essential aspect of critical thinking. In the regression analysis, education accounted for more of the variance associated with cognitive complexity than age and practice experience. When…

Budding Yeast Silencing Complexes and Regulation of Sir2 Activity by Protein-Protein Interactions

PubMed Central

Tanny, Jason C.; Kirkpatrick, Donald S.; Gerber, Scott A.; Gygi, Steven P.; Moazed, Danesh

2004-01-01

Gene silencing in the budding yeast Saccharomyces cerevisiae requires the enzymatic activity of the Sir2 protein, a highly conserved NAD-dependent deacetylase. In order to study the activity of native Sir2, we purified and characterized two budding yeast Sir2 complexes: the Sir2/Sir4 complex, which mediates silencing at mating-type loci and at telomeres, and the RENT complex, which mediates silencing at the ribosomal DNA repeats. Analyses of the protein compositions of these complexes confirmed previously described interactions. We show that the assembly of Sir2 into native silencing complexes does not alter its selectivity for acetylated substrates, nor does it allow the deacetylation of nucleosomal histones. The inability of Sir2 complexes to deacetylate nucleosomes suggests that additional factors influence Sir2 activity in vivo. In contrast, Sir2 complexes show significant enhancement in their affinities for acetylated substrates and their sensitivities to the physiological inhibitor nicotinamide relative to recombinant Sir2. Reconstitution experiments showed that, for the Sir2/Sir4 complex, these differences stem from the physical interaction of Sir2 with Sir4. Finally, we provide evidence that the different nicotinamide sensitivities of Sir2/Sir4 and RENT in vitro could contribute to locus-specific differences in how Sir2 activity is regulated in vivo. PMID:15282295

Construction of "Toxin Complex" in a Mutant Serotype C Strain of Clostridium botulinum Harboring a Defective Neurotoxin Gene.

PubMed

Suzuki, Tomonori; Nagano, Thomas; Niwa, Koichi; Uchino, Masataka; Tomizawa, Motohiro; Sagane, Yoshimasa; Watanabe, Toshihiro

2017-01-01

A non-toxigenic mutant of the toxigenic serotype C Clostridium botulinum strain Stockholm (C-St), C-N71, does not produce the botulinum neurotoxin (BoNT). However, the original strain C-St produces botulinum toxin complex, in which BoNT is associated with non-toxic non-hemagglutinin (NTNHA) and three hemagglutinin proteins (HA-70, HA-33, and HA-17). Therefore, in this study, we aimed to elucidate the effects of bont gene knockout on the formation of the "toxin complex." Nucleotide sequence analysis revealed that a premature stop codon was introduced in the bont gene, whereas other genes were not affected by this mutation. Moreover, we successfully purified the "toxin complex" produced by C-N71. The "toxin complex" was identified as a mixture of NTNHA/HA-70/HA-17/HA-33 complexes with intact NTNHA or C-terminally truncated NTNHA, without BoNT. These results indicated that knockout of the bont gene does not affect the formation of the "toxin complex." Since the botulinum toxin complex has been shown to play an important role in oral toxin transport in the human and animal body, a non-neurotoxic "toxin complex" of C-N71 may be valuable for the development of an oral drug delivery system.

Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 18. Part 1B: Citations with abstracts, sections 10 through 16

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

NONE

1997-09-01

This bibliography contains 3,638 citations with abstracts of documents relevant to environmental restoration, nuclear facility decontamination and decommissioning (D and D), uranium mill tailings management, and site remedial actions. The bibliography contains scientific, technical, financial, and regulatory information that pertains to DOE environmental restoration programs. The citations are separated by topic into 16 sections, including (1) DOE Environmental Restoration Program; (2) DOE D and D Program; (3) Nuclear Facilities Decommissioning; (4) DOE Formerly Utilized sites Remedial Action Program; (5) NORM-Contaminated Site Restoration; (6) DOE Uranium Mill Tailings Remedial Action Project; (7) Uranium Mill Tailings Management; (8) DOE Site-Wide Remedial Actions;more » (9) DOE Onsite Remedial Action Projects; (10) Contaminated Site Remedial Actions; (11) DOE Underground Storage Tank Remediation; (12) DOE Technology Development, Demonstration, and Evaluation; (13) Soil Remediation; (14) Groundwater Remediation; (15) Environmental Measurements, Analysis, and Decision-Making; and (16) Environmental Management Issues.« less

Discovering complex interrelationships between socioeconomic status and health in Europe: A case study applying Bayesian Networks.

PubMed

Alvarez-Galvez, Javier

2016-03-01

Studies assume that socioeconomic status determines individuals' states of health, but how does health determine socioeconomic status? And how does this association vary depending on contextual differences? To answer this question, our study uses an additive Bayesian Networks model to explain the interrelationships between health and socioeconomic determinants using complex and messy data. This model has been used to find the most probable structure in a network to describe the interdependence of these factors in five European welfare state regimes. The advantage of this study is that it offers a specific picture to describe the complex interrelationship between socioeconomic determinants and health, producing a network that is controlled by socio-demographic factors such as gender and age. The present work provides a general framework to describe and understand the complex association between socioeconomic determinants and health. Copyright © 2016 Elsevier Inc. All rights reserved.

THE NGA-DOE GRANT TO EXAMINE CRITICAL ISSUES RELATED TO RADIOACTIVE WASTE AND MATERIALS DISPOSITION INVOLVING DOE FACILITIES

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

Ann M. Beauchesne

1999-07-30

Through the National Governors' Association (NGA) project ''Critical Issues Related to Radioactive Waste and Materials Disposition Involving DOE Facilities'' NGA brings together Governors' policy advisors, state regulators, and DOE officials to examine critical issues related to the cleanup and operation of DOE nuclear weapons and research facilities. Topics explored through this project include: Decisions involving disposal of mixed, low-level, and transuranic (TRU) waste and disposition of nuclear materials; Decisions involving DOE budget requests and their effect on environmental cleanup and compliance at DOE facilities; Strategies to treat mixed, low-level, and transuranic (TRU) waste and their effect on individual sites inmore » the complex; Changes to the FFCA site treatment plans as a result of proposals in the Department's Accelerating Cleanup: Paths to Closure plan and contractor integration analysis; Interstate waste and materials shipments; and Reforms to existing RCRA and CERCLA regulations/guidance to address regulatory overlap and risks posed by DOE wastes. The overarching theme of this project is to help the Department improve coordination of its major program decisions with Governors' offices and state regulators and to ensure such decisions reflect input from these key state officials and stakeholders. This report summarizes activities conducted during the quarter from May 1, 1999, through July 30, 1999, under the NGA grant. The work accomplished by the NGA project team during the past four months can be categorized as follows: maintained open communication with DOE on a variety of activities and issues within the DOE environmental management complex; maintained communication with NGA Federal Facilities Compliance Task Force members regarding DOE efforts to formulate a configuration for mixed low-level waste and low-level treatment and disposal, external regulation of DOE; and continued to facilitate interactions between the states and DOE to develop a foundation for an ongoing substantive relationship between the Governors of key states and Secretary Richardson.« less

Aging and the complexity of cardiovascular dynamics

NASA Technical Reports Server (NTRS)

Kaplan, D. T.; Furman, M. I.; Pincus, S. M.; Ryan, S. M.; Lipsitz, L. A.; Goldberger, A. L.

1991-01-01

Biomedical signals often vary in a complex and irregular manner. Analysis of variability in such signals generally does not address directly their complexity, and so may miss potentially useful information. We analyze the complexity of heart rate and beat-to-beat blood pressure using two methods motivated by nonlinear dynamics (chaos theory). A comparison of a group of healthy elderly subjects with healthy young adults indicates that the complexity of cardiovascular dynamics is reduced with aging. This suggests that complexity of variability may be a useful physiological marker.

EM-21 Retrieval Knowledge Center: Waste Retrieval Challenges

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

Fellinger, Andrew P.; Rinker, Michael W.; Berglin, Eric J.

EM-21 is the Waste Processing Division of the Office of Engineering and Technology, within the U.S. Department of Energy’s (DOE) Office of Environmental Management (EM). In August of 2008, EM-21 began an initiative to develop a Retrieval Knowledge Center (RKC) to provide the DOE, high level waste retrieval operators, and technology developers with centralized and focused location to share knowledge and expertise that will be used to address retrieval challenges across the DOE complex. The RKC is also designed to facilitate information sharing across the DOE Waste Site Complex through workshops, and a searchable database of waste retrieval technology information.more » The database may be used to research effective technology approaches for specific retrieval tasks and to take advantage of the lessons learned from previous operations. It is also expected to be effective for remaining current with state-of-the-art of retrieval technologies and ongoing development within the DOE Complex. To encourage collaboration of DOE sites with waste retrieval issues, the RKC team is co-led by the Savannah River National Laboratory (SRNL) and the Pacific Northwest National Laboratory (PNNL). Two RKC workshops were held in the Fall of 2008. The purpose of these workshops was to define top level waste retrieval functional areas, exchange lessons learned, and develop a path forward to support a strategic business plan focused on technology needs for retrieval. The primary participants involved in these workshops included retrieval personnel and laboratory staff that are associated with Hanford and Savannah River Sites since the majority of remaining DOE waste tanks are located at these sites. This report summarizes and documents the results of the initial RKC workshops. Technology challenges identified from these workshops and presented here are expected to be a key component to defining future RKC-directed tasks designed to facilitate tank waste retrieval solutions.« less

Is meiosis a fundamental cause of inviability among sexual and asexual plants and animals?

PubMed

Levitis, Daniel A; Zimmerman, Kolea; Pringle, Anne

2017-08-16

Differences in viability between asexually and sexually generated offspring strongly influence the selective advantage and therefore the prevalence of sexual reproduction (sex). However, no general principle predicts when sexual offspring will be more viable than asexual offspring. We hypothesize that when any kind of reproduction is based on a more complex cellular process, it will encompass more potential failure points, and therefore lower offspring viability. Asexual reproduction (asex) can be simpler than sex, when offspring are generated using only mitosis. However, when asex includes meiosis and meiotic restitution, gamete production is more complex than in sex. We test our hypothesis by comparing the viability of asexual and closely related sexual offspring across a wide range of plants and animals, and demonstrate that meiotic asex does result in lower viability than sex; without meiosis, asex is mechanistically simple and provides higher viability than sex. This phylogenetically robust pattern is supported in 42 of 44 comparisons drawn from diverse plants and animals, and is not explained by the other variables included in our model. Other mechanisms may impact viability, such as effects of reproductive mode on heterozygosity and subsequent viability, but we propose the complexity of cellular processes of reproduction, particularly meiosis, as a fundamental cause of early developmental failure and mortality. Meiosis, the leading cause of inviability in humans, emerges as a likely explanation of offspring inviability among diverse eukaryotes. © 2017 The Author(s).

A geostatistics-informed hierarchical sensitivity analysis method for complex groundwater flow and transport modeling

NASA Astrophysics Data System (ADS)

Dai, Heng; Chen, Xingyuan; Ye, Ming; Song, Xuehang; Zachara, John M.

2017-05-01

Sensitivity analysis is an important tool for development and improvement of mathematical models, especially for complex systems with a high dimension of spatially correlated parameters. Variance-based global sensitivity analysis has gained popularity because it can quantify the relative contribution of uncertainty from different sources. However, its computational cost increases dramatically with the complexity of the considered model and the dimension of model parameters. In this study, we developed a new sensitivity analysis method that integrates the concept of variance-based method with a hierarchical uncertainty quantification framework. Different uncertain inputs are grouped and organized into a multilayer framework based on their characteristics and dependency relationships to reduce the dimensionality of the sensitivity analysis. A set of new sensitivity indices are defined for the grouped inputs using the variance decomposition method. Using this methodology, we identified the most important uncertainty source for a dynamic groundwater flow and solute transport model at the Department of Energy (DOE) Hanford site. The results indicate that boundary conditions and permeability field contribute the most uncertainty to the simulated head field and tracer plume, respectively. The relative contribution from each source varied spatially and temporally. By using a geostatistical approach to reduce the number of realizations needed for the sensitivity analysis, the computational cost of implementing the developed method was reduced to a practically manageable level. The developed sensitivity analysis method is generally applicable to a wide range of hydrologic and environmental problems that deal with high-dimensional spatially distributed input variables.

A Geostatistics-Informed Hierarchical Sensitivity Analysis Method for Complex Groundwater Flow and Transport Modeling

NASA Astrophysics Data System (ADS)

Dai, H.; Chen, X.; Ye, M.; Song, X.; Zachara, J. M.

2017-12-01

Sensitivity analysis is an important tool for development and improvement of mathematical models, especially for complex systems with a high dimension of spatially correlated parameters. Variance-based global sensitivity analysis has gained popularity because it can quantify the relative contribution of uncertainty from different sources. However, its computational cost increases dramatically with the complexity of the considered model and the dimension of model parameters. In this study we developed a new sensitivity analysis method that integrates the concept of variance-based method with a hierarchical uncertainty quantification framework. Different uncertain inputs are grouped and organized into a multi-layer framework based on their characteristics and dependency relationships to reduce the dimensionality of the sensitivity analysis. A set of new sensitivity indices are defined for the grouped inputs using the variance decomposition method. Using this methodology, we identified the most important uncertainty source for a dynamic groundwater flow and solute transport model at the Department of Energy (DOE) Hanford site. The results indicate that boundary conditions and permeability field contribute the most uncertainty to the simulated head field and tracer plume, respectively. The relative contribution from each source varied spatially and temporally. By using a geostatistical approach to reduce the number of realizations needed for the sensitivity analysis, the computational cost of implementing the developed method was reduced to a practically manageable level. The developed sensitivity analysis method is generally applicable to a wide range of hydrologic and environmental problems that deal with high-dimensional spatially-distributed input variables.

How Do Hunter-Gatherer Children Learn Subsistence Skills? : A Meta-Ethnographic Review.

PubMed

Lew-Levy, Sheina; Reckin, Rachel; Lavi, Noa; Cristóbal-Azkarate, Jurgi; Ellis-Davies, Kate

2017-12-01

Hunting and gathering is, evolutionarily, the defining subsistence strategy of our species. Studying how children learn foraging skills can, therefore, provide us with key data to test theories about the evolution of human life history, cognition, and social behavior. Modern foragers, with their vast cultural and environmental diversity, have mostly been studied individually. However, cross-cultural studies allow us to extrapolate forager-wide trends in how, when, and from whom hunter-gatherer children learn their subsistence skills. We perform a meta-ethnography, which allows us to systematically extract, summarize, and compare both quantitative and qualitative literature. We found 58 publications focusing on learning subsistence skills. Learning begins early in infancy, when parents take children on foraging expeditions and give them toy versions of tools. In early and middle childhood, children transition into the multi-age playgroup, where they learn skills through play, observation, and participation. By the end of middle childhood, most children are proficient food collectors. However, it is not until adolescence that adults (not necessarily parents) begin directly teaching children complex skills such as hunting and complex tool manufacture. Adolescents seek to learn innovations from adults, but they themselves do not innovate. These findings support predictive models that find social learning should occur before individual learning. Furthermore, these results show that teaching does indeed exist in hunter-gatherer societies. And, finally, though children are competent foragers by late childhood, learning to extract more complex resources, such as hunting large game, takes a lifetime.

Two-step recording of visible holographic elements in photo-thermo-refractive glass

NASA Astrophysics Data System (ADS)

Kompan, Fedor; Divliansky, Ivan; Smirnov, Vadim; Glebov, Leonid B.

2018-02-01

Photo-thermo-refractive (PTR) glass) is a photosensitive silicate glass doped with Ce3+ where a permanent refractive index decrement is produced by UV exposure followed by thermal development. This material provides high efficiency and low losses combined with high thermal, ionizing and laser tolerance of holographic optical elements (HOEs). This is why PTR glass is widely used for holographic recording of volume Bragg gratings (trivial holograms produced by interference of two collimated beams) and phase plates operating in near UV, visible, and near IR spectral regions. It would be very beneficial though to record also complex HOEs (lenses and curved mirrors) for those spectral regions. However, PTR is not sensitive to visible or IR radiation and therefore does not allow the recording of nonplanar holograms for these regions. The present paper describes a technique for recording complex HOEs using visible radiation in Ce3+ doped PTR glass. This two-step technique includes a blank exposure to UV radiation followed by structured exposure to a visible beam. It was found that the second exposure decreases the refractive index decrement induced in the UV exposed glass after thermal development. This means that areas, which underwent double exposure, have refractive index lower than in unexposed areas but higher than in just UV exposed ones. Thus, this technique provides refractive index increment after visible irradiation of UV exposed PTR glass. Using this approach, complex holograms (curved mirrors and lenses) operating in the visible region, were recorded in PTR glass.

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

none,

The Office of Analysis within the U.S. Department of Energy (DOE) Office of Environment, Health, Safety and Security (EHSS) publishes the annual DOE Occupational Radiation Exposure Report to provide an overview of the status of radiation protection practices at DOE (including the National Nuclear Security Administration [NNSA]). The DOE 2013 Occupational Radiation Exposure Report provides an evaluation of DOE-wide performance regarding compliance with Title 10, Code of Federal Regulations (C.F.R.), Part 835, Occupational Radiation Protection dose limits and as low as reasonably achievable (ALARA) process requirements. In addition, the report provides data to DOE organizations responsible for developing policies formore » protection of individuals from the adverse health effects of radiation. The report provides a summary and an analysis of occupational radiation exposure information from the monitoring of individuals involved in DOE activities. Over the past five-year period, the occupational radiation exposure information has been analyzed in terms of aggregate data, dose to individuals, and dose by site.« less

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

none,

The U.S. Department of Energy (DOE) Office of Analysis within the Office of Health, Safety and Security (HSS) publishes the annual DOE Occupational Radiation Exposure Report to provide an overview of the status of radiation protection practices at DOE (including the National Nuclear Security Administration [NNSA]). The DOE 2012 Occupational Radiation Exposure Report provides an evaluation of DOE-wide performance regarding compliance with Title 10, Code of Federal Regulations (C.F.R.), Part 835, Occupational Radiation Protection dose limits and as low as reasonably achievable (ALARA) process requirements. In addition, the report provides data to DOE organizations responsible for developing policies for protectionmore » of individuals from the adverse health effects of radiation. The report provides a summary and an analysis of occupational radiation exposure information from the monitoring of individuals involved in DOE activities. Over the past 5-year period, the occupational radiation exposure information is analyzed in terms of aggregate data, dose to individuals, and dose by site.« less

Mechanism of neem limonoids-induced cell death in cancer: role of oxidative phosphorylation

PubMed Central

Yadav, Neelu; Kumar, Sandeep; Kumar, Rahul; Srivastava, Pragya; Sun, Leimin; Rapali, Peter; Marlowe, Timothy; Schneider, Andrea; Inigo, Joseph; O’Malley, Jordan; Londonkar, Ramesh; Gogada, Raghu; Chaudhary, Ajay; Yadava, Nagendra; Chandra, Dhyan

2016-01-01

We have previously reported that neem limonoids (neem) induce multiple cancer cell death pathways. Here we dissect the underlying mechanisms of neem-induced apoptotic cell death in cancer. We observed that neem-induced caspase activation does not require Bax/Bak channel-mediated mitochondrial outer membrane permeabilization, permeability transition pore, and mitochondrial fragmentation. Neem enhanced mitochondrial DNA and mitochondrial biomass. While oxidative phosphorylation (OXPHOS) Complex-I activity was decreased, the activities of other OXPHOS complexes including Complex-II and -IV were unaltered. Increased reactive oxygen species (ROS) levels were associated with an increase in mitochondrial biomass and apoptosis upon neem exposure. Complex-I deficiency due to the loss of Ndufa1-encoded MWFE protein inhibited neem-induced caspase activation and apoptosis, but cell death induction was enhanced. Complex II-deficiency due to the loss of succinate dehydrogenase complex subunit C (SDHC) robustly decreased caspase activation, apoptosis, and cell death. Additionally, the ablation of Complexes-I, -III, -IV, and -V together did not inhibit caspase activation. Together, we demonstrate that neem limonoids target OXPHOS system to induce cancer cell death, which does not require upregulation or activation of proapoptotic Bcl-2 family proteins. PMID:26627937

Mechanism of neem limonoids-induced cell death in cancer: Role of oxidative phosphorylation.

PubMed

Yadav, Neelu; Kumar, Sandeep; Kumar, Rahul; Srivastava, Pragya; Sun, Leimin; Rapali, Peter; Marlowe, Timothy; Schneider, Andrea; Inigo, Joseph R; O'Malley, Jordan; Londonkar, Ramesh; Gogada, Raghu; Chaudhary, Ajay K; Yadava, Nagendra; Chandra, Dhyan

2016-01-01

We have previously reported that neem limonoids (neem) induce multiple cancer cell death pathways. Here we dissect the underlying mechanisms of neem-induced apoptotic cell death in cancer. We observed that neem-induced caspase activation does not require Bax/Bak channel-mediated mitochondrial outer membrane permeabilization, permeability transition pore, and mitochondrial fragmentation. Neem enhanced mitochondrial DNA and mitochondrial biomass. While oxidative phosphorylation (OXPHOS) Complex-I activity was decreased, the activities of other OXPHOS complexes including Complex-II and -IV were unaltered. Increased reactive oxygen species (ROS) levels were associated with an increase in mitochondrial biomass and apoptosis upon neem exposure. Complex-I deficiency due to the loss of Ndufa1-encoded MWFE protein inhibited neem-induced caspase activation and apoptosis, but cell death induction was enhanced. Complex II-deficiency due to the loss of succinate dehydrogenase complex subunit C (SDHC) robustly decreased caspase activation, apoptosis, and cell death. Additionally, the ablation of Complexes-I, -III, -IV, and -V together did not inhibit caspase activation. Together, we demonstrate that neem limonoids target OXPHOS system to induce cancer cell death, which does not require upregulation or activation of proapoptotic Bcl-2 family proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

Summary of International Waste Management Programs (LLNL Input to SNL L3 MS: System-Wide Integration and Site Selection Concepts for Future Disposition Options for HLW)

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

Greenberg, Harris R.; Blink, James A.; Halsey, William G.

2011-08-11

The Used Fuel Disposition Campaign (UFDC) within the Department of Energy’s Office of Nuclear Energy (DOE-NE) Fuel Cycle Technology (FCT) program has been tasked with investigating the disposal of the nation’s spent nuclear fuel (SNF) and high-level nuclear waste (HLW) for a range of potential waste forms and geologic environments. This Lessons Learned task is part of a multi-laboratory effort, with this LLNL report providing input to a Level 3 SNL milestone (System-Wide Integration and Site Selection Concepts for Future Disposition Options for HLW). The work package number is: FTLL11UF0328; the work package title is: Technical Bases / Lessons Learned;more » the milestone number is: M41UF032802; and the milestone title is: “LLNL Input to SNL L3 MS: System-Wide Integration and Site Selection Concepts for Future Disposition Options for HLW”. The system-wide integration effort will integrate all aspects of waste management and disposal, integrating the waste generators, interim storage, transportation, and ultimate disposal at a repository site. The review of international experience in these areas is required to support future studies that address all of these components in an integrated manner. Note that this report is a snapshot of nuclear power infrastructure and international waste management programs that is current as of August 2011, with one notable exception. No attempt has been made to discuss the currently evolving world-wide response to the tragic consequences of the earthquake and tsunami that devastated Japan on March 11, 2011, leaving more than 15,000 people dead and more than 8,000 people missing, and severely damaging the Fukushima Daiichi nuclear power complex. Continuing efforts in FY 2012 will update the data, and summarize it in an Excel spreadsheet for easy comparison and assist in the knowledge management of the study cases.« less

Natural Capital Management: An Evolutionary Paradigm for Sustainable Restoration Investment - 13455

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

Koetz, Maureen T.

2013-07-01

Unlike other forms of capital assets (built infrastructure, labor, financial capital), the supply of usable or accessible air, land, and water elements (termed Natural Capital Assets or NCA) available to enterprise processes is structurally shrinking due to increased demand and regulatory restriction. This supply/demand imbalance is affecting all forms of public and private enterprise (including Federal Facilities) in the form of encroachment, production limits, cost increases, and reduced competitiveness. Department of Energy (DOE) sites are comprised of significant stocks of NCA that function as both conserved capital (providing ecosystem services and other reserve capacity), and as natural infrastructure (supporting majormore » Federal enterprise programs). The current rubric of 'Environmental Stewardship' provides an unduly constrained management paradigm that is focused largely on compliance process metrics, and lacks a value platform for quantifying, documenting, and sustainably re-deploying re-capitalized natural asset capacity and capability. By adopting value-based system concepts similar to built infrastructure accounting and information management, 'stewarded' natural assets relegated to liability- or compliance-focused outcomes become 're-capitalized' operational assets able to support new or expanded mission. This growing need for new accounting and management paradigms to capture natural capital value is achieving global recognition, most recently by the United Nations, world leaders, and international corporations at the Rio+20 Summit in June of 2012. Natural Capital Asset Management (NCAM){sup TM} is such an accounting framework tool. Using a quantification-based design, NCAM{sup TM} provides inventory, capacity and value data to owners or managers of natural assets such as the DOE that parallel comparable information systems currently used for facility assets. Applied to Environmental Management (EM) and other DOE program activities, the natural asset capacity and value generated by EM projects and other investment and operational programming can be recorded and then allocated to mission and/or ecosystem needs as part of overall site, complex, and Federal decision-making. NCAM{sup TM} can also document post-restoration asset capability and value for use in weighing loss mitigation and ecosystem damage claims arising from past operational activities. A prototype NCAM{sup TM} evaluation developed at the Savannah River Site (SRS) demonstrates use of this framework as an advanced paradigm for NCA accounting and decision-making for the larger DOE complex and other enterprise using natural capital in operations. Applying a quantified value paradigm, the framework catalogues the results of activities that sustain, restore, and modernize natural assets for enterprise-wide value beyond that of compliance milestones. Capturing and assigning recapitalization value using NCAM{sup TM} concepts and tools improves effective reuse of taxpayer-sustained assets, records ecosystem service value, enables mission and enterprise optimization, and assures the sustainability of shared natural capital assets in regional pools vital to both complex sites and local and regional economies. (authors)« less

Electrocatalytic Oxidation of Formate with Nickel Diphosphane Dipeptide Complexes. Effect of Ligands Modified with Amino Acids

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

Galan, Brandon R.; Reback, Matthew L.; Jain, Avijita

2013-09-03

A series of nickel bis-diphosphine complexes with dipeptides appended to the ligands were investigated for the catalytic oxidation of formate. Typical rates of ~7 s -1 were found, similar to the parent complex (~8 s -1), with amino acid size and positioning contributing very little to rate or operating potential. Hydroxyl functionalities did result in lower rates, which were recovered by protecting the hydroxyl group. The results suggest that the overall dielectric introduced by the dipeptides does not play an important role in catalysis, but free hydroxyl groups do influence activity suggesting contributions from intra- or intermolecular interactions. These observationsmore » are important in developing a fundamental understanding of the affect that an enzyme-like outer coordination sphere can have upon molecular catalysts. This work was funded by the US DOE Basic Energy Sciences, Chemical Sciences, Geoscience and Biosciences Division (BRG, AJ, AMA, WJS), the US DOE Basic Energy Sciences, Physical Bioscience program (MLR). Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Identifying Specific Genes Controlling Complex Traits Through A Genome-Wide Screen For cis-Acting Regulatory Elements - An Example Using Marek's Disease

USDA-ARS?s Scientific Manuscript database

The identification of specific genes underlying phenotypic variation of complex traits remains one of the greatest challenges in biology despite having genome sequences and more powerful tools. Most genome-wide screens lack sufficient resolving power as they typically depend on linkage. One altern...

Comprehensive Identification Of Specific Genes Controlling Complex Traits Through A Genome-Wide Screen for Cis-Acting Regulatory Elements - An Example Using Marek's Disease

USDA-ARS?s Scientific Manuscript database

The comprehensive identification of genes underlying phenotypic variation of complex traits remains a major challenge. Most genome-wide screens lack sufficient resolving power as they typically depend on linkage. An alternate method is to screen for allele-specific expression (ASE), a simple yet pow...

Recent Experiments Conducted with the Wide-Field Imaging Interferometry Testbed (WIIT)

NASA Technical Reports Server (NTRS)

Leisawitz, David T.; Juanola-Parramon, Roser; Bolcar, Matthew; Iacchetta, Alexander S.; Maher, Stephen F.; Rinehart, Stephen A.

2016-01-01

The Wide-field Imaging Interferometry Testbed (WIIT) was developed at NASA's Goddard Space Flight Center to demonstrate and explore the practical limitations inherent in wide field-of-view double Fourier (spatio-spectral) interferometry. The testbed delivers high-quality interferometric data and is capable of observing spatially and spectrally complex hyperspectral test scenes. Although WIIT operates at visible wavelengths, by design the data are representative of those from a space-based far-infrared observatory. We used WIIT to observe a calibrated, independently characterized test scene of modest spatial and spectral complexity, and an astronomically realistic test scene of much greater spatial and spectral complexity. This paper describes the experimental setup, summarizes the performance of the testbed, and presents representative data.

Long-term in situ oxidation of biogenic uraninite in an alluvial aquifer: impact of dissolved oxygen and calcium.

PubMed

Lezama-Pacheco, Juan S; Cerrato, José M; Veeramani, Harish; Alessi, Daniel S; Suvorova, Elena; Bernier-Latmani, Rizlan; Giammar, Daniel E; Long, Philip E; Williams, Kenneth H; Bargar, John R

2015-06-16

Oxidative dissolution controls uranium release to (sub)oxic pore waters from biogenic uraninite produced by natural or engineered processes, such as bioremediation. Laboratory studies show that uraninite dissolution is profoundly influenced by dissolved oxygen (DO), carbonate, and solutes such as Ca(2+). In complex and heterogeneous subsurface environments, the concentrations of these solutes vary in time and space. Knowledge of dissolution processes and kinetics occurring over the long-term under such conditions is needed to predict subsurface uranium behavior and optimize the selection and performance of uraninite-based remediation technologies over multiyear periods. We have assessed dissolution of biogenic uraninite deployed in wells at the Rifle, CO, DOE research site over a 22 month period. Uraninite loss rates were highly sensitive to DO, with near-complete loss at >0.6 mg/L over this period but no measurable loss at lower DO. We conclude that uraninite can be stable over decadal time scales in aquifers under low DO conditions. U(VI) solid products were absent over a wide range of DO values, suggesting that dissolution proceeded through complexation and removal of oxidized surface uranium atoms by carbonate. Moreover, under the groundwater conditions present, Ca(2+) binds strongly to uraninite surfaces at structural uranium sites, impacting uranium fate.

A Versatile Platform for Nanotechnology Based on Circular Permutation of a Chaperonin Protein

NASA Technical Reports Server (NTRS)

Paavola, Chad; McMillan, Andrew; Trent, Jonathan; Chan, Suzanne; Mazzarella, Kellen; Li, Yi-Fen

2004-01-01

A number of protein complexes have been developed as nanoscale templates. These templates can be functionalized using the peptide sequences that bind inorganic materials. However, it is difficult to integrate peptides into a specific position within a protein template. Integrating intact proteins with desirable binding or catalytic activities is an even greater challenge. We present a general method for modifying protein templates using circular permutation so that additional peptide sequence can be added in a wide variety of specific locations. Circular permutation is a reordering of the polypeptide chain such that the original termini are joined and new termini are created elsewhere in the protein. New sequence can be joined to the protein termini without perturbing the protein structure and with minimal limitation on the size and conformation of the added sequence. We have used this approach to modify a chaperonin protein template, placing termini at five different locations distributed across the surface of the protein complex. These permutants are competent to form the double-ring structures typical of chaperonin proteins. The permuted double-rings also form the same assemblies as the unmodified protein. We fused a fluorescent protein to two representative permutants and demonstrated that it assumes its active structure and does not interfere with assembly of chaperonin double-rings.

COBRApy: COnstraints-Based Reconstruction and Analysis for Python.

PubMed

Ebrahim, Ali; Lerman, Joshua A; Palsson, Bernhard O; Hyduke, Daniel R

2013-08-08

COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. Due to the successes with metabolism, there is an increasing effort to apply COBRA methods to reconstruct and analyze integrated models of cellular processes. The COBRA Toolbox for MATLAB is a leading software package for genome-scale analysis of metabolism; however, it was not designed to elegantly capture the complexity inherent in integrated biological networks and lacks an integration framework for the multiomics data used in systems biology. The openCOBRA Project is a community effort to promote constraints-based research through the distribution of freely available software. Here, we describe COBRA for Python (COBRApy), a Python package that provides support for basic COBRA methods. COBRApy is designed in an object-oriented fashion that facilitates the representation of the complex biological processes of metabolism and gene expression. COBRApy does not require MATLAB to function; however, it includes an interface to the COBRA Toolbox for MATLAB to facilitate use of legacy codes. For improved performance, COBRApy includes parallel processing support for computationally intensive processes. COBRApy is an object-oriented framework designed to meet the computational challenges associated with the next generation of stoichiometric constraint-based models and high-density omics data sets. http://opencobra.sourceforge.net/

Humidity-insensitive water evaporation from molecular complex fluids.

