Designing a new structure for storing nuclear data: Progress of the Working Party for Evaluation Cooperation subgroup #38

DOE PAGES

Mattoon, C. M.; Beck, B. R.

2015-12-24

An international effort is underway to design a new structure for storing and using nuclear reaction data, with the goal of eventually replacing the current standard, ENDF-6. This effort, organized by the Working Party for Evaluation Cooperation, was initiated in 2012 and has resulted in a list of requirements and specifications for how the proposed new structure shall perform. The new structure will take advantage of new developments in computational tools, using a nested hierarchy to store data. Here, the structure can be stored in text form (such as an XML file) for human readability and data sharing, or itmore » can be stored in binary to optimize data access. In this paper, we present the progress towards completing the requirements, specifications and implementation of the new structure.« less

Designing a new structure for storing nuclear data: Progress of the Working Party for Evaluation Cooperation subgroup #38

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

Mattoon, C. M.; Beck, B. R.

An international effort is underway to design a new structure for storing and using nuclear reaction data, with the goal of eventually replacing the current standard, ENDF-6. This effort, organized by the Working Party for Evaluation Cooperation, was initiated in 2012 and has resulted in a list of requirements and specifications for how the proposed new structure shall perform. The new structure will take advantage of new developments in computational tools, using a nested hierarchy to store data. Here, the structure can be stored in text form (such as an XML file) for human readability and data sharing, or itmore » can be stored in binary to optimize data access. In this paper, we present the progress towards completing the requirements, specifications and implementation of the new structure.« less

Field-induced assembly of colloidal ellipsoids into well-defined microtubules

PubMed Central

Crassous, Jérôme J.; Mihut, Adriana M.; Wernersson, Erik; Pfleiderer, Patrick; Vermant, Jan; Linse, Per; Schurtenberger, Peter

2014-01-01

Current theoretical attempts to understand the reversible formation of stable microtubules and virus shells are generally based on shape-specific building blocks or monomers, where the local curvature of the resulting structure is explicitly built-in via the monomer geometry. Here we demonstrate that even simple ellipsoidal colloids can reversibly self-assemble into regular tubular structures when subjected to an alternating electric field. Supported by model calculations, we discuss the combined effects of anisotropic shape and field-induced dipolar interactions on the reversible formation of self-assembled structures. Our observations show that the formation of tubular structures through self-assembly requires much less geometrical and interaction specificity than previously thought, and advance our current understanding of the minimal requirements for self-assembly into regular virus-like structures. PMID:25409686

System requirements specification for SMART structures mode

NASA Technical Reports Server (NTRS)

1992-01-01

Specified here are the functional and informational requirements for software modules which address the geometric and data modeling needs of the aerospace structural engineer. The modules are to be included as part of the Solid Modeling Aerospace Research Tool (SMART) package developed for the Vehicle Analysis Branch (VAB) at the NASA Langley Research Center (LaRC). The purpose is to precisely state what the SMART Structures modules will do, without consideration of how it will be done. Each requirement is numbered for reference in development and testing.

Testis-specific ATP synthase peripheral stalk subunits required for tissue-specific mitochondrial morphogenesis in Drosophila.

PubMed

Sawyer, Eric M; Brunner, Elizabeth C; Hwang, Yihharn; Ivey, Lauren E; Brown, Olivia; Bannon, Megan; Akrobetu, Dennis; Sheaffer, Kelsey E; Morgan, Oshauna; Field, Conroy O; Suresh, Nishita; Gordon, M Grace; Gunnell, E Taylor; Regruto, Lindsay A; Wood, Cricket G; Fuller, Margaret T; Hales, Karen G

2017-03-23

In Drosophila early post-meiotic spermatids, mitochondria undergo dramatic shaping into the Nebenkern, a spherical body with complex internal structure that contains two interwrapped giant mitochondrial derivatives. The purpose of this study was to elucidate genetic and molecular mechanisms underlying the shaping of this structure. The knotted onions (knon) gene encodes an unconventionally large testis-specific paralog of ATP synthase subunit d and is required for internal structure of the Nebenkern as well as its subsequent disassembly and elongation. Knon localizes to spermatid mitochondria and, when exogenously expressed in flight muscle, alters the ratio of ATP synthase complex dimers to monomers. By RNAi knockdown we uncovered mitochondrial shaping roles for other testis-expressed ATP synthase subunits. We demonstrate the first known instance of a tissue-specific ATP synthase subunit affecting tissue-specific mitochondrial morphogenesis. Since ATP synthase dimerization is known to affect the degree of inner mitochondrial membrane curvature in other systems, the effect of Knon and other testis-specific paralogs of ATP synthase subunits may be to mediate differential membrane curvature within the Nebenkern.

Earth Observatory Satellite system definition study. Report no. 3: Design/cost tradeoff studies. Appendix C: EOS program requirements document

NASA Technical Reports Server (NTRS)

1974-01-01

An analysis of the requirements for the Earth Observatory Satellite (EOS) system specifications is presented. The analysis consists of requirements obtained from existing documentation and those derived from functional analysis. The requirements follow the hierarchy of program, mission, system, and subsystem. The code for designating specific requirements is explained. Among the subjects considered are the following: (1) the traffic model, (2) space shuttle related performance, (3) booster related performance, (4) the data collection system, (5) spacecraft structural tests, and (6) the ground support requirements.

Mission-oriented requirements for updating MIL-H-8501. Volume 1: STI proposed structure. [military rotorcraft

NASA Technical Reports Server (NTRS)

Clement, W. F.; Hoh, R. H.; Ferguson, S. W., III; Mitchell, D. G.; Ashkenas, I. L.; Mcruer, D. T.

1985-01-01

The structure of a new flying and ground handling qualities specification for military rotorcraft is presented. This preliminary specification structure is intended to evolve into a replacement for specification MIL-H-8501A. The new structure is designed to accommodate a variety of rotorcraft types, mission flight phases, flight envelopes, and flight environmental characteristics and to provide criteria for three levels of flying qualities, a systematic treatment of failures and reliability, both conventional and multiaxis controllers, and external vision aids which may also incorporate synthetic display content. Existing and new criteria were incorporated into the new structure wherever they could be substantiated.

Direct Administration of Nerve-Specific Contrast to Improve Nerve Sparing Radical Prostatectomy

PubMed Central

Barth, Connor W.; Gibbs, Summer L.

2017-01-01

Nerve damage remains a major morbidity following nerve sparing radical prostatectomy, significantly affecting quality of life post-surgery. Nerve-specific fluorescence guided surgery offers a potential solution by enhancing nerve visualization intraoperatively. However, the prostate is highly innervated and only the cavernous nerve structures require preservation to maintain continence and potency. Systemic administration of a nerve-specific fluorophore would lower nerve signal to background ratio (SBR) in vital nerve structures, making them difficult to distinguish from all nervous tissue in the pelvic region. A direct administration methodology to enable selective nerve highlighting for enhanced nerve SBR in a specific nerve structure has been developed herein. The direct administration methodology demonstrated equivalent nerve-specific contrast to systemic administration at optimal exposure times. However, the direct administration methodology provided a brighter fluorescent nerve signal, facilitating nerve-specific fluorescence imaging at video rate, which was not possible following systemic administration. Additionally, the direct administration methodology required a significantly lower fluorophore dose than systemic administration, that when scaled to a human dose falls within the microdosing range. Furthermore, a dual fluorophore tissue staining method was developed that alleviates fluorescence background signal from adipose tissue accumulation using a spectrally distinct adipose tissue specific fluorophore. These results validate the use of the direct administration methodology for specific nerve visualization with fluorescence image-guided surgery, which would improve vital nerve structure identification and visualization during nerve sparing radical prostatectomy. PMID:28255352

Direct Administration of Nerve-Specific Contrast to Improve Nerve Sparing Radical Prostatectomy.

PubMed

Barth, Connor W; Gibbs, Summer L

2017-01-01

Nerve damage remains a major morbidity following nerve sparing radical prostatectomy, significantly affecting quality of life post-surgery. Nerve-specific fluorescence guided surgery offers a potential solution by enhancing nerve visualization intraoperatively. However, the prostate is highly innervated and only the cavernous nerve structures require preservation to maintain continence and potency. Systemic administration of a nerve-specific fluorophore would lower nerve signal to background ratio (SBR) in vital nerve structures, making them difficult to distinguish from all nervous tissue in the pelvic region. A direct administration methodology to enable selective nerve highlighting for enhanced nerve SBR in a specific nerve structure has been developed herein. The direct administration methodology demonstrated equivalent nerve-specific contrast to systemic administration at optimal exposure times. However, the direct administration methodology provided a brighter fluorescent nerve signal, facilitating nerve-specific fluorescence imaging at video rate, which was not possible following systemic administration. Additionally, the direct administration methodology required a significantly lower fluorophore dose than systemic administration, that when scaled to a human dose falls within the microdosing range. Furthermore, a dual fluorophore tissue staining method was developed that alleviates fluorescence background signal from adipose tissue accumulation using a spectrally distinct adipose tissue specific fluorophore. These results validate the use of the direct administration methodology for specific nerve visualization with fluorescence image-guided surgery, which would improve vital nerve structure identification and visualization during nerve sparing radical prostatectomy.

Rotor systems research aircraft predesign study. Volume 4: Preliminary draft detail specification

NASA Technical Reports Server (NTRS)

Miller, A. N.; Linden, A. W.

1972-01-01

The RSRA requirements are presented in a detail specification format. Coverage of the requirements includes the following headings: (1) aircraft characteristics, (2) general features of design and construction, (3) aerodynamics, (4) structural design criteria, (5) flight control system, (6) propulsion subsystem, and (7) secondary power and distribution subsystem.

Space Generic Open Avionics Architecture (SGOAA) standard specification

NASA Technical Reports Server (NTRS)

Wray, Richard B.; Stovall, John R.

1994-01-01

This standard establishes the Space Generic Open Avionics Architecture (SGOAA). The SGOAA includes a generic functional model, processing structural model, and an architecture interface model. This standard defines the requirements for applying these models to the development of spacecraft core avionics systems. The purpose of this standard is to provide an umbrella set of requirements for applying the generic architecture models to the design of a specific avionics hardware/software processing system. This standard defines a generic set of system interface points to facilitate identification of critical services and interfaces. It establishes the requirement for applying appropriate low level detailed implementation standards to those interfaces points. The generic core avionics functions and processing structural models provided herein are robustly tailorable to specific system applications and provide a platform upon which the interface model is to be applied.

Structuring Formal Control Systems Specifications for Reuse: Surviving Hardware Changes

NASA Technical Reports Server (NTRS)

Thompson, Jeffrey M.; Heimdahl, Mats P. E.; Erickson, Debra M.

2000-01-01

Formal capture and analysis of the required behavior of control systems have many advantages. For instance, it encourages rigorous requirements analysis, the required behavior is unambiguously defined, and we can assure that various safety properties are satisfied. Formal modeling is, however, a costly and time consuming process and if one could reuse the formal models over a family of products, significant cost savings would be realized. In an ongoing project we are investigating how to structure state-based models to achieve a high level of reusability within product families. In this paper we discuss a high-level structure of requirements models that achieves reusability of the desired control behavior across varying hardware platforms in a product family. The structuring approach is demonstrated through a case study in the mobile robotics domain where the desired robot behavior is reused on two diverse platforms-one commercial mobile platform and one build in-house. We use our language RSML (-e) to capture the control behavior for reuse and our tool NIMBUS to demonstrate how the formal specification can be validated and used as a prototype on the two platforms.

Structural Design Requirements and Factors of Safety for Spaceflight Hardware: For Human Spaceflight. Revision A

NASA Technical Reports Server (NTRS)

Bernstein, Karen S.; Kujala, Rod; Fogt, Vince; Romine, Paul

2011-01-01

This document establishes the structural requirements for human-rated spaceflight hardware including launch vehicles, spacecraft and payloads. These requirements are applicable to Government Furnished Equipment activities as well as all related contractor, subcontractor and commercial efforts. These requirements are not imposed on systems other than human-rated spacecraft, such as ground test articles, but may be tailored for use in specific cases where it is prudent to do so such as for personnel safety or when assets are at risk. The requirements in this document are focused on design rather than verification. Implementation of the requirements is expected to be described in a Structural Verification Plan (SVP), which should describe the verification of each structural item for the applicable requirements. The SVP may also document unique verifications that meet or exceed these requirements with NASA Technical Authority approval.

49 CFR 229.141 - Body structure, MU locomotives.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Body structure, MU locomotives. 229.141 Section... Design Requirements § 229.141 Body structure, MU locomotives. (a) MU locomotives built new after April 1... body structure designed to meet or exceed the following minimum specifications: (1) The body structure...

Integrated flight/propulsion control - Subsystem specifications for performance

NASA Technical Reports Server (NTRS)

Neighbors, W. K.; Rock, Stephen M.

1993-01-01

A procedure is presented for calculating multiple subsystem specifications given a number of performance requirements on the integrated system. This procedure applies to problems where the control design must be performed in a partitioned manner. It is based on a structured singular value analysis, and generates specifications as magnitude bounds on subsystem uncertainties. The performance requirements should be provided in the form of bounds on transfer functions of the integrated system. This form allows the expression of model following, command tracking, and disturbance rejection requirements. The procedure is demonstrated on a STOVL aircraft design.

18 CFR 12.35 - Specific inspection requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

...) Seismicity; (ix) Internal stress and hydrostatic pressures in project structures or their foundations or... structures; (iii) The structural adequacy and stability of structures under all credible loading conditions... project works to withstand the loading or overtopping which may occur from a flood up to the probable...

18 CFR 12.35 - Specific inspection requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

...) Seismicity; (ix) Internal stress and hydrostatic pressures in project structures or their foundations or... structures; (iii) The structural adequacy and stability of structures under all credible loading conditions... project works to withstand the loading or overtopping which may occur from a flood up to the probable...

Automatic Dynamic Aircraft Modeler (ADAM) for the Computer Program NASTRAN

NASA Technical Reports Server (NTRS)

Griffis, H.

1985-01-01

Large general purpose finite element programs require users to develop large quantities of input data. General purpose pre-processors are used to decrease the effort required to develop structural models. Further reduction of effort can be achieved by specific application pre-processors. Automatic Dynamic Aircraft Modeler (ADAM) is one such application specific pre-processor. General purpose pre-processors use points, lines and surfaces to describe geometric shapes. Specifying that ADAM is used only for aircraft structures allows generic structural sections, wing boxes and bodies, to be pre-defined. Hence with only gross dimensions, thicknesses, material properties and pre-defined boundary conditions a complete model of an aircraft can be created.

Impact of Requirements Quality on Project Success or Failure

NASA Astrophysics Data System (ADS)

Tamai, Tetsuo; Kamata, Mayumi Itakura

We are interested in the relationship between the quality of the requirements specifications for software projects and the subsequent outcome of the projects. To examine this relationship, we investigated 32 projects started and completed between 2003 and 2005 by the software development division of a large company in Tokyo. The company has collected reliable data on requirements specification quality, as evaluated by software quality assurance teams, and overall project performance data relating to cost and time overruns. The data for requirements specification quality were first converted into a multiple-dimensional space, with each dimension corresponding to an item of the recommended structure for software requirements specifications (SRS) defined in IEEE Std. 830-1998. We applied various statistical analysis methods to the SRS quality data and project outcomes.

Technology update: Tethered aerostat structural design and material developments

NASA Technical Reports Server (NTRS)

Witherow, R. G.

1975-01-01

Requirements exist for an extremely stable, high performance, all-weather tethered aerostat system. This requirement has been satisfied by a 250,000 cubic foot captive buoyant vehicle as demonstrated by over a year of successful field operations. This achievement required significant advancements in several technology areas including composite materials design, aerostatics and aerodynamics, structural design, electro-mechanical design, vehicle fabrication and mooring operations. This paper specifically addresses the materials and structural design aspects of pressurized buoyant vehicles as related to the general class of Lighter Than Air vehicles.

Specific binding of a HeLa cell nuclear protein to RNA sequences in the human immunodeficiency virus transactivating region.

PubMed Central

Gaynor, R; Soultanakis, E; Kuwabara, M; Garcia, J; Sigman, D S

1989-01-01

The transactivator protein, tat, encoded by the human immunodeficiency virus is a key regulator of viral transcription. Activation by the tat protein requires sequences downstream of the transcription initiation site called the transactivating region (TAR). RNA derived from the TAR is capable of forming a stable stem-loop structure and the maintenance of both the stem structure and the loop sequences located between +19 and +44 is required for complete in vivo activation by tat. Gel retardation assays with RNA from both wild-type and mutant TAR constructs generated in vitro with SP6 polymerase indicated specific binding of HeLa nuclear proteins to the TAR. To characterize this RNA-protein interaction, a method of chemical "imprinting" has been developed using photoactivated uranyl acetate as the nucleolytic agent. This reagent nicks RNA under physiological conditions at all four nucleotides in a reaction that is independent of sequence and secondary structure. Specific interaction of cellular proteins with TAR RNA could be detected by enhanced cleavages or imprints surrounding the loop region. Mutations that either disrupted stem base-pairing or extensively changed the primary sequence resulted in alterations in the cleavage pattern of the TAR RNA. Structural features of the TAR RNA stem-loop essential for tat activation are also required for specific binding of the HeLa cell nuclear protein. Images PMID:2544877

Exploration Planetary Surface Structural Systems: Design Requirements and Compliance

NASA Technical Reports Server (NTRS)

Dorsey, John T.

2011-01-01

The Lunar Surface Systems Project developed system concepts that would be necessary to establish and maintain a permanent human presence on the Lunar surface. A variety of specific system implementations were generated as a part of the scenarios, some level of system definition was completed, and masses estimated for each system. Because the architecture studies generally spawned a large number of system concepts and the studies were executed in a short amount of time, the resulting system definitions had very low design fidelity. This paper describes the development sequence required to field a particular structural system: 1) Define Requirements, 2) Develop the Design and 3) Demonstrate Compliance of the Design to all Requirements. This paper also outlines and describes in detail the information and data that are required to establish structural design requirements and outlines the information that would comprise a planetary surface system Structures Requirements document.

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

PubMed

Dong, F; Allawi, H T; Anderson, T; Neri, B P; Lyamichev, V I

2001-08-01

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

A structural-alphabet-based strategy for finding structural motifs across protein families

PubMed Central

Wu, Chih Yuan; Chen, Yao Chi; Lim, Carmay

2010-01-01

Proteins with insignificant sequence and overall structure similarity may still share locally conserved contiguous structural segments; i.e. structural/3D motifs. Most methods for finding 3D motifs require a known motif to search for other similar structures or functionally/structurally crucial residues. Here, without requiring a query motif or essential residues, a fully automated method for discovering 3D motifs of various sizes across protein families with different folds based on a 16-letter structural alphabet is presented. It was applied to structurally non-redundant proteins bound to DNA, RNA, obligate/non-obligate proteins as well as free DNA-binding proteins (DBPs) and proteins with known structures but unknown function. Its usefulness was illustrated by analyzing the 3D motifs found in DBPs. A non-specific motif was found with a ‘corner’ architecture that confers a stable scaffold and enables diverse interactions, making it suitable for binding not only DNA but also RNA and proteins. Furthermore, DNA-specific motifs present ‘only’ in DBPs were discovered. The motifs found can provide useful guidelines in detecting binding sites and computational protein redesign. PMID:20525797

29 CFR 1926.651 - Specific excavation requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... designed by a competent person. Structural ramps used for access or egress of equipment shall be designed by a competent person qualified in structural design, and shall be constructed in accordance with the design. (ii) Ramps and runways constructed of two or more structural members shall have the structural...

29 CFR 1926.651 - Specific excavation requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... designed by a competent person. Structural ramps used for access or egress of equipment shall be designed by a competent person qualified in structural design, and shall be constructed in accordance with the design. (ii) Ramps and runways constructed of two or more structural members shall have the structural...

29 CFR 1926.651 - Specific excavation requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... designed by a competent person. Structural ramps used for access or egress of equipment shall be designed by a competent person qualified in structural design, and shall be constructed in accordance with the design. (ii) Ramps and runways constructed of two or more structural members shall have the structural...

29 CFR 1926.651 - Specific excavation requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... designed by a competent person. Structural ramps used for access or egress of equipment shall be designed by a competent person qualified in structural design, and shall be constructed in accordance with the design. (ii) Ramps and runways constructed of two or more structural members shall have the structural...

29 CFR 1926.651 - Specific excavation requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... designed by a competent person. Structural ramps used for access or egress of equipment shall be designed by a competent person qualified in structural design, and shall be constructed in accordance with the design. (ii) Ramps and runways constructed of two or more structural members shall have the structural...

Concept-based query language approach to enterprise information systems

NASA Astrophysics Data System (ADS)

Niemi, Timo; Junkkari, Marko; Järvelin, Kalervo

2014-01-01

In enterprise information systems (EISs) it is necessary to model, integrate and compute very diverse data. In advanced EISs the stored data often are based both on structured (e.g. relational) and semi-structured (e.g. XML) data models. In addition, the ad hoc information needs of end-users may require the manipulation of data-oriented (structural), behavioural and deductive aspects of data. Contemporary languages capable of treating this kind of diversity suit only persons with good programming skills. In this paper we present a concept-oriented query language approach to manipulate this diversity so that the programming skill requirements are considerably reduced. In our query language, the features which need technical knowledge are hidden in application-specific concepts and structures. Therefore, users need not be aware of the underlying technology. Application-specific concepts and structures are represented by the modelling primitives of the extended RDOOM (relational deductive object-oriented modelling) which contains primitives for all crucial real world relationships (is-a relationship, part-of relationship, association), XML documents and views. Our query language also supports intensional and extensional-intensional queries, in addition to conventional extensional queries. In its query formulation, the end-user combines available application-specific concepts and structures through shared variables.

Experimental demonstration of the control of flexible structures

NASA Technical Reports Server (NTRS)

Schaechter, D. B.; Eldred, D. B.

1984-01-01

The Large Space Structure Technology Flexible Beam Experiment employs a pinned-free flexible beam to demonstrate such required methods as dynamic and adaptive control, as well as various control law design approaches and hardware requirements. An attempt is made to define the mechanization difficulties that may inhere in flexible structures. Attention is presently given to analytical work performed in support of the test facility's development, the final design's specifications, the control laws' synthesis, and experimental results obtained.

Micronucleus-specific histone H1 is required for micronuclear chromosome integrity in Tetrahymena thermophila

PubMed Central

Qiao, Juxia; Xu, Jing; Bo, Tao

2017-01-01

Histone H1 molecules play a key role in establishing and maintaining higher order chromatin structures. They can bind to linker DNA entering and exiting the nucleosome and regulate transcriptional activity. Tetrahymena thermophila has two histone H1, namely, macronuclear histone H1 and micronuclear histone H1 (Mlh1). Mlh1 is specifically localized at micronuclei during growth and starvation stages. Moreover, Mlh1 is localized around micronuclei and forms a specific structure during the conjugation stage. It co-localizes partially with spindle apparatus during micronuclear meiosis. Analysis of MLH1 knock-out revealed that Mlh1 was required for the micronuclear integrity and development during conjugation stage. Overexpression of Mlh1 led to abnormal conjugation progression. RT-PCR analysis indicated that the expression level of HMGB3 increased in ΔMLH1 strains, while the expression level of MLH1 increased in ΔHMGB3 cells during conjugation. These results indicate that micronuclear integrity and sexual development require normal expression level of Mlh1 and that HmgB3 and Mlh1 may functionally compensate each other in regulating micronuclear structure in T. thermophila. PMID:29095884

46 CFR 164.007-5 - Test requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 6 2014-10-01 2014-10-01 false Test requirements. 164.007-5 Section 164.007-5 Shipping...: SPECIFICATIONS AND APPROVAL MATERIALS Structural Insulations § 164.007-5 Test requirements. The insulation value of the specimens for the full scale test shall be such that the average temperature of the...

Heparin/heparan sulfate 6-O-sulfatase from Flavobacterium heparinum: integrated structural and biochemical investigation of enzyme active site and substrate specificity.

PubMed

Myette, James R; Soundararajan, Venkataramanan; Shriver, Zachary; Raman, Rahul; Sasisekharan, Ram

2009-12-11

Heparin and heparan sulfate glycosaminoglycans (HSGAGs) comprise a chemically heterogeneous class of sulfated polysaccharides. The development of structure-activity relationships for this class of polysaccharides requires the identification and characterization of degrading enzymes with defined substrate specificity and enzymatic activity. Toward this end, we report here the molecular cloning and extensive structure-function analysis of a 6-O-sulfatase from the Gram-negative bacterium Flavobacterium heparinum. In addition, we report the recombinant expression of this enzyme in Escherichia coli in a soluble, active form and identify it as a specific HSGAG sulfatase. We further define the mechanism of action of the enzyme through biochemical and structural studies. Through the use of defined substrates, we investigate the kinetic properties of the enzyme. This analysis was complemented by homology-based molecular modeling studies that sought to rationalize the substrate specificity of the enzyme and mode of action through an analysis of the active-site topology of the enzyme including identifying key enzyme-substrate interactions and assigning key amino acids within the active site of the enzyme. Taken together, our structural and biochemical studies indicate that 6-O-sulfatase is a predominantly exolytic enzyme that specifically acts on N-sulfated or N-acetylated 6-O-sulfated glucosamines present at the non-reducing end of HSGAG oligosaccharide substrates. This requirement for the N-acetyl or N-sulfo groups on the glucosamine substrate can be explained through eliciting favorable interactions with key residues within the active site of the enzyme. These findings provide a framework that enables the use of 6-O-sulfatase as a tool for HSGAG structure-activity studies as well as expand our biochemical and structural understanding of this important class of enzymes.

24 CFR 200.944 - Supplementary specific requirements under the HUD building product standards and certification...

Code of Federal Regulations, 2012 CFR

2012-04-01

... rated wood-based structural-use panels. 200.944 Section 200.944 Housing and Urban Development... product standards and certification program for plywood and other performance rated wood-based structural... building product certification program. In the case of plywood and wood-based structural-use panels...

24 CFR 200.944 - Supplementary specific requirements under the HUD building product standards and certification...

Code of Federal Regulations, 2014 CFR

2014-04-01

... rated wood-based structural-use panels. 200.944 Section 200.944 Housing and Urban Development... product standards and certification program for plywood and other performance rated wood-based structural... building product certification program. In the case of plywood and wood-based structural-use panels...

24 CFR 200.944 - Supplementary specific requirements under the HUD building product standards and certification...

Code of Federal Regulations, 2013 CFR

2013-04-01

... rated wood-based structural-use panels. 200.944 Section 200.944 Housing and Urban Development... product standards and certification program for plywood and other performance rated wood-based structural... building product certification program. In the case of plywood and wood-based structural-use panels...

24 CFR 200.944 - Supplementary specific requirements under the HUD building product standards and certification...

Code of Federal Regulations, 2011 CFR

2011-04-01

... rated wood-based structural-use panels. 200.944 Section 200.944 Housing and Urban Development... product standards and certification program for plywood and other performance rated wood-based structural... building product certification program. In the case of plywood and wood-based structural-use panels...

24 CFR 200.944 - Supplementary specific requirements under the HUD building product standards and certification...

Code of Federal Regulations, 2010 CFR

2010-04-01

... rated wood-based structural-use panels. 200.944 Section 200.944 Housing and Urban Development... product standards and certification program for plywood and other performance rated wood-based structural... building product certification program. In the case of plywood and wood-based structural-use panels...

Advanced aeroservoelastic stabilization techniques for hypersonic flight vehicles

NASA Technical Reports Server (NTRS)

Chan, Samuel Y.; Cheng, Peter Y.; Myers, Thomas T.; Klyde, David H.; Magdaleno, Raymond E.; Mcruer, Duane T.