PubMed

Salmon, Jean-Baptiste; Doumenc, Frédéric; Guerrier, Béatrice

2017-09-01

We investigated theoretically water evaporation from concentrated supramolecular mixtures, such as solutions of polymers or amphiphilic molecules, using numerical resolutions of a one-dimensional model based on mass transport equations. Solvent evaporation leads to the formation of a concentrated solute layer at the drying interface, which slows down evaporation in a long-time-scale regime. In this regime, often referred to as the falling rate period, evaporation is dominated by diffusive mass transport within the solution, as already known. However, we demonstrate that, in this regime, the rate of evaporation does not also depend on the ambient humidity for many molecular complex fluids. Using analytical solutions in some limiting cases, we first demonstrate that a sharp decrease of the water chemical activity at high solute concentration leads to evaporation rates which depend weakly on the humidity, as the solute concentration at the drying interface slightly depends on the humidity. However, we also show that a strong decrease of the mutual diffusion coefficient of the solution enhances considerably this effect, leading to nearly independent evaporation rates over a wide range of humidity. The decrease of the mutual diffusion coefficient indeed induces strong concentration gradients at the drying interface, which shield the concentration profiles from humidity variations, except in a very thin region close to the drying interface.

Perspectives on why digital ecologies matter: combining population genetics and ecologically informed agent-based models with GIS for managing dipteran livestock pests.

PubMed

Peck, Steven L

2014-10-01

It is becoming clear that handling the inherent complexity found in ecological systems is an essential task for finding ways to control insect pests of tropical livestock such as tsetse flies, and old and new world screwworms. In particular, challenging multivalent management programs, such as Area Wide Integrated Pest Management (AW-IPM), face daunting problems of complexity at multiple spatial scales, ranging from landscape level processes to those of smaller scales such as the parasite loads of individual animals. Daunting temporal challenges also await resolution, such as matching management time frames to those found on ecological and even evolutionary temporal scales. How does one deal with representing processes with models that involve multiple spatial and temporal scales? Agent-based models (ABM), combined with geographic information systems (GIS), may allow for understanding, predicting and managing pest control efforts in livestock pests. This paper argues that by incorporating digital ecologies in our management efforts clearer and more informed decisions can be made. I also point out the power of these models in making better predictions in order to anticipate the range of outcomes possible or likely. Copyright © 2014 International Atomic Energy Agency 2014. Published by Elsevier B.V. All rights reserved.

Overpopulation question is complex, scientist says.

PubMed

Bauman, J

1998-03-13

This article presents Joel E. Cohen's lecture on the issue of population growth. Cohen, a professor at Rockefeller and Columbia universities, outlined the complexities involved in estimating the world's ability to support humans. He noted that the world has undergone a startling population explosion, with the total number of humans expected to surpass 6 billion in 1998, doubling the population size in only 40 years. Estimates of the total number of humans the planet can support have been varied over the years. However, the only constant element is that there is a wide gap between the standard of living in rich countries with relatively slow population growth and poor countries, where the population is booming. Statistics compiled in the 1960s, 1970s, 1980s, and 1990s attest to this fact. In addition, demographers show that food supply is not a good indicator of how many people an area can support and the fact that food prices are low does not indicate that there is no scarcity. Hence, there is a need to cope with the flourishing worldwide population. To do this, people should understand the complicated relationship between the physical constraints of the planet's carrying capacity and the choices that people must make. Cohen advocated for an improvement in the world's economic climate through better trade relations between developed and poorer countries.

The physical and biological basis of quantitative parameters derived from diffusion MRI

PubMed Central

2012-01-01

Diffusion magnetic resonance imaging is a quantitative imaging technique that measures the underlying molecular diffusion of protons. Diffusion-weighted imaging (DWI) quantifies the apparent diffusion coefficient (ADC) which was first used to detect early ischemic stroke. However this does not take account of the directional dependence of diffusion seen in biological systems (anisotropy). Diffusion tensor imaging (DTI) provides a mathematical model of diffusion anisotropy and is widely used. Parameters, including fractional anisotropy (FA), mean diffusivity (MD), parallel and perpendicular diffusivity can be derived to provide sensitive, but non-specific, measures of altered tissue structure. They are typically assessed in clinical studies by voxel-based or region-of-interest based analyses. The increasing recognition of the limitations of the diffusion tensor model has led to more complex multi-compartment models such as CHARMED, AxCaliber or NODDI being developed to estimate microstructural parameters including axonal diameter, axonal density and fiber orientations. However these are not yet in routine clinical use due to lengthy acquisition times. In this review, I discuss how molecular diffusion may be measured using diffusion MRI, the biological and physical bases for the parameters derived from DWI and DTI, how these are used in clinical studies and the prospect of more complex tissue models providing helpful micro-structural information. PMID:23289085

Security training with interactive laser-video-disk technology

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

Wilson, D.

1988-01-01

DOE, through its contractor EG and G Energy Measurements, Inc., has developed a state-of-the-art interactive-video system for use at the Department of Energy's Central Training Academy. Called the Security Training and Evaluation Shooting System (STRESS), the computer-driven decision shooting system employs the latest is laservideo-disk technology. STRESS is designed to provide realistic and stressful training for security inspectors employed by the DOE and its contractors. The system uses wide-screen video projection, sophisticated scenario-branching technology, and customized video scenarios especially designed for the DOE. Firing a weapon that has been modified to shoot ''laser bullets,'' and wearing a special vest thatmore » detects ''hits'': the security inspector encounters adversaries on the wide screen who can shoot or be shot by the inspector in scenarios that demand fast decisions. Based on those decisions, the computer provides instantaneous branching to different scenes, giving the inspector confrontational training with the realism and variability of real life.« less

THE NGA-DOE GRANT TO EXAMINE CRITICAL ISSUES RELATED TO RADIOACTIVE WASTE AND MATERIALS DISPOSITION INVOLVING DOE FACILITIES

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

Ann M. Beauchesne

1999-04-30

Through the National Governors' Association (NGA) project ''Critical Issues Related to Radioactive Waste and Materials Disposition Involving DOE Facilities'' NGA brings together Governors' policy advisors, state regulators, and DOE officials to examine critical issues related to the cleanup and operation of DOE nuclear weapons and research facilities. Topics explored through this project include: Decisions involving disposal of mixed, low-level, and transuranic (TRU) waste and disposition of nuclear materials; Decisions involving DOE budget requests and their effect on environmental cleanup and compliance at DOE facilities; Strategies to treat mixed, low-level, and transuranic (TRU) waste and their effect on individual sites inmore » the complex; Changes to the FFCA site treatment plans as a result of proposals in the Department's Accelerating Cleanup: Paths to Closure plan and contractor integration analysis; Interstate waste and materials shipments; and Reforms to existing RCRA and CERCLA regulations/guidance to address regulatory overlap and risks posed by DOE wastes. The overarching theme of this project is to help the Department improve coordination of its major program decisions with Governors' offices and state regulators and to ensure such decisions reflect input from these key state officials and stakeholders. This report summarizes activities conducted during the quarter from February 1, 1999, through April 30, 1999, under the NGA grant. The work accomplished by the NGA project team during the past four months can be categorized as follows: maintained open communication with DOE on a variety of activities and issues within the DOE environmental management complex; maintained communication with NGA Federal Facilities Compliance Task Force members regarding DOE efforts to formulate a configuration for mixed low-level waste and low-level treatment and disposal, external regulation of DOE; and EM Integration activities; and continued to serve as a liaison between the NGA FFCA Task Force states and the Department.« less

THE NGA-DOE GRANT TO EXAMINE CRITICAL ISSUES RELATED TO RADIOACTIVE WASTE AND MATERIALS DISPOSITION INVOLVING DOE FACILITIES

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

Ann B. Beauchesne

1998-09-30

Through the National Governors' Association (NGA) project ''Critical Issues Related to Radioactive Waste and Materials Disposition Involving DOE Facilities'' NGA brings together Governors' policy advisors, state regulators, and DOE officials to examine critical issues related to the cleanup and operation of DOE nuclear weapons and research facilities. Topics explored through this project include: (1) Decisions involving disposal of mixed, low-level, and transuranic (TRU) waste and disposition of nuclear materials; (2) Decisions involving DOE budget requests and their effect on environmental cleanup and compliance at DOE facilities; (3) Strategies to treat mixed, low-level, and transuranic (TRU) waste and their effect onmore » individual sites in the complex; (4) Changes to the FFCA site treatment plans as a result of proposals in the Department's Accelerating Cleanup: Paths to Closure plan and contractor integration analysis; (5) Interstate waste and materials shipments; and (6) Reforms to existing RCRA and CERCLA regulations/guidance to address regulatory overlap and risks posed by DOE wastes. The overarching theme of this project is to help the Department improve coordination of its major program decisions with Governors' offices and state regulators and to ensure such decisions reflect input from these key state officials and stakeholders. This report summarizes activities conducted during the quarter from June 1, 1998 through September 30, 1998, under the NGA grant. The work accomplished by the NGA project team during the past four months can be categorized as follows: (1) maintained open communication with DOE on a variety of activities and issues within the DOE environmental management complex; (2) maintained communication with NGA Federal Facilities Compliance Task Force members regarding DOE efforts to formulate a configuration for mixed low-level waste and low-level treatment and disposal, external regulation of DOE; and EM Integration activities; and (3) continued to serve as a liaison between the NGA FFCA Task Force states and the Department.« less

THE NGA-DOE GRANT TO EXAMINE CRITICAL ISSUES RELATED TO RADIOACTIVE WASTE AND MATERIALS DISPOSITION INVOLVING DOE FACILITIES

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

Ann M. Beauchesne

1999-01-31

Through the National Governors' Association (NGA) project ''Critical Issues Related to Radioactive Waste and Materials Disposition Involving DOE Facilities'' NGA brings together Governors' policy advisors, state regulators, and DOE officials to examine critical issues related to the cleanup and operation of DOE nuclear weapons and research facilities. Topics explored through this project include: (1) Decisions involving disposal of mixed, low-level, and transuranic (TRU) waste and disposition of nuclear materials; (2) Decisions involving DOE budget requests and their effect on environmental cleanup and compliance at DOE facilities; (3) Strategies to treat mixed, low-level, and transuranic (TRU) waste and their effect onmore » individual sites in the complex; (4) Changes to the FFCA site treatment plans as a result of proposals in the Department's Accelerating Cleanup: Paths to Closure plan and contractor integration analysis; (5) Interstate waste and materials shipments; and (6) Reforms to existing RCRA and CERCLA regulations/guidance to address regulatory overlap and risks posed by DOE wastes. The overarching theme of this project is to help the Department improve coordination of its major program decisions with Governors' offices and state regulators and to ensure such decisions reflect input from these key state officials and stakeholders. This report summarizes activities conducted during the quarter from October 1, 1998 through January 31, 1999, under the NGA grant. The work accomplished by the NGA project team during the past four months can be categorized as follows: (1) maintained open communication with DOE on a variety of activities and issues within the DOE environmental management complex; (2) maintained communication with NGA Federal Facilities Compliance Task Force members regarding DOE efforts to formulate a configuration for mixed low-level waste and low-level treatment and disposal, external regulation of DOE; and EM Integration activities; and (3) continued to serve as a liaison between the NGA FFCA Task Force states and the Department.« less

EEOC sues employer who demanded janitor take HIV test. Equal Employment Opportunity Commission.

PubMed

1995-07-28

The Equal Employment Opportunity Commission (EEOC) has filed suit on behalf of a former janitor whose employer, [name removed] and Associations, insisted he take an HIV-antibody test and spread rumors that he was HIV-positive. The janitor (known as John Doe) had worked at the Third East Hills Park Cooperative, a low-income housing complex in Pittsburgh, for three years. His employer began speculating about his HIV status when Doe's wife died of AIDS-related complications. The manager of the apartment complex began investigating Doe and asked him to be tested for HIV antibodies. The manager went so far as to call Doe's babysitter to tell her that he thought both Doe and his son were HIV-positive and that she should leave as soon as possible. The lawsuit alleges that [name removed] and Association and Third East Hills Park Cooperative violated Title I of the Americans with Disabilities Act (ADA), which protects employees from intrusive medical questions that are unrelated to job performance. The suit seeks compensatory and punitive damages, and an injunction barring the defendants from engaging in unlawful medical inquiries and harassing workers based on disability.

The Status of the Testing Effect for Complex Materials: Still a Winner

ERIC Educational Resources Information Center

Rawson, Katherine A.

2015-01-01

The target articles in the special issue address a timely and important question concerning whether practice tests enhance learning of complex materials. The consensus conclusion from these articles is that the testing effect does not obtain for complex materials. In this commentary, I discuss why this conclusion is not warranted either by the…

12 CFR 502.27 - How does OTS determine the risk/complexity component for a savings and loan holding company?

Code of Federal Regulations, 2011 CFR

2011-01-01

... classifications and total consolidated holding company assets. OTS will establish these schedules in a Thrift Bulletin. (b) For the purposes of this section, the holding company risk/complexity classification is the most recent risk/complexity classification of which OTS notified the savings and loan holding company...

Infrared Testing of the Wide-field Infrared Survey Telescope Grism Using Computer Generated Holograms

NASA Technical Reports Server (NTRS)

Dominguez, Margaret Z.; Content, David A.; Gong, Qian; Griesmann, Ulf; Hagopian, John G.; Marx, Catherine T; Whipple, Arthur L.

2017-01-01

Infrared Computer Generated Holograms (CGHs) were designed, manufactured and used to measure the performance of the grism (grating prism) prototype which includes testing Diffractive Optical Elements (DOE). The grism in the Wide Field Infrared Survey Telescope (WFIRST) will allow the surveying of a large section of the sky to find bright galaxies.

47 CFR 73.7003 - Point system selection procedures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... stations. (3) State-wide network. Two points for an applicant that does not qualify for the credit for... the diversity credit and the state-wide network credit in any particular application. (4) Technical... following: (1) If the applicant is in a group for which a “B” cut-off notice issued prior to April 21, 2000...

Noncognitive Factors in an Elementary School-Wide Model of Arts Integration

ERIC Educational Resources Information Center

Simpson Steele, Jamie

2016-01-01

Pomaika'i Elementary School has answered a call to improve education by providing content instruction through the arts. How does school wide arts integration in an elementary setting support students as they transition to middle school? This bounded case study examines the experiences of eight families through a series of interviews with students,…

Cooperative monitoring and its role in regional security

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

Biringer, K.; Olsen, J.; Lincoln, R.

1997-03-01

Cooperative monitoring systems can play an important part in promoting the implementation of regional cooperative security agreements. These agreements advance the national security interests of the United States in a post Cold War environment. Regional issues as widely varying as nuclear nonproliferation, trade and environmental pollution can be the source of tensions which may escalate to armed conflict which could have global implications. The Office of National Security Policy Analysis at the US Department of Energy (DOE) has an interest in seeking ways to promote regional cooperation that can reduce the threats posed by regional conflict. DOE technologies and technicalmore » expertise can contribute to developing solutions to a wide variety of these international problems. Much of this DOE expertise has been developed in support of the US nuclear weapons and arms control missions. It is now being made available to other agencies and foreign governments in their search for regional security and cooperation. This report presents two examples of interest to DOE in which monitoring technologies could be employed to promote cooperation through experimentation. The two scenarios include nuclear transparency in Northeast Asia and environmental restoration in the Black Sea. Both offer the potential for the use of technology to promote regional cooperation. The issues associated with both of these monitoring applications are presented along with examples of appropriate monitoring technologies, potential experiments and potential DOE contributions to the scenarios.« less

DOE 2011 occupational radiation exposure

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

none,

2012-12-01

The U.S. Department of Energy (DOE) Office of Analysis within the Office of Health, Safety and Security (HSS) publishes the annual DOE Occupational Radiation Exposure Report to provide an overview of the status of radiation protection practices at DOE (including the National Nuclear Security Administration [NNSA]). The DOE 2011 Occupational Radiation Exposure Report provides an evaluation of DOE-wide performance regarding compliance with Title 10, Code of Federal Regulations (C.F.R.), Part 835, Occupational Radiation Protection dose limits and as low as reasonably achievable (ALARA) process requirements. In addition, the report provides data to DOE organizations responsible for developing policies for protectionmore » of individuals from the adverse health effects of radiation. The report provides a summary and an analysis of occupational radiation exposure information from the monitoring of individuals involved in DOE activities. The occupational radiation exposure information is analyzed in terms of aggregate data, dose to individuals, and dose by site over the past five years.« less

Practical aspects of running DOE for improving growth media for in vitro plants

USDA-ARS?s Scientific Manuscript database

Experiments using DOE software to improve plant tissue culture growth medium are complicated and require complex setups. Once the experimental design is set and the treatment points calculated, media sheets and mixing charts must be developed. Since these experiments require three passages on the sa...

Weak polyelectrolyte complexation driven by associative charging.

PubMed

Rathee, Vikramjit S; Zervoudakis, Aristotle J; Sidky, Hythem; Sikora, Benjamin J; Whitmer, Jonathan K

2018-03-21

Weak polyelectrolytes are relevant for a wide range of fields; in particular, they have been investigated as "smart" materials for chemical separations and drug delivery. The charges on weak polyelectrolytes are dynamic, causing polymer chains to adopt different equilibrium conformations even with relatively small changes to the surrounding environment. Currently, there exists no comprehensive picture of this behavior, particularly where polymer-polymer interactions have the potential to affect charging properties significantly. In this study, we elucidate the novel interplay between weak polyelectrolyte charging and complexation behavior through coupled molecular dynamics and Monte Carlo simulations. Specifically, we investigate a model of two equal-length and oppositely charging polymer chains in an implicit salt solution represented through Debye-Hückel interactions. The charging tendency of each chain, along with the salt concentration, is varied to determine the existence and extent of cooperativity in charging and complexation. Strong cooperation in the charging of these chains is observed at large Debye lengths, corresponding to low salt concentrations, while at lower Debye lengths (higher salt concentrations), the chains behave in apparent isolation. When the electrostatic coupling is long-ranged, we find that a highly charged chain strongly promotes the charging of its partner chain, even if the environment is unfavorable for an isolated version of that partner chain. Evidence of this phenomenon is supported by a drop in the potential energy of the system, which does not occur at the lower Debye lengths where both potential energies and charge fractions converge for all partner chain charging tendencies. The discovery of this cooperation will be helpful in developing "smart" drug delivery mechanisms by allowing for better predictions for the dissociation point of delivery complexes.

Weak polyelectrolyte complexation driven by associative charging

NASA Astrophysics Data System (ADS)

Rathee, Vikramjit S.; Zervoudakis, Aristotle J.; Sidky, Hythem; Sikora, Benjamin J.; Whitmer, Jonathan K.

2018-03-01

Weak polyelectrolytes are relevant for a wide range of fields; in particular, they have been investigated as "smart" materials for chemical separations and drug delivery. The charges on weak polyelectrolytes are dynamic, causing polymer chains to adopt different equilibrium conformations even with relatively small changes to the surrounding environment. Currently, there exists no comprehensive picture of this behavior, particularly where polymer-polymer interactions have the potential to affect charging properties significantly. In this study, we elucidate the novel interplay between weak polyelectrolyte charging and complexation behavior through coupled molecular dynamics and Monte Carlo simulations. Specifically, we investigate a model of two equal-length and oppositely charging polymer chains in an implicit salt solution represented through Debye-Hückel interactions. The charging tendency of each chain, along with the salt concentration, is varied to determine the existence and extent of cooperativity in charging and complexation. Strong cooperation in the charging of these chains is observed at large Debye lengths, corresponding to low salt concentrations, while at lower Debye lengths (higher salt concentrations), the chains behave in apparent isolation. When the electrostatic coupling is long-ranged, we find that a highly charged chain strongly promotes the charging of its partner chain, even if the environment is unfavorable for an isolated version of that partner chain. Evidence of this phenomenon is supported by a drop in the potential energy of the system, which does not occur at the lower Debye lengths where both potential energies and charge fractions converge for all partner chain charging tendencies. The discovery of this cooperation will be helpful in developing "smart" drug delivery mechanisms by allowing for better predictions for the dissociation point of delivery complexes.

Sudden cardiac death in adults with congenital heart disease: does QRS-complex fragmentation discriminate in structurally abnormal hearts?

PubMed

Vehmeijer, Jim T; Koyak, Zeliha; Bokma, Jouke P; Budts, Werner; Harris, Louise; Mulder, Barbara J M; de Groot, Joris R

2018-06-01

Sudden cardiac death (SCD) causes a large portion of all mortality in adult congenital heart disease (ACHD) patients. However, identification of high-risk patients remains challenging. Fragmented QRS-complexes (fQRS) are a marker for SCD in patients with acquired heart disease but data in ACHD patients are lacking. We therefore aim to evaluate the prognostic value of fQRS for SCD in ACHD patients. From a multicentre cohort of 25 790 ACHD patients, we included tachyarrhythmic SCD cases (n = 147), and controls (n = 266) matched by age, gender, congenital defect and (surgical) intervention. fQRS was defined as ≥1 discontinuous deflection in narrow QRS-complexes, and ≥2 in wide QRS-complexes (>120 ms), in two contiguous ECG leads. We calculated odds ratios (OR) using univariable and multivariable conditional logistic regression models correcting for impaired systemic ventricular function, heart failure and QRS duration >120 ms. ECGs of 147 SCD cases (65% male, median age of death 34 years) and of 266 controls were assessed. fQRS was present in 51% of cases and 34% of controls (OR 2.0, P = 0.003). In multivariable analysis, fQRS was independently associated with SCD (OR 1.9, P = 0.01). The most common diagnose of SCD cases was tetralogy of Fallot (ToF, 34 cases). In ToF, fQRS was present in 71% of cases vs. 43% of controls (OR for SCD 2.8, P = 0.03). fQRS was independently associated with SCD in ACHD patients in a cohort of SCD patients and matched controls. fQRS may therefore contribute to the decision when evaluating ACHD patients for primary prevention of SCD.

Structural determinants of enzyme binding affinity: the E1 component of pyruvate dehydrogenase from Escherichia coli in complex with the inhibitor thiamin thiazolone diphosphate.

PubMed

Arjunan, Palaniappa; Chandrasekhar, Krishnamoorthy; Sax, Martin; Brunskill, Andrew; Nemeria, Natalia; Jordan, Frank; Furey, William

2004-03-09

Thiamin thiazolone diphosphate (ThTDP), a potent inhibitor of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc), binds to the enzyme with greater affinity than does the cofactor thiamin diphosphate (ThDP). To identify what determines this difference, the crystal structure of the apo PDHc E1 component complex with ThTDP and Mg(2+) has been determined at 2.1 A and compared to the known structure of the native holoenzyme, PDHc E1-ThDP-Mg(2+) complex. When ThTDP replaces ThDP, reorganization occurs in the protein structure in the vicinity of the active site involving positional and conformational changes in some amino acid residues, a change in the V coenzyme conformation, addition of new hydration sites, and elimination of others. These changes culminate in an increase in the number of hydrogen bonds to the protein, explaining the greater affinity of the apoenzyme for ThTDP. The observed hydrogen bonding pattern is not an invariant feature of ThDP-dependent enzymes but rather specific to this enzyme since the extra hydrogen bonds are made with nonconserved residues. Accordingly, these sequence-related hydrogen bonding differences likewise explain the wide variation in the affinities of different thiamin-dependent enzymes for ThTDP and ThDP. The sequence of each enzyme determines its ability to form hydrogen bonds to the inhibitor or cofactor. Mechanistic roles are suggested for the aforementioned reorganization and its reversal in PDHc E1 catalysis: to promote substrate binding and product release. This study also provides additional insight into the role of water in enzyme inhibition and catalysis.

From global scaling to the dynamics of individual cities

NASA Astrophysics Data System (ADS)

Depersin, Jules; Barthelemy, Marc

2018-03-01

Scaling has been proposed as a powerful tool to analyze the properties of complex systems and in particular for cities where it describes how various properties change with population. The empirical study of scaling on a wide range of urban datasets displays apparent nonlinear behaviors whose statistical validity and meaning were recently the focus of many debates. We discuss here another aspect, which is the implication of such scaling forms on individual cities and how they can be used for predicting the behavior of a city when its population changes. We illustrate this discussion in the case of delay due to traffic congestion with a dataset of 101 US cities in the years 1982–2014. We show that the scaling form obtained by agglomerating all of the available data for different cities and for different years does display a nonlinear behavior, but which appears to be unrelated to the dynamics of individual cities when their population grows. In other words, the congestion-induced delay in a given city does not depend on its population only, but also on its previous history. This strong path dependency prohibits the existence of a simple scaling form valid for all cities and shows that we cannot always agglomerate the data for many different systems. More generally, these results also challenge the use of transversal data for understanding longitudinal series for cities.

Competing spreading processes on multiplex networks: Awareness and epidemics

NASA Astrophysics Data System (ADS)

Granell, Clara; Gómez, Sergio; Arenas, Alex

2014-07-01

Epidemiclike spreading processes on top of multilayered interconnected complex networks reveal a rich phase diagram of intertwined competition effects. A recent study by the authors [C. Granell et al., Phys. Rev. Lett. 111, 128701 (2013)., 10.1103/PhysRevLett.111.128701] presented an analysis of the interrelation between two processes accounting for the spreading of an epidemic, and the spreading of information awareness to prevent infection, on top of multiplex networks. The results in the case in which awareness implies total immunization to the disease revealed the existence of a metacritical point at which the critical onset of the epidemics starts, depending on completion of the awareness process. Here we present a full analysis of these critical properties in the more general scenario where the awareness spreading does not imply total immunization, and where infection does not imply immediate awareness of it. We find the critical relation between the two competing processes for a wide spectrum of parameters representing the interaction between them. We also analyze the consequences of a massive broadcast of awareness (mass media) on the final outcome of the epidemic incidence. Importantly enough, the mass media make the metacritical point disappear. The results reveal that the main finding, i.e., existence of a metacritical point, is rooted in the competition principle and holds for a large set of scenarios.

Lessons in power: Lyndon Johnson revealed. A conversation with historian Robert A. Caro.

PubMed

Caro, Robert A

2006-04-01

No one can lead who does not first acquire power, and no leader can be great who does not know how to use that power. The trouble is that the combination of the two skills is rare. Amassing power requires ambition, a focused pragmatism, and a certain ruthlessness that is often at odds with the daring, idealistic vision needed to achieve great things with that power. The tension is as real in business as it is in politics. This magazine is replete with examples of successful senior managers who could not make the switch from ambitious executive to corporate leader because they did not know what to do with the power they had so expertly accumulated. Robert Caro is a student of power. For the past 27 years, the two-time Pulitzer prize-winning biographer of Robert Moses and Lyndon Johnson has focused on the question of how Johnson amassed and wielded power. Caro's deep understanding of the inner workings of power offers senior executives a nuanced picture of leadership at the highest level. In this wide-ranging conversation, Caro shares his insights about the nature of power, the complexity of ambition, and the role that the greater good can play in the making of a leader. Power doesn't always corrupt, he insists. But what it invariably does is reveal a leader's true nature. "Today, when CEOs have acquired more and more power to change our lives," Caro says,"they have become like presidents in their own right, and they, too, need to align themselves with something greater than themselves if they hope to become truly great leaders."

D and D Knowledge Management Information Tool - 2012 - 12106

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

Upadhyay, H.; Lagos, L.; Quintero, W.

2012-07-01

Deactivation and decommissioning (D and D) work is a high priority activity across the Department of Energy (DOE) complex. Subject matter specialists (SMS) associated with the different ALARA (As-Low-As-Reasonably-Achievable) Centers, DOE sites, Energy Facility Contractors Group (EFCOG) and the D and D community have gained extensive knowledge and experience over the years in the cleanup of the legacy waste from the Manhattan Project. To prevent the D and D knowledge and expertise from being lost over time from the evolving and aging workforce, DOE and the Applied Research Center (ARC) at Florida International University (FIU) proposed to capture and maintainmore » this valuable information in a universally available and easily usable system. D and D KM-IT provides single point access to all D and D related activities through its knowledge base. It is a community driven system. D and D KM-IT makes D and D knowledge available to the people who need it at the time they need it and in a readily usable format. It uses the World Wide Web as the primary source for content in addition to information collected from subject matter specialists and the D and D community. It brings information in real time through web based custom search processes and its dynamic knowledge repository. Future developments include developing a document library, providing D and D information access on mobile devices for the Technology module and Hotline, and coordinating multiple subject matter specialists to support the Hotline. The goal is to deploy a high-end sophisticated and secured system to serve as a single large knowledge base for all the D and D activities. The system consolidates a large amount of information available on the web and presents it to users in the simplest way possible. (authors)« less

How technology transfer issues are managed

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

Sink, C.H.; Easley, K.R.

1991-12-31

In 1989, Secretary of Energy James Watkins made a commitment to accelerate DOE compliance with all applicable laws and standards aimed at protecting human health and the environment. At a minimum, this pledge requires the remediation of the 1989 inventory of chemical, radioactive, and mixed wastes at DOE production sites by 2019. The 1989 Complex inventory consisted of more than 3,700 sites, encompassing more than 26,000 acres contaminated with radioactive, hazardous, and mixed wastes. In addition, over 500 surplus sites are awaiting decontamination and decommissioning (D and D), and approximately 5,000 peripheral properties have contaminated soils (e.g., uranium tailings). Moreover,more » these problems exist at both inactive sites, where the primary focus is on environmental restoration, and at active sites, where the major emphasis is on improved waste management techniques. Although some of DOE`s problems are considered unique due to radioactivity, most forms of contamination resident in the Complex are not; rather, contaminants such as waste chemicals (e.g., inorganics), organics (e.g., fuels and solvents), halogenated organics (e.g., PCBs) and heavy metals commonly result in conventional industrial processes. Although certain other forms of contamination are more unique to DOE operations (e.g., radioactive materials, explosives, and pyrophorics), they are not exclusive to DOE. As DOE develops innovative solutions to these and related waste problems, it is imperative that technology systems and lessons learned be transferred from DOE sites and its R and D laboratories to private industry to maximize the nation`s return on environmental management technology investments.« less

Validation of an intermediate-complexity model for simulating marine biogeochemistry under anoxic conditions in the modern Black Sea

NASA Astrophysics Data System (ADS)

Romaniello, Stephen J.; Derry, Louis A.

2010-08-01

We test the ability of a new 1-D intermediate-complexity box model (ICBM) that includes process-based C, N, P, O, and S biogeochemistry to simulate profiles and fluxes of biogeochemically reactive species across a wide range of ocean redox states. The ICBM was developed to simulate whole ocean processes for paleoceanographic applications and has been tested with data from the modern global ocean. Here we adapt the circulation submodel of the ICBM to simulate water mass exchange and eddy diffusion processes in the Black Sea but make only very minor changes to the biogeochemical submodel. We force the model with estimated natural and anthropogenic inputs of tracers and nutrients to the Black Sea and compare the results of the simulations to modern observations. Ventilation of the Black Sea is modeled by depth-dependent entrainment of Cold Intermediate Layer water into Bosphorus plume water and subsequent intrusion into deep layers. The simulated profiles of circulation tracers θ, salinity, CFC-12, and radiocarbon agree well with available data, suggesting that the model does a reasonable job of representing physical exchange. Vertical profiles of biogeochemically active components are in good overall agreement with observations. The lack of trace metal (Mn and Fe) cycling in the model results in some discrepancies between the simulated profiles and observation across the suboxic zone; however, the overall redox balance is not sensitive to this difference. We compare modeled basin-wide biogeochemical fluxes to available estimates, but in a number of cases uncertainties in modern budgets limit our ability to test the model rigorously. In agreement with earlier work we find that fixed N losses via thiodenitrification are likely a major pathway in the Black Sea N cycle. Overall, the same biogeochemical submodel used to simulate the modern global ocean appears to perform well in simulating Black Sea processes without requiring significant modification. The ability of a single model to perform across a wide range of redox states is an important prerequisite for applying the ICBM to deep time paleoceanographic problems. The model source code is available as MATLAB™ 7 m-files provided as auxiliary material.

International policy and advisory response regarding children's exposure to radio frequency electromagnetic fields (RF-EMF).

PubMed

Redmayne, Mary

2016-01-01

Radiofrequency electromagnetic field (RF-EMF) exposure regulations/guidelines generally only consider acute effects, and not chronic, low exposures. Concerns for children's exposure are warranted due to the amazingly rapid uptake of many wireless devices by increasingly younger children. This review of policy and advice regarding children's RF-EMF exposure draws material from a wide variety of sources focusing on the current situation. This is not a systematic review, but aims to provide a representative cross-section of policy and advisory responses within set boundaries. There are a wide variety of approaches which I have categorized and tabulated ranging from ICNIRP/IEEE guidelines and "no extra precautions needed" to precautionary or scientific much lower maxima and extensive advice to minimize RF-EMF exposure, ban advertising/sale to children, and add exposure information to packaging. Precautionary standards use what I term an exclusion principle. The wide range of policy approaches can be confusing for parents/carers of children. Some consensus among advisory organizations would be helpful acknowledging that, despite extensive research, the highly complex nature of both RF-EMF and the human body, and frequent technological updates, means simple assurance of long-term safety cannot be guaranteed. Therefore, minimum exposure of children to RF-EMF is recommended. This does not indicate need for alarm, but mirrors routine health-and-safety precautions. Simple steps are suggested. ICNIRP guidelines need to urgently publish how the head, torso, and limbs' exposure limits were calculated and what safety margin was applied since this exposure, especially to the abdomen, is now dominant in many children.

DOE Research and Development Accomplishments Frequently Asked Questions

Science.gov Websites

Accomplishments contain? What is the date range of the content? What is an accomplishment? What are the topics in Featured Scientists/Topics pick list, which is at the top of the page. What is the date range of the are the topics in DOE R&D Accomplishments? Topics are wide-ranging and include subjects such as

Energy Assessment Helps Kaiser Aluminum Save Energy and Improve Productivity; DOE Software Adopted as Standard for Analyzing Plant Process Heating Systems Company-Wide

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

Not Available

2008-07-01

This case study describes how the Kaiser Aluminum plant in Sherman, Texas, achieved annual savings of $360,000 and 45,000 MMBtu, and improved furnace energy intensity by 11.1% after receiving a DOE Save Energy Now energy assessment and implementing recommendations to improve the efficiency of its process heating system.

A Genome-Wide Association Study of Autism Incorporating Autism Diagnostic Interview-Revised, Autism Diagnostic Observation Schedule, and Social Responsiveness Scale

ERIC Educational Resources Information Center

Connolly, John J.; Glessner, Joseph T.; Hakonarson, Hakon

2013-01-01

Efforts to understand the causes of autism spectrum disorders (ASDs) have been hampered by genetic complexity and heterogeneity among individuals. One strategy for reducing complexity is to target endophenotypes, simpler biologically based measures that may involve fewer genes and constitute a more homogenous sample. A genome-wide association…

Case report: an unstable wide QRS complexes tachycardia after ablation of a poster-septal accessory pathway: What is the mechanism?

PubMed

Wang, Huan; Che, Xiaoru

2018-03-01

Differentiation of wide QRS complex tachycardia required repeated electrophysiological stimuli and mapping. However, instability of tachycardia would increase the difficulty in differential diagnosis. In this paper, we reported a wide QRS tachycardia following ablation of an atrioventricular reentrant tachycardia participated by a poster-septal accessory pathway. Limited differentiation strategy was performed because the wide QRS tachycardia was self-limited and with unstable hemodynamics. We analyzed the mechanism of the wide QRS tachycardia by only 4 beats ventricular overpacing. On the basis of the last ventricular pacing, an atypical atrioventricular nodal reentrant tachycardia was confirmed. After slow-pathway modification, the wide QRS tachycardia was eliminated. It was an atypical atrial-ventricular node reentrant tachycardia with right bundle branch block. Reasonable analysis based on electrophysiological electrophysiologic knowledge was the basis of successful diagnosis and treatment.

Cost-effective large-scale fabrication of diffractive optical elements by using conventional semiconducting processes.

PubMed

Yoo, Seunghwan; Song, Ho Young; Lee, Junghoon; Jang, Cheol-Yong; Jeong, Hakgeun

2012-11-20

In this article, we introduce a simple fabrication method for SiO(2)-based thin diffractive optical elements (DOEs) that uses the conventional processes widely used in the semiconductor industry. Photolithography and an inductively coupled plasma etching technique are easy and cost-effective methods for fabricating subnanometer-scale and thin DOEs with a refractive index of 1.45, based on SiO(2). After fabricating DOEs, we confirmed the shape of the output light emitted from the laser diode light source and applied to a light-emitting diode (LED) module. The results represent a new approach to mass-produce DOEs and realize a high-brightness LED module.

Can a Reaction's Environment Program its Outcome, and Does it Matter?

NASA Astrophysics Data System (ADS)

Surman, A. J.; Rodriguez-Garcia, M.; Abul-Haija, Y.; Cooper, G. J. T.; Donkers, K.; Planchat i Barbarà, J. M.; Kube, J.; Mullin, M.; Hezwani, M.; Cronin, L.

2017-07-01

Where most eschew reactions producing complex mixtures (‘tar') and prefer to plan ‘clean' syntheses, we embrace complexity. We show that environments can steer ‘messy' reactions, and ask if this can yield significant difference in structure and function.

Vehicle tracking in wide area motion imagery from an airborne platform

NASA Astrophysics Data System (ADS)

van Eekeren, Adam W. M.; van Huis, Jasper R.; Eendebak, Pieter T.; Baan, Jan

2015-10-01

Airborne platforms, such as UAV's, with Wide Area Motion Imagery (WAMI) sensors can cover multiple square kilometers and produce large amounts of video data. Analyzing all data for information need purposes becomes increasingly labor-intensive for an image analyst. Furthermore, the capacity of the datalink in operational areas may be inadequate to transfer all data to the ground station. Automatic detection and tracking of people and vehicles enables to send only the most relevant footage to the ground station and assists the image analysts in effective data searches. In this paper, we propose a method for detecting and tracking vehicles in high-resolution WAMI images from a moving airborne platform. For the vehicle detection we use a cascaded set of classifiers, using an Adaboost training algorithm on Haar features. This detector works on individual images and therefore does not depend on image motion stabilization. For the vehicle tracking we use a local template matching algorithm. This approach has two advantages. In the first place, it does not depend on image motion stabilization and it counters the inaccuracy of the GPS data that is embedded in the video data. In the second place, it can find matches when the vehicle detector would miss a certain detection. This results in long tracks even when the imagery is of low frame-rate. In order to minimize false detections, we also integrate height information from a 3D reconstruction that is created from the same images. By using the locations of buildings and roads, we are able to filter out false detections and increase the performance of the tracker. In this paper we show that the vehicle tracks can also be used to detect more complex events, such as traffic jams and fast moving vehicles. This enables the image analyst to do a faster and more effective search of the data.

VGLUT1 mRNA and protein expression in the visual system of prosimian galagos (Otolemur garnetti)

PubMed Central

Balaram, Pooja; Hackett, Troy A; Kaas, Jon H

2011-01-01

The presynaptic storage and release of glutamate, an excitatory neurotransmitter, is modulated by a family of transport proteins known as vesicular glutamate transporters. Vesicular glutamate transporter 1 (VGLUT1) is widely distributed in the central nervous system of most mammalian and nonmammalian species, and regulates the uptake of glutamate into synaptic vesicles as well as the transport of filled glutamatergic vesicles to the terminal membrane during excitatory transmission. In rodents, VGLUT1 mRNA is primarily found in the neocortex, cerebellum, and hippocampus, and the VGLUT1 transport protein is involved in intercortical and corticothalamic projections that remain distinct from projections involving other VGLUT isoforms. With the exception of a few thalamic sensory nuclei, VGLUT1 mRNA is absent from subcortical areas and does not colocalize with other VGLUT mRNAs. VGLUT1 is similarly restricted to a few thalamic association nuclei and does not colocalize with other VGLUT proteins. However, recent work in primates has shown that VGLUT1 mRNA is also found in several subcortical nuclei as well as cortical areas, and that VGLUT1 may overlap with other VGLUT isoforms in glutamatergic projections. In order to expand current knowledge of VGLUT1 distributions in primates and gain insight on glutamatergic transmission in the visual system of primate species, we examined VGLUT1 mRNA and protein distributions in the lateral geniculate nucleus, pulvinar complex, superior colliculus, V1, V2, and the middle temporal area (MT) of prosimian galagos. We found that, similar to other studies in primates, VGLUT1 mRNA and protein are widely distributed in both subcortical and cortical areas. However, glutamatergic projections involving VGLUT1 are largely limited to intrinsic connections within subcortical and cortical areas, as well as the expected intercortical and corticothalamic projections. Additionally, VGLUT1 expression in galagos allowed us to identify laminar subdivisions of the superior colliculus, V1, V2, and MT. PMID:22912561

Flattening of Caribbean coral reefs: region-wide declines in architectural complexity

PubMed Central

Alvarez-Filip, Lorenzo; Dulvy, Nicholas K.; Gill, Jennifer A.; Côté, Isabelle M.; Watkinson, Andrew R.

2009-01-01

Coral reefs are rich in biodiversity, in large part because their highly complex architecture provides shelter and resources for a wide range of organisms. Recent rapid declines in hard coral cover have occurred across the Caribbean region, but the concomitant consequences for reef architecture have not been quantified on a large scale to date. We provide, to our knowledge, the first region-wide analysis of changes in reef architectural complexity, using nearly 500 surveys across 200 reefs, between 1969 and 2008. The architectural complexity of Caribbean reefs has declined nonlinearly with the near disappearance of the most complex reefs over the last 40 years. The flattening of Caribbean reefs was apparent by the early 1980s, followed by a period of stasis between 1985 and 1998 and then a resumption of the decline in complexity to the present. Rates of loss are similar on shallow (<6 m), mid-water (6–20 m) and deep (>20 m) reefs and are consistent across all five subregions. The temporal pattern of declining architecture coincides with key events in recent Caribbean ecological history: the loss of structurally complex Acropora corals, the mass mortality of the grazing urchin Diadema antillarum and the 1998 El Nino Southern Oscillation-induced worldwide coral bleaching event. The consistently low estimates of current architectural complexity suggest regional-scale degradation and homogenization of reef structure. The widespread loss of architectural complexity is likely to have serious consequences for reef biodiversity, ecosystem functioning and associated environmental services. PMID:19515663

Does Learning a Complex Task Have To Be Complex?: A Study in Learning Decomposition.

ERIC Educational Resources Information Center

Lee, Frank J.; Anderson, John R.

2001-01-01

Decomposed the learning in the Kanfer-Ackerman Air-Traffic Controller Task (P. Ackerman, 1988) down to learning at the keyboard level. Reanalyzed the Ackerman data to show that learning in this complex task reflects learning at the keystroke level. Conducted an eye-tracking experiment with 10 adults that showed that learning at the key stroke…

An artificial guanine that binds cytidine through the cooperative interaction of metal coordination and hydrogen bonding.

PubMed

Mancin, Fabrizio; Chin, Jik

2002-09-18

Cd(II) complex of L binds selectively to cytidine in DMSO with an equilibrium constant of 117 M-1 (where LH is 2-aminomethyl-8-hydroxyquinoline). In contrast, the Zn(II) complex of L does not bind appreciably to any of the four nucleobases under the same condition used for the Cd(II) complex.

78 FR 9953 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-12

... Effectiveness of Proposed Rule Change Related to the Opening of the Complex Order Book February 6, 2013... Exchange's complex order book (``COB'') when the COB opens for trading. Currently the rule does not include... individual orders and quotes in the electronic book or other complex orders in the COB, execute or route for...

Guide of good practices for occupational radiological protection in plutonium facilities

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

NONE

1998-06-01

This Technical Standard (TS) does not contain any new requirements. Its purpose is to provide guides to good practice, update existing reference material, and discuss practical lessons learned relevant to the safe handling of plutonium. the technical rationale is given to allow US Department of Energy (DOE) health physicists to adapt the recommendations to similar situations throughout the DOE complex. Generally, DOE contractor health physicists will be responsible to implement radiation protection activities at DOE facilities and DOE health physicists will be responsible for oversight of those activities. This guidance is meant to be useful for both efforts. This TSmore » replaces PNL-6534, Health Physics Manual of Good Practices for Plutonium Facilities, by providing more complete and current information and by emphasizing the situations that are typical of DOE`s current plutonium operations; safe storage, decontamination, and decommissioning (environmental restoration); and weapons disassembly.« less

THE BIOLOGICAL ACTIVITY OF SOLUBLE ANTIGEN-ANTIBODY COMPLEXES

PubMed Central

Ishizaka, Kimishige; Ishizaka, Teruko; Campbell, Dan H.

1959-01-01

Soluble BSA-anti-BSA complexes, formed in antigen excess, give immediate skin reactions in normal guinea pigs. The mechanism of the reaction is not that of passive or reversed passive anaphylaxis. The complex itself is toxic. Skin activity of the complex depends on its composition. It has become obvious that the complex composed of two antigen molecules and one antibody molecule, (Ag2Ab), does not have the activity, whereas, Ag3Ab2 and more complicated complexes do. The role of complement as well as speculation on the structural changes of antibody-antigen complexes is presented. PMID:13620844

Developmental trauma disorder: pros and cons of including formal criteria in the psychiatric diagnostic systems

PubMed Central

2013-01-01

Background This article reviews the current debate on developmental trauma disorder (DTD) with respect to formalizing its diagnostic criteria. Victims of abuse, neglect, and maltreatment in childhood often develop a wide range of age-dependent psychopathologies with various mental comorbidities. The supporters of a formal DTD diagnosis argue that post-traumatic stress disorder (PTSD) does not cover all consequences of severe and complex traumatization in childhood. Discussion Traumatized individuals are difficult to treat, but clinical experience has shown that they tend to benefit from specific trauma therapy. A main argument against inclusion of formal DTD criteria into existing diagnostic systems is that emphasis on the etiology of the disorder might force current diagnostic systems to deviate from their purely descriptive nature. Furthermore, comorbidities and biological aspects of the disorder may be underdiagnosed using the DTD criteria. Summary Here, we discuss arguments for and against the proposal of DTD criteria and address implications and consequences for the clinical practice. PMID:23286319

Hint of Universal Law for the Financial Gains of Competitive Sport Teams. The case of Tour de France cycle race.

NASA Astrophysics Data System (ADS)

Ausloos, Marcel

2017-12-01

This short note is intended as a "Letter to the Editor" Perspective in order that it serves as a contribution, in view of reaching the physics community caring about rare events and scaling laws and unexpected findings, on a domain of wide interest: sport and money. It is apparent from the data reported and discussed below that the scarcity of such data does not allow to recommend a complex elaboration of an agent based model, - at this time. In some sense, this also means that much data on sport activities is not necessarily given in terms of physics prone materials, but it could be, and would then attract much attention. Nevertheless the findings tie the data to well known scaling laws and physics processes. It is found that a simple scaling law describes the gains of teams in recent bicycle races, like the Tour de France. An analogous case, ranking teams in Formula 1 races, is shown in an Appendix

Designing HIGH-COST Medicine Hospital Surveys, Health Planning, and the Paradox of Progressive Reform

PubMed Central

2010-01-01

Inspired by social medicine, some progressive US health reforms have paradoxically reinforced a business model of high-cost medical delivery that does not match social needs. In analyzing the financial status of their areas’ hospitals, for example, city-wide hospital surveys of the 1910s through 1930s sought to direct capital investments and, in so doing, control competition and markets. The 2 national health planning programs that ran from the mid-1960s to the mid-1980s continued similar strategies of economic organization and management, as did the so-called market reforms that followed. Consequently, these reforms promoted large, extremely specialized, capital-intensive institutions and systems at the expense of less complex (and less costly) primary and chronic care. The current capital crisis may expose the lack of sustainability of such a model and open up new ideas and new ways to build health care designed to meet people's health needs. PMID:20019312

Mitochondrial-associated metabolic disorders: foundations, pathologies and recent progress

PubMed Central

2013-01-01

Research in the last decade has revolutionized the way in which we view mitochondria. Mitochondria are no longer viewed solely as cellular powerhouses; rather, mitochondria are now understood to be vibrant, mobile structures, constantly undergoing fusion and fission, and engaging in intimate interactions with other cellular compartments and structures. Findings have implicated mitochondria in a wide variety of cellular processes and molecular interactions, such as calcium buffering, lipid flux, and intracellular signaling. As such, it does not come as a surprise that an increasing number of human pathologies have been associated with functional defects in mitochondria. The difficulty in understanding and treating human pathologies caused by mitochondrial dysfunction arises from the complex relationships between mitochondria and other cellular processes, as well as the genetic background of such diseases. This review attempts to provide a summary of the background knowledge and recent developments in mitochondrial processes relating to mitochondrial-associated metabolic diseases arising from defects or deficiencies in mitochondrial function, as well as insights into current and future avenues for investigation. PMID:24499129

Oxygen and differentiation status modulate the effect of X-ray irradiation on physiology and mitochondrial proteome of human neuroblastoma cells.

PubMed

Džinić, Tamara; Hartwig, Sonja; Lehr, Stefan; Dencher, Norbert A

2016-12-01

Cytotoxic effects, including oxidative stress, of low linear energy transfer (LET)-ionizing radiation are often underestimated and studies of their mechanisms using cell culture models are widely conducted with cells cultivated at atmospheric oxygen that does not match its physiological levels in body tissues. Also, cell differentiation status plays a role in the outcome of experiments. We compared effects of 2 Gy X-ray irradiation on the physiology and mitochondrial proteome of nondifferentiated and human neuroblastoma (SH-SY5Y) cells treated with retinoic acid cultivated at 21% and 5% O 2 . Irradiation did not affect the amount of subunits of OxPhos complexes and other non-OxPhos mitochondrial proteins, except for heat shock protein 70, which was increased depending on oxygen level and differentiation status. These two factors were proven to modulate mitochondrial membrane potential and the bioenergetic status of cells. We suggest, moreover, that oxygen plays a role in the differentiation of human SH-SY5Y cells.

An Imagineering Approach to the Future of Space Situational Awareness

NASA Astrophysics Data System (ADS)

Luce, R.

It is widely accepted that space is becoming a more congested, contested, and competitive domain. This drives a need not only to track space objects but also to have a clear and constant picture of what the objects are and how they are being operated. Space situational awareness, like most mission areas, suffers from the need to maintain aging, increasingly fragile legacy infrastructure and at the same time acquire increasingly complex materiel solutions that often fall behind schedule and over budget. Imagineering, the name for both the process by which Disney creates new theme park experiences and the corporate division that does the work, offers some new ways of thinking about balancing these needs and providing better bang-for-the-buck. Through a series of personal anecdotes that illustrate key concepts of Imagineering, this paper supports a conclusion that a new way of thinking about the space situational awareness mission area will be needed to ensure mission success moving forward.

A novel structure-aware sparse learning algorithm for brain imaging genetics.

PubMed

Du, Lei; Jingwen, Yan; Kim, Sungeun; Risacher, Shannon L; Huang, Heng; Inlow, Mark; Moore, Jason H; Saykin, Andrew J; Shen, Li

2014-01-01

Brain imaging genetics is an emergent research field where the association between genetic variations such as single nucleotide polymorphisms (SNPs) and neuroimaging quantitative traits (QTs) is evaluated. Sparse canonical correlation analysis (SCCA) is a bi-multivariate analysis method that has the potential to reveal complex multi-SNP-multi-QT associations. Most existing SCCA algorithms are designed using the soft threshold strategy, which assumes that the features in the data are independent from each other. This independence assumption usually does not hold in imaging genetic data, and thus inevitably limits the capability of yielding optimal solutions. We propose a novel structure-aware SCCA (denoted as S2CCA) algorithm to not only eliminate the independence assumption for the input data, but also incorporate group-like structure in the model. Empirical comparison with a widely used SCCA implementation, on both simulated and real imaging genetic data, demonstrated that S2CCA could yield improved prediction performance and biologically meaningful findings.

Air pollution: a smoking gun for cancer.

PubMed

Zhang, Wei; Qian, Chao-Nan; Zeng, Yi-Xin

2014-04-01

Once considered a taboo topic or stigma, cancer is the number one public health enemy in the world. Once a product of an almost untouchable industry, tobacco is indisputably recognized as a major cause of cancer and a target for anticancer efforts. With the emergence of new economic powers in the world, especially in highly populated countries such as China, air pollution has rapidly emerged as a smoking gun for cancer and has become a hot topic for public health debate because of the complex political, economic, scientific, and technologic issues surrounding the air pollution problem. This editorial and the referred articles published in this special issue of the Chinese Journal of Cancer discuss these fundamental questions. Does air pollution cause a wide spectrum of cancers? Should air pollution be considered a necessary evil accompanying economic transformation in developing countries? Is an explosion of cancer incidence coming to China and how soon will it arrive? What must be done to prevent this possible human catastrophe? Finally, the approaches for air pollution control are also discussed.

An Introduction to Markov Modeling: Concepts and Uses

NASA Technical Reports Server (NTRS)

Boyd, Mark A.; Lau, Sonie (Technical Monitor)

1998-01-01

Kharkov modeling is a modeling technique that is widely useful for dependability analysis of complex fault tolerant systems. It is very flexible in the type of systems and system behavior it can model. It is not, however, the most appropriate modeling technique for every modeling situation. The first task in obtaining a reliability or availability estimate for a system is selecting which modeling technique is most appropriate to the situation at hand. A person performing a dependability analysis must confront the question: is Kharkov modeling most appropriate to the system under consideration, or should another technique be used instead? The need to answer this gives rise to other more basic questions regarding Kharkov modeling: what are the capabilities and limitations of Kharkov modeling as a modeling technique? How does it relate to other modeling techniques? What kind of system behavior can it model? What kinds of software tools are available for performing dependability analyses with Kharkov modeling techniques? These questions and others will be addressed in this tutorial.

Performance evaluation of automated segmentation software on optical coherence tomography volume data

PubMed Central

Tian, Jing; Varga, Boglarka; Tatrai, Erika; Fanni, Palya; Somfai, Gabor Mark; Smiddy, William E.

2016-01-01

Over the past two decades a significant number of OCT segmentation approaches have been proposed in the literature. Each methodology has been conceived for and/or evaluated using specific datasets that do not reflect the complexities of the majority of widely available retinal features observed in clinical settings. In addition, there does not exist an appropriate OCT dataset with ground truth that reflects the realities of everyday retinal features observed in clinical settings. While the need for unbiased performance evaluation of automated segmentation algorithms is obvious, the validation process of segmentation algorithms have been usually performed by comparing with manual labelings from each study and there has been a lack of common ground truth. Therefore, a performance comparison of different algorithms using the same ground truth has never been performed. This paper reviews research-oriented tools for automated segmentation of the retinal tissue on OCT images. It also evaluates and compares the performance of these software tools with a common ground truth. PMID:27159849

Synergizing 13C Metabolic Flux Analysis and Metabolic Engineering for Biochemical Production.

PubMed

Guo, Weihua; Sheng, Jiayuan; Feng, Xueyang

Metabolic engineering of industrial microorganisms to produce chemicals, fuels, and drugs has attracted increasing interest as it provides an environment-friendly and renewable route that does not depend on depleting petroleum sources. However, the microbial metabolism is so complex that metabolic engineering efforts often have difficulty in achieving a satisfactory yield, titer, or productivity of the target chemical. To overcome this challenge, 13 C Metabolic Flux Analysis ( 13 C-MFA) has been developed to investigate rigorously the cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, 13 C-MFA has been widely used in academic labs and the biotechnology industry to pinpoint the key issues related to microbial-based chemical production and to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this chapter we introduce the basics of 13 C-MFA and illustrate how 13 C-MFA has been applied to synergize with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production.

A Search Algorithm for Generating Alternative Process Plans in Flexible Manufacturing System

NASA Astrophysics Data System (ADS)

Tehrani, Hossein; Sugimura, Nobuhiro; Tanimizu, Yoshitaka; Iwamura, Koji

Capabilities and complexity of manufacturing systems are increasing and striving for an integrated manufacturing environment. Availability of alternative process plans is a key factor for integration of design, process planning and scheduling. This paper describes an algorithm for generation of alternative process plans by extending the existing framework of the process plan networks. A class diagram is introduced for generating process plans and process plan networks from the viewpoint of the integrated process planning and scheduling systems. An incomplete search algorithm is developed for generating and searching the process plan networks. The benefit of this algorithm is that the whole process plan network does not have to be generated before the search algorithm starts. This algorithm is applicable to large and enormous process plan networks and also to search wide areas of the network based on the user requirement. The algorithm can generate alternative process plans and to select a suitable one based on the objective functions.

Final Report: Conceptual Design of an Electron Accelerator for Bio-Solid Waste Treatment

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

Cooper, Charles

Several studies have identified electron beam (EB) irradiation of municipal wastewater and bio-solids as an effective and promising approach to the environmental remediation of the enormous quantities of human waste created by a growing world-wide population and increased urbanization. However, despite the technical success of experimental and pilot programs over the last several decades, the technique is still not in commercial use anywhere in the world. In addition, the report also identifies the need for “Financial and infrastructure participation from a utility for demonstration project” and “Education and awareness of safety of utilizing electron beam technology” as two additional roadblocksmore » preventing technology adoption of EB treatment for bio-solids. In this concept design, we begin to address these barriers by working with Metropolitan Water Reclamation District of Greater Chicago (MWRD) and by the applying the latest accelerator technologies developed at Fermilab and within the DOE Office of Science laboratory complex.« less

Microbial dextran-hydrolyzing enzymes: fundamentals and applications.

PubMed

Khalikova, Elvira; Susi, Petri; Korpela, Timo

2005-06-01

Dextran is a chemically and physically complex polymer, breakdown of which is carried out by a variety of endo- and exodextranases. Enzymes in many groups can be classified as dextranases according to function: such enzymes include dextranhydrolases, glucodextranases, exoisomaltohydrolases, exoisomaltotriohydrases, and branched-dextran exo-1,2-alpha-glucosidases. Cycloisomalto-oligosaccharide glucanotransferase does not formally belong to the dextranases even though its side reaction produces hydrolyzed dextrans. A new classification system for glycosylhydrolases and glycosyltransferases, which is based on amino acid sequence similarities, divides the dextranases into five families. However, this classification is still incomplete since sequence information is missing for many of the enzymes that have been biochemically characterized as dextranases. Dextran-degrading enzymes have been isolated from a wide range of microorganisms. The major characteristics of these enzymes, the methods for analyzing their activities and biological roles, analysis of primary sequence data, and three-dimensional structures of dextranases have been dealt with in this review. Dextranases are promising for future use in various scientific and biotechnological applications.

Modeling Reality - How Computers Mirror Life

NASA Astrophysics Data System (ADS)

Bialynicki-Birula, Iwo; Bialynicka-Birula, Iwona

2005-01-01

The bookModeling Reality covers a wide range of fascinating subjects, accessible to anyone who wants to learn about the use of computer modeling to solve a diverse range of problems, but who does not possess a specialized training in mathematics or computer science. The material presented is pitched at the level of high-school graduates, even though it covers some advanced topics (cellular automata, Shannon's measure of information, deterministic chaos, fractals, game theory, neural networks, genetic algorithms, and Turing machines). These advanced topics are explained in terms of well known simple concepts: Cellular automata - Game of Life, Shannon's formula - Game of twenty questions, Game theory - Television quiz, etc. The book is unique in explaining in a straightforward, yet complete, fashion many important ideas, related to various models of reality and their applications. Twenty-five programs, written especially for this book, are provided on an accompanying CD. They greatly enhance its pedagogical value and make learning of even the more complex topics an enjoyable pleasure.

A comparison of transport algorithms for premixed, laminar steady state flames

NASA Technical Reports Server (NTRS)

Coffee, T. P.; Heimerl, J. M.

1980-01-01

The effects of different methods of approximating multispecies transport phenomena in models of premixed, laminar, steady state flames were studied. Five approximation methods that span a wide range of computational complexity were developed. Identical data for individual species properties were used for each method. Each approximation method is employed in the numerical solution of a set of five H2-02-N2 flames. For each flame the computed species and temperature profiles, as well as the computed flame speeds, are found to be very nearly independent of the approximation method used. This does not indicate that transport phenomena are unimportant, but rather that the selection of the input values for the individual species transport properties is more important than the selection of the method used to approximate the multispecies transport. Based on these results, a sixth approximation method was developed that is computationally efficient and provides results extremely close to the most sophisticated and precise method used.

First-rank symptoms in schizophrenia: reexamining mechanisms of self-recognition.

PubMed

Waters, Flavie A V; Badcock, Johanna C

2010-05-01

Disturbances of self are a common feature of schizophrenic psychopathology, with patients reporting that their thoughts and actions are controlled by external forces, as shown in first-rank symptoms (FRS). One widely accepted explanatory model of FRS suggests a deficiency in the internal forward model system. Recent studies in the field of cognitive sciences, however, have generated new insights into how complex sensory and motor systems contribute to the sense of self-recognition, and it is becoming clear that the forward model conceptualization does not have unique access to representations about the self. We briefly evaluate the forward model explanation of FRS, reassess the distinction made between the sense of agency and body ownership, and outline recent developments in 4 domains of sensory-motor control that have supplemented our understanding of the processes underlying the sense of self-recognition. The application of these findings to FRS will open up new research directions into the processes underlying these symptoms.

Single functional group interactions with individual carbon nanotubes

NASA Astrophysics Data System (ADS)

Friddle, Raymond W.; Lemieux, Melburne C.; Cicero, Giancarlo; Artyukhin, Alexander B.; Tsukruk, Vladimir V.; Grossman, Jeffrey C.; Galli, Giulia; Noy, Aleksandr

2007-11-01

Carbon nanotubes display a consummate blend of materials properties that affect applications ranging from nanoelectronic circuits and biosensors to field emitters and membranes. These applications use the non-covalent interactions between the nanotubes and chemical functionalities, often involving a few molecules at a time. Despite their wide use, we still lack a fundamental understanding and molecular-level control of these interactions. We have used chemical force microscopy to measure the strength of the interactions of single chemical functional groups with the sidewalls of vapour-grown individual single-walled carbon nanotubes. Surprisingly, the interaction strength does not follow conventional trends of increasing polarity or hydrophobicity, and instead reflects the complex electronic interactions between the nanotube and the functional group. Ab initio calculations confirm the observed trends and predict binding force distributions for a single molecular contact that match the experimental results. Our analysis also reveals the important role of molecular linkage dynamics in determining interaction strength at the single functional group level.

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

Veseli, S.

As the number of sites deploying and adopting EPICS Version 4 grows, so does the need to support PV Access from multiple languages. Especially important are the widely used scripting languages that tend to reduce both software development time and the learning curve for new users. In this paper we describe PvaPy, a Python API for the EPICS PV Access protocol and its accompanying structured data API. Rather than implementing the protocol itself in Python, PvaPy wraps the existing EPICS Version 4 C++ libraries using the Boost.Python framework. This approach allows us to benefit from the existing code base andmore » functionality, and to significantly reduce the Python API development effort. PvaPy objects are based on Python dictionaries and provide users with the ability to access even the most complex of PV Data structures in a relatively straightforward way. Its interfaces are easy to use, and include support for advanced EPICS Version 4 features such as implementation of client and server Remote Procedure Calls (RPC).« less

Progressive Learning of Topic Modeling Parameters: A Visual Analytics Framework.

PubMed

El-Assady, Mennatallah; Sevastjanova, Rita; Sperrle, Fabian; Keim, Daniel; Collins, Christopher

2018-01-01

Topic modeling algorithms are widely used to analyze the thematic composition of text corpora but remain difficult to interpret and adjust. Addressing these limitations, we present a modular visual analytics framework, tackling the understandability and adaptability of topic models through a user-driven reinforcement learning process which does not require a deep understanding of the underlying topic modeling algorithms. Given a document corpus, our approach initializes two algorithm configurations based on a parameter space analysis that enhances document separability. We abstract the model complexity in an interactive visual workspace for exploring the automatic matching results of two models, investigating topic summaries, analyzing parameter distributions, and reviewing documents. The main contribution of our work is an iterative decision-making technique in which users provide a document-based relevance feedback that allows the framework to converge to a user-endorsed topic distribution. We also report feedback from a two-stage study which shows that our technique results in topic model quality improvements on two independent measures.

HotJava: Sun's Animated Interactive World Wide Web Browser for the Internet.

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Examines HotJava and Java, World Wide Web technology for use on the Internet. HotJava, an interactive, animated Web browser, based on the object-oriented Java programming language, is different from HTML-based browsers such as Netscape. Its client/server design does not understand Internet protocols but can dynamically find what it needs to know.…

A framework to analyze hospital-wide patient flow logistics: evidence from an Italian comparative study.