1992-01-01

Advanced high performance vehicles, including Single-Stage-To-Orbit (SSTO) hypersonic flight vehicles, that are statically unstable, require higher bandwidth flight control systems to compensate for the instability resulting in interactions between the flight control system, the engine/propulsion dynamics, and the low frequency structural modes. Military specifications, such as MIL-F-9490D and MIL-F-87242, tend to limit treatment of structural modes to conventional gain stabilization techniques. The conventional gain stabilization techniques, however, introduce low frequency effective time delays which can be troublesome from a flying qualities standpoint. These time delays can be alleviated by appropriate blending of gain and phase stabilization techniques (referred to as Hybrid Phase Stabilization or HPS) for the low frequency structural modes. The potential of using HPS for compensating structural mode interaction was previously explored. It was shown that effective time delay was significantly reduced with the use of HPS; however, the HPS design was seen to have greater residual response than a conventional gain stablized design. Additional work performed to advance and refine the HPS design procedure, to further develop residual response metrics as a basis for alternative structural stability specifications, and to develop strategies for validating HPS design and specification concepts in manned simulation is presented. Stabilization design sensitivity to structural uncertainties and aircraft-centered requirements are also assessed.

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

Goodman, Kerry M.; Yamagata, Masahito; Jin, Xiangshu

Sidekick (Sdk) 1 and 2 are related immunoglobulin superfamily cell adhesion proteins required for appropriate synaptic connections between specific subtypes of retinal neurons. Sdks mediate cell-cell adhesion with homophilic specificity that underlies their neuronal targeting function. Here we report crystal structures of Sdk1 and Sdk2 ectodomain regions, revealing similar homodimers mediated by the four N-terminal immunoglobulin domains (Ig1–4), arranged in a horseshoe conformation. These Ig1–4 horseshoes interact in a novel back-to-back orientation in both homodimers through Ig1:Ig2, Ig1:Ig1 and Ig3:Ig4 interactions. Structure-guided mutagenesis results show that this canonical dimer is required for both Sdk-mediated cell aggregation (viatransinteractions) and Sdk clusteringmore » in isolated cells (viacisinteractions). Sdk1/Sdk2 recognition specificity is encoded across Ig1–4, with Ig1–2 conferring the majority of binding affinity and differential specificity. We suggest that competition betweencisandtransinteractions provides a novel mechanism to sharpen the specificity of cell-cell interactions.« less

Fluid density and concentration measurement using noninvasive in situ ultrasonic resonance interferometry

DOEpatents

Pope, Noah G.; Veirs, Douglas K.; Claytor, Thomas N.

1994-01-01

The specific gravity or solute concentration of a process fluid solution located in a selected structure is determined by obtaining a resonance response spectrum of the fluid/structure over a range of frequencies that are outside the response of the structure itself. A fast fourier transform (FFT) of the resonance response spectrum is performed to form a set of FFT values. A peak value for the FFT values is determined, e.g., by curve fitting, to output a process parameter that is functionally related to the specific gravity and solute concentration of the process fluid solution. Calibration curves are required to correlate the peak FFT value over the range of expected specific gravities and solute concentrations in the selected structure.

Fluid density and concentration measurement using noninvasive in situ ultrasonic resonance interferometry

DOEpatents

Pope, N.G.; Veirs, D.K.; Claytor, T.N.

1994-10-25

The specific gravity or solute concentration of a process fluid solution located in a selected structure is determined by obtaining a resonance response spectrum of the fluid/structure over a range of frequencies that are outside the response of the structure itself. A fast Fourier transform (FFT) of the resonance response spectrum is performed to form a set of FFT values. A peak value for the FFT values is determined, e.g., by curve fitting, to output a process parameter that is functionally related to the specific gravity and solute concentration of the process fluid solution. Calibration curves are required to correlate the peak FFT value over the range of expected specific gravities and solute concentrations in the selected structure. 7 figs.

Fracture control procedures for aircraft structural integrity

NASA Technical Reports Server (NTRS)

Wood, H. A.

1972-01-01

The application of applied fracture mechanics in the design, analysis, and qualification of aircraft structural systems are reviewed. Recent service experiences are cited. Current trends in high-strength materials application are reviewed with particular emphasis on the manner in which fracture toughness and structural efficiency may affect the material selection process. General fracture control procedures are reviewed in depth with specific reference to the impact of inspectability, structural arrangement, and material on proposed analysis requirements for safe crack growth. The relative impact on allowable design stress is indicated by example. Design criteria, material, and analysis requirements for implementation of fracture control procedures are reviewed together with limitations in current available data techniques. A summary of items which require further study and attention is presented.

Just-in-time Design and Additive Manufacture of Patient-specific Medical Implants

NASA Astrophysics Data System (ADS)

Shidid, Darpan; Leary, Martin; Choong, Peter; Brandt, Milan

Recent advances in medical imaging and manufacturing science have enabled the design and production of complex, patient-specific orthopaedic implants. Additive Manufacture (AM) generates three-dimensional structures layer by layer, and is not subject to the constraints associated with traditional manufacturing methods. AM provides significant opportunities for the design of novel geometries and complex lattice structures with enhanced functional performance. However, the design and manufacture of patient-specific AM implant structures requires unique expertise in handling various optimization platforms. Furthermore, the design process for complex structures is computationally intensive. The primary aim of this research is to enable the just-in-time customisation of AM prosthesis; whereby AM implant design and manufacture be completed within the time constraints of a single surgical procedure, while minimising prosthesis mass and optimising the lattice structure to match the stiffness of the surrounding bone tissue. In this research, a design approach using raw CT scan data is applied to the AM manufacture of femoral prosthesis. Using the proposed just-in-time concept, the mass of the prosthesis was rapidly designed and manufactured while satisfying the associated structural requirements. Compressive testing of lattice structures manufactured using proposed method shows that the load carrying capacity of the resected composite bone can be recovered by up to 85% and the compressive stiffness of the AM prosthesis is statistically indistinguishable from the stiffness of the initial bone.

Software reliability: Application of a reliability model to requirements error analysis

NASA Technical Reports Server (NTRS)

Logan, J.

1980-01-01

The application of a software reliability model having a well defined correspondence of computer program properties to requirements error analysis is described. Requirements error categories which can be related to program structural elements are identified and their effect on program execution considered. The model is applied to a hypothetical B-5 requirement specification for a program module.

Spatial Abilities of High-School Students in the Perception of Geologic Structures.

ERIC Educational Resources Information Center

Kali, Yael; Orion, Nir

1996-01-01

Characterizes specific spatial abilities required in geology studies through the examination of the performance of high school students in solving structural geology problems on the geologic spatial ability test (GeoSAT). Concludes that visual penetration ability and the ability to perceive the spatial configuration of the structure are…

Meiosis-Specific Cohesin Component, Stag3 Is Essential for Maintaining Centromere Chromatid Cohesion, and Required for DNA Repair and Synapsis between Homologous Chromosomes

PubMed Central

Hopkins, Jessica; Bedigian, Rick; Oka, Kazuhiro; Overbeek, Paul; Murray, Steve; Jordan, Philip W.

2014-01-01

Cohesins are important for chromosome structure and chromosome segregation during mitosis and meiosis. Cohesins are composed of two structural maintenance of chromosomes (SMC1-SMC3) proteins that form a V-shaped heterodimer structure, which is bridged by a α-kleisin protein and a stromal antigen (STAG) protein. Previous studies in mouse have shown that there is one SMC1 protein (SMC1β), two α-kleisins (RAD21L and REC8) and one STAG protein (STAG3) that are meiosis-specific. During meiosis, homologous chromosomes must recombine with one another in the context of a tripartite structure known as the synaptonemal complex (SC). From interaction studies, it has been shown that there are at least four meiosis-specific forms of cohesin, which together with the mitotic cohesin complex, are lateral components of the SC. STAG3 is the only meiosis-specific subunit that is represented within all four meiosis-specific cohesin complexes. In Stag3 mutant germ cells, the protein level of other meiosis-specific cohesin subunits (SMC1β, RAD21L and REC8) is reduced, and their localization to chromosome axes is disrupted. In contrast, the mitotic cohesin complex remains intact and localizes robustly to the meiotic chromosome axes. The instability of meiosis-specific cohesins observed in Stag3 mutants results in aberrant DNA repair processes, and disruption of synapsis between homologous chromosomes. Furthermore, mutation of Stag3 results in perturbation of pericentromeric heterochromatin clustering, and disruption of centromere cohesion between sister chromatids during meiotic prophase. These defects result in early prophase I arrest and apoptosis in both male and female germ cells. The meiotic defects observed in Stag3 mutants are more severe when compared to single mutants for Smc1β, Rec8 and Rad21l, however they are not as severe as the Rec8, Rad21l double mutants. Taken together, our study demonstrates that STAG3 is required for the stability of all meiosis-specific cohesin complexes. Furthermore, our data suggests that STAG3 is required for structural changes of chromosomes that mediate chromosome pairing and synapsis, DNA repair and progression of meiosis. PMID:24992337

Meiosis-specific cohesin component, Stag3 is essential for maintaining centromere chromatid cohesion, and required for DNA repair and synapsis between homologous chromosomes.

PubMed

Hopkins, Jessica; Hwang, Grace; Jacob, Justin; Sapp, Nicklas; Bedigian, Rick; Oka, Kazuhiro; Overbeek, Paul; Murray, Steve; Jordan, Philip W

2014-07-01

Cohesins are important for chromosome structure and chromosome segregation during mitosis and meiosis. Cohesins are composed of two structural maintenance of chromosomes (SMC1-SMC3) proteins that form a V-shaped heterodimer structure, which is bridged by a α-kleisin protein and a stromal antigen (STAG) protein. Previous studies in mouse have shown that there is one SMC1 protein (SMC1β), two α-kleisins (RAD21L and REC8) and one STAG protein (STAG3) that are meiosis-specific. During meiosis, homologous chromosomes must recombine with one another in the context of a tripartite structure known as the synaptonemal complex (SC). From interaction studies, it has been shown that there are at least four meiosis-specific forms of cohesin, which together with the mitotic cohesin complex, are lateral components of the SC. STAG3 is the only meiosis-specific subunit that is represented within all four meiosis-specific cohesin complexes. In Stag3 mutant germ cells, the protein level of other meiosis-specific cohesin subunits (SMC1β, RAD21L and REC8) is reduced, and their localization to chromosome axes is disrupted. In contrast, the mitotic cohesin complex remains intact and localizes robustly to the meiotic chromosome axes. The instability of meiosis-specific cohesins observed in Stag3 mutants results in aberrant DNA repair processes, and disruption of synapsis between homologous chromosomes. Furthermore, mutation of Stag3 results in perturbation of pericentromeric heterochromatin clustering, and disruption of centromere cohesion between sister chromatids during meiotic prophase. These defects result in early prophase I arrest and apoptosis in both male and female germ cells. The meiotic defects observed in Stag3 mutants are more severe when compared to single mutants for Smc1β, Rec8 and Rad21l, however they are not as severe as the Rec8, Rad21l double mutants. Taken together, our study demonstrates that STAG3 is required for the stability of all meiosis-specific cohesin complexes. Furthermore, our data suggests that STAG3 is required for structural changes of chromosomes that mediate chromosome pairing and synapsis, DNA repair and progression of meiosis.

A virtual intranet and data-warehousing for healthcare co-operation.

PubMed

Kerkri, E M; Quantin, C; Grison, T; Allaert, F A; Tchounikine, A; Yétongnon, K

2001-01-01

As patient's medical data is disseminated in different health structures, developing a medical or epidemiological patient-oriented data warehouse has some specific requirements compared to intra healthcare structure data-warehousing projects. The difference is that the healthcare structures implicated in a patient-oriented data warehouse project require some considerations about the confidentiality of the patient data and of the activities of healthcare structures. Building a data-warehousing system at a regional level, for example in cancerology, requires the participation of all concerned health structures, as well as different health professionals. The heterogeneity of sources medical data of has to be taken into account for choosing between several organizational configurations of the data warehousing system. In top of data warehousing, we propose a concept of Virtual Intranet, which provides a solution to the problem of medical information security arising from heterogeneous sources.

Structural features, substrate specificity, kinetic properties of insect α-amylase and specificity of plant α-amylase inhibitors.

PubMed

Kaur, Rimaljeet; Kaur, Narinder; Gupta, Anil Kumar

2014-11-01

α-Amylase is an important digestive enzyme required for the optimal growth and development of insects. Several insect α-amylases had been purified and their physical and chemical properties were characterized. Insect α-amylases of different orders display variability in structure, properties and substrate specificity. Such diverse properties of amylases could be due to different feeding habits and gut environment of insects. In this review, structural features and properties of several insect α-amylases were compared. This could be helpful in exploring the diversity in characteristics of α-amylase between the members of the same class (insecta). Properties like pH optima are reflected in enzyme structural features. In plants, α-amylase inhibitors (α-AIs) occur as part of natural defense mechanisms against pests by interfering in their digestion process and thus could also provide access to new pest management strategies. AIs are quite specific in their action; therefore, these could be employed according to their effectiveness against target amylases. Potential of transgenics with α-AIs has also been discussed for insect resistance and controlling infestation. The differences in structural features of insect α-amylases provided reasons for their efficient functioning at different pH and the specificity towards various substrates. Various proteinaceous and non-proteinaceous inhibitors discussed could be helpful in controlling pest infestation. In depth detailed studies are required on proteinaceous α-AI-α-amylase interaction at different pH's as well as the insect proteinase action on these inhibitors before selecting the α-AI for making transgenics resistant to particular insect. Copyright © 2014 Elsevier Inc. All rights reserved.

Modeling of additive manufacturing processes for metals: Challenges and opportunities

DOE PAGES

Francois, Marianne M.; Sun, Amy; King, Wayne E.; ...

2017-01-09

Here, with the technology being developed to manufacture metallic parts using increasingly advanced additive manufacturing processes, a new era has opened up for designing novel structural materials, from designing shapes and complex geometries to controlling the microstructure (alloy composition and morphology). The material properties used within specific structural components are also designable in order to meet specific performance requirements that are not imaginable with traditional metal forming and machining (subtractive) techniques.

40 CFR 52.919 - Identification of plan-conditional approval.

Code of Federal Regulations, 2014 CFR

2014-07-01

... sections 110(a)(2)(C) and 110(a)(2)(J) as they both relate to Prevention of Significant Deterioration (PSD... requirements promulgated in the New Source Review (NSR) PM2.5 Rule related to the PM2.5 standard for their PSD... specific enforceable measures related the structural PSD requirements of the PSD and NNSR requirements...

40 CFR 52.919 - Identification of plan-conditional approval.

Code of Federal Regulations, 2013 CFR

2013-07-01

... sections 110(a)(2)(C) and 110(a)(2)(J) as they both relate to Prevention of Significant Deterioration (PSD... requirements promulgated in the New Source Review (NSR) PM2.5 Rule related to the PM2.5 standard for their PSD... specific enforceable measures related the structural PSD requirements of the PSD and NNSR requirements...

Conceptual design of ACB-CP for ITER cryogenic system

NASA Astrophysics Data System (ADS)

Jiang, Yongcheng; Xiong, Lianyou; Peng, Nan; Tang, Jiancheng; Liu, Liqiang; Zhang, Liang

2012-06-01

ACB-CP (Auxiliary Cold Box for Cryopumps) is used to supply the cryopumps system with necessary cryogen in ITER (International Thermonuclear Experimental Reactor) cryogenic distribution system. The conceptual design of ACB-CP contains thermo-hydraulic analysis, 3D structure design and strength checking. Through the thermohydraulic analysis, the main specifications of process valves, pressure safety valves, pipes, heat exchangers can be decided. During the 3D structure design process, vacuum requirement, adiabatic requirement, assembly constraints and maintenance requirement have been considered to arrange the pipes, valves and other components. The strength checking has been performed to crosscheck if the 3D design meets the strength requirements for the ACB-CP.

Aging management program of the reactor building concrete at Point Lepreau Generating Station

NASA Astrophysics Data System (ADS)

Aldea, C.-M.; Shenton, B.; Demerchant, M. M.; Gendron, T.

2011-04-01

In order for New Brunswick Power Nuclear (NBPN) to control the risks of degradation of the concrete reactor building at the Point Lepreau Generating Station (PLGS) the development of an aging management plan (AMP) was initiated. The intention of this plan was to determine the requirements for specific structural components of concrete of the reactor building that require regular inspection and maintenance to ensure the safe and reliable operation of the plant. The document is currently in draft form and presents an integrated methodology for the application of an AMP for the concrete of the reactor building. The current AMP addresses the reactor building structure and various components, such as joint sealant and liners that are integral to the structure. It does not include internal components housed within the structure. This paper provides background information regarding the document developed and the strategy developed to manage potential degradation of the concrete of the reactor building, as well as specific programs and preventive and corrective maintenance activities initiated.

Insight into structural remodeling of the FlhA ring responsible for bacterial flagellar type III protein export

PubMed Central

2018-01-01

The bacterial flagellum is a supramolecular motility machine. Flagellar assembly begins with the basal body, followed by the hook and finally the filament. A carboxyl-terminal cytoplasmic domain of FlhA (FlhAC) forms a nonameric ring structure in the flagellar type III protein export apparatus and coordinates flagellar protein export with assembly. However, the mechanism of this process remains unknown. We report that a flexible linker of FlhAC (FlhAL) is required not only for FlhAC ring formation but also for substrate specificity switching of the protein export apparatus from the hook protein to the filament protein upon completion of the hook structure. FlhAL was required for cooperative ring formation of FlhAC. Alanine substitutions of residues involved in FlhAC ring formation interfered with the substrate specificity switching, thereby inhibiting filament assembly at the hook tip. These observations lead us to propose a mechanistic model for export switching involving structural remodeling of FlhAC. PMID:29707633

Network operating system focus technology

NASA Technical Reports Server (NTRS)

1985-01-01

An activity structured to provide specific design requirements and specifications for the Space Station Data Management System (DMS) Network Operating System (NOS) is outlined. Examples are given of the types of supporting studies and implementation tasks presently underway to realize a DMS test bed capability to develop hands-on understanding of NOS requirements as driven by actual subsystem test beds participating in the overall Johnson Space Center test bed program. Classical operating system elements and principal NOS functions are listed.

Data Mining of Macromolecular Structures.

PubMed

van Beusekom, Bart; Perrakis, Anastassis; Joosten, Robbie P

2016-01-01

The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.

Fragger: a protein fragment picker for structural queries.

PubMed

Berenger, Francois; Simoncini, David; Voet, Arnout; Shrestha, Rojan; Zhang, Kam Y J

2017-01-01

Protein modeling and design activities often require querying the Protein Data Bank (PDB) with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.

Basis of Accreditation for Educational Programs in Designated Health Science Professions.

ERIC Educational Resources Information Center

Canadian Medical Association, Ottawa (Ontario).

Designed as a guide to accreditation for educational programs in designated health science professions in Canada, this report provides educators with guidelines, general requirements, and requirements for specific programs. Following information on the organization, structure, goals, mission, values, philosophy, and terminology of accreditation of…

Identification of emergent off-nominal operational requirements during conceptual architecting of the more electric aircraft

NASA Astrophysics Data System (ADS)

Armstrong, Michael James

Increases in power demands and changes in the design practices of overall equipment manufacturers has led to a new paradigm in vehicle systems definition. The development of unique power systems architectures is of increasing importance to overall platform feasibility and must be pursued early in the aircraft design process. Many vehicle systems architecture trades must be conducted concurrent to platform definition. With an increased complexity introduced during conceptual design, accurate predictions of unit level sizing requirements must be made. Architecture specific emergent requirements must be identified which arise due to the complex integrated effect of unit behaviors. Off-nominal operating scenarios present sizing critical requirements to the aircraft vehicle systems. These requirements are architecture specific and emergent. Standard heuristically defined failure mitigation is sufficient for sizing traditional and evolutionary architectures. However, architecture concepts which vary significantly in terms of structure and composition require that unique failure mitigation strategies be defined for accurate estimations of unit level requirements. Identifying of these off-nominal emergent operational requirements require extensions to traditional safety and reliability tools and the systematic identification of optimal performance degradation strategies. Discrete operational constraints posed by traditional Functional Hazard Assessment (FHA) are replaced by continuous relationships between function loss and operational hazard. These relationships pose the objective function for hazard minimization. Load shedding optimization is performed for all statistically significant failures by varying the allocation of functional capability throughout the vehicle systems architecture. Expressing hazards, and thereby, reliability requirements as continuous relationships with the magnitude and duration of functional failure requires augmentations to the traditional means for system safety assessment (SSA). The traditional two state and discrete system reliability assessment proves insufficient. Reliability is, therefore, handled in an analog fashion: as a function of magnitude of failure and failure duration. A series of metrics are introduced which characterize system performance in terms of analog hazard probabilities. These include analog and cumulative system and functional risk, hazard correlation, and extensions to the traditional component importance metrics. Continuous FHA, load shedding optimization, and analog SSA constitute the SONOMA process (Systematic Off-Nominal Requirements Analysis). Analog system safety metrics inform both architecture optimization (changes in unit level capability and reliability) and architecture augmentation (changes in architecture structure and composition). This process was applied for two vehicle systems concepts (conventional and 'more-electric') in terms of loss/hazard relationships with varying degrees of fidelity. Application of this process shows that the traditional assumptions regarding the structure of the function loss vs. hazard relationship apply undue design bias to functions and components during exploratory design. This bias is illustrated in terms of inaccurate estimations of the system and function level risk and unit level importance. It was also shown that off-nominal emergent requirements must be defined specific to each architecture concept. Quantitative comparisons of architecture specific off-nominal performance were obtained which provide evidence to the need for accurate definition of load shedding strategies during architecture exploratory design. Formally expressing performance degradation strategies in terms of the minimization of a continuous hazard space enhances the system architects ability to accurately predict sizing critical emergent requirements concurrent to architecture definition. Furthermore, the methods and frameworks generated here provide a structured and flexible means for eliciting these architecture specific requirements during the performance of architecture trades.

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

49 CFR 238.209 - Forward end structure of locomotives, including cab cars and MU locomotives.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Forward end structure of locomotives, including... SAFETY STANDARDS Specific Requirements for Tier I Passenger Equipment § 238.209 Forward end structure of... locomotive, including a cab car and an MU locomotive, shall be: (i) Equivalent to a 1/2-inch steel plate with...

Basis of Accreditation for Educational Programs in Allied Medical Disciplines.

ERIC Educational Resources Information Center

Canadian Medical Association, Ottawa (Ontario).

Designed as a guide to accreditation for educational programs in the allied medical disciplines in Canada, this report provides educators with guidelines, general requirements and requirements for specific programs. Following information on the organization, structure, goals and terminology of accreditation of allied medical programs in Canada,…

Software Requirements

DTIC Science & Technology

1990-01-01

Real-Time Systems Specifications 11 Convenient Auto Rental System Marea82 12 Systems Architecture Marca , D. A., and C. L. McGowan. "Static and...Requirements Marca88 Structured Analysis. Orr’s work is worthy of study Marca , D. A., and C. L. McGowan. SADT: Struc- by the instructor, since it enjoys

46 CFR 91.55-5 - Plans and specifications required for new construction.

Code of Federal Regulations, 2010 CFR

2010-10-01

... systems. (e) Marine engineering. For plans required for marine engineering equipment and systems, see... electrical engineering, equipment and systems, see subchapter J (Electrical Engineering) of this chapter. (g... bottoms, etc., and including inboard and outboard profile. (b) Hull structure. 1 (1) *Inner Bottom Plating...

Structural analysis consultation using artificial intelligence

NASA Technical Reports Server (NTRS)

Melosh, R. J.; Marcal, P. V.; Berke, L.

1978-01-01

The primary goal of consultation is definition of the best strategy to deal with a structural engineering analysis objective. The knowledge base to meet the need is designed to identify the type of numerical analysis, the needed modeling detail, and specific analysis data required. Decisions are constructed on the basis of the data in the knowledge base - material behavior, relations between geometry and structural behavior, measures of the importance of time and temperature changes - and user supplied specifics characteristics of the spectrum of analysis types, the relation between accuracy and model detail on the structure, its mechanical loadings, and its temperature states. Existing software demonstrated the feasibility of the approach, encompassing the 36 analysis classes spanning nonlinear, temperature affected, incremental analyses which track the behavior of structural systems.

Crystal Structure of the N-Terminal Half of the Traffic Controller UL37 from Herpes Simplex Virus 1

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

Koenigsberg, Andrea L.; Heldwein, Ekaterina E.; Sandri-Goldin, Rozanne M.

Inner tegument protein UL37 is conserved among all three subfamilies of herpesviruses. Studies of UL37 homologs from two alphaherpesviruses, herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV), have suggested that UL37 plays an essential albeit poorly defined role in intracellular capsid trafficking. At the same time, HSV and PRV homologs cannot be swapped, which suggests that in addition to a conserved function, UL37 homologs also have divergent virus-specific functions. Accurate dissection of UL37 functions requires detailed maps in the form of atomic-resolution structures. Previously, we reported the crystal structure of the N-terminal half of UL37 (UL37N) from PRV. Here,more » we report the crystal structure of HSV-1 UL37N. Comparison of the two structures reveals that UL37 homologs differ in their overall shapes, distributions of surface charges, and locations of projecting loops. In contrast, the previously identified R2 surface region is structurally conserved. We propose that within the N-terminal half of UL37, functional conservation is centered within the R2 surface region, whereas divergent structural elements pinpoint regions mediating virus-specific functions and may engage different binding partners. Together, the two structures can now serve as templates for a structure-guided exploration of both conserved and virus-specific functions of UL37. IMPORTANCEThe ability to move efficiently within host cell cytoplasm is essential for replication in all viruses. It is especially important in the neuroinvasive alphaherpesviruses, such as human herpes simplex virus 1 (HSV-1), HSV-2, and veterinarian pseudorabies virus (PRV), that infect the peripheral nervous system and have to travel long distances along axons. Capsid movement in these viruses is controlled by capsid-associated tegument proteins, yet their specific roles have not yet been defined. Systematic exploration of the roles of tegument proteins in capsid trafficking requires detailed navigational charts in the form of their three-dimensional structures. Here, we determined the crystal structure of the N-terminal half of a conserved tegument protein, UL37, from HSV-1. This structure, along with our previously reported structure of the UL37 homolog from PRV, provides a much needed 3-dimensional template for the dissection of both conserved and virus-specific functions of UL37 in intracellular capsid trafficking.« less

NASA Office of Aeronautical and Space Technology Summer Workshop. Volume 6: Structures and dynamics panel

NASA Technical Reports Server (NTRS)

1975-01-01

Structural requirements for future space missions were defined in relation to technology needs and payloads. Specific areas examined include: large area space structures (antennas, solar array structures, and platforms); a long, slender structure or boom used to support large objects from the shuttle or hold two bodies apart in space; and advanced composite structures for cost effective weight reductions. Other topics discussed include: minimum gage concepts, high temperature components, load and response determination and control, and reliability and life prediction.

NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region.

PubMed Central

Stamatoyannopoulos, J A; Goodwin, A; Joyce, T; Lowrey, C H

1995-01-01

The beta-like globin genes require the upstream locus control region (LCR) for proper expression. The active elements of the LCR coincide with strong erythroid-specific DNase I-hypersensitive sites (HSs). We have used 5' HS4 as a model to study the formation of these HSs. Previously, we identified a 101 bp element that is required for the formation of this HS. This element binds six proteins in vitro. We now report a mutational analysis of the HS4 HS-forming element (HSFE). This analysis indicates that binding sites for the hematopoietic transcription factors NF-E2 and GATA-1 are required for the formation of the characteristic chromatin structure of the HS following stable transfection into murine erythroleukemia cells. Similarly arranged NF-E2 and GATA binding sites are present in the other HSs of the human LCR, as well as in the homologous mouse and goat sequences and the chicken beta-globin enhancer. A combination of DNase I and micrococcal nuclease sensitivity assays indicates that the characteristic erythroid-specific hypersensitivity of HS4 to DNase I is the result of tissue-specific alterations in both nucleosome positioning and tertiary DNA structure. Images PMID:7828582

NASA software specification and evaluation system: Software verification/validation techniques

NASA Technical Reports Server (NTRS)

1977-01-01

NASA software requirement specifications were used in the development of a system for validating and verifying computer programs. The software specification and evaluation system (SSES) provides for the effective and efficient specification, implementation, and testing of computer software programs. The system as implemented will produce structured FORTRAN or ANSI FORTRAN programs, but the principles upon which SSES is designed allow it to be easily adapted to other high order languages.

Structural basis of PP2A activation by PTPA, an ATP-dependent activation chaperone

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

Guo, Feng; Stanevich, Vitali; Wlodarchak, Nathan

Proper activation of protein phosphatase 2A (PP2A) catalytic subunit is central for the complex PP2A regulation and is crucial for broad aspects of cellular function. The crystal structure of PP2A bound to PP2A phosphatase activator (PTPA) and ATPγS reveals that PTPA makes broad contacts with the structural elements surrounding the PP2A active site and the adenine moiety of ATP. PTPA-binding stabilizes the protein fold of apo-PP2A required for activation, and orients ATP phosphoryl groups to bind directly to the PP2A active site. This allows ATP to modulate the metal-binding preferences of the PP2A active site and utilize the PP2A activemore » site for ATP hydrolysis. In vitro, ATP selectively and drastically enhances binding of endogenous catalytic metal ions, which requires ATP hydrolysis and is crucial for acquisition of pSer/Thr-specific phosphatase activity. Furthermore, both PP2A- and ATP-binding are required for PTPA function in cell proliferation and survival. Our results suggest novel mechanisms of PTPA in PP2A activation with structural economy and a unique ATP-binding pocket that could potentially serve as a specific therapeutic target.« less

A graphically oriented specification language for automatic code generation. GRASP/Ada: A Graphical Representation of Algorithms, Structure, and Processes for Ada, phase 1

NASA Technical Reports Server (NTRS)

Cross, James H., II; Morrison, Kelly I.; May, Charles H., Jr.; Waddel, Kathryn C.

1989-01-01

The first phase of a three-phase effort to develop a new graphically oriented specification language which will facilitate the reverse engineering of Ada source code into graphical representations (GRs) as well as the automatic generation of Ada source code is described. A simplified view of the three phases of Graphical Representations for Algorithms, Structure, and Processes for Ada (GRASP/Ada) with respect to three basic classes of GRs is presented. Phase 1 concentrated on the derivation of an algorithmic diagram, the control structure diagram (CSD) (CRO88a) from Ada source code or Ada PDL. Phase 2 includes the generation of architectural and system level diagrams such as structure charts and data flow diagrams and should result in a requirements specification for a graphically oriented language able to support automatic code generation. Phase 3 will concentrate on the development of a prototype to demonstrate the feasibility of this new specification language.

GATOR: Requirements capturing of telephony features

NASA Technical Reports Server (NTRS)

Dankel, Douglas D., II; Walker, Wayne; Schmalz, Mark

1992-01-01

We are developing a natural language-based, requirements gathering system called GATOR (for the GATherer Of Requirements). GATOR assists in the development of more accurate and complete specifications of new telephony features. GATOR interacts with a feature designer who describes a new feature, set of features, or capability to be implemented. The system aids this individual in the specification process by asking for clarifications when potential ambiguities are present, by identifying potential conflicts with other existing features, and by presenting its understanding of the feature to the designer. Through user interaction with a model of the existing telephony feature set, GATOR constructs a formal representation of the new, 'to be implemented' feature. Ultimately GATOR will produce a requirements document and will maintain an internal representation of this feature to aid in future design and specification. This paper consists of three sections that describe (1) the structure of GATOR, (2) POND, GATOR's internal knowledge representation language, and (3) current research issues.

Software requirements: Guidance and control software development specification

NASA Technical Reports Server (NTRS)

Withers, B. Edward; Rich, Don C.; Lowman, Douglas S.; Buckland, R. C.

1990-01-01

The software requirements for an implementation of Guidance and Control Software (GCS) are specified. The purpose of the GCS is to provide guidance and engine control to a planetary landing vehicle during its terminal descent onto a planetary surface and to communicate sensory information about that vehicle and its descent to some receiving device. The specification was developed using the structured analysis for real time system specification methodology by Hatley and Pirbhai and was based on a simulation program used to study the probability of success of the 1976 Viking Lander missions to Mars. Three versions of GCS are being generated for use in software error studies.

Rationale for windshield glass system specification requirements for shuttle orbiter

NASA Technical Reports Server (NTRS)

Hayashida, K.; King, G. L.; Tesinsiky, J.; Wittenburg, D. R.

1972-01-01

A preliminary procurement specification for the space shuttle orbiter windshield pane, and some of the design considerations and rationale leading to its development are presented. The windshield designer is given the necessary methods and procedures for assuring glass pane structural integrity by proof test. These methods and procedures are fully developed for annealed and thermally tempered aluminosilicate, borosilicate, and soda lime glass and for annealed fused silica. Application of the method to chemically tempered glass is considered. Other considerations are vision requirements, protection against bird impact, hail, frost, rain, and meteoroids. The functional requirements of the windshield system during landing, ferrying, boost, space flight, and entry are included.

The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience

PubMed Central

Bug, William J.; Ascoli, Giorgio A.; Grethe, Jeffrey S.; Gupta, Amarnath; Fennema-Notestine, Christine; Laird, Angela R.; Larson, Stephen D.; Rubin, Daniel; Shepherd, Gordon M.; Turner, Jessica A.; Martone, Maryann E.

2009-01-01

A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF. PMID:18975148

The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.

PubMed

Bug, William J; Ascoli, Giorgio A; Grethe, Jeffrey S; Gupta, Amarnath; Fennema-Notestine, Christine; Laird, Angela R; Larson, Stephen D; Rubin, Daniel; Shepherd, Gordon M; Turner, Jessica A; Martone, Maryann E

2008-09-01

A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF.

49 CFR 180.509 - Requirements for inspection and test of specification tank cars.

Code of Federal Regulations, 2012 CFR

2012-10-01

... tank car owner can determine by analysis (e.g., finite element analysis, damage-tolerance analysis, or... missing or loose bolts, nuts, or elements that may make the tank car unsafe for transportation; (5) An... must ensure the structural elements on the tank car qualify with the applicable requirements of this...

49 CFR 180.509 - Requirements for inspection and test of specification tank cars.

Code of Federal Regulations, 2013 CFR

2013-10-01

... tank car owner can determine by analysis (e.g., finite element analysis, damage-tolerance analysis, or... missing or loose bolts, nuts, or elements that may make the tank car unsafe for transportation; (5) An... must ensure the structural elements on the tank car qualify with the applicable requirements of this...

49 CFR 180.509 - Requirements for inspection and test of specification tank cars.

Code of Federal Regulations, 2014 CFR

2014-10-01

... tank car owner can determine by analysis (e.g., finite element analysis, damage-tolerance analysis, or... missing or loose bolts, nuts, or elements that may make the tank car unsafe for transportation; (5) An... must ensure the structural elements on the tank car qualify with the applicable requirements of this...

48 CFR 52.236-9 - Protection of Existing Vegetation, Structures, Equipment, Utilities, and Improvements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... preserve and protect all structures, equipment, and vegetation (such as trees, shrubs, and grass) on or... work required under this contract. The Contractor shall only remove trees when specifically authorized... trees are broken during contract performance, or by the careless operation of equipment, or by workmen...

Implementing Structured English Immersion in Arizona: Benefits, Challenges, and Opportunities

ERIC Educational Resources Information Center

Rios-Aguilar, Cecilia; Gonzalez Canche, Manuel S.; Moll, Luis C.

2012-01-01

Background/Context: Arizona's most recent English Language Learner (ELL) legislation, starting in the school year 2008-2009, requires all such students be educated through a specific Structured English Immersion (SEI) model: the 4-hour English Language Development (ELD) block. The basic premise behind this particular model is that ELL students…

48 CFR 52.236-9 - Protection of Existing Vegetation, Structures, Equipment, Utilities, and Improvements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... preserve and protect all structures, equipment, and vegetation (such as trees, shrubs, and grass) on or... work required under this contract. The Contractor shall only remove trees when specifically authorized... trees are broken during contract performance, or by the careless operation of equipment, or by workmen...

48 CFR 52.236-9 - Protection of Existing Vegetation, Structures, Equipment, Utilities, and Improvements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... preserve and protect all structures, equipment, and vegetation (such as trees, shrubs, and grass) on or... work required under this contract. The Contractor shall only remove trees when specifically authorized... trees are broken during contract performance, or by the careless operation of equipment, or by workmen...

48 CFR 52.236-9 - Protection of Existing Vegetation, Structures, Equipment, Utilities, and Improvements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... preserve and protect all structures, equipment, and vegetation (such as trees, shrubs, and grass) on or... work required under this contract. The Contractor shall only remove trees when specifically authorized... trees are broken during contract performance, or by the careless operation of equipment, or by workmen...

48 CFR 52.236-9 - Protection of Existing Vegetation, Structures, Equipment, Utilities, and Improvements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... preserve and protect all structures, equipment, and vegetation (such as trees, shrubs, and grass) on or... work required under this contract. The Contractor shall only remove trees when specifically authorized... trees are broken during contract performance, or by the careless operation of equipment, or by workmen...

Principles of protein folding--a perspective from simple exact models.

PubMed Central

Dill, K. A.; Bromberg, S.; Yue, K.; Fiebig, K. M.; Yee, D. P.; Thomas, P. D.; Chan, H. S.

1995-01-01

General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics--fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse. PMID:7613459

CRISPR-Cas9 Structures and Mechanisms.

PubMed

Jiang, Fuguo; Doudna, Jennifer A

2017-05-22

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems employ the dual RNA-guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific double-stranded breaks in target DNA. Target recognition strictly requires the presence of a short protospacer adjacent motif (PAM) flanking the target site, and subsequent R-loop formation and strand scission are driven by complementary base pairing between the guide RNA and target DNA, Cas9-DNA interactions, and associated conformational changes. The use of CRISPR-Cas9 as an RNA-programmable DNA targeting and editing platform is simplified by a synthetic single-guide RNA (sgRNA) mimicking the natural dual trans-activating CRISPR RNA (tracrRNA)-CRISPR RNA (crRNA) structure. This review aims to provide an in-depth mechanistic and structural understanding of Cas9-mediated RNA-guided DNA targeting and cleavage. Molecular insights from biochemical and structural studies provide a framework for rational engineering aimed at altering catalytic function, guide RNA specificity, and PAM requirements and reducing off-target activity for the development of Cas9-based therapies against genetic diseases.

Optical fiber designs for beam shaping

NASA Astrophysics Data System (ADS)

Farley, Kevin; Conroy, Michael; Wang, Chih-Hao; Abramczyk, Jaroslaw; Campbell, Stuart; Oulundsen, George; Tankala, Kanishka

2014-03-01

A large number of power delivery applications for optical fibers require beams with very specific output intensity profiles; in particular applications that require a focused high intensity beam typically image the near field (NF) intensity distribution at the exit surface of an optical fiber. In this work we discuss optical fiber designs that shape the output beam profile to more closely correspond to what is required in many real world industrial applications. Specifically we present results demonstrating the ability to transform Gaussian beams to shapes required for industrial applications and how that relates to system parameters such as beam product parameter (BPP) values. We report on the how different waveguide structures perform in the NF and show results on how to achieve flat-top with circular outputs.

Autonomous Assembly of Modular Structures in Space and on Extraterrestrial Locations

NASA Astrophysics Data System (ADS)

Alhorn, Dean C.

2005-02-01

The new U.S. National Vision for Space Exploration requires many new enabling technologies to accomplish the goals of space commercialization and returning humans to the moon and extraterrestrial environments. Traditionally, flight elements are complete sub-systems requiring humans to complete the integration and assembly. These bulky structures also require the use of heavy launch vehicles to send the units to a desired location. This philosophy necessitates a high degree of safety, numerous space walks at a significant cost. Future space mission costs must be reduced and safety increased to reasonably achieve exploration goals. One proposed concept is the autonomous assembly of space structures. This concept is an affordable, reliable solution to in-space and extraterrestrial assembly. Assembly is autonomously performed when two components join after determining that specifications are correct. Local sensors continue monitor joint integrity post assembly, which is critical for safety and structural reliability. Achieving this concept requires a change in space structure design philosophy and the development of innovative technologies to perform autonomous assembly. Assembly of large space structures will require significant numbers of integrity sensors. Thus simple, low-cost sensors are integral to the success of this concept. This paper addresses these issues and proposes a novel concept for assembling space structures autonomously. Core technologies required to achieve in space assembly are presented. These core technologies are critical to the goal of utilizing space in a cost efficient and safe manner. Additionally, these novel technologies can be applied to other systems both on earth and extraterrestrial environments.

Autonomous Assembly of Modular Structures in Space and on Extraterrestrial Locations

NASA Technical Reports Server (NTRS)

Alhorn, Dean C.

2005-01-01

The new U.S. National Vision for Space Exploration requires many new enabling technologies to accomplish the goals of space commercialization and returning humans to the moon and extraterrestrial environments. Traditionally, flight elements are complete subsystems requiring humans to complete the integration and assembly. These bulky structures also require the use of heavy launch vehicles to send the units to a desired location. This philosophy necessitates a high degree of safety, numerous space walks at a significant cost. Future space mission costs must be reduced and safety increased to reasonably achieve exploration goals. One proposed concept is the autonomous assembly of space structures. This concept is an affordable, reliable solution to in-space and extraterrestrial assembly. Assembly is autonomously performed when two components join after determining that specifications are correct. Local sensors continue monitor joint integrity post assembly, which is critical for safety and structural reliability. Achieving this concept requires a change in space structure design philosophy and the development of innovative technologies to perform autonomous assembly. Assembly of large space structures will require significant numbers of integrity sensors. Thus simple, low-cost sensors are integral to the success of this concept. This paper addresses these issues and proposes a novel concept for assembling space structures autonomously. Core technologies required to achieve in space assembly are presented. These core technologies are critical to the goal of utilizing space in a cost efficient and safe manner. Additionally, these novel technologies can be applied to other systems both on earth and extraterrestrial environments.

R2R--software to speed the depiction of aesthetic consensus RNA secondary structures.

PubMed

Weinberg, Zasha; Breaker, Ronald R

2011-01-04

With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

Development of advanced high heat flux and plasma-facing materials

NASA Astrophysics Data System (ADS)

Linsmeier, Ch.; Rieth, M.; Aktaa, J.; Chikada, T.; Hoffmann, A.; Hoffmann, J.; Houben, A.; Kurishita, H.; Jin, X.; Li, M.; Litnovsky, A.; Matsuo, S.; von Müller, A.; Nikolic, V.; Palacios, T.; Pippan, R.; Qu, D.; Reiser, J.; Riesch, J.; Shikama, T.; Stieglitz, R.; Weber, T.; Wurster, S.; You, J.-H.; Zhou, Z.

2017-09-01

Plasma-facing materials and components in a fusion reactor are the interface between the plasma and the material part. The operational conditions in this environment are probably the most challenging parameters for any material: high power loads and large particle and neutron fluxes are simultaneously impinging at their surfaces. To realize fusion in a tokamak or stellarator reactor, given the proven geometries and technological solutions, requires an improvement of the thermo-mechanical capabilities of currently available materials. In its first part this article describes the requirements and needs for new, advanced materials for the plasma-facing components. Starting points are capabilities and limitations of tungsten-based alloys and structurally stabilized materials. Furthermore, material requirements from the fusion-specific loading scenarios of a divertor in a water-cooled configuration are described, defining directions for the material development. Finally, safety requirements for a fusion reactor with its specific accident scenarios and their potential environmental impact lead to the definition of inherently passive materials, avoiding release of radioactive material through intrinsic material properties. The second part of this article demonstrates current material development lines answering the fusion-specific requirements for high heat flux materials. New composite materials, in particular fiber-reinforced and laminated structures, as well as mechanically alloyed tungsten materials, allow the extension of the thermo-mechanical operation space towards regions of extreme steady-state and transient loads. Self-passivating tungsten alloys, demonstrating favorable tungsten-like plasma-wall interaction behavior under normal operation conditions, are an intrinsic solution to otherwise catastrophic consequences of loss-of-coolant and air ingress events in a fusion reactor. Permeation barrier layers avoid the escape of tritium into structural and cooling materials, thereby minimizing the release of tritium under normal operation conditions. Finally, solutions for the unique bonding requirements of dissimilar material used in a fusion reactor are demonstrated by describing the current status and prospects of functionally graded materials.

SSME lifetime prediction and verification, integrating environments, structures, materials: The challenge

NASA Technical Reports Server (NTRS)

Ryan, R. S.; Salter, L. D.; Young, G. M., III; Munafo, P. M.

1985-01-01

The planned missions for the space shuttle dictated a unique and technology-extending rocket engine. The high specific impulse requirements in conjunction with a 55-mission lifetime, plus volume and weight constraints, produced unique structural design, manufacturing, and verification requirements. Operations from Earth to orbit produce severe dynamic environments, which couple with the extreme pressure and thermal environments associated with the high performance, creating large low cycle loads and high alternating stresses above endurance limit which result in high sensitivity to alternating stresses. Combining all of these effects resulted in the requirements for exotic materials, which are more susceptible to manufacturing problems, and the use of an all-welded structure. The challenge of integrating environments, dynamics, structures, and materials into a verified SSME structure is discussed. The verification program and developmental flight results are included. The first six shuttle flights had engine performance as predicted with no failures. The engine system has met the basic design challenges.

Alternative Splicing of Four Trafficking Genes Regulates Myofiber Structure and Skeletal Muscle Physiology.

PubMed

Giudice, Jimena; Loehr, James A; Rodney, George G; Cooper, Thomas A

2016-11-15

During development, transcriptional and post-transcriptional networks are coordinately regulated to drive organ maturation. Alternative splicing contributes by producing temporal-specific protein isoforms. We previously found that genes undergoing splicing transitions during mouse postnatal heart development are enriched for vesicular trafficking and membrane dynamics functions. Here, we show that adult trafficking isoforms are also expressed in adult skeletal muscle and hypothesize that striated muscle utilizes alternative splicing to generate specific isoforms required for function of adult tissue. We deliver morpholinos into flexor digitorum brevis muscles in adult mice to redirect splicing of four trafficking genes to the fetal isoforms. The splicing switch results in multiple structural and functional defects, including transverse tubule (T-tubule) disruption and dihydropyridine receptor alpha (DHPR) and Ryr1 mislocalization, impairing excitation-contraction coupling, calcium handling, and force generation. The results demonstrate a previously unrecognized role for trafficking functions in adult muscle tissue homeostasis and a specific requirement for the adult splice variants. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Molecular principles underlying dual RNA specificity in the Drosophila SNF protein.

PubMed

Weber, Gert; DeKoster, Gregory T; Holton, Nicole; Hall, Kathleen B; Wahl, Markus C

2018-06-07

The first RNA recognition motif of the Drosophila SNF protein is an example of an RNA binding protein with multi-specificity. It binds different RNA hairpin loops in spliceosomal U1 or U2 small nuclear RNAs, and only in the latter case requires the auxiliary U2A' protein. Here we investigate its functions by crystal structures of SNF alone and bound to U1 stem-loop II, U2A' or U2 stem-loop IV and U2A', SNF dynamics from NMR spectroscopy, and structure-guided mutagenesis in binding studies. We find that different loop-closing base pairs and a nucleotide exchange at the tips of the loops contribute to differential SNF affinity for the RNAs. U2A' immobilizes SNF and RNA residues to restore U2 stem-loop IV binding affinity, while U1 stem-loop II binding does not require such adjustments. Our findings show how U2A' can modulate RNA specificity of SNF without changing SNF conformation or relying on direct RNA contacts.

Synthesis of carbon core–shell pore structures and their performance as supercapacitors

DOE PAGES

Ariyanto, Teguh; Dyatkin, Boris; Zhang, Gui-Rong; ...

2015-07-15

High-power supercapacitors require excellent electrolyte mobility within the pore network and high electrical conductivity for maximum capacitance and efficiency. Achieving high power typically requires sacrificing energy densities, as the latter demands a high specific surface area and narrow porosity that impedes ion transport. Here, we present a novel solution for this optimization problem: a nanostructured core–shell carbonaceous material that exhibits a microporous carbon core surrounded by a mesoporous, graphitic shell. The tunable synthesis parameters yielded a structure that features either a sharp or a gradual transition between the core and shell sections. Electrochemical supercapacitor testing using organic electrolyte revealed thatmore » these novel core–shell materials outperform carbons with homogeneous pore structures. The hybrid core–shell materials showed a combination of good capacitance retention, typical for the carbon present in the shell and high specific capacitance, typical for the core material. These materials achieved power densities in excess of 40 kW kg -1 at energy densities reaching 27 Wh kg -1.« less

Analysis and design of lattice materials for large cord and curvature variations in skin panels of morphing wings

NASA Astrophysics Data System (ADS)

Vigliotti, Andrea; Pasini, Damiano

2015-03-01

In the past few decades, several concepts for morphing wings have been proposed with the aim of improving the structural and aerodynamic performance of conventional aircraft wings. One of the most interesting challenges in the design of a morphing wing is represented by the skin, which needs to meet specific deformation requirements. In particular when morphing involves changes of cord or curvature, the skin is required to undergo large recoverable deformation in the actuation direction, while maintaining the desired shape and strength in the others. One promising material concept that can meet these specifications is represented by lattice materials. This paper examines the use of alternative planar lattices in the embodiment of a skin panel for cord and camber morphing of an aircraft wing. We use a structural homogenization scheme capable of capturing large geometric nonlinearity, to examine the structural performance of lattice skin concepts, as well as to tune their mechanical properties in desired directions.

Iraqi Army Facilities Under the Iraq Security Forces Fund, Diyanah and Debecha, Iraq

DTIC Science & Technology

2008-01-17

reinforcement bars and cast each building’s roof flatwork and horizontal beams to complete the structural aspects of the roof system . Steel header...included a mix of new construction and renovation of existing structures and facilities. The Statement of Requirements and Specifications provided...that renovation of existing structures , when possible, was preferred. In addition, the United States government encouraged the contractor to use

Distributed Compression in Camera Sensor Networks

DTIC Science & Technology

2006-02-13

complicated in this context. This effort will make use of the correlation structure of the data given by the plenoptic function n the case of multi-camera...systems. In many cases the structure of the plenoptic function can be estimated without requiring inter-sensor communications, but by using some a...priori global geometrical information. Once the structure of the plenoptic function has been predicted, it is possible to develop specific distributed

Specific sulfation and glycosylation—a structural combination for the anticoagulation of marine carbohydrates

PubMed Central

Pomin, Vitor H.; Mourão, Paulo A. S.

2014-01-01

Based on considered achievements of the last 25 years, specific combinations of sulfation patterns and glycosylation types have been proved to be key structural players for the anticoagulant activity of certain marine glycans. These conclusions were obtained from comparative and systematic analyses on the structure-anticoagulation relationships of chemically well-defined sulfated polysaccharides of marine invertebrates and red algae. These sulfated polysaccharides are known as sulfated fucans (SFs), sulfated galactans (SGs) and glycosaminoglycans (GAGs). The structural combinations necessary for the anticoagulant activities are the 2-sulfation in α-L-SGs, the 2,4-di-sulfation in α-L-fucopyranosyl units found as composing units of certain sea-urchin and sea-cucumber linear SFs, or as branching units of the fucosylated chondroitin sulfate, a unique GAG from sea-cucumbers. Another unique GAG type from marine organisms is the dermatan sulfate isolated from ascidians. The high levels of 4-sulfation at the galactosamine units combined with certain levels of 2-sulfation at the iduronic acid units is the anticoagulant structural requirements of these GAGs. When the backbones of red algal SGs are homogeneous, the anticoagulation is proportionally dependent of their sulfation content. Finally, 4-sulfation was observed to be the structural motif required to enhance the inhibition of thrombin via heparin cofactor-II by invertebrate SFs. PMID:24639954

YAdumper: extracting and translating large information volumes from relational databases to structured flat files.

PubMed

Fernández, José M; Valencia, Alfonso

2004-10-12

Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.

Development of optimized techniques and requirements for computer enhancement of structural weld radiographs. Volume 1: Technical report

NASA Technical Reports Server (NTRS)

Adams, J. R.; Hawley, S. W.; Peterson, G. R.; Salinger, S. S.; Workman, R. A.

1971-01-01

A hardware and software specification covering requirements for the computer enhancement of structural weld radiographs was considered. Three scanning systems were used to digitize more than 15 weld radiographs. The performance of these systems was evaluated by determining modulation transfer functions and noise characteristics. Enhancement techniques were developed and applied to the digitized radiographs. The scanning parameters of spot size and spacing and film density were studied to optimize the information content of the digital representation of the image.

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1981-08-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1980-09-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1979-09-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

electronically excited specied are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Bone microarchitecture of the tibial plateau in skeletal health and osteoporosis.

PubMed

Krause, Matthias; Hubert, Jan; Deymann, Simon; Hapfelmeier, Alexander; Wulff, Birgit; Petersik, Andreas; Püschel, Klaus; Amling, Michael; Hawellek, Thelonius; Frosch, Karl-Heinz

2018-05-07

Impaired bone structure poses a challenge for the treatment of osteoporotic tibial plateau fractures. As knowledge of region-specific structural bone alterations is a prerequisite to achieving successful long-term fixation, the aim of the current study was to characterize tibial plateau bone structure in patients with osteoporosis and the elderly. Histomorphometric parameters were assessed by high-resolution peripheral quantitative computed tomography (HR-pQCT) in 21 proximal tibiae from females with postmenopausal osteoporosis (mean age: 84.3 ± 4.9 years) and eight female healthy controls (45.5 ± 6.9 years). To visualize region-specific structural bony alterations with age, the bone mineral density (Hounsfield units) was additionally analyzed in 168 human proximal tibiae. Statistical analysis was based on evolutionary learning using globally optimal regression trees. Bone structure deterioration of the tibial plateau due to osteoporosis was region-specific. Compared to healthy controls (20.5 ± 4.7%) the greatest decrease in bone volume fraction was found in the medio-medial segments (9.2 ± 3.5%, p < 0.001). The lowest bone volume was found in central segments (tibial spine). Trabecular connectivity was severely reduced. Importantly, in the anterior and posterior 25% of the lateral and medial tibial plateaux, trabecular support and subchondral cortical bone thickness itself were also reduced. Thinning of subchondral cortical bone and marked bone loss in the anterior and posterior 25% of the tibial plateau should require special attention when osteoporotic patients require fracture fixation of the posterior segments. This knowledge may help to improve the long-term, fracture-specific fixation of complex tibial plateau fractures in osteoporosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Transcriptional control by G-quadruplexes: In vivo roles and perspectives for specific intervention.

PubMed

Armas, Pablo; David, Aldana; Calcaterra, Nora B

2017-01-01

G-quadruplexes are non-canonical DNA secondary structures involved in several genomic and molecular processes. Here, we summarize the main G-quadruplex features and evidences proving the in vivo role on the transcriptional regulation of genes required for zebrafish embryonic development. We also discuss alternative strategies for specifically interfering G-quadruplex in vivo.

Long-Range Educational Policy Planning and the Demand for Educated Manpower in Times of Uncertainty.

ERIC Educational Resources Information Center

Bakke, E. K.

1984-01-01

There is no good method of regulating the educational system based on specific, numerical measurements of labor requirements, and it will be important to integrate uncertainty into future forecasts. Adjustments in demand and supply of educated labor in Norway require a decentralized authority structure providing incentives for institutions and the…

24 CFR 3280.904 - Specific requirements for designing the transportation system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... the tire and manufactured home frame or structure to permit unimpeded wheel movement and for changing... alternatives listed in § 3280.903(c) may be accepted in place of such an analysis. (7) Hubs and bearings. Hubs...) Tires, wheels and rims. Tires, wheels and rims shall meet the requirements of § 3280.904(b)(3). Tires...