PubMed

Villa, Stefano; Prenestini, Anna; Giusepi, Isabella

2014-04-01

Through a comparative study of six Italian hospitals, the paper develops and tests a framework to analyze hospital-wide patient flow performance. The framework adopts a system-wide approach to patient flow management and is structured around three different levels: (1) the hospital, (2) the pipelines (possible patient journeys within the hospital) and (3) the production units (physical spaces, such as operating rooms, where service delivery takes places). The focus groups and the data analysis conducted within the study support that the model is a useful tool to investigate hospital-wide implications of patient flows. The paper provides also evidence about the causes of hospital patient flow problems. Particularly, while shortage of capacity does not seem to be a relevant driver, our data shows that patient flow variability caused by inadequate allocation of capacity does represent a key problem. Results also show that the lack of coordination between different pipelines and production units is critical. Finally, the problem of overlapping between elective and unscheduled cases can be solved by setting aside a certain level of capacity for unexpected peaks. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Advanced Post-Irradiation Examination Capabilities Alternatives Analysis Report

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

Jeff Bryan; Bill Landman; Porter Hill

2012-12-01

An alternatives analysis was performed for the Advanced Post-Irradiation Capabilities (APIEC) project in accordance with the U.S. Department of Energy (DOE) Order DOE O 413.3B, “Program and Project Management for the Acquisition of Capital Assets”. The Alternatives Analysis considered six major alternatives: ? No Action ? Modify Existing DOE Facilities – capabilities distributed among multiple locations ? Modify Existing DOE Facilities – capabilities consolidated at a few locations ? Construct New Facility ? Commercial Partnership ? International Partnerships Based on the alternatives analysis documented herein, it is recommended to DOE that the advanced post-irradiation examination capabilities be provided by amore » new facility constructed at the Materials and Fuels Complex at the Idaho National Laboratory.« less

Rigour and Complexity in Educational Research. Conducting Educational Research

ERIC Educational Resources Information Center

Berry, Kathleen; Kincheloe, Joe

2004-01-01

What does it mean to engage in rigorous research? What does a researcher need to know to produce such research? What is specifically involved in multiple method bricolage research? In an era where talk abounds about scientific rigour and evidence-based research in education, this groundbreaking book presents a new and compelling examination of…

Recycled Uranium Mass Balance Project Y-12 National Security Complex Site Report

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

NONE

2000-12-01

This report has been prepared to summarize the findings of the Y-12 National Security Complex (Y-12 Complex) Mass Balance Project and to support preparation of associated U. S. Department of Energy (DOE) site reports. The project was conducted in support of DOE efforts to assess the potential for health and environmental issues resulting from the presence of transuranic (TRU) elements and fission products in recycled uranium (RU) processed by DOE and its predecessor agencies. The United States government used uranium in fission reactors to produce plutonium and tritium for nuclear weapons production. Because uranium was considered scarce relative to demandmore » when these operations began almost 50 years ago, the spent fuel from U.S. fission reactors was processed to recover uranium for recycling. The estimated mass balance for highly enriched RU, which is of most concern for worker exposure and is the primary focus of this project, is summarized in a table. A discrepancy in the mass balance between receipts and shipments (plus inventory and waste) reflects an inability to precisely distinguish between RU and non-RU shipments and receipts involving the Y-12 Complex and Savannah River. Shipments of fresh fuel (non-RU) and sweetener (also non-RU) were made from the Y-12 Complex to Savannah River along with RU shipments. The only way to distinguish between these RU and non-RU streams using available records is by enrichment level. Shipments of {le}90% enrichment were assumed to be RU. Shipments of >90% enrichment were assumed to be non-RU fresh fuel or sweetener. This methodology using enrichment level to distinguish between RU and non-RU results in good estimates of RU flows that are reasonably consistent with Savannah River estimates. Although this is the best available means of distinguishing RU streams, this method does leave a difference of approximately 17.3 MTU between receipts and shipments. Slightly depleted RU streams received by the Y-12 Complex from ORGDP and PGDP are believed to have been returned to the shipping site or disposed of as waste on the Oak Ridge Reservation. No evidence of Y-12 Complex processing of this material was identified in the historical records reviewed by the Project Team.« less

Diffusion, capture and recycling of SCAR/WAVE and Arp2/3 complexes observed in cells by single-molecule imaging.

PubMed

Millius, Arthur; Watanabe, Naoki; Weiner, Orion D

2012-03-01

The SCAR/WAVE complex drives lamellipodium formation by enhancing actin nucleation by the Arp2/3 complex. Phosphoinositides and Rac activate the SCAR/WAVE complex, but how SCAR/WAVE and Arp2/3 complexes converge at sites of nucleation is unknown. We analyzed the single-molecule dynamics of WAVE2 and p40 (subunits of the SCAR/WAVE and Arp2/3 complexes, respectively) in XTC cells. We observed lateral diffusion of both proteins and captured the transition of p40 from diffusion to network incorporation. These results suggest that a diffusive 2D search facilitates binding of the Arp2/3 complex to actin filaments necessary for nucleation. After nucleation, the Arp2/3 complex integrates into the actin network and undergoes retrograde flow, which results in its broad distribution throughout the lamellipodium. By contrast, the SCAR/WAVE complex is more restricted to the cell periphery. However, with single-molecule imaging, we also observed WAVE2 molecules undergoing retrograde motion. WAVE2 and p40 have nearly identical speeds, lifetimes and sites of network incorporation. Inhibition of actin retrograde flow does not prevent WAVE2 association and disassociation with the membrane but does inhibit WAVE2 removal from the actin cortex. Our results suggest that membrane binding and diffusion expedites the recruitment of nucleation factors to a nucleation site independent of actin assembly, but after network incorporation, ongoing actin polymerization facilitates recycling of SCAR/WAVE and Arp2/3 complexes.

Diffusion, capture and recycling of SCAR/WAVE and Arp2/3 complexes observed in cells by single-molecule imaging

PubMed Central

Millius, Arthur; Watanabe, Naoki; Weiner, Orion D.

2012-01-01

The SCAR/WAVE complex drives lamellipodium formation by enhancing actin nucleation by the Arp2/3 complex. Phosphoinositides and Rac activate the SCAR/WAVE complex, but how SCAR/WAVE and Arp2/3 complexes converge at sites of nucleation is unknown. We analyzed the single-molecule dynamics of WAVE2 and p40 (subunits of the SCAR/WAVE and Arp2/3 complexes, respectively) in XTC cells. We observed lateral diffusion of both proteins and captured the transition of p40 from diffusion to network incorporation. These results suggest that a diffusive 2D search facilitates binding of the Arp2/3 complex to actin filaments necessary for nucleation. After nucleation, the Arp2/3 complex integrates into the actin network and undergoes retrograde flow, which results in its broad distribution throughout the lamellipodium. By contrast, the SCAR/WAVE complex is more restricted to the cell periphery. However, with single-molecule imaging, we also observed WAVE2 molecules undergoing retrograde motion. WAVE2 and p40 have nearly identical speeds, lifetimes and sites of network incorporation. Inhibition of actin retrograde flow does not prevent WAVE2 association and disassociation with the membrane but does inhibit WAVE2 removal from the actin cortex. Our results suggest that membrane binding and diffusion expedites the recruitment of nucleation factors to a nucleation site independent of actin assembly, but after network incorporation, ongoing actin polymerization facilitates recycling of SCAR/WAVE and Arp2/3 complexes. PMID:22349699

THE NGA-DOE GRANT TO EXAMINE CRITICAL ISSUES RELATED TO RADIOACTIVE WASTE AND MATERIALS DISPOSITION INVOLVING DOE FACILITIES

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

Ann M. Beauchesne

2000-01-01

Through the National Governors Association (NGA) project ``Critical Issues Related to Radioactive Waste and Materials Disposition Involving DOE Facilities'' NGA brings together Governors' policy advisors, state regulators, and DOE officials to examine critical issues related to the cleanup and operation of DOE nuclear weapons and research facilities. Topics explored through this project include: Decisions involving disposal of mixed, low-level, and transuranic (TRU) waste and disposition of nuclear materials; Decisions involving DOE budget requests and their effect on environmental cleanup and compliance at DOE facilities; Strategies to treat mixed, low-level, and transuranic (TRU) waste and their effect on individual sites inmore » the complex; Changes to the FFCA site treatment plans as a result of proposals in the Department's Accelerating Cleanup: Paths to Closure plan and contractor integration analysis; Interstate waste and materials shipments; and Reforms to existing RCRA and CERCLA regulations/guidance to address regulatory overlap and risks posed by DOE wastes. The overarching theme of this project is to help the Department improve coordination of its major program decisions with Governors' offices and state regulators and to ensure such decisions reflect input from these key state officials and stakeholders. This report summarizes activities conducted during the period from October 1, 1999 through January 31, 2000, under the NGA grant. The work accomplished by the NGA project team during the past three months can be categorized as follows: maintained open communication with DOE on a variety of activities and issues within the DOE environmental management complex; convened and facilitated the October 6--8 NGA FFCA Task Force Meeting in Oak Ridge, Tennessee; maintained communication with NGA Federal Facilities Compliance Task Force members regarding DOE efforts to formulate a configuration for mixed low-level waste and low-level treatment and disposal, external regulation of DOE; and continued to facilitate interactions between the states and DOE to develop a foundation for an ongoing substantive relationship between the Governors of key states and the Department.« less

Tetrahedral aminopeptidase: a novel large protease complex from archaea

PubMed Central

Franzetti, B.; Schoehn, G.; Hernandez, J.-F.; Jaquinod, M.; Ruigrok, R.W.H.; Zaccai, G.

2002-01-01

A dodecameric protease complex with a tetrahedral shape (TET) was isolated from Haloarcula marismortui, a salt-loving archaeon. The 42 kDa monomers in the complex are homologous to metal-binding, bacterial aminopeptidases. TET has a broad aminopeptidase activity and can process peptides of up to 30–35 amino acids in length. TET has a central cavity that is accessible through four narrow channels (<17 Å wide) and through four wider channels (21 Å wide). This architecture is different from that of all the proteolytic complexes described to date that are made up by rings or barrels with a single central channel and only two openings. PMID:11980710

Late Stage Azidation of Complex Molecules

PubMed Central

2016-01-01

Selective functionalization of complex scaffolds is a promising approach to alter the pharmacological profiles of natural products and their derivatives. We report the site-selective azidation of benzylic and aliphatic C–H bonds in complex molecules catalyzed by the combination of Fe(OAc)2 and a PyBox ligand. The same system also catalyzes the trifluoromethyl azidation of olefins to form derivatives of natural products containing both fluorine atoms and azides. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Azides obtained by functionalization of C–H and C=C bonds were converted to the corresponding amines, amides, and triazoles, thus providing a wide variety of nitrogen-containing complex molecules. PMID:27800554

40 CFR 61.141 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., manufacturing, or fabricating operation. This does not include condensed, uncombined water vapor. Waste... such as cliffs, lakes or other large bodies of water, deep and wide ravines, and mountains. Remoteness...

40 CFR 61.141 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., manufacturing, or fabricating operation. This does not include condensed, uncombined water vapor. Waste... such as cliffs, lakes or other large bodies of water, deep and wide ravines, and mountains. Remoteness...

40 CFR 61.141 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., manufacturing, or fabricating operation. This does not include condensed, uncombined water vapor. Waste... such as cliffs, lakes or other large bodies of water, deep and wide ravines, and mountains. Remoteness...

Meteorological Support at the Savanna River Site

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

Addis, Robert P.

2005-10-14

The Department of Energy (DOE) operates many nuclear facilities on large complexes across the United States in support of national defense. The operation of these many and varied facilities and processes require meteorological support for many purposes, including: for routine operations, to respond to severe weather events, such as lightning, tornadoes and hurricanes, to support the emergency response functions in the event of a release of materials to the environment, for engineering baseline and safety documentation, as well as hazards assessments etc. This paper describes a program of meteorological support to the Savannah River Site, a DOE complex located inmore » South Carolina.« less

Strain memory of 2D and 3D rigid inclusion populations in viscous flows - What is clast SPO telling us?

NASA Astrophysics Data System (ADS)

Stahr, Donald W.; Law, Richard D.

2014-11-01

We model the development of shape preferred orientation (SPO) of a large population of two- and three-dimensional (2D and 3D) rigid clasts suspended in a linear viscous matrix deformed by superposed steady and continuously non-steady plane strain flows to investigate the sensitivity of clasts to changing boundary conditions during a single or superposed deformation events. Resultant clast SPOs are compared to one developed by an identical initial population that experienced a steady flow history of constant kinematic vorticity and reached an identical finite strain state, allowing examination of SPO sensitivity to deformation path. Rotation paths of individual triaxial inclusions are complex, even for steady plane strain flow histories. It has been suggested that the 3D nature of the system renders predictions based on 2D models inadequate for applied clast-based kinematic vorticity gauges. We demonstrate that for a large population of clasts, simplification to a 2D model does provide a good approximation to the SPO predicted by full 3D analysis for steady and non-steady plane strain deformation paths. Predictions of shape fabric development from 2D models are not only qualitatively similar to the more complex 3D analysis, but they display the same limitations of techniques based on clast SPO commonly used as a quantitative kinematic vorticity gauge. Our model results from steady, superposed, and non-steady flow histories with a significant pure shearing component at a wide range of finite strain resemble predictions for an identical initial population that experienced a single steady simple shearing deformation. We conclude that individual 2D and 3D clasts respond instantaneously to changes in boundary conditions, however, in aggregate, the SPO of a population of rigid inclusions does not reflect the late-stage kinematics of deformation, nor is it an indicator of the unique 'mean' kinematic vorticity experienced by a deformed rock volume.

Office of the Chief Financial Officer Annual Report 2010

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

Fernandez, Jeffrey

In March, a review team consisting of CFOs from other national laboratories, industry, and members of the University of California Office of the President (UCOP) convened for three days to conduct a comprehensive peer review of the OCFO. This was the first time in almost a decade that the financial operations of the Laboratory had been reviewed. The Committee relayed their observations on our strengths, and their very thoughtful recommendations for improvement, which we are actively pursuing. These improvements, when implemented, will benefit the entire Laboratory for many years to come. The complete report is available on the OCFO websitemore » (www.lbl.gov/Workplace/CFO). In August, the senior management team of the OCFO participated in a strategic planning retreat. The purpose of the two and a half day exercise was, of course, to update our strategic plan, but instead of spending days developing a written document, we enlisted the expertise of a seasoned journalist who also happens to be a very talented graphic artist. He listened carefully to our ideas and committed them to a visual roadmap. All members of the OCFO, Business Managers, and the Laboratory Leadership Team reviewed this draft roadmap. By having a completely visual strategic plan that is posted widely throughout the OCFO, all employees can easily see and identify with the goals that we are all working towards. FY2010 was an extraordinary year. The Laboratory welcomed its seventh Director, Dr. Paul Alivisatos, who wasted no time communicating his vision and priorities for Berkeley Lab. They include five very ambitious initiatives: Carbon Cycle 2.0, The Next Generation Light Source, a Safe and Efficient Lab, Building Community, and Space. In response, the Office of the Chief Financial Officer (OCFO) developed twelve specific initiatives that align completely with these five priorities. We will be very focused on these in the coming fiscal year, but for now, let's review what happened in FY2010. FY2010 was a pivotal year for the Procurement and Property Department. A provision of the management contract that was signed fives years ago required us to achieve cost savings of $30M. I am proud to announce that this last fiscal year we reached that goal, in large part due to the implementation of eBuy, and the negotiation of strategic sourcing contracts. Our last wall-to-wall inventory exceeded all the Department of Energy's (DOE) national targets and DOE approved the LBNL property system unconditionally. Of the total inventory, 92.3% or 25,601 assets were accounted for using barcode scanning that made the inventory process much more efficient. The effective management of the American Recovery and Reinvestment Act (ARRA) funds was strengthened by the continued successful partnership that LBNL shares with our DOE Site Office. They provided authority, support and clarity to this very complex task. The Laboratory's ARRA Stimulus Committee played a critical role in assuring internal controls, compliance with DOE regulations and quality financial management. The LBNL Budget Officer led a DOE complex-wide effort to identify and share how various DOE facilities track and report ARRA-funded projects, share best practices, evaluate issues and discuss solutions. LBNL has been recognized as a leader in this process and will continue to share knowledge and best practices with other DOE laboratories. Continuous education of our staff as well as the greater Laboratory population was still a major focus of the OCFO. With the help of many OCFO senior managers and staff that acted as subject-matter experts, the Core Financial Management Program was completely re-engineered and resulted in a revised classroom and web-based curriculum that will be formally rolled out Lab-wide in early FY2011. The Office of Sponsored Projects and Industry Partnerships (OSPIP) led the effort to select and purchase four Click Commerce software modules for the LBNL electronic Scientific Research Administration (eSRA) project. In early FY2010, the implementation of the Institutional Review Board (IRB) module, responsible for the human subjects review process, began and should be completed in early FY2011. OSPIP also began implementation of the grants and contracts module and we expect an early go-live of 'Grants Express' in mid-FY2011 with a full completion date in FY2012. The peer review's most substantial recommendation for improvement involved the Laboratory's central financial systems. To quote: 'financial reporting system is outdated and inadequate. There is an inability to easily extract data; the field has little confidence in data; people spend more time mining data than analyzing data; requires field users to create & rely upon shadow systems; causes proliferation of program administrators and resource analysts. These issues impact the quality & execution of research; and the data warehouse lacks understanding & ownership.'« less

After Action Report: Advanced Test Reactor Complex 2015 Evaluated Drill October 6, 2015

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

Holmes, Forest Howard

2015-11-01

The Advanced Test Reactor (ATR) Complex, operated by Battelle Energy Alliance, LLC, at the Idaho National Laboratory (INL) conducted an evaluated drill on October 6, 2015, to allow the ATR Complex emergency response organization (ERO) to demonstrate the ability to respond to and mitigate an emergency by implementing the requirements of DOE O 151.1C, “Comprehensive Emergency Management System.”

If you take stand, how can you manage an ecosystem? The complex art of raising a forest.

Treesearch

Sally Duncan

2000-01-01

Managing whole ecosystem is a concept gaining considerable acceptance among forest managers throughout the Northwest, but it does not have a clear or simple definition. Terminology and definitions can be confusing. Forests are complex places, formed by complex processes, and the moment we try to simplify, we are likely to damage the healthy functioning of...

A More Complex Analysis Is Needed.

ERIC Educational Resources Information Center

Lickona, Thomas

1998-01-01

Alfie Kohn's critique of character education in the February 1997 "Kappan" is constructive but not complex enough to provide guidance for the field. Except for briefly describing the Child Development Project, Kohn omits books and articles advocating a comprehensive approach to character education and does not fairly represent some…

Microsurgical management of basilar artery apex aneurysms: a single surgeon's experience from Louisiana State University, Shreveport.

PubMed

Nanda, Anil; Sonig, Ashish; Banerjee, Anirban Deep; Javalkar, Vijay Kumar

2014-01-01

Basilar artery apex aneurysms continue to generate technical challenges and management controversy. Endovascular intervention is becoming the mainstay in the management of these formidable aneurysms, but it has limitations, especially with large/giant or wide neck basilar apex aneurysms. There is paucity of data in the available literature pertaining to the successful management of large/giant, wide neck, and calcified/thrombosed basilar apex aneurysms. We present our experience with consecutively operated complex basilar apex aneurysms so as to present the role of microneurosurgery as a viable management option for these aneurysms. Ours is a retrospective analysis of case-records for operated cases of basilar artery aneurysms spanning 18 years. Basilar apex aneurysms >10 cm, calcified or thrombosed, neck ≥4 mm posterior direction, and retro/subsellar were considered as complex anatomy aneurysms. Basilar apex aneurysms with favorable anatomy were included in the study as a reference group for statistical analysis. Patient demographics, complex features of aneurysms, clinical grade, and outcomes were analyzed. A total of 33 (53.2%) patients had complex anatomy: large (>10 mm) in eight (24.2%); giant aneurysms (>25 mm) in seven (21.2%); wide-neck in 22 (66.7%); and calcified/thrombosed morphology in five (15.1%). The mean age was 48.5 years, and 22 (66.67%) were women. All aneurysms were clipped by the use of various skull base approaches. A total of 71.9% of patients harboring complex aneurysm had good outcomes. If only unruptured and good grade complex aneurysms also are considered, then 86.9% (n = 20) patients had good outcomes. Statistically there was no significant difference in the outcomes of complex and noncomplex aneurysm. Although concerning, the management of large/giant, wide neck, and calcified/thrombosed aneurysms with microneurosurgery is still a competitive alternative to endovascular therapy. After careful selection of appropriate skull base approaches based on the complexity of the basilar apex aneurysm, microneurosurgery can achieve acceptable results. Copyright © 2014 Elsevier Inc. All rights reserved.

Fermi's Motion Produces a Study in Spirograph

NASA Image and Video Library

2017-12-08

The LAT's sensitivity to gamma rays is greatest in the center of its wide field of view and decreases toward the edge. LAT scientists regard the effective limit of the instrument's field of view to be 78.5 degrees (red circle) from its center. View a video of this here: bit.ly/Y2K4LN. Credit: NASA/DOE/Fermi LAT Collaboration ----- NASA's Fermi Gamma-ray Space Telescope orbits our planet every 95 minutes, building up increasingly deeper views of the universe with every circuit. Its wide-eyed Large Area Telescope (LAT) sweeps across the entire sky every three hours, capturing the highest-energy form of light -- gamma rays -- from sources across the universe. These range from supermassive black holes billions of light-years away to intriguing objects in our own galaxy, such as X-ray binaries, supernova remnants and pulsars. Now a Fermi scientist has transformed LAT data of a famous pulsar into a mesmerizing movie that visually encapsulates the spacecraft's complex motion. Click here to continue reading: 1.usa.gov/WhYwCU NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Cranial base morphology and temporal bone pneumatization in Asian Homo erectus.

PubMed

Balzeau, Antoine; Grimaud-Hervé, Dominique

2006-10-01

The external morphological features of the temporal bone are used frequently to determine taxonomic affinities of fossils of the genus Homo. Temporal bone pneumatization has been widely studied in great apes and in early hominids. However, this feature is rarely examined in the later hominids, particularly in Asian Homo erectus. We provide a comparative morphological and quantitative analysis of Asian Homo erectus from the sites of Ngandong, Sambungmacan, and Zhoukoudian, and of Neandertals and anatomically modern Homo sapiens in order to discuss causes and modalities of temporal bone pneumatization during hominid evolution. The evolution of temporal bone pneumatization in the genus Homo is more complex than previously described. Indeed, the Zhoukoudian fossils have a unique pattern of temporal bone pneumatization, whereas Ngandong and Sambungmacan fossils, as well as the Neandertals, more closely resemble the modern human pattern. Moreover, these Chinese fossils are characterized by a wide midvault and a relatively narrow occipital bone. Our results support the point of view that cell development does not play an active role in determining cranial base morphology. Instead, pneumatization is related to available space and to temporal bone morphology, and its development is related to correlated morphology and the relative disposition of the bones and cerebral lobes. Because variation in pneumatization is extensive within the same species, the phyletic implications of pneumatization are limited in the taxa considered here.

Objective definition of rosette shape variation using a combined computer vision and data mining approach.

PubMed

Camargo, Anyela; Papadopoulou, Dimitra; Spyropoulou, Zoi; Vlachonasios, Konstantinos; Doonan, John H; Gay, Alan P

2014-01-01

Computer-vision based measurements of phenotypic variation have implications for crop improvement and food security because they are intrinsically objective. It should be possible therefore to use such approaches to select robust genotypes. However, plants are morphologically complex and identification of meaningful traits from automatically acquired image data is not straightforward. Bespoke algorithms can be designed to capture and/or quantitate specific features but this approach is inflexible and is not generally applicable to a wide range of traits. In this paper, we have used industry-standard computer vision techniques to extract a wide range of features from images of genetically diverse Arabidopsis rosettes growing under non-stimulated conditions, and then used statistical analysis to identify those features that provide good discrimination between ecotypes. This analysis indicates that almost all the observed shape variation can be described by 5 principal components. We describe an easily implemented pipeline including image segmentation, feature extraction and statistical analysis. This pipeline provides a cost-effective and inherently scalable method to parameterise and analyse variation in rosette shape. The acquisition of images does not require any specialised equipment and the computer routines for image processing and data analysis have been implemented using open source software. Source code for data analysis is written using the R package. The equations to calculate image descriptors have been also provided.

Cementitious Barriers Partnership - FY2015 End-Year Report

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

Burns, H. H.; Flach, G. P.; Langton, C. A.

2015-09-17

The DOE-EM Office of Tank Waste Management Cementitious Barriers Partnership (CBP) is chartered with providing the technical basis for implementing cement-based waste forms and radioactive waste containment structures for long-term disposal. Therefore, the CBP ultimate purpose is to support progress in final treatment and disposal of legacy waste and closure of High-Level Waste (HLW) tanks in the DOE complex. This status report highlights the CBP 2015 Software and Experimental Program efforts and accomplishments that support DOE needs in environmental cleanup and waste disposal. DOE needs in this area include: Long-term performance predictions to provide credibility (i.e., a defensible technical basis)more » for regulator and DOE review and approvals, Facility flow sheet development/enhancements, and Conceptual designs for new disposal facilities. In 2015, the CBP developed a beta release of the CBP Software Toolbox – “Version 3.0”, which includes new STADIUM carbonation and damage models, a new SRNL module for estimating hydraulic properties and flow in fractured and intact cementitious materials, and a new LeachXS/ORCHESTRA (LXO) oxidation module. In addition, the STADIUM sulfate attack and chloride models have been improved as well as the LXO modules for sulfate attack, carbonation, constituent leaching, and percolation with radial diffusion (for leaching and transport in cracked cementitious materials). These STADIUM and LXO models are applicable to and can be used by both DOE and the Nuclear Regulatory Commission (NRC) end-users for service life prediction and long-term leaching evaluations of radioactive waste containment structures across the DOE complex.« less

Cosmic cookery: making a stereoscopic 3D animated movie

NASA Astrophysics Data System (ADS)

Holliman, Nick; Baugh, Carlton; Frenk, Carlos; Jenkins, Adrian; Froner, Barbara; Hassaine, Djamel; Helly, John; Metcalfe, Nigel; Okamoto, Takashi

2006-02-01

This paper describes our experience making a short stereoscopic movie visualizing the development of structure in the universe during the 13.7 billion years from the Big Bang to the present day. Aimed at a general audience for the Royal Society's 2005 Summer Science Exhibition, the movie illustrates how the latest cosmological theories based on dark matter and dark energy are capable of producing structures as complex as spiral galaxies and allows the viewer to directly compare observations from the real universe with theoretical results. 3D is an inherent feature of the cosmology data sets and stereoscopic visualization provides a natural way to present the images to the viewer, in addition to allowing researchers to visualize these vast, complex data sets. The presentation of the movie used passive, linearly polarized projection onto a 2m wide screen but it was also required to playback on a Sharp RD3D display and in anaglyph projection at venues without dedicated stereoscopic display equipment. Additionally lenticular prints were made from key images in the movie. We discuss the following technical challenges during the stereoscopic production process; 1) Controlling the depth presentation, 2) Editing the stereoscopic sequences, 3) Generating compressed movies in display specific formats. We conclude that the generation of high quality stereoscopic movie content using desktop tools and equipment is feasible. This does require careful quality control and manual intervention but we believe these overheads are worthwhile when presenting inherently 3D data as the result is significantly increased impact and better understanding of complex 3D scenes.

Sample Skewness as a Statistical Measurement of Neuronal Tuning Sharpness

PubMed Central

Samonds, Jason M.; Potetz, Brian R.; Lee, Tai Sing

2014-01-01

We propose using the statistical measurement of the sample skewness of the distribution of mean firing rates of a tuning curve to quantify sharpness of tuning. For some features, like binocular disparity, tuning curves are best described by relatively complex and sometimes diverse functions, making it difficult to quantify sharpness with a single function and parameter. Skewness provides a robust nonparametric measure of tuning curve sharpness that is invariant with respect to the mean and variance of the tuning curve and is straightforward to apply to a wide range of tuning, including simple orientation tuning curves and complex object tuning curves that often cannot even be described parametrically. Because skewness does not depend on a specific model or function of tuning, it is especially appealing to cases of sharpening where recurrent interactions among neurons produce sharper tuning curves that deviate in a complex manner from the feedforward function of tuning. Since tuning curves for all neurons are not typically well described by a single parametric function, this model independence additionally allows skewness to be applied to all recorded neurons, maximizing the statistical power of a set of data. We also compare skewness with other nonparametric measures of tuning curve sharpness and selectivity. Compared to these other nonparametric measures tested, skewness is best used for capturing the sharpness of multimodal tuning curves defined by narrow peaks (maximum) and broad valleys (minima). Finally, we provide a more formal definition of sharpness using a shape-based information gain measure and derive and show that skewness is correlated with this definition. PMID:24555451

A geostatistics-informed hierarchical sensitivity analysis method for complex groundwater flow and transport modeling: GEOSTATISTICAL SENSITIVITY ANALYSIS

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

Dai, Heng; Chen, Xingyuan; Ye, Ming

Sensitivity analysis is an important tool for quantifying uncertainty in the outputs of mathematical models, especially for complex systems with a high dimension of spatially correlated parameters. Variance-based global sensitivity analysis has gained popularity because it can quantify the relative contribution of uncertainty from different sources. However, its computational cost increases dramatically with the complexity of the considered model and the dimension of model parameters. In this study we developed a hierarchical sensitivity analysis method that (1) constructs an uncertainty hierarchy by analyzing the input uncertainty sources, and (2) accounts for the spatial correlation among parameters at each level ofmore » the hierarchy using geostatistical tools. The contribution of uncertainty source at each hierarchy level is measured by sensitivity indices calculated using the variance decomposition method. Using this methodology, we identified the most important uncertainty source for a dynamic groundwater flow and solute transport in model at the Department of Energy (DOE) Hanford site. The results indicate that boundary conditions and permeability field contribute the most uncertainty to the simulated head field and tracer plume, respectively. The relative contribution from each source varied spatially and temporally as driven by the dynamic interaction between groundwater and river water at the site. By using a geostatistical approach to reduce the number of realizations needed for the sensitivity analysis, the computational cost of implementing the developed method was reduced to a practically manageable level. The developed sensitivity analysis method is generally applicable to a wide range of hydrologic and environmental problems that deal with high-dimensional spatially-distributed parameters.« less

Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts

PubMed Central

2014-01-01

Background Polycomb group proteins form multicomponent complexes that are important for establishing lineage-specific patterns of gene expression. Mammalian cells encode multiple permutations of the prototypic Polycomb repressive complex 1 (PRC1) with little evidence for functional specialization. An aim of this study is to determine whether the multiple orthologs that are co-expressed in human fibroblasts act on different target genes and whether their genomic location changes during cellular senescence. Results Deep sequencing of chromatin immunoprecipitated with antibodies against CBX6, CBX7, CBX8, RING1 and RING2 reveals that the orthologs co-localize at multiple sites. PCR-based validation at representative loci suggests that a further six PRC1 proteins have similar binding patterns. Importantly, sequential chromatin immunoprecipitation with antibodies against different orthologs implies that multiple variants of PRC1 associate with the same DNA. At many loci, the binding profiles have a distinctive architecture that is preserved in two different types of fibroblast. Conversely, there are several hundred loci at which PRC1 binding is cell type-specific and, contrary to expectations, the presence of PRC1 does not necessarily equate with transcriptional silencing. Interestingly, the PRC1 binding profiles are preserved in senescent cells despite changes in gene expression. Conclusions The multiple permutations of PRC1 in human fibroblasts congregate at common rather than specific sites in the genome and with overlapping but distinctive binding profiles in different fibroblasts. The data imply that the effects of PRC1 complexes on gene expression are more subtle than simply repressing the loci at which they bind. PMID:24485159

Does aging impair first impression accuracy? Differentiating emotion recognition from complex social inferences.

PubMed

Krendl, Anne C; Rule, Nicholas O; Ambady, Nalini

2014-09-01

Young adults can be surprisingly accurate at making inferences about people from their faces. Although these first impressions have important consequences for both the perceiver and the target, it remains an open question whether first impression accuracy is preserved with age. Specifically, could age differences in impressions toward others stem from age-related deficits in accurately detecting complex social cues? Research on aging and impression formation suggests that young and older adults show relative consensus in their first impressions, but it is unknown whether they differ in accuracy. It has been widely shown that aging disrupts emotion recognition accuracy, and that these impairments may predict deficits in other social judgments, such as detecting deceit. However, it is unclear whether general impression formation accuracy (e.g., emotion recognition accuracy, detecting complex social cues) relies on similar or distinct mechanisms. It is important to examine this question to evaluate how, if at all, aging might affect overall accuracy. Here, we examined whether aging impaired first impression accuracy in predicting real-world outcomes and categorizing social group membership. Specifically, we studied whether emotion recognition accuracy and age-related cognitive decline (which has been implicated in exacerbating deficits in emotion recognition) predict first impression accuracy. Our results revealed that emotion recognition accuracy did not predict first impression accuracy, nor did age-related cognitive decline impair it. These findings suggest that domains of social perception outside of emotion recognition may rely on mechanisms that are relatively unimpaired by aging. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Investigation of a Complex Space-Time Metric to Describe Precognition of the Future

NASA Astrophysics Data System (ADS)

Rauscher, Elizabeth A.; Targ, Russell

2006-10-01

For more than 100 years scientists have attempted to determine the truth or falsity of claims that some people are able to describe and experience events or information blocked from ordinary perception. For the past 25 years, the authors of this paper - together with researchers in laboratories around the world — have carried out experiments in remote viewing. The evidence for this mode of perception, or direct knowing of distant events and objects, has convinced us of the validity of these claims. It has been widely observed that the accuracy and reliability of this sensory awareness does not diminish with either electromagnetic shielding, nor with increases in temporal or spatial separation between the percipient and the target to be described. Modern physics describes such a time-and-space independent connection between percipient and target as nonlocal. In this paper we present a geometrical model of space-time, which has already been extensively studied in the technical literature of mathematics and physics. This eight-dimensional metric is known as "complex Minkowski space," and has been shown to be consistent with our present understanding of the equations of Newton, Maxwell, Einstein, and Schrödinger. It also has the interesting property of allowing a connection of zero distance between points in the complex manifold, which appear to be separate from one another in ordinary observation. We propose a model that describes the major elements of experimental parapsychology, and at the same time is consistent with the present highly successful structure of modern physics.

Risk-prone individuals prefer the wrong options on a rat version of the Iowa Gambling Task.

PubMed

Rivalan, Marion; Ahmed, Serge H; Dellu-Hagedorn, Françoise

2009-10-15

Decision making in complex and conflicting situations, as measured in the widely used Iowa Gambling Task (IGT), can be profoundly impaired in psychiatric disorders, such as attention-deficit/hyperactivity disorder, drug addiction, and also in healthy individuals for whom immediate gratification prevails over long-term gain. The cognitive processes underlying these deficits are poorly understood, in part due to a lack of suitable animal models assessing complex decision making with good construct validity. We developed a rat gambling task analogous to the IGT that tracks, for the first time, the ongoing decision process within a single session in an operant cage. Rats could choose between various options. Disadvantageous options, as opposed to advantageous ones, offered bigger immediate food reward but were followed by longer, unpredictable penalties (time-out). The majority of rats can evaluate and deduce favorable options more or less rapidly according to task complexity, whereas others systematically choose disadvantageously. These interindividual differences are stable over time and do not depend on task difficulty or on the level of food restriction. We find that poor decision making does not result from a failure to acquire relevant information but from hypersensitivity to reward and higher risk taking in anxiogenic situations. These results suggest that rats, as well as human poor performers, share similar traits to those observed in decision-making related psychiatric disorders. These traits could constitute risk factors of developing such disorders. The rapid identification of poor decision makers using the rat gambling task should promote the discovery of the specific brain dysfunctions that cause maladapted decision making.

Pooled genome wide association detects association upstream of FCRL3 with Graves' disease.

PubMed

Khong, Jwu Jin; Burdon, Kathryn P; Lu, Yi; Laurie, Kate; Leonardos, Lefta; Baird, Paul N; Sahebjada, Srujana; Walsh, John P; Gajdatsy, Adam; Ebeling, Peter R; Hamblin, Peter Shane; Wong, Rosemary; Forehan, Simon P; Fourlanos, Spiros; Roberts, Anthony P; Doogue, Matthew; Selva, Dinesh; Montgomery, Grant W; Macgregor, Stuart; Craig, Jamie E

2016-11-18

Graves' disease is an autoimmune thyroid disease of complex inheritance. Multiple genetic susceptibility loci are thought to be involved in Graves' disease and it is therefore likely that these can be identified by genome wide association studies. This study aimed to determine if a genome wide association study, using a pooling methodology, could detect genomic loci associated with Graves' disease. Nineteen of the top ranking single nucleotide polymorphisms including HLA-DQA1 and C6orf10, were clustered within the Major Histo-compatibility Complex region on chromosome 6p21, with rs1613056 reaching genome wide significance (p = 5 × 10 -8 ). Technical validation of top ranking non-Major Histo-compatablity complex single nucleotide polymorphisms with individual genotyping in the discovery cohort revealed four single nucleotide polymorphisms with p ≤ 10 -4 . Rs17676303 on chromosome 1q23.1, located upstream of FCRL3, showed evidence of association with Graves' disease across the discovery, replication and combined cohorts. A second single nucleotide polymorphism rs9644119 downstream of DPYSL2 showed some evidence of association supported by finding in the replication cohort that warrants further study. Pooled genome wide association study identified a genetic variant upstream of FCRL3 as a susceptibility locus for Graves' disease in addition to those identified in the Major Histo-compatibility Complex. A second locus downstream of DPYSL2 is potentially a novel genetic variant in Graves' disease that requires further confirmation.

Does Central Coherence Relate to the Cognitive Performance of Children with Autism in Dynamic Assessments?

ERIC Educational Resources Information Center

Aljunied, Mariam; Frederickson, Norah

2013-01-01

Central coherence refers to an in-built propensity to form meaningful links over a wide range of stimuli and to generalize over as wide a range of contexts as possible. In children with autism this ability is diminished, and the impact of central coherence deficits in children with autism have previously been observed using static measures of…

Report of official foreign travel to France, June 7--20, 2000

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

J.D. Mason

2000-07-11

The Department of Energy (DOE) has moved rapidly toward electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Like most government agencies, DOE has expressed a preference for openly developed standards over proprietary designs promoted as ``standards'' by vendors. In particular, there is a preference for standards developed by organizations such as the International Organization for Standardization (ISO) and themore » American National Standards Institute (ANSI) that use open, public processes to develop their standards. Among the most widely adopted international standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), to which DOE long ago made a commitment. Besides the official commitment, which has resulted in several specialized projects, DOE makes heavy use of coding derived from SGML: Most documents on the WWW are coded in HTML (Hypertext Markup Language), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Adobe, IBM, Microsoft, Netscape, Oracle, and Sun, is promoting XML (eXtensible Markup Language), a class of SGML applications, for the future of the WWW and the basis for EC. In support of DOE's use of these standards, the authors has served since 1985 as Chairman of the international committee responsible for SGML and related standards, ISO/IEC JTC1/SC34 (SC34) and its predecessor organizations. During his June 2000 trip, he chaired the spring 2000 meeting of SC34 in Paris, France. He also attended a major conference on the use of SGML and XML and led a meeting of the International SGML/XML Users' Group (ISUG). In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there are several SGML-based projects at the Oak Ridge Y-12 Plant. The local project team developed an SGML-based publications system that has been used for several major reports at the Y-12 Plant and Oak Ridge National Laboratory (ORNL). SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at the Y-12 Plant and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). The Ferret system for automated classification analysis will use XML to structure its knowledge base. Supporting standards development allows DOE and the Y-12 plant the opportunity both to provide input into the process and to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML and related topics.« less

Learning Relational Ways of Being: What Globally Engaged Scholars Have Learned about Global Engagement and Sustainable Community Development

ERIC Educational Resources Information Center

Ulrich, Mary Eileen

2016-01-01

How does higher education contribute to finding workable and lasting solutions to complex social issues that face communities globally today? How does higher education contribute to global sustainable development goals? The scholarship of engagement encourages faculty, scholars, and students to work together with communities on solutions to…

A Complexity Approach to Evaluating National Scientific Systems through International Scientific Collaborations

ERIC Educational Resources Information Center

Zelnio, Ryan J.

2013-01-01

This dissertation seeks to contribute to a fuller understanding of how international scientific collaboration has affected national scientific systems. It does this by developing three methodological approaches grounded in social complexity theory and applying them to the evaluation of national scientific systems. The first methodology identifies…

Complexity as a Reflection of the Dimensionality of a Task.

ERIC Educational Resources Information Center

Spilsbury, Georgina

1992-01-01

The hypothesis that a task that increases in complexity (increasing its correlation with a central measure of intelligence) does so by increasing its dimensionality by tapping individual differences or another variable was supported by findings from 46 adults aged 20-70 years performing a mental counting task. (SLD)

Miscellaneous agreements between the U.S. Department of Energy and Federal, State, and local agencies.

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

Meincke, Carol L.

This document identifies and provides access to source documentation for the Site- Wide Environmental Impact Statement for Sandia National Laboratories/New Mexico. Specifically, it lists agreements between the U.S. Department of Energy (DOE), the National Nuclear Security Administration (NNSA), DOE/NNSA/Sandia Site Office (SSO), Sandia Corporation, and local and state government agencies, Department of Defense, Kirtland Air Force Base, and other federal agencies.

Andreev current for low temperature thermometry

NASA Astrophysics Data System (ADS)

Faivre, T.; Golubev, D. S.; Pekola, J. P.

2015-05-01

We demonstrate experimentally that disorder enhanced Andreev current in a tunnel junction between a normal metal and a superconductor provides a method to measure electronic temperature, specifically at temperatures below 200 mK when aluminum is used. This Andreev thermometer has some advantages over conventional quasiparticle thermometers: For instance, it does not conduct heat and its reading does not saturate until at lower temperatures. Another merit is that the responsivity is constant over a wide temperature range.

Does Pacman Have Teeth?

NASA Image and Video Library

2011-10-26

NASA Wide-field Infrared Survey Explorer observed the star-forming cloud NGC 281 in the constellation of Cassiopeia as it appears to be chomping through the cosmos, earning it the nickname the Pacman nebula.

Capsule review of the DOE research and development and field facilities

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

None

1980-09-01

A description is given of the roles of DOE's headquarters, field offices, major multiprogram laboratories, Energy Technology and Mining Technology Centers, and other government-owned, contractor-operated facilities, which are located in all regions of the US. Descriptions of DOE facilities are given for multiprogram laboratories (12); program-dedicated facilities (biomedical and environmental facilities-12, fossil energy facilities-7, fusion energy facility-1, nuclear development facilities-3, physical research facilities-4, safeguards facility-1, and solar facilities-2); and Production, Testing, and Fabrication Facilities (nuclear materials production facilities-5, weapon testing and fabrication complex-8). Three appendices list DOE field and project offices; DOE field facilities by state or territory, names, addresses,more » and telephone numbers; DOE R and D field facilities by type, contractor names, and names of directors. (MCW)« less

A single cognitive heuristic process meets the complexity of domain-specific moral heuristics.

PubMed

Dubljević, Veljko; Racine, Eric

2014-10-01

The inherence heuristic (a) offers modest insights into the complex nature of both the is-ought tension in moral reasoning and moral reasoning per se, and (b) does not reflect the complexity of domain-specific moral heuristics. Formal and general in nature, we contextualize the process described as "inherence heuristic" in a web of domain-specific heuristics (e.g., agent specific; action specific; consequences specific).

Complex Parts, Complex Data: Why You Need to Understand What Radiation Single Event Testing Data Does and Doesn't Show and the Implications Thereof

NASA Technical Reports Server (NTRS)

LaBel, Kenneth A.; Berg, Melanie D.

2015-01-01

Electronic parts (integrated circuits) have grown in complexity such that determining all failure modes and risks from single particle event testing is impossible. In this presentation, the authors will present why this is so and provide some realism on what this means. Its all about understanding actual risks and not making assumptions.

Evidence of complex contagion of information in social media: An experiment using Twitter bots.

PubMed

Mønsted, Bjarke; Sapieżyński, Piotr; Ferrara, Emilio; Lehmann, Sune

2017-01-01

It has recently become possible to study the dynamics of information diffusion in techno-social systems at scale, due to the emergence of online platforms, such as Twitter, with millions of users. One question that systematically recurs is whether information spreads according to simple or complex dynamics: does each exposure to a piece of information have an independent probability of a user adopting it (simple contagion), or does this probability depend instead on the number of sources of exposure, increasing above some threshold (complex contagion)? Most studies to date are observational and, therefore, unable to disentangle the effects of confounding factors such as social reinforcement, homophily, limited attention, or network community structure. Here we describe a novel controlled experiment that we performed on Twitter using 'social bots' deployed to carry out coordinated attempts at spreading information. We propose two Bayesian statistical models describing simple and complex contagion dynamics, and test the competing hypotheses. We provide experimental evidence that the complex contagion model describes the observed information diffusion behavior more accurately than simple contagion. Future applications of our results include more effective defenses against malicious propaganda campaigns on social media, improved marketing and advertisement strategies, and design of effective network intervention techniques.

Environmental Assessment for Selection and Operation of the Proposed Field Research Centers for the Natural and Accelerated Bioremediation Research (NABIR) Program

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

N /A

2000-04-18

The US Department of Energy (DOE) Office of Biological and Environmental Research (OBER), within the Office of Science (SC), proposes to add a Field Research Center (FRC) component to the existing Natural and Accelerated Bioremediation Research (NABIR) Program. The NABIR Program is a ten-year fundamental research program designed to increase the understanding of fundamental biogeochemical processes that would allow the use of bioremediation approaches for cleaning up DOE's contaminated legacy waste sites. An FRC would be integrated with the existing and future laboratory and field research and would provide a means of examining the fundamental biogeochemical processes that influence bioremediationmore » under controlled small-scale field conditions. The NABIR Program would continue to perform fundamental research that might lead to promising bioremediation technologies that could be demonstrated by other means in the future. For over 50 years, DOE and its predecessor agencies have been responsible for the research, design, and production of nuclear weapons, as well as other energy-related research and development efforts. DOE's weapons production and research activities generated hazardous, mixed, and radioactive waste products. Past disposal practices have led to the contamination of soils, sediments, and groundwater with complex and exotic mixtures of compounds. This contamination and its associated costs and risks represents a major concern to DOE and the public. The high costs, long duration, and technical challenges associated with remediating the subsurface contamination at DOE sites present a significant need for fundamental research in the biological, chemical, and physical sciences that will contribute to new and cost-effective solutions. One possible low-cost approach for remediating the subsurface contamination of DOE sites is through the use of a technology known as bioremediation. Bioremediation has been defined as the use of microorganisms to biodegrade or biotransform hazardous organic contaminants to environmentally safe levels in soils, subsurface materials, water, sludges, and residues.. While bioremediation technology is promising, DOE managers and non-DOE scientists have recognized that the fundamental scientific information needed to develop effective bioremediation technologies for cleanup of the legacy waste sites is lacking in many cases. DOE believes that field-based research is needed to realize the full potential of bioremediation. The Department of Energy faces a unique set of challenges associated with cleaning up waste at its former weapons production and research sites. These sites contain complex mixtures of contaminants in the subsurface, including radioactive compounds. In many cases, the fundamental field-based scientific information needed to develop safe and effective remediation and cleanup technologies is lacking. DOE needs fundamental research on the use of microorganisms and their products to assist DOE in the decontamination and cleanup of its legacy waste sites. The existing NABIR program to-date has focused on fundamental scientific research in the laboratory. Because subsurface hydrologic and geologic conditions at contaminated DOE sites cannot easily be duplicated in a laboratory, however, the DOE needs a field component to permit existing and future laboratory research results to be field-tested on a small scale in a controlled outdoor setting. Such field-testing needs to be conducted under actual legacy waste field conditions representative of those that DOE is most in need of remediating. Ideally, these field conditions should be as representative as practicable of the types of subsurface contamination conditions that resulted from legacy wastes from the nuclear weapons program activities. They should also be representative of the types of hydrologic and geologic conditions that exist across the DOE complex.« less

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology.

PubMed

Sudhir, Putty-Reddy; Chen, Chung-Hsuan

2016-03-22

A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology

PubMed Central

Sudhir, Putty-Reddy; Chen, Chung-Hsuan

2016-01-01

A protein complex consists of two or more proteins that are linked together through protein–protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples. PMID:27011181

OSH technical reference manual

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

Not Available

1993-11-01

In an evaluation of the Department of Energy (DOE) Occupational Safety and Health programs for government-owned contractor-operated (GOCO) activities, the Department of Labor`s Occupational Safety and Health Administration (OSHA) recommended a technical information exchange program. The intent was to share written safety and health programs, plans, training manuals, and materials within the entire DOE community. The OSH Technical Reference (OTR) helps support the secretary`s response to the OSHA finding by providing a one-stop resource and referral for technical information that relates to safe operations and practice. It also serves as a technical information exchange tool to reference DOE-wide materials pertinentmore » to specific safety topics and, with some modification, as a training aid. The OTR bridges the gap between general safety documents and very specific requirements documents. It is tailored to the DOE community and incorporates DOE field experience.« less

Graphs, matrices, and the GraphBLAS: Seven good reasons

DOE PAGES

Kepner, Jeremy; Bader, David; Buluç, Aydın; ...

2015-01-01

The analysis of graphs has become increasingly important to a wide range of applications. Graph analysis presents a number of unique challenges in the areas of (1) software complexity, (2) data complexity, (3) security, (4) mathematical complexity, (5) theoretical analysis, (6) serial performance, and (7) parallel performance. Implementing graph algorithms using matrix-based approaches provides a number of promising solutions to these challenges. The GraphBLAS standard (istcbigdata.org/GraphBlas) is being developed to bring the potential of matrix based graph algorithms to the broadest possible audience. The GraphBLAS mathematically defines a core set of matrix-based graph operations that can be used to implementmore » a wide class of graph algorithms in a wide range of programming environments. This paper provides an introduction to the GraphBLAS and describes how the GraphBLAS can be used to address many of the challenges associated with analysis of graphs.« less

Extended hierarchical solvent perturbations from curved surfaces of mesoporous silica particles in a deep eutectic solvent.

PubMed

Hammons, Joshua A; Zhang, Fan; Ilavsky, Jan

2018-06-15

Many applications of deep eutectic solvents (DES) rely on exploitation of their unique yet complex liquid structures. Due to the ionic nature of the DES components, their diffuse structures are perturbed in the presence of a charged surface. We hypothesize that it is possible to perturb the bulk DES structure far (>100 nm) from a curved, charged surface with mesoscopic dimensions. We performed in situ, synchrotron-based ultra-small angle X-ray scattering (USAXS) experiments to study the solvent distribution near the surface of charged mesoporous silica particles (MPS) (≈0.5 µm in diameter) suspended in both water and a common type of DES (1:2 choline Cl-:ethylene glycol). A careful USAXS analysis reveals that the perturbation of electron density distribution within the DES extends ≈1 μm beyond the particle surface, and that this perturbation can be manipulated by the addition of salt ions (AgCl). The concentration of the pore-filling fluid is greatly reduced in the DES. Notably, we extracted the real-space structures of these fluctuations from the USAXS data using a simulated annealing approach that does not require a priori knowledge about the scattering form factor, and can be generalized to a wide range of complex small-angle scattering problems. Copyright © 2018 Elsevier Inc. All rights reserved.

Ordering Unstructured Meshes for Sparse Matrix Computations on Leading Parallel Systems

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Li, Xiaoye; Heber, Gerd; Biswas, Rupak

2000-01-01

The ability of computers to solve hitherto intractable problems and simulate complex processes using mathematical models makes them an indispensable part of modern science and engineering. Computer simulations of large-scale realistic applications usually require solving a set of non-linear partial differential equations (PDES) over a finite region. For example, one thrust area in the DOE Grand Challenge projects is to design future accelerators such as the SpaHation Neutron Source (SNS). Our colleagues at SLAC need to model complex RFQ cavities with large aspect ratios. Unstructured grids are currently used to resolve the small features in a large computational domain; dynamic mesh adaptation will be added in the future for additional efficiency. The PDEs for electromagnetics are discretized by the FEM method, which leads to a generalized eigenvalue problem Kx = AMx, where K and M are the stiffness and mass matrices, and are very sparse. In a typical cavity model, the number of degrees of freedom is about one million. For such large eigenproblems, direct solution techniques quickly reach the memory limits. Instead, the most widely-used methods are Krylov subspace methods, such as Lanczos or Jacobi-Davidson. In all the Krylov-based algorithms, sparse matrix-vector multiplication (SPMV) must be performed repeatedly. Therefore, the efficiency of SPMV usually determines the eigensolver speed. SPMV is also one of the most heavily used kernels in large-scale numerical simulations.

GRB 081029: A Gamma-Ray Burst with a Multi-Component Afterglow

NASA Technical Reports Server (NTRS)

Holland, Stephen T.; DePasquale, Massimiliano; Mao, Jirong; Sakamoto, Taka; Shady, Patricia; Covino, Stefano; Yi-Zhong, Fan; Zhi-Ping, Jin; D'Avanzo, Paolo; Antonelli, Angelo;

Quantitative analysis of periodontal pathogens by ELISA and real-time polymerase chain reaction.

PubMed

Hamlet, Stephen M

2010-01-01

The development of analytical methods enabling the accurate identification and enumeration of bacterial species colonizing the oral cavity has led to the identification of a small number of bacterial pathogens that are major factors in the etiology of periodontal disease. Further, these methods also underpin more recent epidemiological analyses of the impact of periodontal disease on general health. Given the complex milieu of over 700 species of microorganisms known to exist within the complex biofilms found in the oral cavity, the identification and enumeration of oral periodontopathogens has not been an easy task. In recent years however, some of the intrinsic limitations of the more traditional microbiological analyses previously used have been overcome with the advent of immunological and molecular analytical methods. Of the plethora of methodologies reported in the literature, the enzyme-linked immunosorbent assay (ELISA), which combines the specificity of antibody with the sensitivity of simple enzyme assays and the polymerase chain reaction (PCR), has been widely utilized in both laboratory and clinical applications. Although conventional PCR does not allow quantitation of the target organism, real-time PCR (rtPCR) has the ability to detect amplicons as they accumulate in "real time" allowing subsequent quantitation. These methods enable the accurate quantitation of as few as 10(2) (using rtPCR) to 10(4) (using ELISA) periodontopathogens in dental plaque samples.

Double stars with wide separations in the AGK3 - II. The wide binaries and the multiple systems*

NASA Astrophysics Data System (ADS)

Halbwachs, J.-L.; Mayor, M.; Udry, S.

2017-02-01

A large observation programme was carried out to measure the radial velocities of the components of a selection of common proper motion (CPM) stars to select the physical binaries. 80 wide binaries (WBs) were detected, and 39 optical pairs were identified. By adding CPM stars with separations close enough to be almost certain that they are physical, a bias-controlled sample of 116 WBs was obtained, and used to derive the distribution of separations from 100 to 30 000 au. The distribution obtained does not match the log-constant distribution, but agrees with the log-normal distribution. The spectroscopic binaries detected among the WB components were used to derive statistical information about the multiple systems. The close binaries in WBs seem to be like those detected in other field stars. As for the WBs, they seem to obey the log-normal distribution of periods. The number of quadruple systems agrees with the no correlation hypothesis; this indicates that an environment conducive to the formation of WBs does not favour the formation of subsystems with periods shorter than 10 yr.

Patient assessment systems using the World Wide Web.

PubMed

Kohane, I S

1997-02-01

Of the major issues in developing a Web patient assessment system, I have emphasized two main points. First, the World Wide Web can provide substantial leverage in the development of online patient assessment systems. Second, although the existence of Internet technologies does not alter the need to resolve issues that preceded their arrival, current trends suggest that in the home and the office, patient assessment systems will increasingly employ Internet technologies.

Novel Design of Iridium Phosphors with Pyridinylphosphinate Ligands for High-Efficiency Blue Organic Light-emitting Diodes

PubMed Central

Wu, Zheng-Guang; Jing, Yi-Ming; Lu, Guang-Zhao; Zhou, Jie; Zheng, You-Xuan; Zhou, Liang; Wang, Yi; Pan, Yi

2016-01-01

Due to the high quantum efficiency and wide scope of emission colors, iridium (Ir) (III) complexes have been widely applied as guest materials for OLEDs (organic light-emitting diodes). Contrary to well-developed Ir(III)-based red and green phosphorescent complexes, the efficient blue emitters are rare reported. Like the development of the LED, the absence of efficient and stable blue materials hinders the widely practical application of the OLEDs. Inspired by this, we designed two novel ancillary ligands of phenyl(pyridin-2-yl)phosphinate (ppp) and dipyridinylphosphinate (dpp) for efficient blue phosphorescent iridium complexes (dfppy)2Ir(ppp) and (dfppy)2Ir(dpp) (dfppy = 2-(2,4-difluorophenyl)pyridine) with good electron transport property. The devices using the new iridium phosphors display excellent electroluminescence (EL) performances with a peak current efficiency of 58.78 cd/A, a maximum external quantum efficiency of 28.3%, a peak power efficiency of 52.74 lm/W and negligible efficiency roll-off ratios. The results demonstrated that iridium complexes with pyridinylphosphinate ligands are potential blue phosphorescent materials for OLEDs. PMID:27929124

Designing a Feasibility Study: A Starting Point for Considering New Management Initiatives for Working Parents.

ERIC Educational Resources Information Center

Friedman, Dana E.

This brief paper was prepared as a starting point for employers considering the adoption of a new management initiative for working parents. It is not an exhaustive outline of all considerations in the decision-making process, nor does it provide solutions to all the known pitfalls. It does, however, suggest the potential scope and complexity of…

Technical basis, supporting information, and strategy for development and implementation of DOE policy for natural phenomena hazards

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

Murray, R.C.

1991-09-01

Policy for addressing natural phenomenon comprises a hierarchy of interrelated documents. The top level of policy is contained in the code of Federal Regulations which establishes the framework and intent to ensure overall safety of DOE facilities when subjected to the effects of natural phenomena. The natural phenomena to be considered include earthquakes and tsunami, winds, hurricanes and tornadoes, floods, volcano effects and seiches. Natural phenomena criteria have been established for design of new facilities; evaluation of existing facilities; additions, modifications, and upgrades to existing facilities; and evaluation criteria for new or existing sites. Steps needed to implement these fourmore » general criteria are described. The intent of these criteria is to identify WHAT needs to be done to ensure adequate protection from natural phenomena. The commentary provides discussion of WHY this is needed for DOE facilities within the complex. Implementing procedures identifying HOW to carry out these criteria are next identified. Finally, short and long term tasks needed to identify the implementing procedure are tabulated. There is an overall need for consistency throughout the DOE complex related to natural phenomena including consistent terminology, policy, and implementation. 1 fig, 6 tabs.« less

Remedial Action Assessment System (RAAS): A computer-based methodology for conducting feasibility studies

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

Buelt, J.L.; Stottlemyre, J.A.; White, M.K.

1991-09-01

Because of the great complexity and number of potential waste sites facing the US Department of Energy (DOE) for potential cleanup, the DOE is supporting the development of a computer-based methodology to streamline the remedial investigations/feasibility study process required for DOE operable units. DOE operable units are generally more complex in nature because of the existence of multiple waste sites within many of the operable units and the presence of mixed radioactive and hazardous chemical wastes. Consequently, Pacific Northwest Laboratory (PNL) is developing the Remedial Action Assessment System (RAAS), which is aimed at screening, linking, and evaluating establishment technology processmore » options in support of conducting feasibility studies under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA). It is also intended to do the same in support of corrective measures studies requires by the Resource Conservation and Recovery Act (RCRA). This paper presents the characteristics of two RAAS prototypes currently being developed. These include the RAAS Technology Information System, which accesses information on technologies in a graphical and tabular manner, and the main RAAS methodology, which screens, links, and evaluates remedial technologies. 4 refs., 3 figs., 1 tab.« less

Remedial Action Assessment System (RAAS): A computer-based methodology for conducting feasibility studies

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

Buelt, J.L.; Stottlemyre, J.A.; White, M.K.

1991-02-01

Because of the great complexity and number of potential waste sites facing the US Department of Energy (DOE) for potential cleanup, the DOE is supporting the development of a computer-based methodology to streamline the remedial investigation/feasibility study process required for DOE operable units. DOE operable units are generally more complex in nature because of the existence of multiple waste sites within many of the operable units and the presence of mixed radioactive and hazardous chemical wastes. Consequently, Pacific Northwest Laboratory (PNL) is developing the Remedial Action Assessment System (RAAS), which is aimed at screening, linking, and evaluating established technology processmore » options in support of conducting feasibility studies under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA). It is also intended to do the same in support of corrective measures studies required by the Resource Conservation and Recovery Act (RCRA). This paper presents the characteristics of two RAAS prototypes currently being developed. These include the RAAS Technology Information System, which accesses information on technologies in a graphical and tabular manner, and the main RAAS methodology, which screens, links, and evaluates remedial technologies. 4 refs., 3 figs., 1 tab.« less

Purification and characterisation of the fission yeast Ndc80 complex.

PubMed

Matsuo, Yuzy; Maurer, Sebastian P; Surrey, Thomas; Toda, Takashi

2017-07-01

The Ndc80 complex is a conserved outer kinetochore protein complex consisting of Ndc80 (Hec1), Nuf2, Spc24 and Spc25. This complex comprises a major, if not the sole, platform with which the plus ends of the spindle microtubules directly interact. In fission yeast, several studies indicate that multiple microtubule-associated proteins including the Dis1/chTOG microtubule polymerase and the Mal3/EB1 microtubule plus-end tracking protein directly or indirectly bind Ndc80, thereby ensuring stable kinetochore-microtubule attachment. However, the purification of the Ndc80 complex from this yeast has not been achieved, which hampers the in-depth investigation as to how the outer kinetochore attaches to the plus end of the spindle microtubule. Here we report the two-step purification of the fission yeast Ndc80 holo complex from bacteria. First, we purified separately two sub-complexes consisting of Ndc80-Nuf2 and Spc24-Spc25. Then, these two sub-complexes were mixed and applied to size-exclusion chromatography. The reconstituted Ndc80 holo complex is composed of four subunits with equal stoichiometry. The complex possesses microtubule-binding activity, and Total Internal Reflection Fluorescence (TIRF)-microscopy assays show that the complex binds the microtubule lattice. Interestingly, unlike the human complex, the fission yeast complex does not track depolymerising microtubule ends. Further analysis shows that under physiological ionic conditions, the Ndc80 holo complex does not detectably bind Dis1, but instead it interacts with Mal3/EB1, by which the Ndc80 complex tracks the growing microtubule plus end. This result substantiates the notion that the Ndc80 complex plays a crucial role in establishment of the dynamic kinetochore-microtubule interface by cooperating with chTOG and EB1. Copyright © 2017 The Francis Crick Institute. Published by Elsevier Inc. All rights reserved.

Nukes in the Post-Cold War Era A View of the World from Inside the US Nuclear Weapons Program

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

Wood, Blake Philip

Why do we have nuclear weapons? What is in the US stockpile, how is it deployed and controlled, and how it has changed over the years? What is in the “nuclear weapons complex” and what does each lab and plant do? How do the DOE/NNSA Design Labs interact with the Intelligence Community? How does the US stockpile, NW complex, and NW policy compare with those of other countries? What is easy and hard about designing nuclear weapons?

Tiger Team Assessment of the Princeton Plasma Physics Laboratory

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

Not Available

1991-03-01

This report documents the Tiger Team Assessment of the Princeton Plasma Physics Laboratory (PPPL) conducted from February 11 to March 12, 1991. The PPPL is operated for the US Department of Energy (DOE) by Princeton University. The assessment was conducted under the auspices of the Headquarters, DOE, Office of Special Projects which is under the Assistant Secretary for Environment, Safety and Health. Activities of the Tiger Team Assessment resulted in identification of compliance findings or concerns and noteworthy practices and an analysis as to the root causes for noncompliance. The PPPL Tiger Team Assessment is one component of a larger,more » comprehensive DOE Tiger Team Assessment program for DOE facilities that will eventually encompass over 100 of the Department's operating facilities. The objective of the initiative is to provide the Secretary with information on the compliance status of DOE facilities with regard to ES H requirements; root causes for noncompliances; adequacy of DOE and contractor ES H management programs; response actions to address the identified problems areas; and DOE-wide ES H compliance trends and root causes.« less

Appreciating the Complexity of Project Management Execution: Using Simulation in the Classroom

ERIC Educational Resources Information Center

Hartman, Nathan S.; Watts, Charles A.; Treleven, Mark D.