24 CFR 3280.904 - Specific requirements for designing the transportation system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the tire and manufactured home frame or structure to permit unimpeded wheel movement and for changing... alternatives listed in § 3280.903(c) may be accepted in place of such an analysis. (7) Hubs and bearings. Hubs...) Tires, wheels and rims. Tires, wheels and rims shall meet the requirements of § 3280.904(b)(3). Tires...

24 CFR 3280.904 - Specific requirements for designing the transportation system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... the tire and manufactured home frame or structure to permit unimpeded wheel movement and for changing... alternatives listed in § 3280.903(c) may be accepted in place of such an analysis. (7) Hubs and bearings. Hubs...) Tires, wheels and rims. Tires, wheels and rims shall meet the requirements of § 3280.904(b)(3). Tires...

24 CFR 3280.904 - Specific requirements for designing the transportation system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... the tire and manufactured home frame or structure to permit unimpeded wheel movement and for changing... alternatives listed in § 3280.903(c) may be accepted in place of such an analysis. (7) Hubs and bearings. Hubs...) Tires, wheels and rims. Tires, wheels and rims shall meet the requirements of § 3280.904(b)(3). Tires...

Structural Differences between the Streptococcus agalactiae Housekeeping and Pilus-Specific Sortases: SrtA and SrtC1

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

Khare, B.; Krishnan, V.; Rajashankar, K.R.

2011-10-21

The assembly of pili on the cell wall of Gram-positive bacteria requires transpeptidase enzymes called sortases. In Streptococcus agalactiae, the PI-1 pilus island of strain 2603V/R encodes two pilus-specific sortases (SrtC1 and SrtC2) and three pilins (GBS80, GBS52 and GBS104). Although either pilus-specific sortase is sufficient for the polymerization of the major pilin, GBS80, incorporation of the minor pilins GBS52 and GBS104 into the pilus structure requires SrtC1 and SrtC2, respectively. The S. agalactiae housekeeping sortase, SrtA, whose gene is present at a different location and does not catalyze pilus polymerization, was shown to be involved in cell wall anchoringmore » of pilus polymers. To understand the structural basis of sortases involved in such diverse functions, we determined the crystal structures of S. agalactiae SrtC1 and SrtA. Both enzymes are made of an eight-stranded beta-barrel core with variations in their active site architecture. SrtA exhibits a catalytic triad arrangement similar to that in Streptococcus pyogenes SrtA but different from that in Staphylococcus aureus SrtA. In contrast, the SrtC1 enzyme contains an N-terminal helical domain and a 'lid' in its putative active site, which is similar to that seen in Streptococcus pneumoniae pilus-specific sortases, although with subtle differences in positioning and composition. To understand the effect of such differences on substrate recognition, we have also determined the crystal structure of a SrtC1 mutant, in which the conserved DP(W/F/Y) motif was replaced with the sorting signal motif of GBS80, IPNTG. By comparing the structures of WT wild type SrtA and SrtC1 and the 'lid' mutant of SrtC1, we propose that structural elements within the active site and the lid may be important for defining the role of specific sortase in pili biogenesis.« less

Validation of a SysML based design for wireless sensor networks

NASA Astrophysics Data System (ADS)

Berrachedi, Amel; Rahim, Messaoud; Ioualalen, Malika; Hammad, Ahmed

2017-07-01

When developing complex systems, the requirement for the verification of the systems' design is one of the main challenges. Wireless Sensor Networks (WSNs) are examples of such systems. We address the problem of how WSNs must be designed to fulfil the system requirements. Using the SysML Language, we propose a Model Based System Engineering (MBSE) specification and verification methodology for designing WSNs. This methodology uses SysML to describe the WSNs requirements, structure and behaviour. Then, it translates the SysML elements to an analytic model, specifically, to a Deterministic Stochastic Petri Net. The proposed approach allows to design WSNs and study their behaviors and their energy performances.

Evolution of the arginase fold and functional diversity

PubMed Central

Dowling, Daniel P.; Costanzo, Luigi Di; Gennadios, Heather A.; Christianson, David W.

2009-01-01

The large number of protein structures deposited in the Protein Data Bank allows for the identification of novel structural superfamilies based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. Here, we review the unique α/β fold first observed in the manganese metalloenzyme rat liver arginase, consisting of a parallel 8 stranded β-sheet surrounded by several helices, and its evolutionary relationship with the zinc-requiring and/or iron-requiring histone deacetylases and acetylpolyamine amidohydrolases. Structural comparisons reveal key features of the core α/β fold that contribute to the divergent metal ion specificity and stoichiometry required for the chemical and biological functions of these enzymes. PMID:18360740

Development of flame-resistant structures for use in the Apollo and Skylab programs

NASA Technical Reports Server (NTRS)

Coskren, R. J.

1973-01-01

Flame-resistant materials have been designed and fabricated to meet certain end-use criteria established by NASA with emphasis on meeting established flammability standards. The program had three general phases: (1) fabrication of candidate sample structures for evaluation by the Structures and Mechanics Division and/or NASA contractors; (2) physical testing of the structures developed; and (3) supply of required quantities of specific items for fabrication into prototype and/or flight items for the Apollo and Skylab programs.

Hardwood Press-Lam Crossties: Processing and Performance.

DTIC Science & Technology

1979-01-01

replacements (24) Earlier reports by the American Railway EngineeringA Association ( AREA ) indicated more failures due to splitting and decay (62 pct...to emphasize a M 4 %441 higher percen’age of structural failures An AREA specification (3) on f concrete ties represents the first performance...specification for any type of tie. The AREA specification for timber c r crosstles addresses only species, *t .- requirements (2) A tie size of 7 inches

Swa2, the yeast homolog of mammalian auxilin, is specifically required for the propagation of the prion variant [URE 3‐1

PubMed Central

Troisi, Elizabeth M.; Rockman, Michael E.; Nguyen, Phil P.; Oliver, Emily E.

2015-01-01

Summary Yeast prions require a core set of chaperone proteins including Sis1, Hsp70 and Hsp104 to generate new amyloid templates for stable propagation, yet emerging studies indicate that propagation of some prions requires additional chaperone activities, demonstrating chaperone specificity beyond the common amyloid requirements. To comprehensively assess such prion‐specific requirements for the propagation of the [URE 3] prion variant [URE 3‐1], we screened 12 yeast cytosolic J‐proteins, and here we report a novel role for the J‐protein Swa2/Aux1. Swa2 is the sole yeast homolog of the mammalian protein auxilin, which, like Swa2, functions in vesicle‐mediated endocytosis by disassembling the structural lattice formed by the protein clathrin. We found that, in addition to Sis1, [URE 3‐1] is specifically dependent upon Swa2, but not on any of the 11 other J‐proteins. Further, we show that [URE 3‐1] propagation requires both a functional J‐domain and the tetratricopeptide repeat (TPR) domain, but surprisingly does not require Swa2‐clathrin binding. Because the J‐domain of Swa2 can be replaced with the J‐domains of other proteins, our data strongly suggest that prion‐chaperone specificity arises from the Swa2 TPR domain and supports a model where Swa2 acts through Hsp70, most likely to provide additional access points for Hsp104 to promote prion template generation. PMID:26031938

Some design constraints required for the assembly of software components: The incorporation of atomic abstract types into generically structured abstract types

NASA Technical Reports Server (NTRS)

Johnson, Charles S.

1986-01-01

It is nearly axiomatic, that to take the greatest advantage of the useful features available in a development system, and to avoid the negative interactions of those features, requires the exercise of a design methodology which constrains their use. A major design support feature of the Ada language is abstraction: for data, functions processes, resources, and system elements in general. Atomic abstract types can be created in packages defining those private types and all of the overloaded operators, functions, and hidden data required for their use in an application. Generically structured abstract types can be created in generic packages defining those structured private types, as buildups from the user-defined data types which are input as parameters. A study is made of the design constraints required for software incorporating either atomic or generically structured abstract types, if the integration of software components based on them is to be subsequently performed. The impact of these techniques on the reusability of software and the creation of project-specific software support environments is also discussed.

Structural dynamics technology research in NASA: Perspective on future needs

NASA Technical Reports Server (NTRS)

1979-01-01

The perspective of a NASA ad hoc study group on future research needs in structural dynamics within the aerospace industry is presented. The common aspects of the design process across the industry are identified and the role of structural dynamics is established through a discussion of various design considerations having their basis in structural dynamics. The specific structural dynamics issues involved are identified and assessed as to their current technological status and trends. Projections of future requirements based on this assessment are made and areas of research to meet them are identified.

Structural materials issues for the next generation fission reactors

NASA Astrophysics Data System (ADS)

Chant, I.; Murty, K. L.

2010-09-01

Generation-IV reactor design concepts envisioned thus far cater to a common goal of providing safer, longer lasting, proliferation-resistant, and economically viable nuclear power plants. The foremost consideration in the successful development and deployment of Gen-W reactor systems is the performance and reliability issues involving structural materials for both in-core and out-of-core applications. The structural materials need to endure much higher temperatures, higher neutron doses, and extremely corrosive environments, which are beyond the experience of the current nuclear power plants. Materials under active consideration for use in different reactor components include various ferritic/martensitic steels, austenitic stainless steels, nickel-base superalloys, ceramics, composites, etc. This article addresses the material requirements for these advanced fission reactor types, specifically addressing structural materials issues depending on the specific application areas.

Advances in Lithium-Sulfur Rechargeable Batteries Powering the Electronic Future

NASA Technical Reports Server (NTRS)

Skotheim, Terje; Akridge, Jim; Hyland, Bob

2001-01-01

This viewgraph presentation discusses the Moltech Corporation's history and structure, power systems development, product attributes, Li-S adapted products, cell construction, specific energy comparisons, and product requirements necessary for use in spacecraft applications.

DTFM Modeling and Analysis Method for Gossamer Structures

NASA Technical Reports Server (NTRS)

Fang, Hou-Fei; Lou, Michael; Broduer, Steve (Technical Monitor)

2001-01-01

Gossamer systems are mostly composed of support structures formed by highly flexible, long tubular elements and pre-tensioned thin-film membranes. These systems offer order-of-magnitude reductions in mass and launch volume and will revolutionize the architecture and design of space flight systems that require large in-orbit configurations and apertures. A great interest has been generated in recent years to fly gossamer systems on near-term and future space missions. Modeling and analysis requirements for gossamer structures are unique. Simulation of in-space performance issues of gossamer structures, such as inflation deployment of flexible booms, formation and effects of wrinkle in tensioned membranes, synthesis of tubular and membrane elements into a complete structural system, usually cannot be accomplished by using the general-purpose finite-element structural analysis codes. This has led to the need of structural modeling and analysis capabilities specifically suitable for gossamer structures. The Distributed Transfer Function Method (DTFM) can potentially meet this urgent need. Additional information is contained in the original extended abstract.

Specific application for Oak Ridge National Laboratory dismantlement of Building 3004. Appendix A -- Quality assurance plan; Appendix B -- Records management plan

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

NONE

This quality assurance (QA) plan defines the QA requirements for the dismantlement and removal of Building 3004 at Oak Ridge National Laboratory (ORNL). The building is a four-story wooden trained structure with wooden siding, which resides approximately 150 ft west of the Bulk Shielding Reactor, and only several feet away from the visitors entrance to the Graphite Reactor museum. Complete descriptions and sketches are in the Performance Specification document for this project. This project is being conducted as a non-CERCLA maintenance action. This plan is an appendix to the QA plan for the ORNL Environmental Restoration (ER) Program. ORNL/ER-225, whichmore » is the source of the project QA requirements, tailors those QA requirements to the specific needs of this project as defined in ORNL/ER-225. Project-specific description and organization are also provided in this plan. Appendix B, Records Management Plan, is included.« less

Power Extension Package (PEP) system definition extension, orbital service module systems analysis study. Volume 4: PEP functional specification

NASA Technical Reports Server (NTRS)

1979-01-01

The functional, performance, design, and test requirements for the Orbiter power extension package and its associated ground support equipment are defined. Both government and nongovernment standards and specifications are cited for the following subsystems: electrical power, structural/mechanical, avionics, and thermal control. Quality control assurance provisions and preparation for delivery are also discussed.

Transcriptional control by G-quadruplexes: In vivo roles and perspectives for specific intervention

PubMed Central

Armas, Pablo; David, Aldana; Calcaterra, Nora B.

2017-01-01

ABSTRACT G-quadruplexes are non-canonical DNA secondary structures involved in several genomic and molecular processes. Here, we summarize the main G-quadruplex features and evidences proving the in vivo role on the transcriptional regulation of genes required for zebrafish embryonic development. We also discuss alternative strategies for specifically interfering G-quadruplex in vivo. PMID:27696937

Spatial characteristics of early successional habitat across the Upper Great Lakes states

Treesearch

Brian G. Tavernia; Mark D. Nelson; James D. Garner; Charles H. (Hobie) Perry

2016-01-01

Creation and management of early successional forest (ESF) is needed to halt and reverse declines of bird species dependent on pioneering plant species or young forests. ESF-dependent bird species require specific structural forest classes and are sensitive to forest age (a surrogate for forest structure), patch size, proximity to patch edges, and the juxtaposition of...

Bacterialike (filamentous) structures associated with pyritized burrow linings, Arnheim Formation (Upper Ordovician), southeastern Indiana

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

Blackwell, W.H.; Martin, A.J.

Much naturally occurring pyritization is biologically mediated, with specific types of bacteria (sulfate reducers) promoting the reactions. Among the criteria required for pyritization in a marine environment are the presence of: (1) interstitial iron ions, (2) a primarily anaerobic (reducing) environment; (3) an organic-rich substrate, and (4) sulfate-reducing bacteria (releasing sulfide). However, the direct connection between pyritization and bacteria (microfloral remains) is difficult to visualize in the fossil record. This study focuses specifically on pyritized burrow linings that occur in strongly bioturbated wackestones from the Arnheim Formation (Cincinnatian Series, Upper Ordovician). Specific reducing microenvironments (i.e. mucoidal burrow linings) were themore » sites of early diagenetic pyritization in otherwise oxygenated, organic-rich sediments. Material examined under both the light and electron microscopes revealed occasional evidence of pyrite associated with filamentous structures. These structures possess a shape and size consistent with certain types of bacteria. This relationship, bacterialike structures with pyrite, may be more common in the fossil record than previously suspected.« less

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity.

PubMed

Nicoludis, John M; Lau, Sze-Yi; Schärfe, Charlotta P I; Marks, Debora S; Weihofen, Wilhelm A; Gaudet, Rachelle

2015-11-03

Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1-EC3, containing the homophilic specificity-determining region, of two mouse clustered Pcdh isoforms (PcdhγA1 and PcdhγC3) to investigate the nature of the homophilic interaction. Within the crystal lattices, we observe antiparallel interfaces consistent with a role in trans cell-cell contact. Antiparallel dimerization is supported by evolutionary correlations. Two interfaces, located primarily on EC2-EC3, involve distinctive clustered Pcdh structure and sequence motifs, lack predicted glycosylation sites, and contain residues highly conserved in orthologs but not paralogs, pointing toward their biological significance as homophilic interaction interfaces. These two interfaces are similar yet distinct, reflecting a possible difference in interaction architecture between clustered Pcdh subfamilies. These structures initiate a molecular understanding of clustered Pcdh assemblies that are required to produce functional neuronal networks. Copyright © 2015 Elsevier Ltd. All rights reserved.

S-phase-specific activation of Cds1 kinase defines a subpathway of the checkpoint response in Schizosaccharomyces pombe

PubMed Central

Lindsay, Howard D.; Griffiths, Dominic J.F.; Edwards, Rhian J.; Christensen, Per U.; Murray, Johanne M.; Osman, Fekret; Walworth, Nancy; Carr, Antony M.

1998-01-01

Checkpoints that respond to DNA structure changes were originally defined by the inability of yeast mutants to prevent mitosis following DNA damage or S-phase arrest. Genetic analysis has subsequently identified subpathways of the DNA structure checkpoints, including the reversible arrest of DNA synthesis. Here, we show that the Cds1 kinase is required to slow S phase in the presence of DNA-damaging agents. Cds1 is phosphorylated and activated by S-phase arrest and activated by DNA damage during S phase, but not during G1 or G2. Activation of Cds1 during S phase is dependent on all six checkpoint Rad proteins, and Cds1 interacts both genetically and physically with Rad26. Unlike its Saccharomyces cerevisiae counterpart Rad53, Cds1 is not required for the mitotic arrest checkpoints and, thus, defines an S-phase specific subpathway of the checkpoint response. We propose a model for the DNA structure checkpoints that offers a new perspective on the function of the DNA structure checkpoint proteins. This model suggests that an intrinsic mechanism linking S phase and mitosis may function independently of the known checkpoint proteins. PMID:9450932

Structural variants of yeast prions show conformer-specific requirements for chaperone activity

PubMed Central

Stein, Kevin C.; True, Heather L.

2016-01-01

Summary Molecular chaperones monitor protein homeostasis and defend against the misfolding and aggregation of proteins that is associated with protein conformational disorders. In these diseases, a variety of different aggregate structures can form. These are called prion strains, or variants, in prion diseases, and cause variation in disease pathogenesis. Here, we use variants of the yeast prions [RNQ+] and [PSI+] to explore the interactions of chaperones with distinct aggregate structures. We found that prion variants show striking variation in their relationship with Hsp40s. Specifically, the yeast Hsp40 Sis1, and its human ortholog Hdj1, had differential capacities to process prion variants, suggesting that Hsp40 selectivity has likely changed through evolution. We further show that such selectivity involves different domains of Sis1, with some prion conformers having a greater dependence on particular Hsp40 domains. Moreover, [PSI+] variants were more sensitive to certain alterations in Hsp70 activity as compared to [RNQ+] variants. Collectively, our data indicate that distinct chaperone machinery is required, or has differential capacity, to process different aggregate structures. Elucidating the intricacies of chaperone-client interactions, and how these are altered by particular client structures, will be crucial to understanding how this system can go awry in disease and contribute to pathological variation. PMID:25060529

Structure and anticoagulant activity of a sulfated galactan from the red alga, Gelidium crinale. Is there a specific structural requirement for the anticoagulant action?

PubMed

Pereira, Maria G; Benevides, Norma M B; Melo, Marcia R S; Valente, Ana Paula; Melo, Fábio R; Mourão, Paulo A S

2005-09-05

Marine red algae are an abundant source of sulfated galactans with potent anticoagulant activity. However, the specific structural motifs that confer biological activity remain to be elucidated. We have now isolated and purified a sulfated galactan from the marine red alga, Gellidium crinale. The structure of this polysaccharide was determined using NMR spectroscopy. It is composed of the repeating structure -4-alpha-Galp-(1-->3)-beta-Galp1--> but with a variable sulfation pattern. Clearly 15% of the total alpha-units are 2,3-di-sulfated and another 55% are 2-sulfated. No evidence for the occurrence of 3,6-anhydro alpha-galactose units was observed in the NMR spectra. We also compared the anticoagulant activity of this sulfated galactan with a polysaccharide from the species, Botryocladia occidentalis, with a similar saccharide chain but with higher amounts of 2,3-di-sulfated alpha-units. The sulfated galactan from G. crinale has a lower anticoagulant activity on a clotting assay when compared with the polysaccharide from B. occidentalis. When tested in assays using specific proteases and coagulation inhibitors, these two galactans showed significant differences in their activity. They do not differ in thrombin inhibition mediated by antithrombin, but in assays where heparin cofactor II replaces antithrombin, the sulfated galactan from G. crinale requires a significantly higher concentration to achieve the same inhibitory effect as the polysaccharide from B. occidentalis. In contrast, when factor Xa instead of thrombin is used as the target protease, the sulfated galactan from G. crinale is a more potent anticoagulant. These observations suggest that the proportion and/or the distribution of 2,3-di-sulfated alpha-units along the galactan chain may be a critical structural motif to promote the interaction of the protease with specific protease and coagulation inhibitors.

Recent progress in NASA Langley Research Center textile reinforced composites program

NASA Technical Reports Server (NTRS)

Dexter, H. Benson; Harris, Charles E.; Johnston, Norman J.

1992-01-01

Research was conducted to explore the benefits of textile reinforced composites for transport aircraft primary structures. The objective is to develop and demonstrate the potential of affordable textile reinforced composite materials to meet design properties and damage tolerance requirements of advanced aircraft structural concepts. Some program elements include development of textile preforms, processing science, mechanics of materials, experimental characterization of materials, and development and evaluation of textile reinforced composite structural elements and subcomponents. Textile 3-D weaving, 3-D braiding, and knitting and/or stitching are being compared with conventional laminated tape processes for improved damage tolerance. Through-the-thickness reinforcements offer significant damage tolerance improvements. However, these gains must be weighted against potential loss in in-plane properties such as strength and stiffness. Analytical trade studies are underway to establish design guidelines for the application of textile material forms to meet specific loading requirements. Fabrication and testing of large structural parts are required to establish the potential of textile reinforced composite materials.

Generalized Information Architecture for Managing Requirements in IBM?s Rational DOORS(r) Application.

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

Aragon, Kathryn M.; Eaton, Shelley M.; McCornack, Marjorie Turner

When a requirements engineering effort fails to meet expectations, often times the requirements management tool is blamed. Working with numerous project teams at Sandia National Laboratories over the last fifteen years has shown us that the tool is rarely the culprit; usually it is the lack of a viable information architecture with well- designed processes to support requirements engineering. This document illustrates design concepts with rationale, as well as a proven information architecture to structure and manage information in support of requirements engineering activities for any size or type of project. This generalized information architecture is specific to IBM's Rationalmore » DOORS (Dynamic Object Oriented Requirements System) software application, which is the requirements management tool in Sandia's CEE (Common Engineering Environment). This generalized information architecture can be used as presented or as a foundation for designing a tailored information architecture for project-specific needs. It may also be tailored for another software tool. Version 1.0 4 November 201« less

Materials and structures

NASA Astrophysics Data System (ADS)

Saito, Theodore T.; Langenbeck, Sharon L.; Al-Jamily, Ghanim; Arnold, Joe; Barbee, Troy; Coulter, Dan; Dolgin, Ben; Fichter, Buck; George, Patricia; Gorenstein, Paul

1992-08-01

Materials and structures technology covers a wide range of technical areas. Some of the most pertinent issues for the Astrotech 21 missions include dimensionally stable structural materials, advanced composites, dielectric coatings, optical metallic coatings for low scattered light applications, low scattered light surfaces, deployable and inflatable structures (including optical), support structures in 0-g and 1-g environments, cryogenic optics, optical blacks, contamination hardened surfaces, radiation hardened glasses and crystals, mono-metallic telescopes and instruments, and materials characterization. Some specific examples include low coefficients of thermal expansion (CTE) structures (0.01 ppm/K), lightweight thermally stable mirror materials, thermally stable optical assemblies, high reliability/accuracy (1 micron) deployable structures, and characterization of nanometer level behavior of materials/structures for interferometry concepts. Large filled-aperture concepts will require materials with CTE's of 10(exp 9) at 80 K, anti-contamination coatings, deployable and erectable structures, composite materials with CTE's less than 0.01 ppm/K and thermal hysteresis, 0.001 ppm/K. Gravitational detection systems such as LAGOS will require rigid/deployable structures, dimensionally stable components, lightweight materials with low conductivity, and high stability optics. The Materials and Structures panel addressed these issues and the relevance of the Astrotech 21 mission requirements by dividing materials and structures technology into five categories. These categories, the necessary development, and applicable mission/program development phasing are summarized. For each of these areas, technology assessments were made and development plans were defined.

Visualizing Viral Protein Structures in Cells Using Genetic Probes for Correlated Light and Electron Microscopy

PubMed Central

Ou, Horng D.; Deerinck, Thomas J.; Bushong, Eric; Ellisman, Mark H.; O’Shea, Clodagh C.

2015-01-01

Structural studies of viral proteins most often use high-resolution techniques such as X-ray crystallography, nuclear magnetic resonance, single particle negative stain, or cryo-electron microscopy (EM) to reveal atomic interactions of soluble, homogeneous viral proteins or viral protein complexes. Once viral proteins or complexes are separated from their host’s cellular environment, their natural in-situ structure and details of how they interact with other cellular components may be lost. EM has been an invaluable tool in virology since its introduction in the late 1940’s and subsequent application to cells in the 1950’s. EM studies have expanded our knowledge of viral entry, viral replication, alteration of cellular components, and viral lysis. Most of these early studies were focused on conspicuous morphological cellular changes, because classic EM metal stains were designed to highlight classes of cellular structures rather than specific molecular structures. Much later, to identify viral proteins inducing specific structural configurations at the cellular level, immunostaining with a primary antibody followed by colloidal gold secondary antibody was employed to mark the location of specific viral proteins. This technique can suffer from artifacts in cellular ultrastructure due to compromises required to provide access to the immuno-reagents. Immunolocalization methods also require the generation of highly specific antibodies, which may not be available for every viral protein. Here we discuss new methods to visualize viral proteins and structures at high resolutions in-situ using correlated light and electron microscopy (CLEM). We discuss the use of genetically encoded protein fusions that oxidize diaminobenzidine (DAB) into an osmiophilic polymer that can be visualized by EM. Detailed protocols for applying the genetically encoded photo-oxidizing protein MiniSOG to a viral protein, photo-oxidation of the fusion protein to yield DAB polymer staining, and preparation of photo-oxidized samples for TEM and serial block-face scanning EM (SBEM) for large-scale volume EM data acquisition are also presented. As an example, we discuss the recent multi-scale analysis of Adenoviral protein E4-ORF3 that reveals a new type of multi-functional polymer that disrupts multiple cellular proteins. This new capability to visualize unambiguously specific viral protein structures at high resolutions in the native cellular environment is revealing new insights into how they usurp host proteins and functions to drive pathological viral replication. PMID:26066760

Visualizing viral protein structures in cells using genetic probes for correlated light and electron microscopy.

PubMed

Ou, Horng D; Deerinck, Thomas J; Bushong, Eric; Ellisman, Mark H; O'Shea, Clodagh C

2015-11-15

Structural studies of viral proteins most often use high-resolution techniques such as X-ray crystallography, nuclear magnetic resonance, single particle negative stain, or cryo-electron microscopy (EM) to reveal atomic interactions of soluble, homogeneous viral proteins or viral protein complexes. Once viral proteins or complexes are separated from their host's cellular environment, their natural in situ structure and details of how they interact with other cellular components may be lost. EM has been an invaluable tool in virology since its introduction in the late 1940's and subsequent application to cells in the 1950's. EM studies have expanded our knowledge of viral entry, viral replication, alteration of cellular components, and viral lysis. Most of these early studies were focused on conspicuous morphological cellular changes, because classic EM metal stains were designed to highlight classes of cellular structures rather than specific molecular structures. Much later, to identify viral proteins inducing specific structural configurations at the cellular level, immunostaining with a primary antibody followed by colloidal gold secondary antibody was employed to mark the location of specific viral proteins. This technique can suffer from artifacts in cellular ultrastructure due to compromises required to provide access to the immuno-reagents. Immunolocalization methods also require the generation of highly specific antibodies, which may not be available for every viral protein. Here we discuss new methods to visualize viral proteins and structures at high resolutions in situ using correlated light and electron microscopy (CLEM). We discuss the use of genetically encoded protein fusions that oxidize diaminobenzidine (DAB) into an osmiophilic polymer that can be visualized by EM. Detailed protocols for applying the genetically encoded photo-oxidizing protein MiniSOG to a viral protein, photo-oxidation of the fusion protein to yield DAB polymer staining, and preparation of photo-oxidized samples for TEM and serial block-face scanning EM (SBEM) for large-scale volume EM data acquisition are also presented. As an example, we discuss the recent multi-scale analysis of Adenoviral protein E4-ORF3 that reveals a new type of multi-functional polymer that disrupts multiple cellular proteins. This new capability to visualize unambiguously specific viral protein structures at high resolutions in the native cellular environment is revealing new insights into how they usurp host proteins and functions to drive pathological viral replication. Copyright © 2015 Elsevier Inc. All rights reserved.