2013-01-01

As the popularity and importance of project management increase, so does the need for well-prepared project managers. This article discusses our experiences using a project management simulation in undergraduate and MBA classes to help students better grasp the complexity of project management. This approach gives students hands-on experience with…

Creating a Shared Context for Value-Based Collaboration & Decision Making

ERIC Educational Resources Information Center

Guckert, Donald J.; King, Jeri Ripley

2012-01-01

How does one succinctly communicate the breadth, complexity, and forward-thinking approaches that are necessary for facilities management organizations to operate in today's complex and ever-changing environment? Recently, the authors were asked to do just that at the University of Iowa Department of Facilities Management. In this article, they…

Does the Detection of Misunderstanding Lead to Its Revision?

ERIC Educational Resources Information Center

García-Rodicio, Héctor; Sánchez, Emilio

2014-01-01

When dealing with complex conceptual systems, low-prior- knowledge learners develop fragmentary and incorrect understanding. To learn complex topics deeply, these learners have to (a) monitor understanding to detect flaws and (b) generate explanations to revise and repair the flaws. In this research we explored if the detection of a flaw in…

School Nurses and Care Coordination for Children with Complex Needs: An Integrative Review

ERIC Educational Resources Information Center

McClanahan, Rachel; Weismuller, Penny C.

2015-01-01

Health care for students with chronic needs can be complex and specialized, resulting in fragmentation, duplication, and inefficiencies. Students who miss school due to chronic conditions lose valuable educational exposure that contributes to academic success. As health-related disabilities increase in prevalence so does the need for the…

How does complex terrain influence responses of carbon and water cycle processes to climate variability and climate change?

EPA Science Inventory

We are pursuing the ambitious goal of understanding how complex terrain influences the responses of carbon and water cycle processes to climate variability and climate change. Our studies take place in H.J. Andrews Experimental Forest, an LTER (Long Term Ecological Research) site...

CYLD Deubiquitinates RIP1 in the TNFα-Induced Necrosome to Facilitate Kinase Activation and Programmed Necrosis

PubMed Central

Moquin, David M.; McQuade, Thomas; Chan, Francis Ka-Ming

2013-01-01

Background Necroptosis/programmed necrosis is initiated by a macro-molecular protein complex termed the necrosome. Receptor interacting protein kinase 1 (RIPK1/RIP1) and RIP3 are key components of the necrosome. TNFα is a prototypic inducer of necrosome activation, and it is widely believed that deubiquitination of RIP1 at the TNFR-1 signaling complex precedes transition of RIP1 into the cytosol where it forms the RIP1-RIP3 necrosome. Cylindromatosis (CYLD) is believed to promote programmed necrosis by facilitating RIP1 deubiquitination at this membrane receptor complex. Methodology/Principal Findings We demonstrate that RIP1 is indeed the primary target of CYLD in TNFα-induced programmed necrosis. We observed that CYLD does not regulate RIP1 ubiquitination at the TNF receptor. TNF and zVAD-induced programmed necrosis was highly attenuated in CYLD-/- cells. However, in the presence of cycloheximide or SMAC mimetics, programmed necrosis was only moderately reduced in CYLD-/- cells. Under the latter conditions, RIP1-RIP3 necrosome formation is only delayed, but not abolished in CYLD-/- cells. We further demonstrate that RIP1 within the NP-40 insoluble necrosome is ubiquitinated and that CYLD regulates RIP1 ubiquitination in this compartment. Hence, RIP1 ubiquitination in this late-forming complex is greatly increased in CYLD-/- cells. Increased RIP1 ubiquitination impairs RIP1 and RIP3 phosphorylation, a signature of kinase activation. Conclusions/Significance Our results show that CYLD regulates RIP1 ubiquitination in the TNFα-induced necrosome, but not in the TNFR-1 signaling complex. In cells sensitized to programmed necrosis with SMAC mimetics, CYLD is not essential for necrosome assembly. Since SMAC mimetics induces the loss of the E3 ligases cIAP1 and cIAP2, reduced RIP1 ubiquitination could lead to reduced requirement for CYLD to remove ubiquitin chains from RIP1 in the TNFR-1 complex. As increased RIP1 ubiquitination in the necrosome correlates with impaired RIP1 and RIP3 phosphorylation and function, these results suggest that CYLD controls RIP1 kinase activity during necrosome assembly. PMID:24098568

Competition and facilitation between a native and a domestic herbivore: trade-offs between forage quantity and quality.

PubMed

Augustine, David J; Springer, Tim L

2013-06-01

Potential competition between native and domestic herbivores is a major consideration influencing the management and conservation of native herbivores in rangeland ecosystems. In grasslands of the North American Great Plains, black-tailed prairie dogs (Cynomys ludovicianus) are widely viewed as competitors with cattle but are also important for biodiversity conservation due to their role in creating habitat for other native species. We examined spatiotemporal variation in prairie dog effects on growing-season forage quality and quantity using measurements from three colony complexes in Colorado and South Dakota and from a previous study of a fourth complex in Montana. At two complexes experiencing below-average precipitation, forage availability both on and off colonies was so low (12-54 g/m2) that daily forage intake rates of cattle were likely constrained by instantaneous intake rates and daily foraging time. Under these dry conditions, prairie dogs (1) substantially reduced forage availability, thus further limiting cattle daily intake rates, and (2) had either no or a small positive effect on forage digestibility. Under such conditions, prairie dogs are likely to compete with cattle in direct proportion to their abundance. For two complexes experiencing above-average precipitation, forage quantity on and off colonies (77-208 g/m2) was sufficient for daily forage intake of cattle to be limited by digestion rather than instantaneous forage intake. At one complex where prairie dogs enhanced forage digestibility and [N] while having no effect on forage quantity, prairie dogs are predicted to facilitate cattle mass gains regardless of prairie dog abundance. At the second complex where prairie dogs enhanced digestibility and [N] but reduced forage quantity, effects on cattle can vary from competition to facilitation depending on prairie dog abundance. Our findings show that the high spatiotemporal variation in vegetation dynamics characteristic of semiarid grasslands is paralleled by variability in the magnitude of competition between native and domestic grazers. Competitive interactions evident during dry periods may be partially or wholly offset by facilitation during periods when forage digestibility is enhanced and forage quantity does not limit the daily intake rate of cattle.

Preparation, characterization, and thermal stability of β-cyclodextrin/soybean lecithin inclusion complex.

PubMed

Wang, Xinge; Luo, Zhigang; Xiao, Zhigang

2014-01-30

β-Cyclodextrin (β-CD), which is widely used to increase the stability, solubility, and bioavailability of guests, can form host-guest inclusion complexes with a wide variety of organic molecules. In this study the β-CD/soybean lecithin inclusion complex was prepared. The effect of reaction parameters such as reaction temperature, reaction time and the molar ratio of β-CD/soybean lecithin on inclusion ratio were studied. The inclusion ratio of the product prepared under the optimal conditions of β-CD/soybean lecithin molar ratio 2:1, reaction temperature 60°C reaction time 2h was 40.2%. The results of UV-vis, DSC, XRD and FT-IR spectrum indicated the formation of inclusion complex. The thermal stability experiment indicated that the thermal stability of soybean lecithin in inclusion complex was significantly improved compared with free soybean lecithin. Copyright © 2013 Elsevier Ltd. All rights reserved.

Transition and closeout of the Fernald Closure Project

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

Bilson, H.E.; Terry, T.; Reising, J.

The U.S. Department of Energy (DOE) and Fluor Fernald have completed the majority of the cleanup of the Fernald Site. The over 1,000 acre complex for processing uranium has been demolished and soil contamination has been remediated. With acres of wetlands and prairies replacing the buildings and waste pits. At the end of the project the focus shifted to developing demonstrating the completion of the project and the contract, as well as ensuring a smooth transition of the facility from the DOE's Environmental Management (EM) Program to the DOE's Legacy Management (LM) Program. Working with the DOE, each portion ofmore » the closure contract was examined for specific closure definition. From this negotiation effort the Comprehensive Exit and Transition Plan (CE/T Plan) was written. The CE/T Plan is intended to assist DOE in the analysis that the site is ready for transfer into long-term stewardship (LTS) (also referred to as legacy management) and that Fluor Fernald, Inc. has satisfactorily completed the closure contract statement of work elements. Following the Lessons Learned from the closure of the Rocky Flats Site, the DOE's Legacy Management Program created a matrix of Transition Elements required to ensure adequate information was in place to allow the new prime contractor to perform the Legacy Management scope of work. The transition plan included over 1,000 elements broken down into functional areas and relied on specific Fernald Responsibility Transition Packages (RTPs) for detailed transition actions. The template for Closure and Transition Planning used at the Fernald Site was developed using the best Lessons Learned from across the DOE Complex. The template could be used for other sites, and lessons learned from this closure and transition will be appropriate for all closure projects. (authors)« less

Antifungal Activity of Eupolauridine and Its Action on DNA Topoisomerases

PubMed Central

Khan, Shabana I.; Nimrod, Alison C.; Mehrpooya, Mohammed; Nitiss, John L.; Walker, Larry A.; Clark, Alice M.

2002-01-01

The azafluoranthene alkaloid eupolauridine has previously been shown to have in vitro antifungal activity and selective inhibition of fungal topoisomerase I. The present study was undertaken to examine further its selectivity and mode of action. Eupolauridine completely inhibits the DNA relaxation activity of purified fungal topoisomerase I at 50 μg/ml, but it does not stabilize the cleavage complex of either human or fungal topoisomerase I. Cleavage complex stabilization is the mode of action of topoisomerase I targeting drugs of the camptothecin family. Also, unlike camptothecin, eupolauridine does not cause significant cytotoxicity in mammalian cells. To determine if the inhibition of topoisomerase I is the principal mode of antifungal action of eupolauridine, Saccharomyces cerevisiae strains with alterations in topoisomerase genes were used in clonogenic assays. The antifungal activity of eupolauridine was not diminished in the absence of topoisomerase I; rather, the cells lacking the enzyme were more sensitive to the drug. Cell-killing activity of eupolauridine was also more pronounced in cells that overexpressed topoisomerase II. In vitro assays with the purified yeast enzyme confirmed that eupolauridine stabilized topoisomerase II covalent complexes. These results indicate that a major target for fungal cell killing by eupolauridine is DNA topoisomerase II rather than topoisomerase I, but does not exclude the possibility that the drug also acts against other targets. PMID:12019091

Antifungal activity of eupolauridine and its action on DNA topoisomerases.

PubMed

Khan, Shabana I; Nimrod, Alison C; Mehrpooya, Mohammed; Nitiss, John L; Walker, Larry A; Clark, Alice M

2002-06-01

The azafluoranthene alkaloid eupolauridine has previously been shown to have in vitro antifungal activity and selective inhibition of fungal topoisomerase I. The present study was undertaken to examine further its selectivity and mode of action. Eupolauridine completely inhibits the DNA relaxation activity of purified fungal topoisomerase I at 50 microg/ml, but it does not stabilize the cleavage complex of either human or fungal topoisomerase I. Cleavage complex stabilization is the mode of action of topoisomerase I targeting drugs of the camptothecin family. Also, unlike camptothecin, eupolauridine does not cause significant cytotoxicity in mammalian cells. To determine if the inhibition of topoisomerase I is the principal mode of antifungal action of eupolauridine, Saccharomyces cerevisiae strains with alterations in topoisomerase genes were used in clonogenic assays. The antifungal activity of eupolauridine was not diminished in the absence of topoisomerase I; rather, the cells lacking the enzyme were more sensitive to the drug. Cell-killing activity of eupolauridine was also more pronounced in cells that overexpressed topoisomerase II. In vitro assays with the purified yeast enzyme confirmed that eupolauridine stabilized topoisomerase II covalent complexes. These results indicate that a major target for fungal cell killing by eupolauridine is DNA topoisomerase II rather than topoisomerase I, but does not exclude the possibility that the drug also acts against other targets.

USSR and Eastern Europe Scientific Abstracts, Cybernetics, Computers and Automation Technology, Number 35

DTIC Science & Technology

1978-09-12

the population. Only a socialist, planned economy can cope with such problems. However, the in- creasing complexity of the tasks faced’ by...the development of systems allowing man-machine dialogue does not decrease, but rather increase the complexity of the systems involved, simply...shifting the complexity to another sphere, where it is invisible to the human utilizing the system. Figures 5; refer- ences 3: 2 Russian, 1 Western

Department of Energy Air Emissions Annual Report Oak Ridge Reservation, Oak Ridge, Tennessee 40 Code of Federal Regulations (CFR) 61, Subpart H Calendar Year 2016

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

Martin, Richard

As defined in the preamble of the final rule, the entire DOE facility on the Oak Ridge Reservation (ORR) must meet the 10 mrem/yr ED standard.1 In other words, the combined ED from all radiological air emission sources from Y-12 National Security Complex (Y-12 Complex), Oak Ridge National Laboratory (ORNL), East Tennessee Technology Park (ETTP), Oak Ridge Institute for Science and Education (ORISE) and any other DOE operation on the reservation must meet the 10 mrem/yr standard. Compliance with the standard is demonstrated through emission sampling, monitoring, calculations and radiation dose modeling in accordance with approved EPA methodologies and procedures.more » DOE estimates the ED to many individuals or receptor points in the vicinity of ORR, but it is the dose to the maximally exposed individual (MEI) that determines compliance with the standard.« less

Hydrothermal transport and deposition of the rare earth elements by fluorine-bearing aqueous liquids

NASA Astrophysics Data System (ADS)

Migdisov, Art A.; Williams-Jones, A. E.

2014-12-01

New technologies, particularly those designed to address environmental concerns, have created a great demand for the rare earth elements (REE), and focused considerable attention on the processes by which they are concentrated to economically exploitable levels in the Earth's crust. There is widespread agreement that hydrothermal fluids played an important role in the formation of the world's largest economic REE deposit, i.e. Bayan Obo, China. Until recently, many researchers have assumed that hydrothermal transport of the REE in fluorine-bearing ore-forming systems occurs mainly due to the formation of REE-fluoride complexes. Consequently, hydrothermal models for REE concentration have commonly involved depositional mechanisms based on saturation of the fluid with REE minerals due to destabilization of REE-fluoride complexes. Here, we demonstrate that these complexes are insignificant in REE transport, and that the above models are therefore flawed. The strong association of H+ and F- as HF° and low solubility of REE-F solids greatly limit transport of the REE as fluoride complexes. However, this limitation does not apply to REE-chloride complexes. Because of this, the high concentration of Cl- in the ore fluids, and the relatively high stability of REE-chloride complexes, the latter can transport appreciable concentrations of REE at low pH. The limitation also does not apply to sulphate complexes and in some fluids, the concentration of sulphate may be sufficient to transport significant concentrations of REE as sulphate complexes, particularly at weakly acidic pH. This article proposes new models for hydrothermal REE deposition based on the transport of the REE as chloride and sulphate complexes.

Performance Analysis of a Hardware Implemented Complex Signal Kurtosis Radio-Frequency Interference Detector

NASA Technical Reports Server (NTRS)

Schoenwald, Adam J.; Bradley, Damon C.; Mohammed, Priscilla N.; Piepmeier, Jeffrey R.; Wong, Mark

2016-01-01

In the field of microwave radiometry, Radio Frequency Interference (RFI) consistently degrades the value of scientific results. Through the use of digital receivers and signal processing, the effects of RFI on scientific measurements can be reduced depending on certain circumstances. As technology allows us to implement wider band digital receivers for radiometry, the problem of RFI mitigation changes. Our work focuses on finding a detector that outperforms real kurtosis in wide band scenarios. The algorithm implemented is a complex signal kurtosis detector which was modeled and simulated. The performance of both complex and real signal kurtosis is evaluated for continuous wave, pulsed continuous wave, and wide band quadrature phase shift keying (QPSK) modulations. The use of complex signal kurtosis increased the detectability of interference.

Identifying Complex Dynamics in Social Systems: A New Methodological Approach Applied to Study School Segregation

ERIC Educational Resources Information Center

Spaiser, Viktoria; Hedström, Peter; Ranganathan, Shyam; Jansson, Kim; Nordvik, Monica K.; Sumpter, David J. T.

2018-01-01

It is widely recognized that segregation processes are often the result of complex nonlinear dynamics. Empirical analyses of complex dynamics are however rare, because there is a lack of appropriate empirical modeling techniques that are capable of capturing complex patterns and nonlinearities. At the same time, we know that many social phenomena…

Guide to good practices for operations and administration updates through required reading

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

NONE

1998-12-01

This Guide to Good Practices is written to enhance understanding of, and provide direction for, Required Reading, Chapter XIV of Department of Energy (DOE) Order 5480.19, Conduct of Operations Requirements for DOE Facilities. The practices in this guide should be considered when planning or reviewing programs for updating personnel with operations and administration information through required reading. Contractors are advised to adopt procedures that meet the intent of DOE Order 5480.19. Required Reading is an element of an effective Conduct of Operations program. The complexity and array of activities performed in DOE facilities dictate the necessity for a coordinated requiredmore » reading program to promote safe and efficient operations.« less

Rat Muc4 (sialomucin complex) reduces binding of anti-ErbB2 antibodies to tumor cell surfaces, a potential mechanism for herceptin resistance.

PubMed

Price-Schiavi, Shari A; Jepson, Scott; Li, Peter; Arango, Maria; Rudland, Philip S; Yee, Lisa; Carraway, Kermit L

2002-06-20

Muc4 (also called sialomucin complex), the rat homolog of human MUC4, is a heterodimeric glycoprotein complex that consists of a peripheral O-glycosylated mucin subunit, ASGP-1, tightly but noncovalently linked to a N-glycosylated transmembrane subunit, ASGP-2. The complex is expressed in a number of normal, vulnerable epithelial tissues, including mammary gland, uterus, colon, cornea and trachea. Muc4/SMC is also overexpressed or aberrantly expressed on a number of human tumors including breast tumors. Overexpression of Muc4/SMC has been shown to block cell-cell and cell-matrix interactions, protect tumor cells from immune surveillance and promote metastasis. In addition, as a ligand for ErbB2, Muc4/SMC can potentiate phosphorylation of ErbB2 and potentially alter signals generated from this receptor. Using A375 human melanoma cells and MCF7 human breast adenocarcinoma cells stably transfected with tetracycline regulatable Muc4, we have investigated whether overexpression of Muc4/SMC can repress antibody binding to cell surface-expressed ErbB2. Overexpression of Muc4/SMC does not affect the level of ErbB2 expression in either cell line, but it does reduce binding of a number of anti-ErbB2 antibodies, including Herceptin. Interestingly, overexpression of ErbB2 does not block binding of other unrelated antibodies of the same isotype, suggesting that the reduction in ErbB2 antibody binding is due to complex formation of Muc4/SMC and ErbB2. Furthermore, capping of Muc4/SMC with anti-Muc4/SMC antibodies reduces antibody binding to ErbB2 instead of increasing binding, again suggesting that reduced antibody binding to ErbB2 is due to steric hindrance from complex formation of Muc4/SMC and ErbB2. Thus, overexpression of Muc4/SMC on tumor cells may have both prognostic and therapeutic relevance. Copyright 2002 Wiley-Liss, Inc.

Shannon information, LMC complexity and Rényi entropies: a straightforward approach.

PubMed

López-Ruiz, Ricardo

2005-04-01

The LMC complexity, an indicator of complexity based on a probabilistic description, is revisited. A straightforward approach allows us to establish the time evolution of this indicator in a near-equilibrium situation and gives us a new insight for interpreting the LMC complexity for a general non equilibrium system. Its relationship with the Rényi entropies is also explained. One of the advantages of this indicator is that its calculation does not require a considerable computational effort in many cases of physical and biological interest.

24 CFR 599.303 - Rating of applications.

Code of Federal Regulations, 2014 CFR

2014-04-01

... the area poverty rate, area unemployment rate, and for urban areas, the percentage of families below... jurisdiction in the nominated area, does not exceed by more than 25% the nation-wide 1999 Crime Index rate per...

24 CFR 599.303 - Rating of applications.

Code of Federal Regulations, 2013 CFR

2013-04-01

... the area poverty rate, area unemployment rate, and for urban areas, the percentage of families below... jurisdiction in the nominated area, does not exceed by more than 25% the nation-wide 1999 Crime Index rate per...

24 CFR 599.303 - Rating of applications.

Code of Federal Regulations, 2012 CFR

2012-04-01

... the area poverty rate, area unemployment rate, and for urban areas, the percentage of families below... jurisdiction in the nominated area, does not exceed by more than 25% the nation-wide 1999 Crime Index rate per...

24 CFR 599.303 - Rating of applications.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the area poverty rate, area unemployment rate, and for urban areas, the percentage of families below... jurisdiction in the nominated area, does not exceed by more than 25% the nation-wide 1999 Crime Index rate per...

Menopausal Hormone Therapy and Cancer

MedlinePlus

... FDA-approved hormone products, sometimes referred to as “bio-identical hormones,” are widely promoted and sold without ... about these products in Menopausal Hormone Therapy and “Bio-identical” Hormones . Where does evidence about risks and ...

75 FR 72739 - Compliance Testing Procedures: Correction Factor for Room Air Conditioners

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-26

... industry practices or consensus body testing standards which have been superseded by standards which are... accurate. With these facts in mind, DOE compliance enforcement forbearance, or an industry-wide waiver or...

Thoughts on a Pedagogy OF Complexity

ERIC Educational Resources Information Center

Byrne, David

2014-01-01

There is now a developed and extensive literature on the implications of the "complexity frame of reference" (Castellani & Hafferty, 2009) for education in general and pedagogy in particular. This includes a wide range of interesting contributions which consider how complexity can inform, inter alia, research on educational systems…

DOE's Oak Ridge Site Kick Off Demolition of the K-27 Building

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

Cange, Sue; Rueter, Ken

2016-02-10

DOE's Oak Ridge Office of Environmental Management kicked off demolition of the K-27 Building this month, moving closer to fulfilling Vision 2016 — removal of all gaseous diffusion buildings from the site by year’s end. As the site's last uranium enrichment building falls, it will mark the first-ever demolition and cleanup of a gaseous diffusion complex anywhere.

"Does Knowing Stuff like PSHE and Citizenship Make Me a Better Teacher?": Student Teachers in the Teacher Training Figuration

ERIC Educational Resources Information Center

Velija, Philippa; Capel, Susan; Katene, Will; Hayes, Sid

2008-01-01

One of the key elements of figurational sociology is the emphasis on understanding complex networks of interdependencies in which people are involved. The focal point of this paper is the process of initial teacher training (ITT) and the relationships of which student teachers are part during their ITT course. The paper does not look at what…

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

Goldston, W.T.

DOE issued Order 435.1, ''Radioactive Waste Management,'' on July 9, 1999 for immediate implementation. The requirements for Low Level Mixed, Transuranic, and High Level Waste have been completely rewritten. The entire DOE complex has been struggling with how to implement these new requirements within the one year required timeframe. This paper will chronicle the implementation strategy and actual results of the work to carry out that strategy at the Savannah River Site.

Report: complexation of β-sitosterol with tris (dibenzylideneacetone) dipalladium and its anti-microbial activity.

PubMed

Mahmood, Talat; Bibi, Yasmeen; Zafar, Raana; Wahab, Aneela; Mahmood, Iffat; Arshad, Nuzhat; Sherwani, Sikandar Khan

2015-03-01

β-sitosterol is a naturally occurring plant sterol (phytosterol) present in many fruits and vegetables. Scientific research has proven that β-sitosterol is helpful in maintaining the proper functioning of our body. Previously we described the complexation of β-sitosterol with trace metals (Mahmood et al., 2013). Trace metals after the formation of complex unable to absorb in the body and hence eliminated out from the body thus reducing metal toxicity (Marsha, 1996). The present article describes the complexation of μ-sitosterol with Palladium (Pd) metal. Palladium is a toxic metal and due to polluted and hazardous environment traces of this metal can be transferred into the body, which is harmful for human health. Our aim is to make Pd-sterol complex so that this toxic metal (Pd) does not absorb in the body and hence excreted out from the body in the complex form. In order to form this complex μ-sitosterol (Ib) is reacted with Tris (dibenzylideneacetone) dipalladium or [Pd(2) (DBA)(3)] (Ia) in 2:1 ratio in an inert atmosphere and dimethylformamid (DMF) added as a solvent. The resulting complex [Pd(2) (DBA)(3).(β-sitosterol) (Ic) was identified by various spectroscopic techniques such as IR, Mass and (1)H-NMR. This new organo metallic complex (Ic) also showed significant antibacterial and antifungal activity. The present work revealed that Pd-sterol complex does not only reduce metal toxicity but also helpful in minimizing bacterial and fungal infections present in the body. Our research also concluded that we must take plenty of fruits and vegetables in our diet so that natural plant sterol such as β-sitosterol can enhance our defense mechanism and maintain other functions of our body.

Multiple-Zone Diffractive Optic Element for Laser Ranging Applications

NASA Technical Reports Server (NTRS)

Ramos-Izquierdo, Luis A.

2011-01-01

A diffractive optic element (DOE) can be used as a beam splitter to generate multiple laser beams from a single input laser beam. This technology has been recently used in LRO s Lunar Orbiter Laser Altimeter (LOLA) instrument to generate five laser beams that measure the lunar topography from a 50-km nominal mapping orbit (see figure). An extension of this approach is to use a multiple-zone DOE to allow a laser altimeter instrument to operate over a wider range of distances. In particular, a multiple-zone DOE could be used for applications that require both mapping and landing on a planetary body. In this case, the laser altimeter operating range would need to extend from several hundred kilometers down to a few meters. The innovator was recently involved in an investigation how to modify the LOLA instrument for the OSIRIS asteroid mapping and sample return mission. One approach is to replace the DOE in the LOLA laser beam expander assembly with a multiple-zone DOE that would allow for the simultaneous illumination of the asteroid with mapping and landing laser beams. The proposed OSIRIS multiple-zone DOE would generate the same LOLA five-beam output pattern for high-altitude topographic mapping, but would simultaneously generate a wide divergence angle beam using a small portion of the total laser energy for the approach and landing portion of the mission. Only a few percent of the total laser energy is required for approach and landing operations as the return signal increases as the inverse square of the ranging height. A wide divergence beam could be implemented by making the center of the DOE a diffractive or refractive negative lens. The beam energy and beam divergence characteristics of a multiple-zone DOE could be easily tailored to meet the requirements of other missions that require laser ranging data. Current single-zone DOE lithographic manufacturing techniques could also be used to fabricate a multiple-zone DOE by masking the different DOE zones during the manufacturing process, and the same space-compatible DOE substrates (fused silica, sapphire) that are used on standard DOE s could be used for multiple- zone DOE s. DOEs are an elegant and cost-effective optical design option for spacebased laser altimeters that require multiple output laser beams. The use of multiple-zone DOEs would allow for the design and optimization of a laser altimeter instrument required to operate over a large range of target distances, such as those designed to both map and land on a planetary body. In addition to space-based laser altimeters, this technology could find applications in military or commercial unmanned aerial vehicles (UAVs) that fly at an altitude of several kilometers and need to land. It is also conceivable that variations of this approach could be used in land-based applications such as collision avoidance and robotic control of cars, trains, and ships.

New Developments in the Technology Readiness Assessment Process in US DOE-EM - 13247

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

Krahn, Steven; Sutter, Herbert; Johnson, Hoyt

2013-07-01

A Technology Readiness Assessment (TRA) is a systematic, metric-based process and accompanying report that evaluates the maturity of the technologies used in systems; it is designed to measure technology maturity using the Technology Readiness Level (TRL) scale pioneered by the National Aeronautics and Space Administration (NASA) in the 1980's. More recently, DoD has adopted and provided systematic guidance for performing TRAs and determining TRLs. In 2007 the GAO recommended that the DOE adopt the NASA/DoD methodology for evaluating technology maturity. Earlier, in 2006-2007, DOE-EM had conducted pilot TRAs on a number of projects at Hanford and Savannah River. In Marchmore » 2008, DOE-EM issued a process guide, which established TRAs as an integral part of DOE-EM's Project Management Critical Decision Process. Since the development of its detailed TRA guidance in 2008, DOE-EM has continued to accumulate experience in the conduct of TRAs and the process for evaluating technology maturity. DOE has developed guidance on TRAs applicable department-wide. DOE-EM's experience with the TRA process, the evaluations that led to recently developed proposed revisions to the DOE-EM TRA/TMP Guide; the content of the proposed changes that incorporate the above lessons learned and insights are described. (authors)« less

U.S. Department of Energy's Bioenergy Research Centers An Overview of the Science

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

None

2010-07-01

Alternative fuels from renewable cellulosic biomass - plant stalks, trunks, stems, and leaves - are expected to significantly reduce U.S. dependence on imported oil while enhancing national energy security and decreasing the environmental impacts of energy use. Ethanol and other advanced biofuels from cellulosic biomass are renewable alternatives that could increase domestic production of transportation fuels, revitalize rural economies, and reduce carbon dioxide and pollutant emissions. According to U.S. Secretary of Energy Steven Chu, 'Developing the next generation of biofuels is key to our effort to end our dependence on foreign oil and address the climate crisis while creating millionsmore » of new jobs that can't be outsourced.' Although cellulosic ethanol production has been demonstrated on a pilot level, developing a cost-effective, commercial-scale cellulosic biofuel industry will require transformational science to significantly streamline current production processes. Woodchips, grasses, cornstalks, and other cellulosic biomass are widely abundant but more difficult to break down into sugars than corn grain - the primary source of U.S. ethanol fuel production today. Biological research is key to accelerating the deconstruction of cellulosic biomass into sugars that can be converted to biofuels. The Department of Energy (DOE) Office of Science continues to play a major role in inspiring, supporting, and guiding the biotechnology revolution over the past 30 years. The DOE Genomic Science program is advancing a new generation of research focused on achieving whole-systems understanding of biology. This program is bringing together scientists in diverse fields to understand the complex biology underlying solutions to DOE missions in energy production, environmental remediation, and climate change science. For more information on the Genomic Science program, see p. 26. To focus the most advanced biotechnology-based resources on the biological challenges of biofuel production, DOE established three Bioenergy Research Centers (BRCs) in September 2007. Each center is pursuing the basic research underlying a range of high-risk, high-return biological solutions for bioenergy applications. Advances resulting from the BRCs are providing the knowledge needed to develop new biobased products, methods, and tools that the emerging biofuel industry can use (see sidebar, Bridging the Gap from Fundamental Biology to Industrial Innovation for Bioenergy, p. 6). The DOE BRCs have developed automated, high-throughput analysis pipelines that will accelerate scientific discovery for biology-based biofuel research. The three centers, which were selected through a scientific peer-review process, are based in geographically diverse locations - the Southeast, the Midwest, and the West Coast - with partners across the nation (see U.S. map, DOE Bioenergy Research Centers and Partners, on back cover). DOE's Lawrence Berkeley National Laboratory leads the DOE Joint BioEnergy Institute (JBEI) in California; DOE's Oak Ridge National Laboratory leads the BioEnergy Science Center (BESC) in Tennessee; and the University of Wisconsin-Madison leads the Great Lakes Bioenergy Research Center (GLBRC). Each center represents a multidisciplinary partnership with expertise spanning the physical and biological sciences, including genomics, microbial and plant biology, analytical chemistry, computational biology and bioinformatics, and engineering. Institutional partners include DOE national laboratories, universities, private companies, and nonprofit organizations.« less

Sr-isotopic composition of marbles from the Puerto Galera area (Mindoro, Philippines): additional evidence for a Paleozoic age of a metamorphic complex in the Philippine island arc

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

Knittel, U.; Daniels, U.

1987-02-01

The Sr-isotopic composition of marbles from the Puerto Galera area (Mindoro, Philippines) is compatible with either a Tertiary or a Paleozoic age. The former is considered as unlikely because nonmetamorphic sediments of that age overlie the metamorphic complex. This implies that the metamorphic complex does not represent the basement of the Philippine arc but is an accreted terrane.

Complexity reduction of biochemical rate expressions.

PubMed

Schmidt, Henning; Madsen, Mads F; Danø, Sune; Cedersund, Gunnar

2008-03-15

The current trend in dynamical modelling of biochemical systems is to construct more and more mechanistically detailed and thus complex models. The complexity is reflected in the number of dynamic state variables and parameters, as well as in the complexity of the kinetic rate expressions. However, a greater level of complexity, or level of detail, does not necessarily imply better models, or a better understanding of the underlying processes. Data often does not contain enough information to discriminate between different model hypotheses, and such overparameterization makes it hard to establish the validity of the various parts of the model. Consequently, there is an increasing demand for model reduction methods. We present a new reduction method that reduces complex rational rate expressions, such as those often used to describe enzymatic reactions. The method is a novel term-based identifiability analysis, which is easy to use and allows for user-specified reductions of individual rate expressions in complete models. The method is one of the first methods to meet the classical engineering objective of improved parameter identifiability without losing the systems biology demand of preserved biochemical interpretation. The method has been implemented in the Systems Biology Toolbox 2 for MATLAB, which is freely available from http://www.sbtoolbox2.org. The Supplementary Material contains scripts that show how to use it by applying the method to the example models, discussed in this article.

Descriptive Model of Generic WAMS

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

Hauer, John F.; DeSteese, John G.

The Department of Energy’s (DOE) Transmission Reliability Program is supporting the research, deployment, and demonstration of various wide area measurement system (WAMS) technologies to enhance the reliability of the Nation’s electrical power grid. Pacific Northwest National Laboratory (PNNL) was tasked by the DOE National SCADA Test Bed Program to conduct a study of WAMS security. This report represents achievement of the milestone to develop a generic WAMS model description that will provide a basis for the security analysis planned in the next phase of this study.

The Role of the Environmental Management Site Specific Advisory Board under the Federal Advisory Committee Act, With Emphasis on the Northern New Mexico Citizens' Advisory Board - 12482

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

Santistevan, Menice B.

2012-07-01

The Environmental Management Site Specific Advisory Board (EM SSAB) is comprised of eight Citizens' Advisory Boards, chartered under the Federal Advisory Committee Act (FACA) by the Assistant Secretary for Environmental Management for the U. S. Department of Energy (DOE). The purpose of the EM SSAB is to provide the DOE with recommendations regarding Environmental Management issues from legacy waste produced at major sites across the DOE Complex. The Northern New Mexico Citizens' Advisory Board (NNMCAB) is the site specific advisory board to the DOE on issues of environmental monitoring, remediation, waste management and long-term stewardship at Los Alamos National Laboratorymore » (LANL). The other boards are located at: Hanford, Idaho, Nevada, Paducah, Portsmouth, Oak Ridge and Savannah River. Using broad citizen outreach and input, the SSAB provides an official mechanism for the citizenry at each of these sites to monitor current activities affecting the region and also to have input into the prioritization of future activities. 'The mission of the EM SSAB is to more directly involve stakeholders in EM Planning and decision-making processes for the nuclear weapons complex cleanup. DOE has various means of involving the public in its planning and decision-making processes; the EM SSAB is only one component of EM's public participation program, and is not intended to be an exclusive means of public participation. It is the policy of DOE and EM to conduct it programs in an open and responsive manner, thereby encouraging and providing the opportunity for public participation in its planning and decision-making processes. EM SSAB members are appointed to a two year term and may serve up to three terms. During this time, members are able to hear many presentation from subject matter experts, attend several site tours at their site and across the DOE complex and are able to express their concerns and give input to the prioritization of clean up at each site. It is an excellent education and it is hoped that these members will go out to their communities, friends and family and discuss these issues in an informed manner. Many times our citizens rely only on newspaper articles or the Internet, which are sometimes replete with fear and misinformation. The more stakeholders are able to be truly informed, the more accurate the discourse will be at each of the DOE sites. (author)« less

School-Age Children Talk about Chess: Does Knowledge Drive Syntactic Complexity?

ERIC Educational Resources Information Center

Nippold, Marilyn A.

2009-01-01

Purpose: This study examined language productivity and syntactic complexity in school-age children in relation to their knowledge of the topic of discussion--the game of chess. Method: Children (N = 32; mean age = 10;11 [years;months]) who played chess volunteered to be interviewed by an adult examiner who had little or no experience playing…

Cueing Complex Animations: Does Direction of Attention Foster Learning Processes?

ERIC Educational Resources Information Center

Lowe, Richard; Boucheix, Jean-Michel

2011-01-01

The time course of learners' processing of a complex animation was studied using a dynamic diagram of a piano mechanism. Over successive repetitions of the material, two forms of cueing (standard colour cueing and anti-cueing) were administered either before or during the animated segment of the presentation. An uncued group and two other control…

Embedded Clause Effects on Recall: Does High Prior Knowledge of Content Domain Overcome Syntactic Complexity in Students of Spanish?

ERIC Educational Resources Information Center

Barry, Sue; Lazarte, Alejandro A.

1995-01-01

This study tested the effect of embedded clauses on recall for 48 English-speaking high school students reading Spanish historical texts. It found that the complexity of sentence structure seemed to cancel the advantage of previous exposure to the content domain. Contains 39 references. (MDM)

Confirmation of Non-Impacted Status (TA16-280 Complex)

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

Ruedig, Elizabeth

2017-12-07

EPC-ES finds that the materials associated with TA16-280 complex (see Figure 1) are candidates for release to the public for recycle or as sanitary/commercial waste. This finding is consistent with the requirements of DOE Order 458.1 Radiation Protection of the Public and the Environment and LANL Policy 412 Environmental Radiation Protection.

Activation of Hsp90/NOS and increased NO generation does not impair mitochondrial respiratory chain by competitive binding at cytochrome C Oxidase in low oxygen concentrations

PubMed Central

Presley, Tennille; Vedam, Kaushik; Liu, Xiaoping; Zweier, Jay L.

2009-01-01

Nitric oxide (NO) is known to regulate mitochondrial respiration, especially during metabolic stress and disease, by nitrosation of the mitochondrial electron transport chain (ETC) complexes (irreversible) and by a competitive binding at O2 binding site of cytochrome c oxidase (CcO) in complex IV (reversible). In this study, by using bovine aortic endothelial cells, we demonstrate that the inhibitory effect of endogenously generated NO by nitric oxide synthase (NOS) activation, by either NOS stimulators or association with heat shock protein 90 (Hsp90), is significant only at high prevailing pO2 through nitrosation of mitochondrial ETC complexes, but it does not inhibit the respiration by competitive binding at CcO at very low pO2. ETC complexes activity measurements confirmed that significant reduction in complex IV activity was noticed at higher pO2, but it was unaffected at low pO2 in these cells. This was further extended to heat-shocked cells, where NOS was activated by the induction/activation of (Hsp90) through heat shock at an elevated temperature of 42°C. From these results, we conclude that the entire attenuation of respiration by endogenous NO is due to irreversible inhibition by nitrosation of ETC complexes but not through reversible inhibition by competing with O2 binding at CcO at complex IV. PMID:19412660

Attacking cancer dormacy using game theory

NASA Astrophysics Data System (ADS)

Austin, Robert

Here is the problem: Cancer kills primarily by re-emergence from a period of dormancy after initial treatment. The presence of driver mutations and subsequent clonal expansion by Darwinian evolution does not explain dormancy and re-emergence of cancer from a community of cancer and host cells (including stromal and immune cells), nor does it explain our inability to predict the emergence of metastasis, by far the real killer in cancer. Dormancy appears to be a slow-driven, multi-cell interaction-dominated, threshold system with a poor prognosis once the cancer emerges from dormancy. The mission here is to try and model the phenomena of dormancy using game theory ideas, and in an in vitro complex ecology designed to emulate the true complexity of an in vivo tumor.

A 1:2 crystalline complex of ApA:proflavine: a model for binding to single-stranded regions in RNA.

PubMed Central

Neidle, S; Taylor, G; Sanderson, M

1978-01-01

The structure of a 1"2 complex of adenylyl-(3',5')-adenosine phosphate and proflavine hemisulfate has been determined using the methods of x-ray crystallography. Since the ApA does not form a mini double helix, it may serve as a model for the interaction of planar molecules with single stranded nucleic acids. The dinucleotide adopts an extended conformation with the adenines in adjacent molecules forming base pairs. A most unusual feature of the molecule is that it does not obey the "rigid nucleotide" concept although none of the torsion angles occur in energetically unfavourable regions. This is most probably due to the strong interactions between the proflavine and the oligonucleotide. PMID:724521

Simple replacement of violaxanthin by zeaxanthin in LHC-II does not cause chlorophyll fluorescence quenching.

PubMed

Dreuw, Andreas; Wormit, Michael

2008-03-01

Recently, a mechanism for the energy-dependent component (qE) of non-photochemical quenching (NPQ), the fundamental photo-protection mechanism in green plants, has been suggested. Replacement of violaxanthin by zeaxanthin in the binding pocket of the major light harvesting complex LHC-II may be sufficient to invoke efficient chlorophyll fluorescence quenching. Our quantum chemical calculations, however, show that the excited state energies of violaxanthin and zeaxanthin are practically identical when their geometry is constrained to the naturally observed structure of violaxanthin in LHC-II. Therefore, since violaxanthin does not quench LHC-II, zeaxanthin should not either. This theoretical finding is nicely in agreement with experimental results obtained by femtosecond spectroscopy on LHC-II complexes containing violaxanthin or zeaxanthin.

HALOS: fast, autonomous, holographic adaptive optics

NASA Astrophysics Data System (ADS)

Andersen, Geoff P.; Gelsinger-Austin, Paul; Gaddipati, Ravi; Gaddipati, Phani; Ghebremichael, Fassil

2014-08-01

We present progress on our holographic adaptive laser optics system (HALOS): a compact, closed-loop aberration correction system that uses a multiplexed hologram to deconvolve the phase aberrations in an input beam. The wavefront characterization is based on simple, parallel measurements of the intensity of fixed focal spots and does not require any complex calculations. As such, the system does not require a computer and is thus much cheaper, less complex than conventional approaches. We present details of a fully functional, closed-loop prototype incorporating a 32-element MEMS mirror, operating at a bandwidth of over 10kHz. Additionally, since the all-optical sensing is made in parallel, the speed is independent of actuator number - running at the same bandwidth for one actuator as for a million.

Defining and Assessing Chinese Syntactic Complexity via TC-Units

ERIC Educational Resources Information Center

Yu, Qiaona

2016-01-01

The triad dimensions of complexity, accuracy, and fluency (CAF) has been widely used for assessing second language performance and development. Unlike accuracy and fluency, the construct of Chinese syntactic complexity has not been comprehensibly conceptualized or operationalized. Moreover, not tailored to the typological differences such as the…

WHC significant lessons learned 1993--1995

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

Bickford, J.C.

1997-12-12

A lesson learned as defined in DOE-STD-7501-95, Development of DOE Lessons Learned Programs, is: A ``good work practice`` or innovative approach that is captured and shared to promote repeat applications or an adverse work practice or experience that is captured and shared to avoid a recurrence. The key word in both parts of this definition is ``shared``. This document was published to share a wide variety of recent Hanford experiences with other DOE sites. It also provides a valuable tool to be used in new employee and continuing training programs at Hanford facilities and at other DOE locations. This manualmore » is divided into sections to facilitate extracting appropriate subject material when developing training modules. Many of the bulletins could be categorized into more than one section, however, so examination of other related sections is encouraged.« less

Analyzing Genome-Wide Association Studies with an FDR Controlling Modification of the Bayesian Information Criterion

PubMed Central

Dolejsi, Erich; Bodenstorfer, Bernhard; Frommlet, Florian

2014-01-01

The prevailing method of analyzing GWAS data is still to test each marker individually, although from a statistical point of view it is quite obvious that in case of complex traits such single marker tests are not ideal. Recently several model selection approaches for GWAS have been suggested, most of them based on LASSO-type procedures. Here we will discuss an alternative model selection approach which is based on a modification of the Bayesian Information Criterion (mBIC2) which was previously shown to have certain asymptotic optimality properties in terms of minimizing the misclassification error. Heuristic search strategies are introduced which attempt to find the model which minimizes mBIC2, and which are efficient enough to allow the analysis of GWAS data. Our approach is implemented in a software package called MOSGWA. Its performance in case control GWAS is compared with the two algorithms HLASSO and d-GWASelect, as well as with single marker tests, where we performed a simulation study based on real SNP data from the POPRES sample. Our results show that MOSGWA performs slightly better than HLASSO, where specifically for more complex models MOSGWA is more powerful with only a slight increase in Type I error. On the other hand according to our simulations GWASelect does not at all control the type I error when used to automatically determine the number of important SNPs. We also reanalyze the GWAS data from the Wellcome Trust Case-Control Consortium and compare the findings of the different procedures, where MOSGWA detects for complex diseases a number of interesting SNPs which are not found by other methods. PMID:25061809

Development of Quality Assessment Techniques for Large Eddy Simulation of Propulsion and Power Systems in Complex Geometries

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

Lacaze, Guilhem; Oefelein, Joseph

Large-eddy-simulation (LES) is quickly becoming a method of choice for studying complex thermo-physics in a wide range of propulsion and power systems. It provides a means to study coupled turbulent combustion and flow processes in parameter spaces that are unattainable using direct-numerical-simulation (DNS), with a degree of fidelity that can be far more accurate than conventional engineering methods such as the Reynolds-averaged Navier-Stokes (RANS) approx- imation. However, development of predictive LES is complicated by the complex interdependence of different type of errors coming from numerical methods, algorithms, models and boundary con- ditions. On the other hand, control of accuracy hasmore » become a critical aspect in the development of predictive LES for design. The objective of this project is to create a framework of metrics aimed at quantifying the quality and accuracy of state-of-the-art LES in a manner that addresses the myriad of competing interdependencies. In a typical simulation cycle, only 20% of the computational time is actually usable. The rest is spent in case preparation, assessment, and validation, because of the lack of guidelines. This work increases confidence in the accuracy of a given solution while min- imizing the time obtaining the solution. The approach facilitates control of the tradeoffs between cost, accuracy, and uncertainties as a function of fidelity and methods employed. The analysis is coupled with advanced Uncertainty Quantification techniques employed to estimate confidence in model predictions and calibrate model's parameters. This work has provided positive conse- quences on the accuracy of the results delivered by LES and will soon have a broad impact on research supported both by the DOE and elsewhere.« less

Fault Management Guiding Principles

NASA Technical Reports Server (NTRS)

Newhouse, Marilyn E.; Friberg, Kenneth H.; Fesq, Lorraine; Barley, Bryan

2011-01-01

Regardless of the mission type: deep space or low Earth orbit, robotic or human spaceflight, Fault Management (FM) is a critical aspect of NASA space missions. As the complexity of space missions grows, the complexity of supporting FM systems increase in turn. Data on recent NASA missions show that development of FM capabilities is a common driver for significant cost overruns late in the project development cycle. Efforts to understand the drivers behind these cost overruns, spearheaded by NASA's Science Mission Directorate (SMD), indicate that they are primarily caused by the growing complexity of FM systems and the lack of maturity of FM as an engineering discipline. NASA can and does develop FM systems that effectively protect mission functionality and assets. The cost growth results from a lack of FM planning and emphasis by project management, as well the maturity of FM as an engineering discipline, which lags behind the maturity of other engineering disciplines. As a step towards controlling the cost growth associated with FM development, SMD has commissioned a multi-institution team to develop a practitioner's handbook representing best practices for the end-to-end processes involved in engineering FM systems. While currently concentrating primarily on FM for science missions, the expectation is that this handbook will grow into a NASA-wide handbook, serving as a companion to the NASA Systems Engineering Handbook. This paper presents a snapshot of the principles that have been identified to guide FM development from cradle to grave. The principles range from considerations for integrating FM into the project and SE organizational structure, the relationship between FM designs and mission risk, and the use of the various tools of FM (e.g., redundancy) to meet the FM goal of protecting mission functionality and assets.

Cardiac-resynchronization therapy in heart failure with a narrow QRS complex.

PubMed

Ruschitzka, Frank; Abraham, William T; Singh, Jagmeet P; Bax, Jeroen J; Borer, Jeffrey S; Brugada, Josep; Dickstein, Kenneth; Ford, Ian; Gorcsan, John; Gras, Daniel; Krum, Henry; Sogaard, Peter; Holzmeister, Johannes

2013-10-10

Cardiac-resynchronization therapy (CRT) reduces morbidity and mortality in chronic systolic heart failure with a wide QRS complex. Mechanical dyssynchrony also occurs in patients with a narrow QRS complex, which suggests the potential usefulness of CRT in such patients. We conducted a randomized trial involving 115 centers to evaluate the effect of CRT in patients with New York Heart Association class III or IV heart failure, a left ventricular ejection fraction of 35% or less, a QRS duration of less than 130 msec, and echocardiographic evidence of left ventricular dyssynchrony. All patients underwent device implantation and were randomly assigned to have CRT capability turned on or off. The primary efficacy outcome was the composite of death from any cause or first hospitalization for worsening heart failure. On March 13, 2013, the study was stopped for futility on the recommendation of the data and safety monitoring board. At study closure, the 809 patients who had undergone randomization had been followed for a mean of 19.4 months. The primary outcome occurred in 116 of 404 patients in the CRT group, as compared with 102 of 405 in the control group (28.7% vs. 25.2%; hazard ratio, 1.20; 95% confidence interval [CI], 0.92 to 1.57; P=0.15). There were 45 deaths in the CRT group and 26 in the control group (11.1% vs. 6.4%; hazard ratio, 1.81; 95% CI, 1.11 to 2.93; P=0.02). In patients with systolic heart failure and a QRS duration of less than 130 msec, CRT does not reduce the rate of death or hospitalization for heart failure and may increase mortality. (Funded by Biotronik and GE Healthcare; EchoCRT ClinicalTrials.gov number, NCT00683696.).

An endosomal syntaxin and the AP-3 complex are required for formation and maturation of candidate lysosome-related secretory organelles (mucocysts) in Tetrahymena thermophila.

PubMed

Kaur, Harsimran; Sparvoli, Daniela; Osakada, Hiroko; Iwamoto, Masaaki; Haraguchi, Tokuko; Turkewitz, Aaron P

2017-06-01

The ciliate Tetrahymena thermophila synthesizes large secretory vesicles called mucocysts. Mucocyst biosynthesis shares features with dense core granules (DCGs) in animal cells, including proteolytic processing of cargo proteins during maturation. However, other molecular features have suggested relatedness to lysosome-related organelles (LROs). LROs, which include diverse organelles in animals, are formed via convergence of secretory and endocytic trafficking. Here we analyzed Tetrahymena syntaxin 7-like 1 (Stx7l1p), a Qa-SNARE whose homologues in other lineages are linked with vacuoles/LROs. Stx7l1p is targeted to both immature and mature mucocysts and is essential in mucocyst formation. In STX7L1 -knockout cells, the two major classes of mucocyst cargo proteins localize independently, accumulating in largely nonoverlapping vesicles. Thus initial formation of immature mucocysts involves heterotypic fusion, in which a subset of mucocyst proteins is delivered via an endolysosomal compartment. Further, we show that subsequent maturation requires AP-3, a complex widely implicated in LRO formation. Knockout of the µ-subunit gene does not impede delivery of any known mucocyst cargo but nonetheless arrests mucocyst maturation. Our data argue that secretory organelles in ciliates may represent a new class of LROs and reveal key roles of an endosomal syntaxin and AP-3 in the assembly of this complex compartment. © 2017 Kaur et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Ferrocene-oligonucleotide conjugates for electrochemical probing of DNA.

PubMed Central

Ihara, T; Maruo, Y; Takenaka, S; Takagi, M

1996-01-01

Toward the development of a universal, sensitive and convenient method of DNA (or RNA) detection, electrochemically active oligonucleotides were prepared by covalent linkage of a ferrocenyl group to the 5'-aminohexyl-terminated synthetic oligonucleotides. Using these electrochemically active probes, we have been able to demonstrate the detection of DNA and RNA at femtomole levels by HPLC equipped with an ordinary electrochemical detector (ECD) [Takenaka,S., Uto,Y., Kondo,H., Ihara,T. and Takagi,M. (1994) Anal. Biochem., 218, 436-443]. Thermodynamic and electrochemical studies of the interaction between the probes and the targets are presented here. The thermodynamics obtained revealed that the conjugation stabilizes the triple-helix complexes by 2-3 kcal mol-1 (1-2 orders increment in binding constant) at 298 K, which corresponds to the effect of elongation of additional several base triplets. The main cause of this thermodynamic stabilization by the conjugation is likely to be the overall conformational change of whole structure of the conjugate rather than the additional local interaction. The redox potential of the probe was independent of the target structure, which is either single- or double stranded. However, the potential is slightly dependent (with a 10-30 mV negative shift on complexation) on the extra sequence in the target, probably because the individual sequence is capable of contacting or interacting with the ferrocenyl group in a slightly different way from each other. This small potential shift itself, however, does not cause any inconvenience on practical applications in detecting the probes by using ECD. These results lead to the conclusion that the redox-active probes are very useful for the microanalysis of nucleic acids due to the stability of the complexes, high detection sensitivity and wide applicability to the target structures (DNA and RNA; single- and double strands) and the sequences. PMID:8932383

Efficient Use of Distributed Systems for Scientific Applications

NASA Technical Reports Server (NTRS)

Taylor, Valerie; Chen, Jian; Canfield, Thomas; Richard, Jacques

2000-01-01

Distributed computing has been regarded as the future of high performance computing. Nationwide high speed networks such as vBNS are becoming widely available to interconnect high-speed computers, virtual environments, scientific instruments and large data sets. One of the major issues to be addressed with distributed systems is the development of computational tools that facilitate the efficient execution of parallel applications on such systems. These tools must exploit the heterogeneous resources (networks and compute nodes) in distributed systems. This paper presents a tool, called PART, which addresses this issue for mesh partitioning. PART takes advantage of the following heterogeneous system features: (1) processor speed; (2) number of processors; (3) local network performance; and (4) wide area network performance. Further, different finite element applications under consideration may have different computational complexities, different communication patterns, and different element types, which also must be taken into consideration when partitioning. PART uses parallel simulated annealing to partition the domain, taking into consideration network and processor heterogeneity. The results of using PART for an explicit finite element application executing on two IBM SPs (located at Argonne National Laboratory and the San Diego Supercomputer Center) indicate an increase in efficiency by up to 36% as compared to METIS, a widely used mesh partitioning tool. The input to METIS was modified to take into consideration heterogeneous processor performance; METIS does not take into consideration heterogeneous networks. The execution times for these applications were reduced by up to 30% as compared to METIS. These results are given in Figure 1 for four irregular meshes with number of elements ranging from 30,269 elements for the Barth5 mesh to 11,451 elements for the Barth4 mesh. Future work with PART entails using the tool with an integrated application requiring distributed systems. In particular this application, illustrated in the document entails an integration of finite element and fluid dynamic simulations to address the cooling of turbine blades of a gas turbine engine design. It is not uncommon to encounter high-temperature, film-cooled turbine airfoils with 1,000,000s of degrees of freedom. This results because of the complexity of the various components of the airfoils, requiring fine-grain meshing for accuracy. Additional information is contained in the original.

EM Properties of Magnetic Minerals at RADAR Frequencies

NASA Technical Reports Server (NTRS)

Stillman, D. E.; Olhoeft, G. R.

2005-01-01

Previous missions to Mars have revealed that Mars surface is magnetic at DC frequency. Does this highly magnetic surface layer attenuate RADAR energy as it does in certain locations on Earth? It has been suggested that the active magnetic mineral on Mars is titanomaghemite and/or titanomagnetite. When titanium is incorporated into a maghemite or magnetite crystal, the Curie temperature can be significantly reduced. Mars has a wide range of daily temperature fluctuations (303K - 143K), which could allow for daily passes through the Curie temperature. Hence, the global dust layer on Mars could experience widely varying magnetic properties as a function of temperature, more specifically being ferromagnetic at night and paramagnetic during the day. Measurements of EM properties of magnetic minerals were made versus frequency and temperature (300K- 180K). Magnetic minerals and Martian analog samples were gathered from a number of different locations on Earth.

Y-12 Site Sustainability Plan

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

Spencer, Charles G

2012-12-01

The accomplishments to date and the long-range planning of the Y-12 Energy Management and Sustainability and Stewardship programs support the U.S. Department of Energy (DOE) and the National Nuclear Security Administration (NNSA) vision for a commitment to energy effi ciency and sustainability and to achievement of the Guiding Principles. Specifi cally, the Y-12 vision is to support the Environment, Safety and Health Policy and the DOE Strategic Sustainability Performance Plan, while promoting overall sustainability and reduction of greenhouse gas emissions. The mission of the Y-12 Energy Management program is to incorporate energy-effi cient technologies site-wide and to position Y-12 tomore » meet NNSA energy requirement needs through 2025 and beyond. The plan addresses greenhouse gases, buildings, fleet management, water use, pollution prevention, waste reduction, sustainable acquisition, electronic stewardship and data centers, site innovation and government-wide support.« less

Pleistocene barrier bar seaward of ooid shoal complex near Miami, Florida

USGS Publications Warehouse

Halley, Robert B.; Shinn, Eugene A.; Hudson, J. Harold; Lidz, Barbara H.

1977-01-01

An ooid sand barrier bar of Pleistocene age was deposited along the seaward side of an ooid shoal complex southwest of Miami, Florida. The bar is 35 km long, about 0.8 km wide, elongate parallel with the trend of the ooid shoal complex and perpendicular to channels between individual shoals. A depression 1.6 km wide, interpreted as a back-barrier channel, isolates the bar from the ooid shoals. During sea-level fall and subaerial exposure of the bar, the ooid sand was cemented in place, preventing migration of the barrier. No Holocene analogue of this sand body is recognized, perhaps because of the relative youthfulness of Holocene ooid shoals. This Pleistocene ooid shoal complex, with its reservoir-size barrier bar, may serve as a refined model for exploration in ancient ooid sand belts.

Complex Fluids and Hydraulic Fracturing.

PubMed

Barbati, Alexander C; Desroches, Jean; Robisson, Agathe; McKinley, Gareth H

2016-06-07

Nearly 70 years old, hydraulic fracturing is a core technique for stimulating hydrocarbon production in a majority of oil and gas reservoirs. Complex fluids are implemented in nearly every step of the fracturing process, most significantly to generate and sustain fractures and transport and distribute proppant particles during and following fluid injection. An extremely wide range of complex fluids are used: naturally occurring polysaccharide and synthetic polymer solutions, aqueous physical and chemical gels, organic gels, micellar surfactant solutions, emulsions, and foams. These fluids are loaded over a wide range of concentrations with particles of varying sizes and aspect ratios and are subjected to extreme mechanical and environmental conditions. We describe the settings of hydraulic fracturing (framed by geology), fracturing mechanics and physics, and the critical role that non-Newtonian fluid dynamics and complex fluids play in the hydraulic fracturing process.

Tiger Team Assessment of the Fermi National Accelerator Laboratory

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

Not Available

1992-06-01

This draft report documents the Tiger Team Assessment of the Fermi National Accelerator Laboratory (Fermilab) located in Batavia, Illinois. Fermilab is a program-dedicated national laboratory managed by the Universities Research Association, Inc. (URA) for the US Department of Energy (DOE). The Tiger Team Assessment was conducted from May 11 to June 8, 1992, under the auspices of DOE`s Office of Special Projects (OSP) under the Office of the Assistant Secretary for Environment, Safety and Health (EH). The assessment was comprehensive, encompassing environmental, safety and health (ES&H), and quality assurance (QA) disciplines; site remediation; facilities management; and waste management operations. Compliancemore » with applicable Federal , State of Illinois, and local regulations; applicable DOE Orders; best management practices; and internal Fermilab requirements was addressed. In addition, an evaluation of the effectiveness of DOE and Fermilab management of the ES&H/QA and self-assessment programs was conducted. The Fermilab Tiger Team Assessment is part a larger, comprehensive DOE Tiger Team Independent Assessment Program planned for DOE facilities. The objective of the initiative is to provide the Secretary of Energy with information on the compliance status of DOE facilities with regard to ES&H requirements, root causes for noncompliance, adequacy of DOE and contractor ES&H management programs, response actions to address the identified problem areas, and DOE-wide ES&H compliance trends and root causes.« less

Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion

PubMed Central

Duroc, Yann; Kumar, Rajeev; Ranjha, Lepakshi; Adam, Céline; Guérois, Raphaël; Md Muntaz, Khan; Marsolier-Kergoat, Marie-Claude; Dingli, Florent; Laureau, Raphaëlle; Loew, Damarys; Llorente, Bertrand; Charbonnier, Jean-Baptiste; Cejka, Petr; Borde, Valérie

2017-01-01

Gene conversions resulting from meiotic recombination are critical in shaping genome diversification and evolution. How the extent of gene conversions is regulated is unknown. Here we show that the budding yeast mismatch repair related MutLβ complex, Mlh1-Mlh2, specifically interacts with the conserved meiotic Mer3 helicase, which recruits it to recombination hotspots, independently of mismatch recognition. This recruitment is essential to limit gene conversion tract lengths genome-wide, without affecting crossover formation. Contrary to expectations, Mer3 helicase activity, proposed to extend the displacement loop (D-loop) recombination intermediate, does not influence the length of gene conversion events, revealing non-catalytical roles of Mer3. In addition, both purified Mer3 and MutLβ preferentially recognize D-loops, providing a mechanism for limiting gene conversion in vivo. These findings show that MutLβ is an integral part of a new regulatory step of meiotic recombination, which has implications to prevent rapid allele fixation and hotspot erosion in populations. DOI: http://dx.doi.org/10.7554/eLife.21900.001 PMID:28051769

Sunspot seismology: accounting for magnetohydrodynamic wave processes using imaging spectropolarimetry

NASA Astrophysics Data System (ADS)

Rajaguru, S. P.

Effects of acoustic wave absorption, mode conversion and transmission by a sunspot on the helioseismic inferences are widely discussed, yet accounting for them has proved difficult for lack of a consistent framework within helioseismic modelling. Here, following a discussion of problems and issues that the near-surface magnetohydrodynamics hosts through a complex interplay of radiative transfer, measurement issues, and MHD wave processes, I present some possibilities entirely from observational analyses based on imaging spectropolarimetry. In particular, I present some results on wave evolution as a function of observation height and inclination of magnetic field to the vertical, derived from a high-cadence imaging spectropolarimetric observation of a sunspot and its surroundings using the instrument IBIS (NSO/Sac Peak, USA). These observations were made in magnetically sensitive (Fe I 6173 Å) and insensitive (Fe I 7090 Å) upper photospheric absorption lines. Wave travel time contributions from within the photospheric layers of a sunspot estimated here would then need to be removed from the inversion modelling procedure, that does not have the provision to account for them.

Surface Relief of Mapping

NASA Astrophysics Data System (ADS)

Costa, Manuel F.; Almeida, Jose B.

1989-02-01

We will describe in this communication a noncont act method of measuring surface profile, it does not require any surface preparation, and it can be used with a very large range of surfaces from highly reflecting to non reflecting ones and as complex as textile surfaces. This method is reasonably immune to dispersion and diffraction, which usually make very difficult the application of non contact profilometry methods to a wide range of materials and situations, namely on quality control systems in industrial production lines. The method is based on the horizontal shift of the bright spot on a horizontal surface when this is illuminated with an oblique beam and moved vertically. in order to make the profilometry the sample is swept by an oblique light beam and the bright spot position is compared with a reference position. The bright spot must be as small as possible, particularly in very irregular surfaces; so the light beam diameter must be as small as possible and the incidence angle must not be too small. The sensivity of a system based on this method will be given, mostly, by the reception optical system.

The global counterfeit drug trade: patient safety and public health risks.

PubMed

Mackey, Tim K; Liang, Bryan A

2011-11-01

Counterfeit drugs are a global problem with significant and well-documented consequences for global health and patient safety, including drug resistance and patient deaths. This multibillion-dollar industry does not respect geopolitical borders, and threatens public health in both rich and resource-poor nations alike. The epidemiology of counterfeits is also wide in breadth and scope, including thousands of counterfeit incidents per year, encompassing all types of therapeutic classes, and employing a complex global supply chain network enabling this illegal activity. In addition, information technologies available through the Internet and sales via online pharmacies have allowed the criminal element to thrive in an unregulated environment of anonymity, deception, and lack of adequate enforcement. Though recent global enforcement efforts have led to arrests of online counterfeit sellers, such actions have not stemmed supplies from illegal online sellers or kept up with their creativity in illegally selling their products. To address this issue, we propose a global policy framework utilizing public-private partnership models with centralized surveillance reporting that would enable cooperation and coordination to combat this global health crisis. Copyright © 2011 Wiley-Liss, Inc.

Superabsorbing, Artificial Metal Films Constructed from Semiconductor Nanoantennas.