Estimating survival rates with time series of standing age‐structure data

USGS Publications Warehouse

Udevitz, Mark S.; Gogan, Peter J.

2012-01-01

It has long been recognized that age‐structure data contain useful information for assessing the status and dynamics of wildlife populations. For example, age‐specific survival rates can be estimated with just a single sample from the age distribution of a stable, stationary population. For a population that is not stable, age‐specific survival rates can be estimated using techniques such as inverse methods that combine time series of age‐structure data with other demographic data. However, estimation of survival rates using these methods typically requires numerical optimization, a relatively long time series of data, and smoothing or other constraints to provide useful estimates. We developed general models for possibly unstable populations that combine time series of age‐structure data with other demographic data to provide explicit maximum likelihood estimators of age‐specific survival rates with as few as two years of data. As an example, we applied these methods to estimate survival rates for female bison (Bison bison) in Yellowstone National Park, USA. This approach provides a simple tool for monitoring survival rates based on age‐structure data.

Structural mechanism underlying capsaicin binding and activation of TRPV1 ion channel

PubMed Central

Cheng, Wei; Yang, Wei; Yu, Peilin; Song, Zhenzhen; Yarov-Yarovoy, Vladimir; Zheng, Jie

2015-01-01

Capsaicin bestows spiciness by activating TRPV1 channel with exquisite potency and selectivity. Capsaicin-bound channel structure was previously resolved by cryo-EM at 4.2-to-4.5 Å resolution, however important details required for mechanistic understandings are unavailable: capsaicin was registered as a small electron density, reflecting neither its chemical structure nor specific ligand-channel interactions. We obtained the missing atomic-level details by iterative computation, which were confirmed by systematic site-specific functional tests. We observed that the bound capsaicin takes “tail-up, head-down” configurations. The vanillyl and amide groups form specific interactions to anchor its bound position, while the aliphatic tail may sample a range of conformations, making it invisible in cryo-EM images. Capsaicin stabilizes the open state by “pull-and-contact” interactions between the vanillyl group and the S4-S5 linker. Our study provided a structural mechanism for the agonistic function of capsaicin and its analogs, and demonstrated an effective approach to obtain atomic level information from cryo-EM structures. PMID:26053297

Extreme disorder in an ultrahigh-affinity protein complex

NASA Astrophysics Data System (ADS)

Borgia, Alessandro; Borgia, Madeleine B.; Bugge, Katrine; Kissling, Vera M.; Heidarsson, Pétur O.; Fernandes, Catarina B.; Sottini, Andrea; Soranno, Andrea; Buholzer, Karin J.; Nettels, Daniel; Kragelund, Birthe B.; Best, Robert B.; Schuler, Benjamin

2018-03-01

Molecular communication in biology is mediated by protein interactions. According to the current paradigm, the specificity and affinity required for these interactions are encoded in the precise complementarity of binding interfaces. Even proteins that are disordered under physiological conditions or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring defined binding sites or interactions between specific individual residues. Proteome-wide sequence analysis suggests that this interaction mechanism may be abundant in eukaryotes.

Shape optimization of disc-type flywheels

NASA Technical Reports Server (NTRS)

Nizza, R. S.

1976-01-01

Techniques were developed for presenting an analytical and graphical means for selecting an optimum flywheel system design, based on system requirements, geometric constraints, and weight limitations. The techniques for creating an analytical solution are formulated from energy and structural principals. The resulting flywheel design relates stress and strain pattern distribution, operating speeds, geometry, and specific energy levels. The design techniques incorporate the lowest stressed flywheel for any particular application and achieve the highest specific energy per unit flywheel weight possible. Stress and strain contour mapping and sectional profile plotting reflect the results of the structural behavior manifested under rotating conditions. This approach toward flywheel design is applicable to any metal flywheel, and permits the selection of the flywheel design to be based solely on the criteria of the system requirements that must be met, those that must be optimized, and those system parameters that may be permitted to vary.

Data standards for clinical research data collection forms: current status and challenges.

PubMed

Richesson, Rachel L; Nadkarni, Prakash

2011-05-01

Case report forms (CRFs) are used for structured-data collection in clinical research studies. Existing CRF-related standards encompass structural features of forms and data items, content standards, and specifications for using terminologies. This paper reviews existing standards and discusses their current limitations. Because clinical research is highly protocol-specific, forms-development processes are more easily standardized than is CRF content. Tools that support retrieval and reuse of existing items will enable standards adoption in clinical research applications. Such tools will depend upon formal relationships between items and terminological standards. Future standards adoption will depend upon standardized approaches for bridging generic structural standards and domain-specific content standards. Clinical research informatics can help define tools requirements in terms of workflow support for research activities, reconcile the perspectives of varied clinical research stakeholders, and coordinate standards efforts toward interoperability across healthcare and research data collection.

Topology optimization for nonlinear dynamic problems: Considerations for automotive crashworthiness

NASA Astrophysics Data System (ADS)

Kaushik, Anshul; Ramani, Anand

2014-04-01

Crashworthiness of automotive structures is most often engineered after an optimal topology has been arrived at using other design considerations. This study is an attempt to incorporate crashworthiness requirements upfront in the topology synthesis process using a mathematically consistent framework. It proposes the use of equivalent linear systems from the nonlinear dynamic simulation in conjunction with a discrete-material topology optimizer. Velocity and acceleration constraints are consistently incorporated in the optimization set-up. Issues specific to crash problems due to the explicit solution methodology employed, nature of the boundary conditions imposed on the structure, etc. are discussed and possible resolutions are proposed. A demonstration of the methodology on two-dimensional problems that address some of the structural requirements and the types of loading typical of frontal and side impact is provided in order to show that this methodology has the potential for topology synthesis incorporating crashworthiness requirements.

Field documentation and client presentation of IR inspections on new masonry structures

NASA Astrophysics Data System (ADS)

McMullan, Phillip C.

1991-03-01

With the adoption of American Concrete Institute's Design Standard 530 (ACI 530-88/ASCE 5-88) and Specifications (ACI 530.1-88/ASCE 6-88) by more governing bodies throughout the United States, the level and method of inspecting masonry structures is rapidly changing. These new standards set forth inspection criteria such that the Professional of Record (i.e., Architect), can determine the level of inspection based on the type and complexity of the structure being built. For example, a hospital would require considerably more inspection than a Seven-Eleven mini-market. However, the standards require that all new masonry buildings must be inspected. Infrared thermography has proven to be an effective tool to assist in the required inspections. These inspections focus on evaluating masonry for compliance with the design specifications with regard to material, structural strength and thermal performance, the use of video infrared thermography provides a thorough systematic method for inspection of structural solids and thermal integrity of masonry structures. In conducting masonry inspections, the creation of a permanent, well-documented record is valuable in avoiding potential controversy over the inspection findings. Therefore, the inspection method, verification of findings, and presentation of the inspection data are key to the successful use of infrared thermography as an inspection tool. This paper will focus on the method of inspection which TSI employs in conducting new masonry inspections. Additionally, an important component of any work is the presentation of the data. We will look at the information which is generated during this type of inspection and how that data can be converted into a usable report for the various parties involved in construction of a new masonry building.

Telomere Capping Proteins are Structurally Related to RPA with an additional Telomere-Specific Domain

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

Gelinas, A.; Paschini, M; Reyes, F

Telomeres must be capped to preserve chromosomal stability. The conserved Stn1 and Ten1 proteins are required for proper capping of the telomere, although the mechanistic details of how they contribute to telomere maintenance are unclear. Here, we report the crystal structures of the C-terminal domain of the Saccharomyces cerevisiae Stn1 and the Schizosaccharomyces pombe Ten1 proteins. These structures reveal striking similarities to corresponding subunits in the replication protein A complex, further supporting an evolutionary link between telomere maintenance proteins and DNA repair complexes. Our structural and in vivo data of Stn1 identify a new domain that has evolved to supportmore » a telomere-specific role in chromosome maintenance. These findings endorse a model of an evolutionarily conserved mechanism of DNA maintenance that has developed as a result of increased chromosomal structural complexity.« less

Development and Sizing of the JWST Integrated Science Instrument Module (ISIM) Metering Structure

NASA Technical Reports Server (NTRS)

Johnston, John; Kunt, Cengiz; Bartoszyk, Andrew; Hendricks, Steve; Cofie, Emmanuel

2006-01-01

The JWST Integrated Science Instrument Module (ISIM) includes a large metering structure (approx. 2m x 2m x 1.5m) that houses the science instruments and guider. Stringent dimensional stability and repeatability requirements combined with mass limitations led to the selection of a composite bonded frame design comprised of biased laminate tubes. Even with the superb material specific stiffness, achieving the required frequency for the given mass allocations in conjunction with severe spatial limitations imposed by the instrument complement has proven challenging. In response to the challenge, the ISIM structure team considered literally over 100 primary structure topology and kinematic mount configurations, and settled on a concept comprised of over 70 m of tubes, over 50 bonded joint assemblies, and a "split bi-pod" kinematic mount configuration. In this paper, we review the evolution of the ISIM primary structure topology and kinematic mount configuration to the current baseline concept.

Proving Correctness for Pointer Programs in a Verifying Compiler

NASA Technical Reports Server (NTRS)

Kulczycki, Gregory; Singh, Amrinder

2008-01-01

This research describes a component-based approach to proving the correctness of programs involving pointer behavior. The approach supports modular reasoning and is designed to be used within the larger context of a verifying compiler. The approach consists of two parts. When a system component requires the direct manipulation of pointer operations in its implementation, we implement it using a built-in component specifically designed to capture the functional and performance behavior of pointers. When a system component requires pointer behavior via a linked data structure, we ensure that the complexities of the pointer operations are encapsulated within the data structure and are hidden to the client component. In this way, programs that rely on pointers can be verified modularly, without requiring special rules for pointers. The ultimate objective of a verifying compiler is to prove-with as little human intervention as possible-that proposed program code is correct with respect to a full behavioral specification. Full verification for software is especially important for an agency like NASA that is routinely involved in the development of mission critical systems.

Shuttle/TDRSS Ku-band downlink study

NASA Technical Reports Server (NTRS)

Meyer, R.

1976-01-01

Assessing the adequacy of the baseline signal design approach, developing performance specifications for the return link hardware, and performing detailed design and parameter optimization tasks was accomplished by completing five specific study tasks. The results of these tasks show that the basic signal structure design is sound and that the goals can be met. Constraints placed on return link hardware by this structure allow reasonable specifications to be written so that no extreme technical risk areas in equipment design are foreseen. A third channel can be added to the PM mode without seriously degrading the other services. The feasibility of using only a PM mode was shown to exist, however, this will require use of some digital TV transmission techniques. Each task and its results are summarized.

Integrated support structure for GASCAN 2

NASA Technical Reports Server (NTRS)

1990-01-01

The focus of the Worcester Polytechnic Institute (WPI) Advanced Space Design Program was the preliminary design of the Integrated Support Structure for GASCAN II, a Get Away Special canister donated by the MITRE Corporation. Two teams of three students each worked on the support structure. There was a structural design team and a thermal design team. The structure will carry three experiments also undergoing preliminary design this year, the mu-gravity Ignition Experiment, the Rotational Flow in Low Gravity Experiment, and the Ionospheric Properties and Propagation Experiment. The structural design team was responsible for the layout of the GASCAN and the preliminary design of the structure itself. They produced the physical interface specifications defining the baseline weights and volumes for the equipment and produced layout drawings of the system. The team produced static and modal finite element analysis of the structure using ANSYS. The thermal design team was responsible for the power and timing requirements of the payload and for the identification and preliminary analysis of potential thermal problems. The team produced the power, timing, and energy interface specifications and assisted in the development of the specification of the battery pack. The thermal parameters of each experiment were cataloged and the experiments were subjected to worst case heat transfer scenarios.

A space station Structures and Assembly Verification Experiment, SAVE

NASA Technical Reports Server (NTRS)

Russell, R. A.; Raney, J. P.; Deryder, L. J.

1986-01-01

The Space Station structure has been baselined to be a 5 M (16.4 ft) erectable truss. This structure will provide the overall framework to attach laboratory modules and other systems, subsystems and utilities. The assembly of this structure represents a formidable EVA challenge. To validate this capability the Space Station Structures/Dynamics Technical Integration Panel (TIP) met to develop the necessary data for an integrated STS structures flight experiment. As a result of this meeting, the Langley Research Center initiated a joint Langley/Boeing Aerospace Company study which supported the structures/dynamics TIP in developing the preliminary definition and design of a 5 M erectable space station truss and the resources required for a proposed flight experiment. The purpose of the study was to: (1) devise methods of truss assembly by astronauts; (2) define a specific test matrix for dynamic characterization; (3) identify instrumentation and data system requirements; (4) determine the power, propulsion and control requirements for the truss on-orbit for 3 years; (5) study the packaging of the experiment in the orbiter cargo bay; (6) prepare a preliminary cost estimate and schedule for the experiment; and (7) provide a list of potential follow-on experiments using the structure as a free flyer. The results of this three month study are presented.

Notochord vacuoles are lysosome-related organelles that function in axis and spine morphogenesis.

PubMed

Ellis, Kathryn; Bagwell, Jennifer; Bagnat, Michel

2013-03-04

The notochord plays critical structural and signaling roles during vertebrate development. At the center of the vertebrate notochord is a large fluid-filled organelle, the notochord vacuole. Although these highly conserved intracellular structures have been described for decades, little is known about the molecular mechanisms involved in their biogenesis and maintenance. Here we show that zebrafish notochord vacuoles are specialized lysosome-related organelles whose formation and maintenance requires late endosomal trafficking regulated by the vacuole-specific Rab32a and H(+)-ATPase-dependent acidification. We establish that notochord vacuoles are required for body axis elongation during embryonic development and identify a novel role in spine morphogenesis. Thus, the vertebrate notochord plays important structural roles beyond early development.

Space construction system analysis. Part 2: Construction analysis

NASA Technical Reports Server (NTRS)

Roebuck, J. A.; Buck, P. A.; Gimlich, G. W.; Greenberg, H. S.; Hart, R. J.; Indrikis, J.; Lefever, A. E.; Lillenas, A. N.; Mcbaine, C. K.

1980-01-01

The construction methods specific to the end to end construction process for building the ETVP in low Earth orbit, using the space shuttle orbiter as a construction base, are analyzed. The analyses concerned three missions required to build the basic platform. The first mission involved performing the fabrication of beams in space and assembling the beams into a basic structural framework. The second mission was to install the forward support structure and aft support structure, the forward assembly, and a TT&C antenna. The third mission plan was to complete the construction of the platform and activate it to begin operations in low Earth orbit. The integration of the activities for each mission is described along with the construction requirements and construction logic.

Notochord vacuoles are lysosome-related organelles that function in axis and spine morphogenesis

PubMed Central

Ellis, Kathryn; Bagwell, Jennifer

2013-01-01

The notochord plays critical structural and signaling roles during vertebrate development. At the center of the vertebrate notochord is a large fluid-filled organelle, the notochord vacuole. Although these highly conserved intracellular structures have been described for decades, little is known about the molecular mechanisms involved in their biogenesis and maintenance. Here we show that zebrafish notochord vacuoles are specialized lysosome-related organelles whose formation and maintenance requires late endosomal trafficking regulated by the vacuole-specific Rab32a and H+-ATPase–dependent acidification. We establish that notochord vacuoles are required for body axis elongation during embryonic development and identify a novel role in spine morphogenesis. Thus, the vertebrate notochord plays important structural roles beyond early development. PMID:23460678

Geocoded data structures and their applications to Earth science investigations

NASA Technical Reports Server (NTRS)

Goldberg, M.

1984-01-01

A geocoded data structure is a means for digitally representing a geographically referenced map or image. The characteristics of representative cellular, linked, and hybrid geocoded data structures are reviewed. The data processing requirements of Earth science projects at the Goddard Space Flight Center and the basic tools of geographic data processing are described. Specific ways that new geocoded data structures can be used to adapt these tools to scientists' needs are presented. These include: expanding analysis and modeling capabilities; simplifying the merging of data sets from diverse sources; and saving computer storage space.

Integrated Requirements Analysis and Technology Roadmaps

NASA Technical Reports Server (NTRS)

1997-01-01

In fiscal year 1997, Strategic Insight performed analytical studies for NASA's Highly Reusable Space Transportation (HRST) program, creating program documents which illuminated technical requirements and critical research opportunities. Studies were performed to structure and confirm HRST's evolving technical requirements, building on Marshall's Phase 1 work, which defined HRST system concepts, analytical tools and high-level issues for assessment in Phase 2. Specifically, Strategic Insight: (1) Performed a requirements analysis to update HRST: An Advanced Concepts Study, Study Guidelines, Version 2.0 of January 22, 1996; only minor changes were recommended for the given parameters of interest to concept designers; (2) Conducted mini-workshops during HRST Working Group meetings on April 14-15, 1997 and July 22-24, 1997; and (3) Created structures for technology road maps of candidate HRST concepts, both subsystem and end-to-end concepts, emerging from the 13 cooperative agreement projects.

Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1*

PubMed Central

Musayev, Faik N.; Zarate-Perez, Francisco; Bishop, Clayton; Burgner, John W.; Escalante, Carlos R.

2015-01-01

Adeno-associated virus (AAV) is the only eukaryotic virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC repeats that are recognized by the AAV non-structural Rep proteins. These proteins are multifunctional, with an N-terminal origin-binding domain (OBD) and a helicase domain joined together by a short linker. As a first step to understand the process of site-specific integration, we proceeded to characterize the recognition and assembly of Rep68 onto the AAVS1 site. We first determined the x-ray structure of AAV-2 Rep68 OBD in complex with the AAVS1 DNA site. Specificity is achieved through the interaction of a glycine-rich loop that binds the major groove and an α-helix that interacts with a downstream minor groove on the same face of the DNA. Although the structure shows a complex with three OBD molecules bound to the AAVS1 site, we show by using analytical centrifugation and electron microscopy that the full-length Rep68 forms a heptameric complex. Moreover, we determined that a minimum of two direct repeats is required to form a stable complex and to melt DNA. Finally, we show that although the individual domains bind DNA poorly, complex assembly requires oligomerization and cooperation between its OBD, helicase, and the linker domains. PMID:26370092

Uncertainty in stormwater drainage adaptation: what matters and how much is too much?

NASA Astrophysics Data System (ADS)

Stack, L. J.; Simpson, M. H.; Moore, T.; Gulliver, J. S.; Roseen, R.; Eberhart, L.; Smith, J. B.; Gruber, J.; Yetka, L.; Wood, R.; Lawson, C.

2014-12-01

Published research continues to report that long-term, local-scale precipitation forecasts are too uncertain to support local-scale adaptation. Numerous studies quantify the range of uncertainty in downscaled model output; compare this with uncertainty from other sources such as hydrological modeling; and propose circumventing uncertainty via "soft" or "low regret" actions, or adaptive management. Yet non-structural adaptations alone are likely insufficient. Structural adaptation requires quantified engineering design specifications. However, the literature does not define a tolerable level of uncertainty. Without such a benchmark, how can we determine whether the climate-change-cognizant design specifications that we are capable of, for example the climate change factors increasingly utilized in European practice, are viable? The presentation will explore this question, in the context of reporting results and observations from an ongoing ten-year program assessing local-scale stormwater drainage system vulnerabilities, required capacities, and adaptation options and costs. This program has studied stormwater systems of varying complexity in a variety of regions, topographies, and levels of urbanization, in northern-New England and the upper-Midwestern United States. These studies demonstrate the feasibility of local-scale design specifications, and provide tangible information on risk to enable valid cost/benefit decisions. The research program has found that stormwater planners and engineers have routinely accepted, in the normal course of professional practice, a level of uncertainty in hydrological modeling comparable to that in long-term precipitation projections. Moreover, the ability to quantify required capacity and related construction costs for specific climate change scenarios, the insensitivity of capacity and costs to uncertainty, and the percentage of pipes and culverts that never require upsizing, all serve to limit the impact of uncertainty inherent in climate change projections.

12 CFR 1022.72 - General requirements for risk-based pricing notices.

Code of Federal Regulations, 2012 CFR

2012-01-01

... consumer by placing the consumer within one of a discrete number of pricing tiers for a specific type of...-priced tier). For example, a person that uses a tiered pricing structure with annual percentage rates of...

Milne boost from Galilean gauge theory

NASA Astrophysics Data System (ADS)

Banerjee, Rabin; Mukherjee, Pradip

2018-03-01

Physical origin of Milne boost invariance of the Newton Cartan spacetime is traced to the effect of local Galilean boosts in its metric structure, using Galilean gauge theory. Specifically, we do not require any gauge field to understand Milne boost invariance.

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

PubMed Central

2011-01-01

Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file. PMID:21205310

Logistics Integration: Closing the Gap

DTIC Science & Technology

2012-05-18

explain how a common understanding occurs as part of JOPP. More importantly, the structure of JOPP Jacks a specific process of collaboration between...create unity of effort. Flexibility is how logistic structures and procedures improvise and adapt to the chaos of the battlefield. This requires... prefabricated harbors or artificial ports.26 The two prefabricated harbors were to be constructed as soon as the beachheads were secured utilizing the

Charge-coupled device image sensor study

NASA Technical Reports Server (NTRS)

1973-01-01

The design specifications and predicted performance characteristics of a Charge-Coupled Device Area Imager and a Charge-Coupled Device Linear Imager are presented. The Imagers recommended are intended for use in space-borne imaging systems and therefore would meet the requirements for the intended application. A unique overlapping metal electrode structure and a buried channel structure are described. Reasons for the particular imager designs are discussed.

Tactical Unit Data and Decision Requirements for Urban Operations

DTIC Science & Technology

2008-10-01

maneuverability, sensor optimization, weapon effects, terrain), and develop rich but lightweight information structures and architecture . Specifically, the goal...tion structure and systemic architecture that enable sharing common data in near real-time, and mission planning and analysis software for U-BE...Building Function Verify mosque and identify possi- ble schools or meeting places Identify types of cinema (stage/theatre) or other similar nearby

THE CRYSTALLOGRAPHIC INVESTIGATION OF AuCl /center dot/ PCl$sub 3$ AND IBOGAINE /center dot/ HBr

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

Arai-wessel, G.J.

1960-01-01

The structure of the two compounds is completely dlfferent, one being an inorganic complex and the other being an organic alkaloid complex. The difference in crystal constitution caused a difference in behavior with regard to radiation, requiring the use of specific crysthllographic methods for each. Interferences involved in determining their crystal structure are compared and discussed. (N.W.R.)

A resource for benchmarking the usefulness of protein structure models.

PubMed

Carbajo, Daniel; Tramontano, Anna

2012-08-02

Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

Hardware Specific Integration Strategy for Impedance-Based Structural Health Monitoring of Aerospace Systems

NASA Technical Reports Server (NTRS)

Owen, Robert B.; Gyekenyesi, Andrew L.; Inman, Daniel J.; Ha, Dong S.

2011-01-01

The Integrated Vehicle Health Management (IVHM) Project, sponsored by NASA's Aeronautics Research Mission Directorate, is conducting research to advance the state of highly integrated and complex flight-critical health management technologies and systems. An effective IVHM system requires Structural Health Monitoring (SHM). The impedance method is one such SHM technique for detection and monitoring complex structures for damage. This position paper on the impedance method presents the current state of the art, future directions, applications and possible flight test demonstrations.

The PubChem chemical structure sketcher

PubMed Central

2009-01-01

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

16 CFR 640.3 - General requirements for risk-based pricing notices.

Code of Federal Regulations, 2013 CFR

2013-01-01

... within one of a discrete number of pricing tiers for a specific type of credit product, based in whole or... that uses a tiered pricing structure with annual percentage rates of 8, 10, 12, and 14 percent would...

12 CFR 222.72 - General requirements for risk-based pricing notices.

Code of Federal Regulations, 2013 CFR

2013-01-01

... within one of a discrete number of pricing tiers for a specific type of credit product, based in whole or... that uses a tiered pricing structure with annual percentage rates of 8, 10, 12, and 14 percent would...

16 CFR 640.3 - General requirements for risk-based pricing notices.

Code of Federal Regulations, 2014 CFR

2014-01-01

... within one of a discrete number of pricing tiers for a specific type of credit product, based in whole or... that uses a tiered pricing structure with annual percentage rates of 8, 10, 12, and 14 percent would...

12 CFR 222.72 - General requirements for risk-based pricing notices.

Code of Federal Regulations, 2014 CFR

2014-01-01

... within one of a discrete number of pricing tiers for a specific type of credit product, based in whole or... that uses a tiered pricing structure with annual percentage rates of 8, 10, 12, and 14 percent would...

16 CFR 640.3 - General requirements for risk-based pricing notices.

Code of Federal Regulations, 2012 CFR

2012-01-01

... within one of a discrete number of pricing tiers for a specific type of credit product, based in whole or... that uses a tiered pricing structure with annual percentage rates of 8, 10, 12, and 14 percent would...

Expanding the Scope of Site-Specific Recombinases for Genetic and Metabolic Engineering

PubMed Central

Gaj, Thomas; Sirk, Shannon J.; Barbas, Carlos F.

2014-01-01

Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. PMID:23982993

Structural Feature Ions for Distinguishing N- and O-Linked Glycan Isomers by LC-ESI-IT MS/MS

NASA Astrophysics Data System (ADS)

Everest-Dass, Arun V.; Abrahams, Jodie L.; Kolarich, Daniel; Packer, Nicolle H.; Campbell, Matthew P.

2013-06-01

Glycomics is the comprehensive study of glycan expression in an organism, cell, or tissue that relies on effective analytical technologies to understand glycan structure-function relationships. Owing to the macro- and micro-heterogeneity of oligosaccharides, detailed structure characterization has required an orthogonal approach, such as a combination of specific exoglycosidase digestions, LC-MS/MS, and the development of bioinformatic resources to comprehensively profile a complex biological sample. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) has emerged as a key tool in the structural analysis of oligosaccharides because of its high sensitivity, resolution, and robustness. Here, we present a strategy that uses LC-ESI-MS/MS to characterize over 200 N- and O-glycans from human saliva glycoproteins, complemented by sequential exoglycosidase treatment, to further verify the annotated glycan structures. Fragment-specific substructure diagnostic ions were collated from an extensive screen of the literature available on the detailed structural characterization of oligosaccharides and, together with other specific glycan structure feature ions derived from cross-ring and glycosidic-linkage fragmentation, were used to characterize the glycans and differentiate isomers. The availability of such annotated mass spectrometric fragmentation spectral libraries of glycan structures, together with such substructure diagnostic ions, will be key inputs for the future development of the automated elucidation of oligosaccharide structures from MS/MS data.

Towards Formal Implementation of PUS Standard

NASA Astrophysics Data System (ADS)

Ilić, D.

2009-05-01

As an effort to promote the reuse of on-board and ground systems ESA developed a standard for packet telemetry and telecommand - PUS. It defines a set of standard service models with the corresponding structures of the associated telemetry and telecommand packets. Various missions then can choose to implement those standard PUS services that best conform to their specific requirements. In this paper we propose a formal development (based on the Event-B method) of reusable service patterns, which can be instantiated for concrete application. Our formal models allow us to formally express and verify specific service properties including various telecommand and telemetry packet structure validation.

Characterization of large 2219 aluminum alloy hand forgings for the space shuttle solid rocket booster

NASA Technical Reports Server (NTRS)

Brennecke, M. W.

1978-01-01

The mechanical properties, including fracture toughness, and stress corrosion properties of four types of 2219-T852 aluminum alloy hand forgings are presented. Weight of the forgings varied between 450 and 3500 lb at the time of heat treatment and dimensions exceeded the maximum covered in existing specifications. The forgings were destructively tested to develop reliable mechanical property data to replace estimates employed in the design of the Space Shuttle Solid Rocket Booster (SRB) and to establish minimum guaranteed properties for structural refinement and for entry into specification revisions. The report summarizes data required from the forgers and from the SRB Structures contractor.

DESAP 1: A structural design program with stress and displacement constraints. Volume 1: Theoretical and user's manual

NASA Technical Reports Server (NTRS)

Kiusalaas, J.; Reddy, G. B.

1977-01-01

A finite element program is presented for computer-automated, minimum weight design of elastic structures with constraints on stresses (including local instability criteria) and displacements. Volume 1 of the report contains the theoretical and user's manual of the program. Sample problems and the listing of the program are included in Volumes 2 and 3. The element subroutines are organized so as to facilitate additions and changes by the user. As a result, a relatively minor programming effort would be required to make DESAP 1 into a special purpose program to handle the user's specific design requirements and failure criteria.

Employing Intelligence, Surveillance, and Reconnaissance: Organizing, Training, and Equipping to Get It Right

DTIC Science & Technology

2014-02-01

facilitate effective employment across all spectra and that an adequate ISR- specific C2 structure be established. Lastly, it addresses artificial seams...becomes too great. Thus, unless an individual is specifically tasked to perform a tactical controller role under the senior intelli - gence duty...into joint operations enabling rapid decisions based on actionable intelli - gence.൚ It also highlights the requirement of synchronizing all actions

Automatic specification of reliability models for fault-tolerant computers

NASA Technical Reports Server (NTRS)

Liceaga, Carlos A.; Siewiorek, Daniel P.

1993-01-01

The calculation of reliability measures using Markov models is required for life-critical processor-memory-switch structures that have standby redundancy or that are subject to transient or intermittent faults or repair. The task of specifying these models is tedious and prone to human error because of the large number of states and transitions required in any reasonable system. Therefore, model specification is a major analysis bottleneck, and model verification is a major validation problem. The general unfamiliarity of computer architects with Markov modeling techniques further increases the necessity of automating the model specification. Automation requires a general system description language (SDL). For practicality, this SDL should also provide a high level of abstraction and be easy to learn and use. The first attempt to define and implement an SDL with those characteristics is presented. A program named Automated Reliability Modeling (ARM) was constructed as a research vehicle. The ARM program uses a graphical interface as its SDL, and it outputs a Markov reliability model specification formulated for direct use by programs that generate and evaluate the model.

Binding affinities of vascular endothelial growth factor (VEGF) for heparin-derived oligosaccharides

PubMed Central

Zhao, Wenjing; McCallum, Scott A.; Xiao, Zhongping; Zhang, Fuming; Linhardt, Robert J.

2011-01-01

Heparin and heparan sulphate (HS) exert their wide range of biological activities by interacting with extracellular protein ligands. Among these important protein ligands are various angiogenic growth factors and cytokines. HS-binding to vascular endothelial growth factor (VEGF) regulates multiple aspects of vascular development and function through its specific interaction with HS. Many studies have focused on HS-derived or HS-mimicking structures for the characterization of VEGF165 interaction with HS. Using a heparinase 1-prepared small library of heparin-derived oligosaccharides ranging from hexasaccharide to octadecasaccharide, we systematically investigated the heparin-specific structural features required for VEGF binding. We report the apparent affinities for the association between the heparin-derived oligosaccharides with both VEGF165 and VEGF55, a peptide construct encompassing exclusively the heparin-binding domain of VEGF165. An octasaccharide was the minimum size of oligosaccharide within the library to efficiently bind to both forms of VEGF and that a tetradecasaccharide displayed an effective binding affinity to VEGF165 comparable to unfractionated heparin. The range of relative apparent binding affinities among VEGF and the panel of heparin-derived oligosaccharides demonstrate that VEGF binding affinity likely depends on the specific structural features of these oligosaccharides including their degree of sulphation and sugar ring stereochemistry and conformation. Notably, the unique 3-O-sulpho group found within the specific antithrombin binding site of heparin is not required for VEGF165 binding. These findings afford new insight into the inherent kinetics and affinities for VEGF association with heparin and heparin-derived oligosaccharides with key residue specific modifications and may potentially benefit the future design of oligosaccharide-based anti-angiogenesis drugs. PMID:21658003

Secondary structure propensity and chirality of the amyloidophilic peptide p5 and its analogues impacts ligand binding - In vitro characterization

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

Wall, Jonathan S.; Williams, Angela; Wooliver, Craig

Here, polybasic helical peptides, such as peptide p5, bind human amyloid extracts and synthetic amyloid fibrils. When radio labeled, peptide p5 has been shown to specifically bind amyloid in vivo thereby allowing imaging of the disease. Structural requirements for heparin and amyloid binding have been studied using analogues of p5 that modify helicity and chirality.

RNA polymerase I-Rrn3 complex at 4.8 Å resolution

NASA Astrophysics Data System (ADS)

Engel, Christoph; Plitzko, Jürgen; Cramer, Patrick

2016-07-01

Transcription of ribosomal DNA by RNA polymerase I (Pol I) requires the initiation factor Rrn3. Here we report the cryo-EM structure of the Pol I-Rrn3 complex at 4.8 Å resolution. The structure reveals how Rrn3 binding converts an inactive Pol I dimer into an initiation-competent monomeric complex and provides insights into the mechanisms of Pol I-specific initiation and regulation.

Sierra Structural Dynamics User's Notes

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

Reese, Garth M.

2015-10-19

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a users guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

Secondary structure propensity and chirality of the amyloidophilic peptide p5 and its analogues impacts ligand binding - In vitro characterization

DOE PAGES

Wall, Jonathan S.; Williams, Angela; Wooliver, Craig; ...

2016-08-11

Here, polybasic helical peptides, such as peptide p5, bind human amyloid extracts and synthetic amyloid fibrils. When radio labeled, peptide p5 has been shown to specifically bind amyloid in vivo thereby allowing imaging of the disease. Structural requirements for heparin and amyloid binding have been studied using analogues of p5 that modify helicity and chirality.

The Chromatin Remodeler SPLAYED Regulates Specific Stress Signaling Pathways

PubMed Central

Walley, Justin W.; Rowe, Heather C.; Xiao, Yanmei; Chehab, E. Wassim; Kliebenstein, Daniel J.; Wagner, Doris; Dehesh, Katayoon

2008-01-01

Organisms are continuously exposed to a myriad of environmental stresses. Central to an organism's survival is the ability to mount a robust transcriptional response to the imposed stress. An emerging mechanism of transcriptional control involves dynamic changes in chromatin structure. Alterations in chromatin structure are brought about by a number of different mechanisms, including chromatin modifications, which covalently modify histone proteins; incorporation of histone variants; and chromatin remodeling, which utilizes ATP hydrolysis to alter histone-DNA contacts. While considerable insight into the mechanisms of chromatin remodeling has been gained, the biological role of chromatin remodeling complexes beyond their function as regulators of cellular differentiation and development has remained poorly understood. Here, we provide genetic, biochemical, and biological evidence for the critical role of chromatin remodeling in mediating plant defense against specific biotic stresses. We found that the Arabidopsis SWI/SNF class chromatin remodeling ATPase SPLAYED (SYD) is required for the expression of selected genes downstream of the jasmonate (JA) and ethylene (ET) signaling pathways. SYD is also directly recruited to the promoters of several of these genes. Furthermore, we show that SYD is required for resistance against the necrotrophic pathogen Botrytis cinerea but not the biotrophic pathogen Pseudomonas syringae. These findings demonstrate not only that chromatin remodeling is required for selective pathogen resistance, but also that chromatin remodelers such as SYD can regulate specific pathways within biotic stress signaling networks. PMID:19079584

The chromatin remodeler SPLAYED regulates specific stress signaling pathways.

PubMed

Walley, Justin W; Rowe, Heather C; Xiao, Yanmei; Chehab, E Wassim; Kliebenstein, Daniel J; Wagner, Doris; Dehesh, Katayoon

2008-12-01

Organisms are continuously exposed to a myriad of environmental stresses. Central to an organism's survival is the ability to mount a robust transcriptional response to the imposed stress. An emerging mechanism of transcriptional control involves dynamic changes in chromatin structure. Alterations in chromatin structure are brought about by a number of different mechanisms, including chromatin modifications, which covalently modify histone proteins; incorporation of histone variants; and chromatin remodeling, which utilizes ATP hydrolysis to alter histone-DNA contacts. While considerable insight into the mechanisms of chromatin remodeling has been gained, the biological role of chromatin remodeling complexes beyond their function as regulators of cellular differentiation and development has remained poorly understood. Here, we provide genetic, biochemical, and biological evidence for the critical role of chromatin remodeling in mediating plant defense against specific biotic stresses. We found that the Arabidopsis SWI/SNF class chromatin remodeling ATPase SPLAYED (SYD) is required for the expression of selected genes downstream of the jasmonate (JA) and ethylene (ET) signaling pathways. SYD is also directly recruited to the promoters of several of these genes. Furthermore, we show that SYD is required for resistance against the necrotrophic pathogen Botrytis cinerea but not the biotrophic pathogen Pseudomonas syringae. These findings demonstrate not only that chromatin remodeling is required for selective pathogen resistance, but also that chromatin remodelers such as SYD can regulate specific pathways within biotic stress signaling networks.

Earthquake ground motion: Chapter 3

USGS Publications Warehouse

Luco, Nicolas; Kircher, Charles A.; Crouse, C. B.; Charney, Finley; Haselton, Curt B.; Baker, Jack W.; Zimmerman, Reid; Hooper, John D.; McVitty, William; Taylor, Andy

2016-01-01

Most of the effort in seismic design of buildings and other structures is focused on structural design. This chapter addresses another key aspect of the design process—characterization of earthquake ground motion into parameters for use in design. Section 3.1 describes the basis of the earthquake ground motion maps in the Provisions and in ASCE 7 (the Standard). Section 3.2 has examples for the determination of ground motion parameters and spectra for use in design. Section 3.3 describes site-specific ground motion requirements and provides example site-specific design and MCER response spectra and example values of site-specific ground motion parameters. Section 3.4 discusses and provides an example for the selection and scaling of ground motion records for use in various types of response history analysis permitted in the Standard.

Membranes linked by trans-SNARE complexes require lipids prone to non-bilayer structure for progression to fusion.

PubMed

Zick, Michael; Stroupe, Christopher; Orr, Amy; Douville, Deborah; Wickner, William T

2014-01-01

Like other intracellular fusion events, the homotypic fusion of yeast vacuoles requires a Rab GTPase, a large Rab effector complex, SNARE proteins which can form a 4-helical bundle, and the SNARE disassembly chaperones Sec17p and Sec18p. In addition to these proteins, specific vacuole lipids are required for efficient fusion in vivo and with the purified organelle. Reconstitution of vacuole fusion with all purified components reveals that high SNARE levels can mask the requirement for a complex mixture of vacuole lipids. At lower, more physiological SNARE levels, neutral lipids with small headgroups that tend to form non-bilayer structures (phosphatidylethanolamine, diacylglycerol, and ergosterol) are essential. Membranes without these three lipids can dock and complete trans-SNARE pairing but cannot rearrange their lipids for fusion. DOI: http://dx.doi.org/10.7554/eLife.01879.001.

Shaping skeletal growth by modular regulatory elements in the Bmp5 gene.

PubMed

Guenther, Catherine; Pantalena-Filho, Luiz; Kingsley, David M

2008-12-01

Cartilage and bone are formed into a remarkable range of shapes and sizes that underlie many anatomical adaptations to different lifestyles in vertebrates. Although the morphological blueprints for individual cartilage and bony structures must somehow be encoded in the genome, we currently know little about the detailed genomic mechanisms that direct precise growth patterns for particular bones. We have carried out large-scale enhancer surveys to identify the regulatory architecture controlling developmental expression of the mouse Bmp5 gene, which encodes a secreted signaling molecule required for normal morphology of specific skeletal features. Although Bmp5 is expressed in many skeletal precursors, different enhancers control expression in individual bones. Remarkably, we show here that different enhancers also exist for highly restricted spatial subdomains along the surface of individual skeletal structures, including ribs and nasal cartilages. Transgenic, null, and regulatory mutations confirm that these anatomy-specific sequences are sufficient to trigger local changes in skeletal morphology and are required for establishing normal growth rates on separate bone surfaces. Our findings suggest that individual bones are composite structures whose detailed growth patterns are built from many smaller lineage and gene expression domains. Individual enhancers in BMP genes provide a genomic mechanism for controlling precise growth domains in particular cartilages and bones, making it possible to separately regulate skeletal anatomy at highly specific locations in the body.

Degree of Biomimicry of Artificial Spider Silk Spinning Assessed by NMR Spectroscopy.

PubMed

Otikovs, Martins; Andersson, Marlene; Jia, Qiupin; Nordling, Kerstin; Meng, Qing; Andreas, Loren B; Pintacuda, Guido; Johansson, Jan; Rising, Anna; Jaudzems, Kristaps

2017-10-02

Biomimetic spinning of artificial spider silk requires that the terminal domains of designed minispidroins undergo specific structural changes in concert with the β-sheet conversion of the repetitive region. Herein, we combine solution and solid-state NMR methods to probe domain-specific structural changes in the NT2RepCT minispidroin, which allows us to assess the degree of biomimicry of artificial silk spinning. In addition, we show that the structural effects of post-spinning procedures can be examined. By studying the impact of NT2RepCT fiber drying, we observed a reversible beta-to-alpha conversion. We think that this approach will be useful for guiding the optimization of artificial spider silk fibers. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study of flutter related computational procedures for minimum weight structural sizing of advanced aircraft, supplemental data

NASA Technical Reports Server (NTRS)

Oconnell, R. F.; Hassig, H. J.; Radovcich, N. A.

1975-01-01

Computational aspects of (1) flutter optimization (minimization of structural mass subject to specified flutter requirements), (2) methods for solving the flutter equation, and (3) efficient methods for computing generalized aerodynamic force coefficients in the repetitive analysis environment of computer-aided structural design are discussed. Specific areas included: a two-dimensional Regula Falsi approach to solving the generalized flutter equation; method of incremented flutter analysis and its applications; the use of velocity potential influence coefficients in a five-matrix product formulation of the generalized aerodynamic force coefficients; options for computational operations required to generate generalized aerodynamic force coefficients; theoretical considerations related to optimization with one or more flutter constraints; and expressions for derivatives of flutter-related quantities with respect to design variables.

Characterization of Novel Plasmonic, Photonic, and Semiconductor Microstructures

NASA Astrophysics Data System (ADS)

Sears, Jasmine Soria

The fields of telecommunications and optoelectronics are under constant pressure to shrink devices and reduce power consumption. Micro-scale photonic and plasmonic structures can trap light and enhance the brightness of active emitters; thus, these types of structures are promising avenues to accomplishing the goals of miniaturization and efficiency. A deeper understanding of specific structures is important in order to gauge their suitability for specific applications. In this dissertation, two types of microstructures are explored: one-dimensional silicon photonic crystals and self-assembled indium islands. This dissertation will provide novel characterization of these structures and a description of how to utilize or compensate for the observed features. A photonic crystal can act as a tiny resonator for certain wavelengths, making it a promising structure for applications that require extremely small lasers. However, because of silicon’s indirect bandgap, a silicon photonic crystal cavity would require the addition of an active emitter to function as a light source. Attempts to incorporate erbium into these cavities, and the observation of an unusual coupling phenomenon, will be discussed. Self-assembled indium islands are plasmonic structures that can be grown via molecular beam epitaxy. In theory, these islands should be pure indium nanoantennas on top of a smooth gallium arsenide substrate. In practice, the component materials are less segregated than predicted, giving rise to unexpected hollow dome shapes and a sub-surface indium layer. Although these features were not an intended result of indium island growth, they provide information regarding the island formation process and potentially contribute additional applications.

A three-dimensional actuated origami-inspired transformable metamaterial with multiple degrees of freedom

NASA Astrophysics Data System (ADS)

Overvelde, Johannes T. B.; de Jong, Twan A.; Shevchenko, Yanina; Becerra, Sergio A.; Whitesides, George M.; Weaver, James C.; Hoberman, Chuck; Bertoldi, Katia

2016-03-01

Reconfigurable devices, whose shape can be drastically altered, are central to expandable shelters, deployable space structures, reversible encapsulation systems and medical tools and robots. All these applications require structures whose shape can be actively controlled, both for deployment and to conform to the surrounding environment. While most current reconfigurable designs are application specific, here we present a mechanical metamaterial with tunable shape, volume and stiffness. Our approach exploits a simple modular origami-like design consisting of rigid faces and hinges, which are connected to form a periodic structure consisting of extruded cubes. We show both analytically and experimentally that the transformable metamaterial has three degrees of freedom, which can be actively deformed into numerous specific shapes through embedded actuation. The proposed metamaterial can be used to realize transformable structures with arbitrary architectures, highlighting a robust strategy for the design of reconfigurable devices over a wide range of length scales.

Space platform expendables resupply concept definition study. Volume 3: Work breakdown structure and work breakdown structure dictionary

NASA Technical Reports Server (NTRS)

1984-01-01

The work breakdown structure (WBS) for the Space Platform Expendables Resupply Concept Definition Study is described. The WBS consists of a list of WBS elements, a dictionary of element definitions, and an element logic diagram. The list and logic diagram identify the interrelationships of the elements. The dictionary defines the types of work that may be represented by or be classified under each specific element. The Space Platform Expendable Resupply WBS was selected mainly to support the program planning, scheduling, and costing performed in the programmatics task (task 3). The WBS is neither a statement-of-work nor a work authorization document. Rather, it is a framework around which to define requirements, plan effort, assign responsibilities, allocate and control resources, and report progress, expenditures, technical performance, and schedule performance. The WBS element definitions are independent of make-or-buy decisions, organizational structure, and activity locations unless exceptions are specifically stated.

Elucidating nitric oxide synthase domain interactions by molecular dynamics.

PubMed

Hollingsworth, Scott A; Holden, Jeffrey K; Li, Huiying; Poulos, Thomas L

2016-02-01

Nitric oxide synthase (NOS) is a multidomain enzyme that catalyzes the production of nitric oxide (NO) by oxidizing L-Arg to NO and L-citrulline. NO production requires multiple interdomain electron transfer steps between the flavin mononucleotide (FMN) and heme domain. Specifically, NADPH-derived electrons are transferred to the heme-containing oxygenase domain via the flavin adenine dinucleotide (FAD) and FMN containing reductase domains. While crystal structures are available for both the reductase and oxygenase domains of NOS, to date there is no atomic level structural information on domain interactions required for the final FMN-to-heme electron transfer step. Here, we evaluate a model of this final electron transfer step for the heme-FMN-calmodulin NOS complex based on the recent biophysical studies using a 105-ns molecular dynamics trajectory. The resulting equilibrated complex structure is very stable and provides a detailed prediction of interdomain contacts required for stabilizing the NOS output state. The resulting equilibrated complex model agrees well with previous experimental work and provides a detailed working model of the final NOS electron transfer step required for NO biosynthesis. © 2015 The Protein Society.

Job-related stress in psychiatric nurses in Japan caring for elderly patients with dementia.

PubMed

Yada, Hironori; Abe, Hiroshi; Lu, Xi; Wakizaki, Yuko; Omori, Hisamitsu; Matsuo, Hisae; Ishida, Yasushi; Katoh, Takahiko

2014-11-01

We investigated the specificity and structures of job-related stress in psychiatric dementia nurses (PDNs) caring for elderly patients with serious behavioral and psychological symptoms of dementia who required substantial assistance with activities of daily living, in order to obtain fundamental knowledge toward providing mental health care for these nurses. Subjects were 244 nurses [63 PDNs and 181 other psychiatric nurses (OPNs)] Analysis of covariance to examine the specificity of job-related stress in PDNs revealed physical workload and work environment to be more significant stressors, and irritability and anxiety to be more significant stress reactions in PDNs than in OPNs. An examination of PDNs' job-related stress structures established in a structural equation model with two stress reactions confirmed as specific outcomes for PDNs revealed a significant positive influence of work environment on irritability; utilization of techniques for anxiety and physical workload influenced both stress reactions. Our findings highlight the importance of reducing physical workload and environment and establishing a structure for nursing techniques in psychiatric dementia wards to improve the mental health of PDNs.

Structural hot spots for the solubility of globular proteins

PubMed Central

Ganesan, Ashok; Siekierska, Aleksandra; Beerten, Jacinte; Brams, Marijke; Van Durme, Joost; De Baets, Greet; Van der Kant, Rob; Gallardo, Rodrigo; Ramakers, Meine; Langenberg, Tobias; Wilkinson, Hannah; De Smet, Frederik; Ulens, Chris; Rousseau, Frederic; Schymkowitz, Joost

2016-01-01

Natural selection shapes protein solubility to physiological requirements and recombinant applications that require higher protein concentrations are often problematic. This raises the question whether the solubility of natural protein sequences can be improved. We here show an anti-correlation between the number of aggregation prone regions (APRs) in a protein sequence and its solubility, suggesting that mutational suppression of APRs provides a simple strategy to increase protein solubility. We show that mutations at specific positions within a protein structure can act as APR suppressors without affecting protein stability. These hot spots for protein solubility are both structure and sequence dependent but can be computationally predicted. We demonstrate this by reducing the aggregation of human α-galactosidase and protective antigen of Bacillus anthracis through mutation. Our results indicate that many proteins possess hot spots allowing to adapt protein solubility independently of structure and function. PMID:26905391

Structures, performance, benefit, cost study. [gas turbine engines

NASA Technical Reports Server (NTRS)

Feder, E.

1981-01-01

Aircraft engine structures were studied to identify the advanced structural technologies that would provide the most benefits to future aircraft operations. A series of studies identified engine systems with the greatest potential for improvements. Based on these studies, six advanced generic structural concepts were selected and conceptually designed. The benefits of each concept were quantitatively assessed in terms of thrust specific fuel consumption, weight, cost, maintenance cost, fuel burned and direct operating cost plus interest. The probability of success of each concept was also determined. The concepts were ranked and the three most promising were selected for further study which consisted of identifying and comprehensively outlining the advanced technologies required to develop these concepts for aircraft engine application. Analytic, fabrication, and test technology developments are required. The technology programs outlined emphasize the need to provide basic, fundamental understanding of technology to obtain the benefit goals.

Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway

DOE PAGES

Saxton, Robert A.; Knockenhauer, Kevin E.; Wolfson, Rachel L.; ...

2015-11-19

Eukaryotic cells coordinate growth with the availability of nutrients through mTOR complex 1 (mTORC1), a master growth regulator. Leucine is of particular importance and activates mTORC1 via the Rag GTPases and their regulators GATOR1 and GATOR2. Sestrin2 interacts with GATOR2 and is a leucine sensor. We present the 2.7-Å crystal structure of Sestrin2 in complex with leucine. Leucine binds through a single pocket that coordinates its charged functional groups and confers specificity for the hydrophobic side chain. A loop encloses leucine and forms a lid-latch mechanism required for binding. A structure-guided mutation in Sestrin2 that decreases its affinity for leucinemore » leads to a concomitant increase in the leucine concentration required for mTORC1 activation in cells. Lastly, these results provide a structural mechanism of amino acid sensing by the mTORC1 pathway.« less

Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway

PubMed Central

Saxton, Robert A.; Knockenhauer, Kevin E.; Wolfson, Rachel L.; Chantranupong, Lynne; Pacold, Michael E.; Wang, Tim; Schwartz, Thomas U.; Sabatini, David M.

2015-01-01

Eukaryotic cells coordinate growth with the availability of nutrients through mTOR complex 1 (mTORC1), a master growth regulator. Leucine is of particular importance and activates mTORC1 via the Rag GTPases and their regulators GATOR1 and GATOR2. Sestrin2 interacts with GATOR2 and is a leucine sensor. We present the 2.7-Å crystal structure of Sestrin2 in complex with leucine. Leucine binds through a single pocket that coordinates its charged functional groups and confers specificity for the hydrophobic side chain. A loop encloses leucine and forms a lid-latch mechanism required for binding. A structure-guided mutation in Sestrin2 that decreases its affinity for leucine leads to a concomitant increase in the leucine concentration required for mTORC1 activation in cells. These results provide a structural mechanism of amino acid sensing by the mTORC1 pathway. PMID:26586190

An Exquisitely Specific PDZ/Target Recognition Revealed by the Structure of INAD PDZ3 in Complex with TRP Channel Tail.

PubMed

Ye, Fei; Liu, Wei; Shang, Yuan; Zhang, Mingjie

2016-03-01

The vast majority of PDZ domains are known to bind to a few C-terminal tail residues of target proteins with modest binding affinities and specificities. Such promiscuous PDZ/target interactions are not compatible with highly specific physiological functions of PDZ domain proteins and their targets. Here, we report an unexpected PDZ/target binding occurring between the scaffold protein inactivation no afterpotential D (INAD) and transient receptor potential (TRP) channel in Drosophila photoreceptors. The C-terminal 15 residues of TRP are required for the specific interaction with INAD PDZ3. The INAD PDZ3/TRP peptide complex structure reveals that only the extreme C-terminal Leu of TRP binds to the canonical αB/βB groove of INAD PDZ3. The rest of the TRP peptide, by forming a β hairpin structure, binds to a surface away from the αB/βB groove of PDZ3 and contributes to the majority of the binding energy. Thus, the INAD PDZ3/TRP channel interaction is exquisitely specific and represents a new mode of PDZ/target recognitions. Copyright © 2016 Elsevier Ltd. All rights reserved.

76 FR 75435 - Fatigue Tolerance Evaluation of Metallic Structures

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-02

..., Regulations and Policy Group, Rotorcraft Directorate, ASW-111, Federal Aviation Administration, 2601 Meacham... designed and manufactured, performs properly, and meets the regulations and minimum standards prescribed... amended rule requires a specific result (that is, inspection, retirement times, or equivalent means to...

Technology's Impact on Library Interior Planning.

ERIC Educational Resources Information Center

Michaels, David Leroy

1987-01-01

Discusses issues to be considered in planning a library that will anticipate the needs of the future. Power and telecommunications capacity are stressed, and a checklist of items requiring specific writing services is included. Recommendations for workstation design and structural elements are offered. (MES)

URBAN MORPHOLOGY FOR HOUSTON TO DRIVE MODELS-3/CMAQ AT NEIGHBORHOOD SCALES

EPA Science Inventory

Air quality simulation models applied at various horizontal scales require different degrees of treatment in the specifications of the underlying surfaces. As we model neighborhood scales ( 1 km horizontal grid spacing), the representation of urban morphological structures (e....

Surface resistivity as an alternative for rapid chloride permeability test of hardened concrete.

DOT National Transportation Integrated Search

2015-03-01

Kansas experiences harsh winters that require frequent use of de-icing salts, making it critical to the long-term : durability of concrete structures that the permeability is kept under control. Under current KDOT specification, the : Rapid Chloride ...

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2010 CFR

2010-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2014 CFR

2014-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2012 CFR

2012-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2013 CFR

2013-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

10 CFR 61.12 - Specific technical information.

Code of Federal Regulations, 2011 CFR

2011-01-01

... NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE... of the land disposal facility and the disposal units. For near-surface disposal, the description must...; structural stability of backfill, wastes, and covers; contact of wastes with standing water; disposal site...

MultiLIS: A Description of the System Design and Operational Features.

ERIC Educational Resources Information Center

Kelly, Glen J.; And Others

1988-01-01

Describes development, hardware requirements, and features of the MultiLIS integrated library software package. A system profile provides pricing information, operational characteristics, and technical specifications. Sidebars discuss MultiLIS integration structure, incremental architecture, and NCR Tower Computers. (4 references) (MES)

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

PubMed Central

Dasgupta, Bhaskar; Kasahara, Kota; Kamiya, Narutoshi; Nakamura, Haruki; Kinjo, Akira R.