PubMed

Kim, Soo Jin; Park, Junghyun; Esfandyarpour, Majid; Pecora, Emanuele F; Kik, Pieter G; Brongersma, Mark L

2016-06-08

In 1934, Wilhelm Woltersdorff demonstrated that the absorption of light in an ultrathin, freestanding film is fundamentally limited to 50%. He concluded that reaching this limit would require a film with a real-valued sheet resistance that is exactly equal to R = η/2 ≈ 188.5Ω/□, where [Formula: see text] is the impedance of free space. This condition can be closely approximated over a wide frequency range in metals that feature a large imaginary relative permittivity εr″, that is, a real-valued conductivity σ = ε0εr″ω. A thin, continuous sheet of semiconductor material does not facilitate such strong absorption as its complex-valued permittivity with both large real and imaginary components preclude effective impedance matching. In this work, we show how a semiconductor metafilm constructed from optically resonant semiconductor nanostructures can be created whose optical response mimics that of a metallic sheet. For this reason, the fundamental absorption limit mentioned above can also be reached with semiconductor materials, opening up new opportunities for the design of ultrathin optoelectronic and light harvesting devices.

Non-Cartesian MRI Reconstruction With Automatic Regularization Via Monte-Carlo SURE

PubMed Central

Weller, Daniel S.; Nielsen, Jon-Fredrik; Fessler, Jeffrey A.

2013-01-01

Magnetic resonance image (MRI) reconstruction from undersampled k-space data requires regularization to reduce noise and aliasing artifacts. Proper application of regularization however requires appropriate selection of associated regularization parameters. In this work, we develop a data-driven regularization parameter adjustment scheme that minimizes an estimate (based on the principle of Stein’s unbiased risk estimate—SURE) of a suitable weighted squared-error measure in k-space. To compute this SURE-type estimate, we propose a Monte-Carlo scheme that extends our previous approach to inverse problems (e.g., MRI reconstruction) involving complex-valued images. Our approach depends only on the output of a given reconstruction algorithm and does not require knowledge of its internal workings, so it is capable of tackling a wide variety of reconstruction algorithms and nonquadratic regularizers including total variation and those based on the ℓ1-norm. Experiments with simulated and real MR data indicate that the proposed approach is capable of providing near mean squared-error (MSE) optimal regularization parameters for single-coil undersampled non-Cartesian MRI reconstruction. PMID:23591478

Attractive design: an elution solvent optimization platform for magnetic-bead-based fractionation using digital microfluidics and design of experiments.

PubMed

Lafrenière, Nelson M; Mudrik, Jared M; Ng, Alphonsus H C; Seale, Brendon; Spooner, Neil; Wheeler, Aaron R

2015-04-07

There is great interest in the development of integrated tools allowing for miniaturized sample processing, including solid phase extraction (SPE). We introduce a new format for microfluidic SPE relying on C18-functionalized magnetic beads that can be manipulated in droplets in a digital microfluidic platform. This format provides the opportunity to tune the amount (and potentially the type) of stationary phase on-the-fly, and allows the removal of beads after the extraction (to enable other operations in same device-space), maintaining device reconfigurability. Using the new method, we employed a design of experiments (DOE) operation to enable automated on-chip optimization of elution solvent composition for reversed phase SPE of a model system. Further, conditions were selected to enable on-chip fractionation of multiple analytes. Finally, the method was demonstrated to be useful for online cleanup of extracts from dried blood spot (DBS) samples. We anticipate this combination of features will prove useful for separating a wide range of analytes, from small molecules to peptides, from complex matrices.

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

Li, Minghai; Duan, Mojie; Fan, Jue

The thermodynamics and kinetics of protein folding and protein conformational changes are governed by the underlying free energy landscape. However, the multidimensional nature of the free energy landscape makes it difficult to describe. We propose to use a weighted-graph approach to depict the free energy landscape with the nodes on the graph representing the conformational states and the edge weights reflecting the free energy barriers between the states. Our graph is constructed from a molecular dynamics trajectory and does not involve projecting the multi-dimensional free energy landscape onto a low-dimensional space defined by a few order parameters. The calculation ofmore » free energy barriers was based on transition-path theory using the MSMBuilder2 package. We compare our graph with the widely used transition disconnectivity graph (TRDG) which is constructed from the same trajectory and show that our approach gives more accurate description of the free energy landscape than the TRDG approach even though the latter can be organized into a simple tree representation. The weighted-graph is a general approach and can be used on any complex system.« less

How Does a Divided Population Respond to Change?

PubMed Central

Qubbaj, Murad R.; Muneepeerakul, Rachata; Aggarwal, Rimjhim M.; Anderies, John M.

2015-01-01

Most studies on the response of socioeconomic systems to a sudden shift focus on long-term equilibria or end points. Such narrow focus forgoes many valuable insights. Here we examine the transient dynamics of regime shift on a divided population, exemplified by societies divided ideologically, politically, economically, or technologically. Replicator dynamics is used to investigate the complex transient dynamics of the population response. Though simple, our modeling approach exhibits a surprisingly rich and diverse array of dynamics. Our results highlight the critical roles played by diversity in strategies and the magnitude of the shift. Importantly, it allows for a variety of strategies to arise organically as an integral part of the transient dynamics—as opposed to an independent process—of population response to a regime shift, providing a link between the population's past and future diversity patterns. Several combinations of different populations' strategy distributions and shifts were systematically investigated. Such rich dynamics highlight the challenges of anticipating the response of a divided population to a change. The findings in this paper can potentially improve our understanding of a wide range of socio-ecological and technological transitions. PMID:26161859

Fermi's Motion Produces a Study in Spirograph

NASA Image and Video Library

2013-02-27

Final still from Fermi video [bit.ly/Y2K4LN]. Credit: NASA/DOE/Fermi LAT Collaboration ----- NASA's Fermi Gamma-ray Space Telescope orbits our planet every 95 minutes, building up increasingly deeper views of the universe with every circuit. Its wide-eyed Large Area Telescope (LAT) sweeps across the entire sky every three hours, capturing the highest-energy form of light -- gamma rays -- from sources across the universe. These range from supermassive black holes billions of light-years away to intriguing objects in our own galaxy, such as X-ray binaries, supernova remnants and pulsars. Now a Fermi scientist has transformed LAT data of a famous pulsar into a mesmerizing movie that visually encapsulates the spacecraft's complex motion. Click here to continue reading: 1.usa.gov/WhYwCU NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

How Does a Divided Population Respond to Change?

PubMed

Qubbaj, Murad R; Muneepeerakul, Rachata; Aggarwal, Rimjhim M; Anderies, John M

2015-01-01

Most studies on the response of socioeconomic systems to a sudden shift focus on long-term equilibria or end points. Such narrow focus forgoes many valuable insights. Here we examine the transient dynamics of regime shift on a divided population, exemplified by societies divided ideologically, politically, economically, or technologically. Replicator dynamics is used to investigate the complex transient dynamics of the population response. Though simple, our modeling approach exhibits a surprisingly rich and diverse array of dynamics. Our results highlight the critical roles played by diversity in strategies and the magnitude of the shift. Importantly, it allows for a variety of strategies to arise organically as an integral part of the transient dynamics--as opposed to an independent process--of population response to a regime shift, providing a link between the population's past and future diversity patterns. Several combinations of different populations' strategy distributions and shifts were systematically investigated. Such rich dynamics highlight the challenges of anticipating the response of a divided population to a change. The findings in this paper can potentially improve our understanding of a wide range of socio-ecological and technological transitions.

CW-SSIM kernel based random forest for image classification

NASA Astrophysics Data System (ADS)

Fan, Guangzhe; Wang, Zhou; Wang, Jiheng

2010-07-01

Complex wavelet structural similarity (CW-SSIM) index has been proposed as a powerful image similarity metric that is robust to translation, scaling and rotation of images, but how to employ it in image classification applications has not been deeply investigated. In this paper, we incorporate CW-SSIM as a kernel function into a random forest learning algorithm. This leads to a novel image classification approach that does not require a feature extraction or dimension reduction stage at the front end. We use hand-written digit recognition as an example to demonstrate our algorithm. We compare the performance of the proposed approach with random forest learning based on other kernels, including the widely adopted Gaussian and the inner product kernels. Empirical evidences show that the proposed method is superior in its classification power. We also compared our proposed approach with the direct random forest method without kernel and the popular kernel-learning method support vector machine. Our test results based on both simulated and realworld data suggest that the proposed approach works superior to traditional methods without the feature selection procedure.

Fuzzy Logic Controller Stability Analysis Using a Satisfiability Modulo Theories Approach

NASA Technical Reports Server (NTRS)

Arnett, Timothy; Cook, Brandon; Clark, Matthew A.; Rattan, Kuldip

2017-01-01

While many widely accepted methods and techniques exist for validation and verification of traditional controllers, at this time no solutions have been accepted for Fuzzy Logic Controllers (FLCs). Due to the highly nonlinear nature of such systems, and the fact that developing a valid FLC does not require a mathematical model of the system, it is quite difficult to use conventional techniques to prove controller stability. Since safety-critical systems must be tested and verified to work as expected for all possible circumstances, the fact that FLC controllers cannot be tested to achieve such requirements poses limitations on the applications for such technology. Therefore, alternative methods for verification and validation of FLCs needs to be explored. In this study, a novel approach using formal verification methods to ensure the stability of a FLC is proposed. Main research challenges include specification of requirements for a complex system, conversion of a traditional FLC to a piecewise polynomial representation, and using a formal verification tool in a nonlinear solution space. Using the proposed architecture, the Fuzzy Logic Controller was found to always generate negative feedback, but inconclusive for Lyapunov stability.

Does the introduced brook trout ( Salvelinus fontinalis) affect growth of the native brown trout ( Salmo trutta)?

NASA Astrophysics Data System (ADS)

Korsu, Kai; Huusko, Ari; Muotka, Timo

2009-03-01

Non-native brook trout have become widely established in North European streams. We combined evidence from an artificial-stream experiment and drainage-scale field surveys to examine whether brook trout suppressed the growth of the native brown trout (age 0 to age 2). Our experimental results demonstrated that brown trout were unaffected by the presence of brook trout but that brook trout showed reduced growth in the presence of brown trout. However, the growth reduction only appeared in the experimental setting, indicating that the reduced spatial constraint of the experimental system may have forced the fish to unnaturally intense interactions. Indeed, in the field, no effect of either species on the growth of the putative competitor was detected. These results caution against uncritical acceptance of findings from small-scale experiments because they rarely scale up to more complex field situations. This and earlier work suggest that the establishment of brook trout in North European streams has taken place mainly because of the availability of unoccupied (or underutilized) niche space, rather than as a result of species trait combinations or interspecific competition per se.

Multiensemble Markov models of molecular thermodynamics and kinetics.

PubMed

Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank

2016-06-07

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models-clustering of high-dimensional spaces and modeling of complex many-state systems-with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein-ligand binding model.

Multiensemble Markov models of molecular thermodynamics and kinetics

PubMed Central

Wu, Hao; Paul, Fabian; Noé, Frank

2016-01-01

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models—clustering of high-dimensional spaces and modeling of complex many-state systems—with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein–ligand binding model. PMID:27226302

3D Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Parnell, Clare E.; Maclean, Rhona C.; Haynes, Andrew L.; Galsgaard, Klaus

2011-08-01

Magnetic reconnection is an important process that is prevalent in a wide range of astrophysical bodies. It is the mechanism that permits magnetic fields to relax to a lower energy state through the global restructuring of the magnetic field and is thus associated with a range of dynamic phenomena such as solar flares and CMEs. The characteristics of three-dimensional reconnection are reviewed revealing how much more diverse it is than reconnection in two dimensions. For instance, three-dimensional reconnection can occur both in the vicinity of null points, as well as in the absence of them. It occurs continuously and continually throughout a diffusion volume, as opposed to at a single point, as it does in two dimensions. This means that in three-dimensions field lines do not reconnect in pairs of lines making the visualisation and interpretation of three-dimensional reconnection difficult. By considering particular numerical 3D magnetohydrodynamic models of reconnection, we consider how magnetic reconnection can lead to complex magnetic topologies and current sheet formation. Indeed, it has been found that even simple interactions, such as the emergence of a flux tube, can naturally give rise to `turbulent-like' reconnection regions.

Low-complexity DOA estimation from short data snapshots for ULA systems using the annihilating filter technique

NASA Astrophysics Data System (ADS)

Bellili, Faouzi; Amor, Souheib Ben; Affes, Sofiène; Ghrayeb, Ali

2017-12-01

This paper addresses the problem of DOA estimation using uniform linear array (ULA) antenna configurations. We propose a new low-cost method of multiple DOA estimation from very short data snapshots. The new estimator is based on the annihilating filter (AF) technique. It is non-data-aided (NDA) and does not impinge therefore on the whole throughput of the system. The noise components are assumed temporally and spatially white across the receiving antenna elements. The transmitted signals are also temporally and spatially white across the transmitting sources. The new method is compared in performance to the Cramér-Rao lower bound (CRLB), the root-MUSIC algorithm, the deterministic maximum likelihood estimator and another Bayesian method developed precisely for the single snapshot case. Simulations show that the new estimator performs well over a wide SNR range. Prominently, the main advantage of the new AF-based method is that it succeeds in accurately estimating the DOAs from short data snapshots and even from a single snapshot outperforming by far the state-of-the-art techniques both in DOA estimation accuracy and computational cost.

Understanding Radionuclide Interactions with Layered Materials

NASA Astrophysics Data System (ADS)

Wang, Y.

2015-12-01

Layered materials play an important role in nuclear waste management and environmental cleanup. Better understanding of radionuclide interactions with those materials is critical for engineering high-performance materials for various applications. This presentation will provide an overview on radionuclide interactions with two general categories of layered materials - cationic clays and anionic clays - from a perspective of nanopore confinement. Nanopores are widely present in layered materials, either as the interlayers or as inter-particle space. Nanopore confinement can significantly modify chemical reactions in those materials. This effect may cause the preferential enrichment of radionuclides in nanopores and therefore directly impact the mobility of the radionuclides. This effect also implies that conventional sorption measurements using disaggregated samples may not represent chemical conditions in actual systems. The control of material structures on ion exchange, surface complexation, and diffusion in layered materials will be systematically examined, and the related modeling approaches will be discussed. This work was performed at Sandia National Laboratories, which is a multiprogram laboratory operated by Sandia Corporation, a Lockheed-Martin Company, for the DOE under contract DE-AC04-94AL8500.

The Structure of Coronal Loops

NASA Technical Reports Server (NTRS)

Antiochos, Spiro K.

2009-01-01

It is widely believed that the simple coronal loops observed by XUV imagers, such as EIT, TRACE, or XRT, actually have a complex internal structure consisting of many (perhaps hundreds) of unresolved, interwoven "strands". According to the nanoflare model, photospheric motions tangle the strands, causing them to reconnect and release the energy required to produce the observed loop plasma. Although the strands, themselves, are unresolved by present-generation imagers, there is compelling evidence for their existence and for the nanoflare model from analysis of loop intensities and temporal evolution. A problem with this scenario is that, although reconnection can eliminate some of the strand tangles, it cannot destroy helicity, which should eventually build up to observable scales. we consider, therefore, the injection and evolution of helicity by the nanoflare process and its implications for the observed structure of loops and the large-scale corona. we argue that helicity does survive and build up to observable levels, but on spatial and temporal scales larger than those of coronal loops. we discuss the implications of these results for coronal loops and the corona, in general .

Optimal Modality Selection for Cooperative Human-Robot Task Completion.

PubMed

Jacob, Mithun George; Wachs, Juan P

2016-12-01

Human-robot cooperation in complex environments must be fast, accurate, and resilient. This requires efficient communication channels where robots need to assimilate information using a plethora of verbal and nonverbal modalities such as hand gestures, speech, and gaze. However, even though hybrid human-robot communication frameworks and multimodal communication have been studied, a systematic methodology for designing multimodal interfaces does not exist. This paper addresses the gap by proposing a novel methodology to generate multimodal lexicons which maximizes multiple performance metrics over a wide range of communication modalities (i.e., lexicons). The metrics are obtained through a mixture of simulation and real-world experiments. The methodology is tested in a surgical setting where a robot cooperates with a surgeon to complete a mock abdominal incision and closure task by delivering surgical instruments. Experimental results show that predicted optimal lexicons significantly outperform predicted suboptimal lexicons (p <; 0.05) in all metrics validating the predictability of the methodology. The methodology is validated in two scenarios (with and without modeling the risk of a human-robot collision) and the differences in the lexicons are analyzed.

Trying to prevent abortion.

PubMed

Bromham, D R; Oloto, E J

1997-06-01

It is known that, since antiquity, women confronted with an unwanted pregnancy have used abortion as a means of resolving their dilemma. Although undoubtedly widely used in all historical ages, abortion has come to be regarded as an event preferably avoided because of the impact on the women concerned as well as considerations for fetal life. Policies to reduce numbers and rates of abortion must acknowledge certain observations. Criminalization does not prevent abortion but increases maternal risks. A society's 'openness' in discussing sexual matters inversely correlates with abortion rates. Correlation between contraceptive use and abortion is also inverse but relates most closely to the efficacy of contraceptive methods used. 'Revolution' in the range of contraceptive methods used will have an equivalent impact on abortion rates. Secondary or emergency contraceptive methods have a considerable role to play in the reduction of abortion numbers. Good sex (and 'relationships') education programs may delay sexual debut, increase contraceptive usage and be associated with reduced abortion. Finally, interaction between socioeconomic factors and the choice between abortion and ongoing pregnancy are complex. Abortion is not necessarily chosen by those least able to support a child financially.

DNA combing on low-pressure oxygen plasma modified polysilsesquioxane substrates for single-molecule studies

PubMed Central

Sriram, K. K.; Chang, Chun-Ling; Rajesh Kumar, U.; Chou, Chia-Fu

2014-01-01

Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versatility of microfluidics regarding robustness, buffer exchange capability, and molecule manipulation using external forces for single molecule studies. Here, we demonstrate a simple one-step combing process involving only low-pressure oxygen (O2) plasma modified polysilsesquioxane (PSQ) polymer layer to facilitate both room temperature microfluidic device bonding and immobilization of stretched single DNA molecules without molecular functionalization step. Atomic force microscopy and Kelvin probe force microscopy experiments revealed a significant increase in surface roughness and surface potential on low-pressure O2 plasma treated PSQ, in contrast to that with high-pressure O2 plasma treatment, which are proposed to be responsible for enabling effective DNA immobilization. We further demonstrate the use of our platform to observe DNA-RNA polymerase complexes and cancer drug cisplatin induced DNA condensation using wide-field fluorescence imaging. PMID:25332730

Increasing Energy Access in Sub-Saharan Africa: Exploring Public-Private Models for Intervention

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

Bazilian, Morgan; Pless, Jacquelyn

This report, by Morgan Bazilian and Jacquelyn Pless, examines ways that Energy+ could make a large impact in providing energy access to the poor, focusing on four promising models. While there remains a focus on a technology (PV), and a region (SSA) in this report, the models the authors explore are amenable to other specifications as well. Thus, the models presented provide an opportunity for stakeholders and the international community to collaborate and leverage capacities, resources, and networks. Of course, these models are only a few of the very wide range of possible mechanisms. They also are somewhat focused onmore » engaging the private sector. The report does not provide a full context for the complex landscape of energy access and energy poverty. Rather, the paper is focused around the specifics of the interventions. It remains the case that the fundamental building blocks of capacity building, good governance and planning, and the ability to find funding for 'upfront' due diligence and analysis remain critical. Those items are, however, largely outside the scope of this short report.« less

Air pollution: a smoking gun for cancer

PubMed Central

Zhang, Wei; Qian, Chao-Nan; Zeng, Yi-Xin

2014-01-01

Once considered a taboo topic or stigma, cancer is the number one public health enemy in the world. Once a product of an almost untouchable industry, tobacco is indisputably recognized as a major cause of cancer and a target for anticancer efforts. With the emergence of new economic powers in the world, especially in highly populated countries such as China, air pollution has rapidly emerged as a smoking gun for cancer and has become a hot topic for public health debate because of the complex political, economic, scientific, and technologic issues surrounding the air pollution problem. This editorial and the referred articles published in this special issue of the Chinese Journal of Cancer discuss these fundamental questions. Does air pollution cause a wide spectrum of cancers? Should air pollution be considered a necessary evil accompanying economic transformation in developing countries? Is an explosion of cancer incidence coming to China and how soon will it arrive? What must be done to prevent this possible human catastrophe? Finally, the approaches for air pollution control are also discussed. PMID:24636233

Current knowledge in Polypodium leucotomos effect on skin protection.

PubMed

Palomino, Olga María

2015-04-01

This article provides an overview of pharmacology, toxicity, pharmacokinetics and clinical data of Polypodium leucotomos L. (PL). PL aerial part has proven to exert antioxidant, photoprotective and immunomodulatory activities; its mechanism of action is complex and includes several activities: (1) PL diminishes the production of reactive oxygen and nitrogen species (ROS, RNS); (2) PL inhibits the photoisomerization of trans-urocanic acid (t-UCA); (3) PL inhibits apoptosis induced by ultraviolet radiation; (4) PL prevents damage to genetic material and (5) PL enhances DNA repair. PL is not mutagenic and does not induce acute or chronic toxicity. Its biological effects have been proved in cell cultures, animal models, murine models and in human beings. Photoprotective activity has been assessed in healthy volunteers as well as in patients suffering from several cutaneous diseases such as vitiligo, psoriasis, idiopathic photodermatosis or melasma. PL results to be an efficient treatment especially for sensitive cutaneous phototypes and adds extra protection when ultraviolet radiation (UVR) exposure cannot be avoided, such as wide or narrow band UVB phototherapy or treatment with psoralens plus UVA exposure radiation.

A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa.

PubMed

Ficklin, Stephen P; Feltus, Frank Alex

2013-01-01

Many traits of biological and agronomic significance in plants are controlled in a complex manner where multiple genes and environmental signals affect the expression of the phenotype. In Oryza sativa (rice), thousands of quantitative genetic signals have been mapped to the rice genome. In parallel, thousands of gene expression profiles have been generated across many experimental conditions. Through the discovery of networks with real gene co-expression relationships, it is possible to identify co-localized genetic and gene expression signals that implicate complex genotype-phenotype relationships. In this work, we used a knowledge-independent, systems genetics approach, to discover a high-quality set of co-expression networks, termed Gene Interaction Layers (GILs). Twenty-two GILs were constructed from 1,306 Affymetrix microarray rice expression profiles that were pre-clustered to allow for improved capture of gene co-expression relationships. Functional genomic and genetic data, including over 8,000 QTLs and 766 phenotype-tagged SNPs (p-value < = 0.001) from genome-wide association studies, both covering over 230 different rice traits were integrated with the GILs. An online systems genetics data-mining resource, the GeneNet Engine, was constructed to enable dynamic discovery of gene sets (i.e. network modules) that overlap with genetic traits. GeneNet Engine does not provide the exact set of genes underlying a given complex trait, but through the evidence of gene-marker correspondence, co-expression, and functional enrichment, site visitors can identify genes with potential shared causality for a trait which could then be used for experimental validation. A set of 2 million SNPs was incorporated into the database and serve as a potential set of testable biomarkers for genes in modules that overlap with genetic traits. Herein, we describe two modules found using GeneNet Engine, one with significant overlap with the trait amylose content and another with significant overlap with blast disease resistance.

A Systems-Genetics Approach and Data Mining Tool to Assist in the Discovery of Genes Underlying Complex Traits in Oryza sativa

PubMed Central

Ficklin, Stephen P.; Feltus, Frank Alex

2013-01-01

Many traits of biological and agronomic significance in plants are controlled in a complex manner where multiple genes and environmental signals affect the expression of the phenotype. In Oryza sativa (rice), thousands of quantitative genetic signals have been mapped to the rice genome. In parallel, thousands of gene expression profiles have been generated across many experimental conditions. Through the discovery of networks with real gene co-expression relationships, it is possible to identify co-localized genetic and gene expression signals that implicate complex genotype-phenotype relationships. In this work, we used a knowledge-independent, systems genetics approach, to discover a high-quality set of co-expression networks, termed Gene Interaction Layers (GILs). Twenty-two GILs were constructed from 1,306 Affymetrix microarray rice expression profiles that were pre-clustered to allow for improved capture of gene co-expression relationships. Functional genomic and genetic data, including over 8,000 QTLs and 766 phenotype-tagged SNPs (p-value < = 0.001) from genome-wide association studies, both covering over 230 different rice traits were integrated with the GILs. An online systems genetics data-mining resource, the GeneNet Engine, was constructed to enable dynamic discovery of gene sets (i.e. network modules) that overlap with genetic traits. GeneNet Engine does not provide the exact set of genes underlying a given complex trait, but through the evidence of gene-marker correspondence, co-expression, and functional enrichment, site visitors can identify genes with potential shared causality for a trait which could then be used for experimental validation. A set of 2 million SNPs was incorporated into the database and serve as a potential set of testable biomarkers for genes in modules that overlap with genetic traits. Herein, we describe two modules found using GeneNet Engine, one with significant overlap with the trait amylose content and another with significant overlap with blast disease resistance. PMID:23874666

A Multi-Breed Genome-Wide Association Analysis for Canine Hypothyroidism Identifies a Shared Major Risk Locus on CFA12.

PubMed

Bianchi, Matteo; Dahlgren, Stina; Massey, Jonathan; Dietschi, Elisabeth; Kierczak, Marcin; Lund-Ziener, Martine; Sundberg, Katarina; Thoresen, Stein Istre; Kämpe, Olle; Andersson, Göran; Ollier, William E R; Hedhammar, Åke; Leeb, Tosso; Lindblad-Toh, Kerstin; Kennedy, Lorna J; Lingaas, Frode; Rosengren Pielberg, Gerli

2015-01-01

Hypothyroidism is a complex clinical condition found in both humans and dogs, thought to be caused by a combination of genetic and environmental factors. In this study we present a multi-breed analysis of predisposing genetic risk factors for hypothyroidism in dogs using three high-risk breeds--the Gordon Setter, Hovawart and the Rhodesian Ridgeback. Using a genome-wide association approach and meta-analysis, we identified a major hypothyroidism risk locus shared by these breeds on chromosome 12 (p = 2.1x10(-11)). Further characterisation of the candidate region revealed a shared ~167 kb risk haplotype (4,915,018-5,081,823 bp), tagged by two SNPs in almost complete linkage disequilibrium. This breed-shared risk haplotype includes three genes (LHFPL5, SRPK1 and SLC26A8) and does not extend to the dog leukocyte antigen (DLA) class II gene cluster located in the vicinity. These three genes have not been identified as candidate genes for hypothyroid disease previously, but have functions that could potentially contribute to the development of the disease. Our results implicate the potential involvement of novel genes and pathways for the development of canine hypothyroidism, raising new possibilities for screening, breeding programmes and treatments in dogs. This study may also contribute to our understanding of the genetic etiology of human hypothyroid disease, which is one of the most common endocrine disorders in humans.

A Multi-Breed Genome-Wide Association Analysis for Canine Hypothyroidism Identifies a Shared Major Risk Locus on CFA12

PubMed Central

Massey, Jonathan; Dietschi, Elisabeth; Kierczak, Marcin; Lund-Ziener, Martine; Sundberg, Katarina; Thoresen, Stein Istre; Kämpe, Olle; Andersson, Göran; Ollier, William E. R.; Hedhammar, Åke; Leeb, Tosso; Lindblad-Toh, Kerstin; Kennedy, Lorna J.; Lingaas, Frode; Rosengren Pielberg, Gerli

2015-01-01

Hypothyroidism is a complex clinical condition found in both humans and dogs, thought to be caused by a combination of genetic and environmental factors. In this study we present a multi-breed analysis of predisposing genetic risk factors for hypothyroidism in dogs using three high-risk breeds—the Gordon Setter, Hovawart and the Rhodesian Ridgeback. Using a genome-wide association approach and meta-analysis, we identified a major hypothyroidism risk locus shared by these breeds on chromosome 12 (p = 2.1x10-11). Further characterisation of the candidate region revealed a shared ~167 kb risk haplotype (4,915,018–5,081,823 bp), tagged by two SNPs in almost complete linkage disequilibrium. This breed-shared risk haplotype includes three genes (LHFPL5, SRPK1 and SLC26A8) and does not extend to the dog leukocyte antigen (DLA) class II gene cluster located in the vicinity. These three genes have not been identified as candidate genes for hypothyroid disease previously, but have functions that could potentially contribute to the development of the disease. Our results implicate the potential involvement of novel genes and pathways for the development of canine hypothyroidism, raising new possibilities for screening, breeding programmes and treatments in dogs. This study may also contribute to our understanding of the genetic etiology of human hypothyroid disease, which is one of the most common endocrine disorders in humans. PMID:26261983

Network-wide BGP route prediction for traffic engineering

NASA Astrophysics Data System (ADS)

Feamster, Nick; Rexford, Jennifer

2002-07-01

The Internet consists of about 13,000 Autonomous Systems (AS's) that exchange routing information using the Border Gateway Protocol (BGP). The operators of each AS must have control over the flow of traffic through their network and between neighboring AS's. However, BGP is a complicated, policy-based protocol that does not include any direct support for traffic engineering. In previous work, we have demonstrated that network operators can adapt the flow of traffic in an efficient and predictable fashion through careful adjustments to the BGP policies running on their edge routers. Nevertheless, many details of the BGP protocol and decision process make predicting the effects of these policy changes difficult. In this paper, we describe a tool that predicts traffic flow at network exit points based on the network topology, the import policy associated with each BGP session, and the routing advertisements received from neighboring AS's. We present a linear-time algorithm that computes a network-wide view of the best BGP routes for each destination prefix given a static snapshot of the network state, without simulating the complex details of BGP message passing. We describe how to construct this snapshot using the BGP routing tables and router configuration files available from operational routers. We verify the accuracy of our algorithm by applying our tool to routing and configuration data from AT&T's commercial IP network. Our route prediction techniques help support the operation of large IP backbone networks, where interdomain routing is an important aspect of traffic engineering.

Ultra-thin and strong formvar-based membranes with controlled porosity for micro- and nano-scale systems

DOE PAGES

Auchter, Eric Lawrence; Marquez, Justin Ryan; Stevens, Garrison Nicole; ...

2018-03-28

Here, we present a methodology for developing ultra-thin and strong formvar-based membranes with controlled morphologies. Formvar is a thin hydrophilic and oleophilic polymer inert to most chemicals and resistant to radiation. The formvar-based membranes are viable materials as support structures in micro- and macro-scale systems depending on thinness and porosity control. Tunable sub-micron thick porous membranes with 20%–65% porosity were synthesized by controlling the ratios of formvar, glycerol, and chloroform. This synthesis process does not require complex separation or handling methods and allows for the production of strong, thin, and porous formvar-based membranes. An expansive array of these membrane characterizationsmore » including chemical compatibility, mechanical responses, wettability, as well as the mathematical simulations as a function of porosity has been presented. The wide range of chemical compatibility allows for membrane applications in various environments, where other polymers would not be suitable. Our formvar-based membranes were found to have an elastic modulus of 7.8 GPa, a surface free energy of 50 mN m -1 and an average thickness of 125 nm. Stochastic model simulations indicate that formvar with the porosity of ~50% is the optimal membrane formulation, allowing the most material transfer across the membrane while also withstanding the highest simulated pressure loadings before tearing. Development of novel, resilient and versatile membranes with controlled porosity offers a wide range of exciting applications in the fields of nanoscience, microfluidics, and MEMS.« less

Examination of Association to Autism of Common Genetic Variation in Genes Related to Dopamine

PubMed Central

Anderson, B.M.; Schnetz-Boutaud, N.; Bartlett, J.; Wright, H.H.; Abramson, R.K.; Cuccaro, M.L.; Gilbert, J.R.; Pericak-Vance, M.A.; Haines, J.L.

2010-01-01

Autism is a severe neurodevelopmental disorder characterized by a triad of complications. Autistic individuals display significant disturbances in language and reciprocal social interactions, combined with repetitive and stereotypic behaviors. Prevalence studies suggest that autism is more common than originally believed, with recent estimates citing a rate of one in 150. Although this genomic approach has yielded multiple suggestive regions, a specific risk locus has yet to be identified and widely confirmed. Because many etiologies have been suggested for this complex syndrome, we hypothesize that one of the difficulties in identifying autism genes is that multiple genetic variants may be required to significantly increase the risk of developing autism. Thus we took the alternative approach of examining 14 prominent dopamine pathway candidate genes for detailed study by genotyping 28 SNPs. Although we did observe a nominally significant association for rs2239535 (p=.008) on chromosome 20, single locus analysis did not reveal any results as significant after correction for multiple comparisons. No significant interaction was identified when Multifactor Dimensionality Reduction (MDR) was employed to test specifically for multilocus effects. Although genome-wide linkage scans in autism have provided support for linkage to various loci along the dopamine pathway, our study does not provide strong evidence of linkage or association to any specific gene or combination of genes within the pathway. These results demonstrate that common genetic variation within the tested genes located within this pathway at most play a minor to moderate role in overall autism pathogenesis. PMID:19360691