2014-01-01

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics. PMID:24625758

The challenge of developing structural materials for fusion power systems

NASA Astrophysics Data System (ADS)

Bloom, Everett E.

1998-10-01

Nuclear fusion can be one of the most attractive sources of energy from the viewpoint of safety and minimal environmental impact. Central in the goal of designing a safe, environmentally benign, and economically competitive fusion power system is the requirement for high performance, low activation materials. The general performance requirements for such materials have been defined and it is clear that materials developed for other applications (e.g. aerospace, nuclear fission, fossil energy systems) will not fully meet the needs of fusion. Advanced materials, with composition and microstructure tailored to yield properties that will satisfy the specific requirements of fusion must be developed. The international fusion programs have made significant progress towards this goal. Compositional requirements for low activation lead to a focus of development efforts on silicon carbide composites, vanadium alloys, and advanced martensitic steels as candidate structural material systems. Control of impurities will be critically important in actually achieving low activation but this appears possible. Neutron irradiation produces significant changes in the mechanical and physical properties of each of these material systems raising feasibility questions and design limitations. A focus of the research and development effort is to understand these effects, and through the development of specific compositions and microstructures, produce materials with improved and adequate performance. Other areas of research that are synergistic with the development of radiation resistant materials include fabrication, joining technology, chemical compatibility with coolants and tritium breeders and specific questions relating to the unique characteristics of a given material (e.g. coatings to reduce gas permeation in SiC composites) or design concept (e.g. electrical insulator coatings for liquid metal concepts).

Efficient design of nanoplasmonic waveguide devices using the space mapping algorithm.

PubMed

Dastmalchi, Pouya; Veronis, Georgios

2013-12-30

We show that the space mapping algorithm, originally developed for microwave circuit optimization, can enable the efficient design of nanoplasmonic waveguide devices which satisfy a set of desired specifications. Space mapping utilizes a physics-based coarse model to approximate a fine model accurately describing a device. Here the fine model is a full-wave finite-difference frequency-domain (FDFD) simulation of the device, while the coarse model is based on transmission line theory. We demonstrate that simply optimizing the transmission line model of the device is not enough to obtain a device which satisfies all the required design specifications. On the other hand, when the iterative space mapping algorithm is used, it converges fast to a design which meets all the specifications. In addition, full-wave FDFD simulations of only a few candidate structures are required before the iterative process is terminated. Use of the space mapping algorithm therefore results in large reductions in the required computation time when compared to any direct optimization method of the fine FDFD model.

Ligand Recognition by A-Class Eph Receptors: Crystal Structures of the EphA2 Ligand-Binding Domain and the EphA2/ephrin-A1 Complex

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

Himanen, J.; Goldgur, Y; Miao, H

2009-01-01

Ephrin (Eph) receptor tyrosine kinases fall into two subclasses (A and B) according to preferences for their ephrin ligands. All published structural studies of Eph receptor/ephrin complexes involve B-class receptors. Here, we present the crystal structures of an A-class complex between EphA2 and ephrin-A1 and of unbound EphA2. Although these structures are similar overall to their B-class counterparts, they reveal important differences that define subclass specificity. The structures suggest that the A-class Eph receptor/ephrin interactions involve smaller rearrangements in the interacting partners, better described by a 'lock-and-key'-type binding mechanism, in contrast to the 'induced fit' mechanism defining the B-class molecules.more » This model is supported by structure-based mutagenesis and by differential requirements for ligand oligomerization by the two subclasses in cell-based Eph receptor activation assays. Finally, the structure of the unligated receptor reveals a homodimer assembly that might represent EphA2-specific homotypic cell adhesion interactions.« less

Psychometric modeling of abuse and dependence symptoms across six illicit substances indicates novel dimensions of misuse

PubMed Central

Clark, Shaunna L.; Gillespie, Nathan A.; Adkins, Daniel E.; Kendler, Kenneth S.; Neale, Michael C.

2015-01-01

Aims This study explored the factor structure of DSM III-R/IV symptoms for substance abuse and dependence across six illicit substance categories in a population-based sample of males. Method DSM III-R/IV drug abuse and dependence symptoms for cannabis, sedatives, stimulants, cocaine, opioids and hallucinogens from 4179 males born 1940-1970 from the population-based Virginia Adult Twin Study of Psychiatric and Substance Use Disorders were analyzed. Confirmatory factor analyses tested specific hypotheses regarding the latent structure of substance misuse for a comprehensive battery of 13 misuse symptoms measured across six illicit substance categories (78 items). Results Among the models fit, the latent structure of substance misuse was best represented by a combination of substance-specific factors and misuse symptom-specific factors. We found no support for a general liability factor to illicit substance misuse. Conclusions Results indicate that liability to misuse illicit substances is drug class specific, with little evidence for a general liability factor. Additionally, unique dimensions capturing propensity toward specific misuse symptoms (e.g., tolerance, withdrawal) across substances were identified. While this finding requires independent replication, the possibility of symptom-specific misuse factors, present in multiple substances, raises the prospect of genetic, neurobiological and behavioral predispositions toward distinct, narrowly defined features of drug abuse and dependence. PMID:26517709

MR Anatomy of Deep Brain Nuclei with Special Reference to Specific Diseases and Deep Brain Stimulation Localization

PubMed Central

Telford, Ryan; Vattoth, Surjith

2014-01-01

Summary Diseases affecting the basal ganglia and deep brain structures vary widely in etiology and include metabolic, infectious, ischemic, and neurodegenerative conditions. Some neurologic diseases, such as Wernicke encephalopathy or pseudohypoparathyroidism, require specific treatments, which if unrecognized could lead to further complications. Other pathologies, such as hypertrophic olivary degeneration, if not properly diagnosed may be mistaken for a primary medullary neoplasm and create unnecessary concern. The deep brain structures are complex and can be difficult to distinguish on routine imaging. It is imperative that radiologists first understand the intrinsic anatomic relationships between the different basal ganglia nuclei and deep brain structures with magnetic resonance (MR) imaging. It is important to understand the "normal" MR signal characteristics, locations, and appearances of these structures. This is essential to recognizing diseases affecting the basal ganglia and deep brain structures, especially since most of these diseases result in symmetrical, and therefore less noticeable, abnormalities. It is also crucial that neurosurgeons correctly identify the deep brain nuclei presurgically for positioning deep brain stimulator leads, the most important being the subthalamic nucleus for Parkinson syndromes and the thalamic ventral intermediate nucleus for essential tremor. Radiologists will be able to better assist clinicians in diagnosis and treatment once they are able to accurately localize specific deep brain structures. PMID:24571832

Structure of a designed protein cage that self-assembles into a highly porous cube

DOE PAGES

Lai, Yen-Ting; Reading, Eamonn; Hura, Greg L.; ...

2014-11-10

Natural proteins can be versatile building blocks for multimeric, self-assembling structures. Yet, creating protein-based assemblies with specific geometries and chemical properties remains challenging. Highly porous materials represent particularly interesting targets for designed assembly. Here we utilize a strategy of fusing two natural protein oligomers using a continuous alpha-helical linker to design a novel protein that self assembles into a 750 kDa, 225 Å diameter, cube-shaped cage with large openings into a 130 Å diameter inner cavity. A crystal structure of the cage showed atomic level agreement with the designed model, while electron microscopy, native mass spectrometry, and small angle x-raymore » scattering revealed alternate assembly forms in solution. These studies show that accurate design of large porous assemblies with specific shapes is feasible, while further specificity improvements will likely require limiting flexibility to select against alternative forms. Finally, these results provide a foundation for the design of advanced materials with applications in bionanotechnology, nanomedicine and material sciences.« less

Modulation of the Pyrococcus abyssi NucS Endonuclease Activity by Replication Clamp at Functional and Structural Levels*

PubMed Central

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P.; Khun, Joelle; Vos, Marten H.; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-01-01

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5′ and 3′ flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction. PMID:22431731

Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels.

PubMed

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P; Khun, Joelle; Vos, Marten H; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-05-04

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction.

Use of reduction rate as a quantitative knob for controlling the twin structure and shape of palladium nanocrystals.

PubMed

Wang, Yi; Peng, Hsin-Chieh; Liu, Jingyue; Huang, Cheng Zhi; Xia, Younan

2015-02-11

Kinetic control is a powerful means for maneuvering the twin structure and shape of metal nanocrystals and thus optimizing their performance in a variety of applications. However, there is only a vague understanding of the explicit roles played by reaction kinetics due to the lack of quantitative information about the kinetic parameters. With Pd as an example, here we demonstrate that kinetic parameters, including rate constant and activation energy, can be derived from spectroscopic measurements and then used to calculate the initial reduction rate and further have this parameter quantitatively correlated with the twin structure of a seed and nanocrystal. On a quantitative basis, we were able to determine the ranges of initial reduction rates required for the formation of nanocrystals with a specific twin structure, including single-crystal, multiply twinned, and stacking fault-lined. This work represents a major step forward toward the deterministic syntheses of colloidal noble-metal nanocrystals with specific twin structures and shapes.

Silicon nitride ceramic development in Thales Alenia Space : qualification achievement and further developments for future applications

NASA Astrophysics Data System (ADS)

Cornillon, L.; Devilliers, C.; Behar-Lafenetre, S.; Ait-Zaid, S.; Berroth, K.; Bravo, A. C.

2017-11-01

Dealing with ceramic materials for more than two decades, Thales Alenia Space - France has identified Silicon Nitride Si3N4 as a high potential material for the manufacturing of stiff, stable and lightweight truss structure for future large telescopes. Indeed, for earth observation or astronomic observation, space mission requires more and more telescopes with high spatial resolution, which leads to the use of large primary mirrors, and a long distance between primary and secondary mirrors. Therefore current and future large space telescopes require a huge truss structure to hold and locate precisely the mirrors. Such large structure requires very strong materials with high specific stiffness and a low coefficient of thermal expansion (CTE). Based on the silicon nitride performances and on the know how of FCT Ingenieurkeramik to manufacture complex parts, Thales Alenia Space (TAS) has engaged, in cooperation with FCT, activities to develop and qualify silicon nitride parts for other applications for space projects.

Silicon nitride ceramic development in Thales Alenia Space: qualification achiement and further developments for future applications

NASA Astrophysics Data System (ADS)

Cornillon, L.; Devilliers, C.; Behar-Lafenetre, S.; Ait-Zaid, S.; Berroth, K.; Bravo, A. C.

2017-11-01

Dealing with ceramic materials for more than two decades, Thales Alenia Space - France has identified Silicon Nitride Si3N4 as a high potential material for the manufacturing of stiff, stable and lightweight truss structure for future large telescopes. Indeed, for earth observation or astronomic observation, space mission requires more and more telescopes with high spatial resolution, which leads to the use of large primary mirrors, and a long distance between primary and secondary mirrors. Therefore current and future large space telescopes require a huge truss structure to hold and locate precisely the mirrors. Such large structure requires very strong materials with high specific stiffness and a low coefficient of thermal expansion (CTE). Based on the silicon nitride performances and on the know how of FCT Ingenieurkeramik to manufacture complex parts, Thales Alenia Space (TAS) has engaged, in cooperation with FCT, activities to develop and qualify silicon nitride parts for other applications for space projects.

A reduced adaptive observer for multivariable systems. [using reduced dynamic ordering

NASA Technical Reports Server (NTRS)

Carroll, R. L.; Lindorff, D. P.

1973-01-01

An adaptive observer for multivariable systems is presented for which the dynamic order of the observer is reduced, subject to mild restrictions. The observer structure depends directly upon the multivariable structure of the system rather than a transformation to a single-output system. The number of adaptive gains is at most the sum of the order of the system and the number of input parameters being adapted. Moreover, for the relatively frequent specific cases for which the number of required adaptive gains is less than the sum of system order and input parameters, the number of these gains is easily determined by inspection of the system structure. This adaptive observer possesses all the properties ascribed to the single-input single-output adpative observer. Like the other adaptive observers some restriction is required of the allowable system command input to guarantee convergence of the adaptive algorithm, but the restriction is more lenient than that required by the full-order multivariable observer. This reduced observer is not restricted to cycle systems.

18 CFR 12.35 - Specific inspection requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... from monitoring instruments; and (vi) The quality and adequacy of maintenance, surveillance, and... life or cause significant property damage, the independent consultant must evaluate the ability of... endanger the project works. (2) If structural failure would not present a hazard to human life of cause...

18 CFR 12.35 - Specific inspection requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... from monitoring instruments; and (vi) The quality and adequacy of maintenance, surveillance, and... life or cause significant property damage, the independent consultant must evaluate the ability of... endanger the project works. (2) If structural failure would not present a hazard to human life of cause...

38 CFR 1.15 - Standards for program evaluation.

Code of Federal Regulations, 2011 CFR

2011-07-01

... the data. (f) Each program evaluation requires a systematic research design to collect the data necessary to measure the objectives. This research design should conform to the following: (1) Rationale. The research design for each evaluation should contain a specific rationale and should be structured...

Surface resistivity as an alternative for rapid chloride permeability test of hardened concrete : [technical summary].

DOT National Transportation Integrated Search

2015-03-01

Kansas experiences harsh winters that require frequent use of de-icing salts, making it : critical to the long-term durability of concrete structures that the permeability is kept : under control. Under current KDOT specification, the Rapid Chloride ...

Elimination sequence optimization for SPAR

NASA Technical Reports Server (NTRS)

Hogan, Harry A.

1986-01-01

SPAR is a large-scale computer program for finite element structural analysis. The program allows user specification of the order in which the joints of a structure are to be eliminated since this order can have significant influence over solution performance, in terms of both storage requirements and computer time. An efficient elimination sequence can improve performance by over 50% for some problems. Obtaining such sequences, however, requires the expertise of an experienced user and can take hours of tedious effort to affect. Thus, an automatic elimination sequence optimizer would enhance productivity by reducing the analysts' problem definition time and by lowering computer costs. Two possible methods for automating the elimination sequence specifications were examined. Several algorithms based on the graph theory representations of sparse matrices were studied with mixed results. Significant improvement in the program performance was achieved, but sequencing by an experienced user still yields substantially better results. The initial results provide encouraging evidence that the potential benefits of such an automatic sequencer would be well worth the effort.

In vitro selection of catalytic RNAs

NASA Technical Reports Server (NTRS)

Chapman, K. B.; Szostak, J. W.

1994-01-01

In vitro selection techniques are poised to allow a rapid expansion of the study of catalysis by RNA enzymes (ribozymes). This truly molecular version of genetics has already been applied to the study of the structures of known ribozymes and to the tailoring of their catalytic activity to meet specific requirements of substrate specificity or reaction conditions. During the past year, in vitro selection has been successfully used to isolate novel RNA catalysts from random sequence pools.

Interface Specifications for the A-7E Shared Services Module.

DTIC Science & Technology

1982-09-08

To illustrate the principles, the onboard software for the Navy’s A-7E aircraft will be redesigned and rewritten. The Shared Services module provides...purpose of the Shared Services module is to allow the remainder of the software to remain unchanged when the requirements-based rules for these values and...services change. This report describes the modular structure of the Shared Services module, and contains the abstract interface specifications for all

Manned remote work station development article. Volume 3: Development test plan. Appendix A: Manufacturing requirements/schedule

NASA Technical Reports Server (NTRS)

1979-01-01

The tests and procedures for the manned remote work station (MRWS) open cherry picker (OCP) development test article (DTA) are described to validate systems requirements and performance specifications. A development test program is outlined to evaluate key design issues and man/machine interfaces when the MRWS OCP is used in a shuttle support role of satellite servicing and in orbit construction of large structures.

Hybrid CMS methods with model reduction for assembly of structures

NASA Technical Reports Server (NTRS)

Farhat, Charbel

1991-01-01

Future on-orbit structures will be designed and built in several stages, each with specific control requirements. Therefore there must be a methodology which can predict the dynamic characteristics of the assembled structure, based on the dynamic characteristics of the subassemblies and their interfaces. The methodology developed by CSC to address this issue is Hybrid Component Mode Synthesis (HCMS). HCMS distinguishes itself from standard component mode synthesis algorithms in the following features: (1) it does not require the subcomponents to have displacement compatible models, which makes it ideal for analyzing the deployment of heterogeneous flexible multibody systems, (2) it incorporates a second-level model reduction scheme at the interface, which makes it much faster than other algorithms and therefore suitable for control purposes, and (3) it does answer specific questions such as 'how does the global fundamental frequency vary if I change the physical parameters of substructure k by a specified amount?'. Because it is based on an energy principle rather than displacement compatibility, this methodology can also help the designer to define an assembly process. Current and future efforts are devoted to applying the HCMS method to design and analyze docking and berthing procedures in orbital construction.

Expanding the scope of site-specific recombinases for genetic and metabolic engineering.

PubMed

Gaj, Thomas; Sirk, Shannon J; Barbas, Carlos F

2014-01-01

Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. © 2013 Wiley Periodicals, Inc.

Research requirements to reduce empty weight of helicopters by use of advanced materials

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

Hoffstedt, D.J.

1976-12-01

Utilization of the new, lightweight, high-strength, aerospace structural-composite (filament/matrix) materials, when specifically designed into a new aircraft, promises reductions in structural empty weight of 12% at recurring costs competetive with metals. A program of basic and applied research and demonstration is identified with the objective of advancing the state of the art to the point where civil helicopters are confidently designed, produced, certified, and marketed by 1985. A structural empty-weight reduction of 12% was shown to significantly reduce energy consumption in modern high-performance helicopters.

Spatial Query for Planetary Data

NASA Technical Reports Server (NTRS)

Shams, Khawaja S.; Crockett, Thomas M.; Powell, Mark W.; Joswig, Joseph C.; Fox, Jason M.

2011-01-01

Science investigators need to quickly and effectively assess past observations of specific locations on a planetary surface. This innovation involves a location-based search technology that was adapted and applied to planetary science data to support a spatial query capability for mission operations software. High-performance location-based searching requires the use of spatial data structures for database organization. Spatial data structures are designed to organize datasets based on their coordinates in a way that is optimized for location-based retrieval. The particular spatial data structure that was adapted for planetary data search is the R+ tree.

Popcorn-Derived Porous Carbon Flakes with an Ultrahigh Specific Surface Area for Superior Performance Supercapacitors.

PubMed

Hou, Jianhua; Jiang, Kun; Wei, Rui; Tahir, Muhammad; Wu, Xiaoge; Shen, Ming; Wang, Xiaozhi; Cao, Chuanbao

2017-09-13

Popcorn-derived porous carbon flakes have been successfully fabricated from the biomass of maize. Utilizing the "puffing effect", the nubby maize grain turned into materials with an interconnected honeycomb-like porous structure composed of carbon flakes. The following chemical activation method enabled the as-prepared products to possess optimized porous structures for electrochemical energy-storage devices, such as multilayer flake-like structures, ultrahigh specific surface area (S BET : 3301 m 2 g -1 ), and a high content of micropores (microporous surface area of 95%, especially the optimized sub-nanopores with the size of 0.69 nm) that can increase the specific capacitance. The as-obtained sample displayed excellent specific capacitance of 286 F g -1 at 90 A g -1 for supercapacitors. Moreover, the unique porous structure demonstrated an ideal way to improve the volumetric energy density performance. A high energy density of 103 Wh kg -1 or 53 Wh L -1 has been obtained in the case of ionic liquid electrolyte, which is the highest among reported biomass-derived carbon materials and will satisfy the urgent requirements of a primary power source for electric vehicles. This work may prove to be a fast, green, and large-scale synthesis route by using the large nubby granular materials to synthesize applicable porous carbons in energy-storage devices.

Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme

PubMed Central

Mustoe, Anthony M.; Al-Hashimi, Hashim M.; Brooks, Charles L.

2016-01-01

A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions form with low conformational free energy, while non-native tetraloop/tetraloop–receptor interactions are penalized by high conformational free energies. Topological constraints also give rise to strong cooperativity between distal tertiary interactions, quantitatively matching prior experimental measurements. The specificity of the folding landscape is further enhanced as tertiary contacts place additional constraints on the conformational space, progressively funneling the molecule to the native state. These results indicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary folding landscape, and further emphasize topological constraints as a key force in RNA folding. PMID:26481360

Towards methodical modelling: Differences between the structure and output dynamics of multiple conceptual models

NASA Astrophysics Data System (ADS)

Knoben, Wouter; Woods, Ross; Freer, Jim

2016-04-01

Conceptual hydrologic models consist of a certain arrangement of spatial and temporal dynamics consisting of stores, fluxes and transformation functions, depending on the modeller's choices and intended use. They have the advantages of being computationally efficient, being relatively easy model structures to reconfigure and having relatively low input data demands. This makes them well-suited for large-scale and large-sample hydrology, where appropriately representing the dominant hydrologic functions of a catchment is a main concern. Given these requirements, the number of parameters in the model cannot be too high, to avoid equifinality and identifiability issues. This limits the number and level of complexity of dominant hydrologic processes the model can represent. Specific purposes and places thus require a specific model and this has led to an abundance of conceptual hydrologic models. No structured overview of these models exists and there is no clear method to select appropriate model structures for different catchments. This study is a first step towards creating an overview of the elements that make up conceptual models, which may later assist a modeller in finding an appropriate model structure for a given catchment. To this end, this study brings together over 30 past and present conceptual models. The reviewed model structures are simply different configurations of three basic model elements (stores, fluxes and transformation functions), depending on the hydrologic processes the models are intended to represent. Differences also exist in the inner workings of the stores, fluxes and transformations, i.e. the mathematical formulations that describe each model element's intended behaviour. We investigate the hypothesis that different model structures can produce similar behavioural simulations. This can clarify the overview of model elements by grouping elements which are similar, which can improve model structure selection.

Fluid-Structure Interaction and Structural Analyses using a Comprehensive Mitral Valve Model with 3D Chordal Structure

PubMed Central

Toma, Milan; Einstein, Daniel R.; Bloodworth, Charles H.; Cochran, Richard P.; Yoganathan, Ajit P.; Kunzelman, Karyn S.

2016-01-01

Over the years, three-dimensional models of the mitral valve have generally been organized around a simplified anatomy. Leaflets have been typically modeled as membranes, tethered to discrete chordae typically modeled as one-dimensional, non-linear cables. Yet, recent, high-resolution medical images have revealed that there is no clear boundary between the chordae and the leaflets. In fact, the mitral valve has been revealed to be more of a webbed structure whose architecture is continuous with the chordae and their extensions into the leaflets. Such detailed images can serve as the basis of anatomically accurate, subject-specific models, wherein the entire valve is modeled with solid elements that more faithfully represent the chordae, the leaflets, and the transition between the two. These models have the potential to enhance our understanding of mitral valve mechanics, and to re-examine the role of the mitral valve chordae, which heretofore have been considered to be “invisible” to the fluid and to be of secondary importance to the leaflets. However, these new models also require a rethinking of modeling assumptions. In this study, we examine the conventional practice of loading the leaflets only and not the chordae in order to study the structural response of the mitral valve apparatus. Specifically, we demonstrate that fully resolved 3D models of the mitral valve require a fluid-structure interaction analysis to correctly load the valve even in the case of quasi-static mechanics. While a fluid-structure interaction mode is still more computationally expensive than a structural-only model, we also show that advances in GPU computing have made such models tractable. PMID:27342229

Fluid-structure interaction and structural analyses using a comprehensive mitral valve model with 3D chordal structure.

PubMed

Toma, Milan; Einstein, Daniel R; Bloodworth, Charles H; Cochran, Richard P; Yoganathan, Ajit P; Kunzelman, Karyn S

2017-04-01

Over the years, three-dimensional models of the mitral valve have generally been organized around a simplified anatomy. Leaflets have been typically modeled as membranes, tethered to discrete chordae typically modeled as one-dimensional, non-linear cables. Yet, recent, high-resolution medical images have revealed that there is no clear boundary between the chordae and the leaflets. In fact, the mitral valve has been revealed to be more of a webbed structure whose architecture is continuous with the chordae and their extensions into the leaflets. Such detailed images can serve as the basis of anatomically accurate, subject-specific models, wherein the entire valve is modeled with solid elements that more faithfully represent the chordae, the leaflets, and the transition between the two. These models have the potential to enhance our understanding of mitral valve mechanics and to re-examine the role of the mitral valve chordae, which heretofore have been considered to be 'invisible' to the fluid and to be of secondary importance to the leaflets. However, these new models also require a rethinking of modeling assumptions. In this study, we examine the conventional practice of loading the leaflets only and not the chordae in order to study the structural response of the mitral valve apparatus. Specifically, we demonstrate that fully resolved 3D models of the mitral valve require a fluid-structure interaction analysis to correctly load the valve even in the case of quasi-static mechanics. While a fluid-structure interaction mode is still more computationally expensive than a structural-only model, we also show that advances in GPU computing have made such models tractable. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Model-Drive Architecture for Agent-Based Systems

NASA Technical Reports Server (NTRS)

Gradanin, Denis; Singh, H. Lally; Bohner, Shawn A.; Hinchey, Michael G.

2004-01-01

The Model Driven Architecture (MDA) approach uses a platform-independent model to define system functionality, or requirements, using some specification language. The requirements are then translated to a platform-specific model for implementation. An agent architecture based on the human cognitive model of planning, the Cognitive Agent Architecture (Cougaar) is selected for the implementation platform. The resulting Cougaar MDA prescribes certain kinds of models to be used, how those models may be prepared and the relationships of the different kinds of models. Using the existing Cougaar architecture, the level of application composition is elevated from individual components to domain level model specifications in order to generate software artifacts. The software artifacts generation is based on a metamodel. Each component maps to a UML structured component which is then converted into multiple artifacts: Cougaar/Java code, documentation, and test cases.

Structural considerations for fabrication and mounting of the AXAF HRMA optics

NASA Technical Reports Server (NTRS)

Cohen, Lester M.; Cernoch, Larry; Mathews, Gary; Stallcup, Michael

1990-01-01

A methodology is described which minimizes optics distortion in the fabrication, metrology, and launch configuration phases. The significance of finite element modeling and breadboard testing is described with respect to performance analyses of support structures and material effects in NASA's AXAF X-ray optics. The paper outlines the requirements for AXAF performance, optical fabrication, metrology, and glass support fixtures, as well as the specifications for mirror sensitivity and the high-resolution mirror assembly. Analytical modeling of the tools is shown to coincide with grinding and polishing experiments, and is useful for designing large-area polishing and grinding tools. Metrological subcomponents that have undergone initial testing show evidence of meeting force requirements.

Structures of ribonucleoprotein particle modification enzymes

PubMed Central

Liang, Bo; Li, Hong

2016-01-01

Small nucleolar and Cajal body ribonucleoprotein particles (RNPs) are required for the maturation of ribosomes and spliceosomes. They consist of small nucleolar RNA or Cajal body RNA combined with partner proteins and represent the most complex RNA modification enzymes. Recent advances in structure and function studies have revealed detailed information regarding ribonucleoprotein assembly and substrate binding. These enzymes form intertwined RNA–protein assemblies that facilitate reversible binding of the large ribosomal RNA or small nuclear RNA. These revelations explain the specificity among the components in enzyme assembly and substrate modification. The multiple conformations of individual components and those of complete RNPs suggest a dynamic assembly process and justify the requirement of many assembly factors in vivo. PMID:21108865

Ultra high molecular weight polyethylene: Optical features at millimeter wavelengths

NASA Astrophysics Data System (ADS)

D'Alessandro, G.; Paiella, A.; Coppolecchia, A.; Castellano, M. G.; Colantoni, I.; de Bernardis, P.; Lamagna, L.; Masi, S.

2018-05-01

The next generation of experiments for the measurement of the Cosmic Microwave Background (CMB) requires more and more the use of advanced materials, with specific physical and structural properties. An example is the material used for receiver's cryostat windows and internal lenses. The large throughput of current CMB experiments requires a large diameter (of the order of 0.5 m) of these parts, resulting in heavy structural and optical requirements on the material to be used. Ultra High Molecular Weight (UHMW) polyethylene (PE) features high resistance to traction and good transmissivity in the frequency range of interest. In this paper, we discuss the possibility of using UHMW PE for windows and lenses in experiments working at millimeter wavelengths, by measuring its optical properties: emissivity, transmission and refraction index. Our measurements show that the material is well suited to this purpose.

Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides thetaiotaomicron BT2127 is an Inorganic Pyrophosphatase+

PubMed Central

Huang, Hua; Yury, Patskovsky; Toro, Rafael; Farelli, Jeremiah D.; Pandya, Chetanya; Almo, Steven C.; Allen, Karen N.; Dunaway-Mariano, Debra

2012-01-01

The explosion of protein sequence information requires that current strategies for function assignment must evolve to complement experimental approaches with computationally-based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown Haloalkanoate Dehalogenase superfamily member BT2127 (Uniprot accession # Q8A5V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics/structure/mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with kcat/Km value for pyrophosphate of ∼1 × 105 M−1 s−1), together with the gene context, supports the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of the wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure guided site directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain-domain association. Based on this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172 and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue β-phosphoglucomutase control the leaving group size (phosphate vs. glucose-phosphate) and the position of the Asp acid/base in the open vs. closed conformations. HADSF pyrophosphatases represent a third mechanistic and fold type for bacterial pyrophosphatases. PMID:21894910

Industrial approach to piezoelectric damping of large fighter aircraft components

NASA Astrophysics Data System (ADS)

Simpson, John; Schweiger, Johannes

1998-06-01

Different concepts to damp structural vibrations of the vertical tail of fighter aircraft are reported. The various requirements for a vertical tail bias an integrated approach for the design. Several active vibrations suppression concepts had been investigated during the preparatory phase of a research program shared by Daimler-Benz Aerospace Military Aircraft (Dasa), Daimler-Benz Forschung (DBF) and Deutsche Forschungsandstalt fuer Luftund Raumfahrt (DLR). Now in the main phase of the programme, four concepts were finally chosen: two concepts with aerodynamic control surfaces and two concepts with piezoelectric components. One piezo concept approach will be described rigorously, the other concepts are briefly addressed. In the Dasa concept, thin surface piezo actuators are set out carefully to flatten the dynamic portion of the combined static and dynamic maximum bending moment loading case directly in the shell structure. The second piezo concept by DLR involves pre-loaded lead zirconate titanate (PZT)-block actuators at host structure fixtures. To this end a research apparatus was designed and built as a full scale simplified fin box with carbon fiber reinformed plastic skins and an aluminium stringer-rib substructure restrained by relevant aircraft fixtures. It constitutes a benchmark 3D-structural impedance. The engineering design incorporates 7kg of PZT surface actuators. The structural system then should be excited to more than 15mm tip displacement amplitude. This prepares the final step to total A/C integration. Typical analysis methods using cyclic thermal analogies adapted to induced load levels are compared. Commercial approaches leading onto basic state space model interpretation wrt. actuator sizing and positioning, structural integrity constraints, FE-validation and testing are described. Both piezoelectric strategies are aimed at straight open-loop performance related to concept weight penalty and input electric power. The required actuators, power and integration are then enhanced to specification standards. An adapted qualification program plan is used to improve analytical read across, specifications, manufacturing decisions, handling requirements. The next research goals are outlined.

49 CFR 179.10 - Tank mounting.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 3 2012-10-01 2012-10-01 false Tank mounting. 179.10 Section 179.10... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) SPECIFICATIONS FOR TANK CARS General Design Requirements § 179.10 Tank mounting. (a) The manner in which tanks are attached to the car structure shall be...

49 CFR 179.10 - Tank mounting.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 3 2013-10-01 2013-10-01 false Tank mounting. 179.10 Section 179.10... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) SPECIFICATIONS FOR TANK CARS General Design Requirements § 179.10 Tank mounting. (a) The manner in which tanks are attached to the car structure shall be...

49 CFR 179.10 - Tank mounting.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 3 2011-10-01 2011-10-01 false Tank mounting. 179.10 Section 179.10... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) SPECIFICATIONS FOR TANK CARS General Design Requirements § 179.10 Tank mounting. (a) The manner in which tanks are attached to the car structure shall be...

49 CFR 179.10 - Tank mounting.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 3 2014-10-01 2014-10-01 false Tank mounting. 179.10 Section 179.10... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) SPECIFICATIONS FOR TANK CARS General Design Requirements § 179.10 Tank mounting. (a) The manner in which tanks are attached to the car structure shall be...

Outdoor Leadership Skills: A Program Perspective

ERIC Educational Resources Information Center

Shooter, Wynn; Sibthorp, Jim; Paisley, Karen

2009-01-01

Successful hiring, training, and pairing or grouping of staff requires administrators to consider the relationship between their programs' goals and the specific outdoor leadership skills of individual leaders. Authors have divided outdoor leadership skills into a three-category structure, and models of outdoor leadership have focused on skills…

HAL/S-FC compiler system functional specification

NASA Technical Reports Server (NTRS)

1974-01-01

Compiler organization is discussed, including overall compiler structure, internal data transfer, compiler development, and code optimization. The user, system, and SDL interfaces are described, along with compiler system requirements. Run-time software support package and restrictions and dependencies are also considered of the HAL/S-FC system.

46 CFR 56.50-96 - Keel cooler installations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PIPING SYSTEMS AND APPURTENANCES Design Requirements Pertaining to Specific Systems § 56.50-96 Keel cooler installations. (a) Keel... forming part of the tube and satisfies all of the following: (i) The cooler structure is fabricated from...

Iron Containing Metal-Organic Frameworks: Structure, Synthesis, and Applications in Environmental Remediation.

PubMed

Liu, Xiaocheng; Zhou, Yaoyu; Zhang, Jiachao; Tang, Lin; Luo, Lin; Zeng, Guangming

2017-06-21

Metal-organic frameworks (MOFs) with Fe content are gradually developing into an independent branch in environmental remediation, requiring economical, effective, low-toxicity strategies to the complete procedure. In this review, recent advancements in the structure, synthesis, and environmental application focusing on the mechanism are presented. The unique structure of novel design proposed specific characteristics of different iron-containing MOFs with potential innovation. Synthesis of typical MILs, NH 2 -MILs and MILs based materials reveal the basis and defect of the current method, indicating the optimal means for the actual requirements. The adsorption of various contamination with multiple interaction as well as the catalytic degradation over radicals or electron-hole pairs are reviewed. This review implied considerable prospects of iron-containing MOFs in the field of environment and a more comprehensive cognition into the challenges and potential improvement.

Non-Axisymmetric Inflatable Pressure Structure (NAIPS) Full-Scale Pressure Test

NASA Technical Reports Server (NTRS)

Jones, Thomas C.; Doggett, William R.; Warren, Jerry E.; Watson, Judith J.; Shariff, Khadijah; Makino, Alberto; Yount, Bryan C.

2017-01-01

Inflatable space structures have the potential to significantly reduce the required launch volume for large pressure vessels required for exploration applications including habitats, airlocks and tankage. In addition, mass savings can be achieved via the use of high specific strength softgoods materials, and the reduced design penalty from launching the structure in a densely packaged state. Large inclusions however, such as hatches, induce a high mass penalty at the interfaces with the softgoods and in the added rigid structure while reducing the packaging efficiency. A novel, Non-Axisymmetric Inflatable Pressure Structure (NAIPS) was designed and recently tested at NASA Langley Research Center to demonstrate an elongated inflatable architecture that could provide areas of low stress along a principal axis in the surface. These low stress zones will allow the integration of a flexible linear seal that substantially reduces the added mass and volume of a heritage rigid hatch structure. This paper describes the test of the first full-scale engineering demonstration unit (EDU) of the NAIPS geometry and a comparison of the results to finite element analysis.

Fusion peptide of influenza hemagglutinin requires a fixed angle boomerang structure for activity.

PubMed

Lai, Alex L; Park, Heather; White, Judith M; Tamm, Lukas K

2006-03-03

The fusion peptide of influenza hemagglutinin is crucial for cell entry of this virus. Previous studies showed that this peptide adopts a boomerang-shaped structure in lipid model membranes at the pH of membrane fusion. To examine the role of the boomerang in fusion, we changed several residues proposed to stabilize the kink in this structure and measured fusion. Among these, mutants E11A and W14A expressed hemagglutinins with hemifusion and no fusion activities, and F9A and N12A had no effect on fusion, respectively. Binding enthalpies and free energies of mutant peptides to model membranes and their ability to perturb lipid bilayer structures correlated well with the fusion activities of the parent full-length molecules. The structure of W14A determined by NMR and site-directed spin labeling features a flexible kink that points out of the membrane, in sharp contrast to the more ordered boomerang of the wild-type, which points into the membrane. A specific fixed angle boomerang structure is thus required to support membrane fusion.

Requirements for Space Settlement Design

NASA Astrophysics Data System (ADS)

Gale, Anita E.; Edwards, Richard P.

2004-02-01

When large space settlements are finally built, inevitably the customers who pay for them will start the process by specifying requirements with a Request for Proposal (RFP). Although we are decades away from seeing the first of these documents, some of their contents can be anticipated now, and provide insight into the variety of elements that must be researched and developed before space settlements can happen. Space Settlement Design Competitions for High School students present design challenges in the form of RFPs, which predict basic requirements for space settlement attributes in the future, including structural features, infrastructure, living conveniences, computers, business areas, and safety. These requirements are generically summarized, and unique requirements are noted for specific space settlement locations and applications.

Functional and Structural Correlates of Motor Speed in the Cerebellar Anterior Lobe

PubMed Central

Wenzel, Uwe; Taubert, Marco; Ragert, Patrick; Krug, Jürgen; Villringer, Arno

2014-01-01

In athletics, motor performance is determined by different abilities such as technique, endurance, strength and speed. Based on animal studies, motor speed is thought to be encoded in the basal ganglia, sensorimotor cortex and the cerebellum. The question arises whether there is a unique structural feature in the human brain, which allows “power athletes” to perform a simple foot movement significantly faster than “endurance athletes”. We acquired structural and functional brain imaging data from 32 track-and-field athletes. The study comprised of 16 “power athletes” requiring high speed foot movements (sprinters, jumpers, throwers) and 16 endurance athletes (distance runners) which in contrast do not require as high speed foot movements. Functional magnetic resonance imaging (fMRI) was used to identify speed specific regions of interest in the brain during fast and slow foot movements. Anatomical MRI scans were performed to assess structural grey matter volume differences between athletes groups (voxel based morphometry). We tested maximum movement velocity of plantarflexion (PF-Vmax) and acquired electromyographical activity of the lateral and medial gastrocnemius muscle. Behaviourally, a significant difference between the two groups of athletes was noted in PF-Vmax and fMRI indicates that fast plantarflexions are accompanied by increased activity in the cerebellar anterior lobe. The same region indicates increased grey matter volume for the power athletes compared to the endurance counterparts. Our results suggest that speed-specific neuro-functional and -structural differences exist between power and endurance athletes in the peripheral and central nervous system. PMID:24800742

Verb bias and verb-specific competition effects on sentence production

PubMed Central

Thothathiri, Malathi; Evans, Daniel G.; Poudel, Sonali

2017-01-01

How do speakers choose between structural options for expressing a given meaning? Overall preference for some structures over others as well as prior statistical association between specific verbs and sentence structures (“verb bias”) are known to broadly influence language use. However, the effects of prior statistical experience on the planning and execution of utterances and the mechanisms that facilitate structural choice for verbs with different biases have not been fully explored. In this study, we manipulated verb bias for English double-object (DO) and prepositional-object (PO) dative structures: some verbs appeared solely in the DO structure (DO-only), others solely in PO (PO-only) and yet others equally in both (Equi). Structural choices during subsequent free-choice sentence production revealed the expected dispreference for DO overall but critically also a reliable linear trend in DO production that was consistent with verb bias (DO-only > Equi > PO-only). Going beyond the general verb bias effect, three results suggested that Equi verbs, which were associated equally with the two structures, engendered verb-specific competition and required additional resources for choosing the dispreferred DO structure. First, DO production with Equi verbs but not the other verbs correlated with participants’ inhibition ability. Second, utterance duration prior to the choice of a DO structure showed a quadratic trend (DO-only < Equi > PO-only) with the longest durations for Equi verbs. Third, eye movements consistent with reimagining the event also showed a quadratic trend (DO-only < Equi > PO-only) prior to choosing DO, suggesting that participants used such recall particularly for Equi verbs. Together, these analyses of structural choices, utterance durations, eye movements and individual differences in executive functions shed light on the effects of verb bias and verb-specific competition on sentence production and the role of different executive functions in choosing between sentence structures. PMID:28672009

Specification and Design Methodologies for High-Speed Fault-Tolerant Array Algorithms and Structures for VLSI.

DTIC Science & Technology

1987-06-01

evaluation and chip layout planning for VLSI digital systems. A high-level applicative (functional) language, implemented at UCLA, allows combining of...operating system. 2.1 Introduction The complexity of VLSI requires the application of CAD tools at all levels of the design process. In order to be...effective, these tools must be adaptive to the specific design. In this project we studied a design method based on the use of applicative languages

The practical implementation of fatigue requirements to military aircraft and helicopters in the United Kingdom

NASA Technical Reports Server (NTRS)

Maxwell, R. D. J.

1972-01-01

The methods adopted in the United Kingdom to ensure the structural integrity of military aeroplanes and helicopters from the fatigue point of view are described. The procedure adopted from the writing of the specification to the monitoring of fatigue life in service are presented along with the requirements to be met and the way in which they are satisfied. Some of the outstanding problems that remain to be solved are indicated.

Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: implications for the design of new and efficient ribozymes with high sequence specificity

PubMed Central

Kasai, Yasuhiro; Shizuku, Hideki; Takagi, Yasuomi; Warashina, Masaki; Taira, Kazunari

2002-01-01

Exploitation of ribozymes in a practical setting requires high catalytic activity and strong specificity. The hammerhead ribozyme R32 has considerable potential in this regard since it has very high catalytic activity. In this study, we have examined how R32 recognizes and cleaves a specific substrate, focusing on the mechanism behind the specificity. Comparing rates of cleavage of a substrate in a mixture that included the correct substrate and various substrates with point mutations, we found that R32 cleaved the correct substrate specifically and at a high rate. To clarify the source of this strong specificity, we quantified the weak interactions between R32 and various truncated substrates, using truncated substrates as competitive inhibitors since they were not readily cleaved during kinetic measurements of cleavage of the correct substrate, S11. We found that the strong specificity of the cleavage reaction was due to a closed form of R32 with a hairpin structure. The self-complementary structure within R32 enabled the ribozyme to discriminate between the correct substrate and a mismatched substrate. Since this hairpin motif did not increase the Km (it did not inhibit the binding interaction) or decrease the kcat (it did not decrease the cleavage rate), this kind of hairpin structure might be useful for the design of new ribozymes with strong specificity and high activity. PMID:12034825

Probabilistic assessment of smart composite structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Shiao, Michael C.

1994-01-01

A composite wing with spars and bulkheads is used to demonstrate the effectiveness of probabilistic assessment of smart composite structures to control uncertainties in distortions and stresses. Results show that a smart composite wing can be controlled to minimize distortions and to have specified stress levels in the presence of defects. Structural responses such as changes in angle of attack, vertical displacements, and stress in the control and controlled plies are probabilistically assessed to quantify their respective uncertainties. Sensitivity factors are evaluated to identify those parameters that have the greatest influence on a specific structural response. Results show that smart composite structures can be configured to control both distortions and ply stresses to satisfy specified design requirements.

Using SysML for MBSE analysis of the LSST system

NASA Astrophysics Data System (ADS)

Claver, Charles F.; Dubois-Felsmann, Gregory; Delgado, Francisco; Hascall, Pat; Marshall, Stuart; Nordby, Martin; Schalk, Terry; Schumacher, German; Sebag, Jacques

2010-07-01

The Large Synoptic Survey Telescope is a complex hardware - software system of systems, making up a highly automated observatory in the form of an 8.4m wide-field telescope, a 3.2 billion pixel camera, and a peta-scale data processing and archiving system. As a project, the LSST is using model based systems engineering (MBSE) methodology for developing the overall system architecture coded with the Systems Modeling Language (SysML). With SysML we use a recursive process to establish three-fold relationships between requirements, logical & physical structural component definitions, and overall behavior (activities and sequences) at successively deeper levels of abstraction and detail. Using this process we have analyzed and refined the LSST system design, ensuring the consistency and completeness of the full set of requirements and their match to associated system structure and behavior. As the recursion process proceeds to deeper levels we derive more detailed requirements and specifications, and ensure their traceability. We also expose, define, and specify critical system interfaces, physical and information flows, and clarify the logic and control flows governing system behavior. The resulting integrated model database is used to generate documentation and specifications and will evolve to support activities from construction through final integration, test, and commissioning, serving as a living representation of the LSST as designed and built. We discuss the methodology and present several examples of its application to specific systems engineering challenges in the LSST design.

SPS structures and control: A perspective

NASA Technical Reports Server (NTRS)

Ried, R. C.

1980-01-01

The characteristics and design requirements for the structure and control systems for a solar power satellite were evaluated. A simplistic, indicative analysis on a representative configuration was developed. Representative configuration masses and dimensions are given in convenient approximate magnitudes. The significance of structure control interaction and the significance of stiffness to the minimization of dynamic energy was demonstrated. It was found that the thermal environment for the SPS was dominated by solar radiation and waste heat rejection by the antenna. A more in-depth assessment of the control system design and associated system performance is still needed, specifically the inter-relatonships between control sensors, actuators, and structural response.

Hoxd11 specifies a program of metanephric kidney development within the intermediate mesoderm of the mouse embryo.

PubMed

Mugford, Joshua W; Sipilä, Petra; Kobayashi, Akio; Behringer, Richard R; McMahon, Andrew P

2008-07-15

The mammalian kidney consists of an array of tubules connected to a ductal system that collectively function to control water/salt balance and to remove waste from the organisms' circulatory system. During mammalian embryogenesis, three kidney structures form within the intermediate mesoderm. The two most anterior structures, the pronephros and the mesonephros, are transitory and largely non-functional, while the most posterior, the metanephros, persists as the adult kidney. We have explored the mechanisms underlying regional specific differentiation of the kidney forming mesoderm. Previous studies have shown a requirement for Hox11 paralogs (Hoxa11, Hoxc11 and Hoxd11) in metanephric development. Mice lacking all Hox11 activity fail to form metanephric kidney structures. We demonstrate that the Hox11 paralog expression is restricted in the intermediate mesoderm to the posterior, metanephric level. When Hoxd11 is ectopically activated in the anterior mesonephros, we observe a partial transformation to a metanephric program of development. Anterior Hoxd11(+) cells activate Six2, a transcription factor required for the maintenance of metanephric tubule progenitors. Additionally, Hoxd11(+) mesonephric tubules exhibit an altered morphology and activate several metanephric specific markers normally confined to distal portions of the functional nephron. Collectively, our data support a model where Hox11 paralogs specify a metanephric developmental program in responsive intermediate mesoderm. This program maintains tubule forming progenitors and instructs a metanephric specific pattern of nephron differentiation.

Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome.

PubMed

Schuecker, Jannis; Schmidt, Maximilian; van Albada, Sacha J; Diesmann, Markus; Helias, Moritz

2017-02-01

The continuous integration of experimental data into coherent models of the brain is an increasing challenge of modern neuroscience. Such models provide a bridge between structure and activity, and identify the mechanisms giving rise to experimental observations. Nevertheless, structurally realistic network models of spiking neurons are necessarily underconstrained even if experimental data on brain connectivity are incorporated to the best of our knowledge. Guided by physiological observations, any model must therefore explore the parameter ranges within the uncertainty of the data. Based on simulation results alone, however, the mechanisms underlying stable and physiologically realistic activity often remain obscure. We here employ a mean-field reduction of the dynamics, which allows us to include activity constraints into the process of model construction. We shape the phase space of a multi-scale network model of the vision-related areas of macaque cortex by systematically refining its connectivity. Fundamental constraints on the activity, i.e., prohibiting quiescence and requiring global stability, prove sufficient to obtain realistic layer- and area-specific activity. Only small adaptations of the structure are required, showing that the network operates close to an instability. The procedure identifies components of the network critical to its collective dynamics and creates hypotheses for structural data and future experiments. The method can be applied to networks involving any neuron model with a known gain function.

False Belief and Language Comprehension in Cantonese-Speaking Children

ERIC Educational Resources Information Center

Cheung, Him

2006-01-01

The current research compared two accounts of the relation between language and false belief in children, namely that (a) language is generally related to false belief because both require secondary representation in a social-interactional context and that (b) specific language structures that explicitly code meta representation contribute…

Telecom Link--A Competitive Simulated Design Exercise.

ERIC Educational Resources Information Center

Freeman, J.; Allen, J.

1982-01-01

Telecom link is a structured design exercise concerned with building a telecommunications link between London and Amsterdam. Designed for A-level physics, the simulation requires a minimum of 10 hours. Aims of the exercise, design specifications and technical aspects, and summaries of four possible technologies used in the simulation are…

The Incorporation of Animal-Assisted Interventions in Social Work Education

ERIC Educational Resources Information Center

Tedeschi, Philip; Fitchett, Jennifer; Molidor, Christian E.

2005-01-01

Successful social work practice requires orientation to diverse social and cultural characteristics which structure the framework for our communities and families. This paper explores the necessity of incorporating the connection between people and non-human relationships in our understanding of social support systems. Specifically, we examine our…

Humorous Relations: Attentiveness, Pleasure and Risk

ERIC Educational Resources Information Center

Mayo, Cris

2014-01-01

This article focuses on the structures of humor and joke telling that require particular kinds of attentiveness and particular relationships between speaker and audience, or more specifically, between classmates. First, I will analyze the pedagogical and relational preconditions that are necessary for humor to work. If humor is to work well, the…

MANUAL OF PLANNING STANDARDS FOR SCHOOL BUILDINGS.

ERIC Educational Resources Information Center

New York State Education Dept., Albany.

THIS MANUAL CONTAINS THE REQUIREMENTS AND RECOMMENDATIONS FOR DEVELOPMENT AND DESIGN IN ERECTION, REPAIR, ENLARGEMENT, AND REMODELING OF SCHOOL BUILDINGS, IN TERMS OF HEALTH, COMFORT, AND SAFETY OF PUPILS ATTENDING THE PUBLIC SCHOOLS. SPECIFIC AREAS COVERED BY THIS MANUAL INCLUDE--(1) STRUCTURE AND SAFETY PLANNING, (2) MATERIALS, (3) VISUAL…

77 FR 38781 - Notice of Intent To Prepare an Environmental Impact Statement for the Proposed Naval Base...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-29

... organizational structure and mandated mission requirements. The specific arrangement of built assets, number of... that would provide for indoor classroom and tactical training instruction, and equipment use... to support logistics, equipment use and maintenance training, classroom and tactical skills...

Memory for Context becomes Less Specific with Time

ERIC Educational Resources Information Center

Wiltgen, Brian J.; Silva, Alcino J.

2007-01-01

Context memories initially require the hippocampus, but over time become independent of this structure. This shift reflects a consolidation process whereby memories are gradually stored in distributed regions of the cortex. The function of this process is thought to be the extraction of statistical regularities and general knowledge from specific…

Left Dislocation in Near-Native French

ERIC Educational Resources Information Center

Donaldson, Bryan

2011-01-01

The present study is concerned with the upper limits of SLA--specifically, mastery of the syntax-discourse interface in successful endstate learners of second-language (L2) French (near-native speakers). Left dislocation (LD) is a syntactic means of structuring spoken French discourse by marking topic. Its use requires speakers to coordinate…

Sequence-specific bias correction for RNA-seq data using recurrent neural networks.

PubMed

Zhang, Yao-Zhong; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru

2017-01-25

The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning to bare on a host of bioinformatical problems. Deep learning is ideally suited for biological problems that require automatic or hierarchical feature representation for biological data when prior knowledge is limited. In this work, we address the sequence-specific bias correction problem for RNA-seq data redusing Recurrent Neural Networks (RNNs) to model nucleotide sequences without pre-determining sequence structures. The sequence-specific bias of a read is then calculated based on the sequence probabilities estimated by RNNs, and used in the estimation of gene abundance. We explore the application of two popular RNN recurrent units for this task and demonstrate that RNN-based approaches provide a flexible way to model nucleotide sequences without knowledge of predetermined sequence structures. Our experiments show that training a RNN-based nucleotide sequence model is efficient and RNN-based bias correction methods compare well with the-state-of-the-art sequence-specific bias correction method on the commonly used MAQC-III data set. RNNs provides an alternative and flexible way to calculate sequence-specific bias without explicitly pre-determining sequence structures.

The Effect of Differentially Designed Fusion Proteins to Elicit Efficient Anti-human Thyroid Stimulating Hormone Immune Responses.

PubMed

Mard-Soltani, Maysam; Rasaee, Mohamad Javad; Khalili, Saeed; Sheikhi, Abdol-Karim; Hedayati, Mehdi; Ghaderi-Zefrehi, Hossein; Alasvand, Milad

2018-04-01

The production of human thyroid stimulating hormone (hTSH) immunoassays requires specific antibodies against hTSH which is a cumbersome process. Therefore, producing specific polyclonal antibodies against engineered recombinant fusion hTSH antigens would be of great significance. The best immunogenic region of the hTSH was selected based on in silico analyses and equipped with two different fusions. Standard methods were used for protein expression, purification, verification, structural evaluation, and immunizations of the white New Zealand rabbits. Ultimately, immunized serums were used for antibody titration, purification and characterization (specificity, sensitivity and cross reactivity). The desired antigens were successfully designed, sub-cloned, expressed, confirmed and used for in vivo immunization. Structural analyses indicated that only the bigger antigen has showed changed 2 dimensional (2D) and 3D structural properties in comparison to the smaller antigen. The raised polyclonal antibodies were capable of specific and sensitive hTSH detection, while the cross reactivity with the other members of the glycoprotein hormone family was minimum and negligible. The fusion which was solely composed of the tetanus toxin epitopes led to better protein folding and was capable of immunizing the host animals resulting into high titer antibody. Therefore, the minimal fusion sequences seem to be more effective in eliciting specific antibody responses.

SU-E-T-544: A Radiation Oncology-Specific Multi-Institutional Federated Database: Initial Implementation

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

Hendrickson, K; Phillips, M; Fishburn, M

Purpose: To implement a common database structure and user-friendly web-browser based data collection tools across several medical institutions to better support evidence-based clinical decision making and comparative effectiveness research through shared outcomes data. Methods: A consortium of four academic medical centers agreed to implement a federated database, known as Oncospace. Initial implementation has addressed issues of differences between institutions in workflow and types and breadth of structured information captured. This requires coordination of data collection from departmental oncology information systems (OIS), treatment planning systems, and hospital electronic medical records in order to include as much as possible the multi-disciplinary clinicalmore » data associated with a patients care. Results: The original database schema was well-designed and required only minor changes to meet institution-specific data requirements. Mobile browser interfaces for data entry and review for both the OIS and the Oncospace database were tailored for the workflow of individual institutions. Federation of database queries--the ultimate goal of the project--was tested using artificial patient data. The tests serve as proof-of-principle that the system as a whole--from data collection and entry to providing responses to research queries of the federated database--was viable. The resolution of inter-institutional use of patient data for research is still not completed. Conclusions: The migration from unstructured data mainly in the form of notes and documents to searchable, structured data is difficult. Making the transition requires cooperation of many groups within the department and can be greatly facilitated by using the structured data to improve clinical processes and workflow. The original database schema design is critical to providing enough flexibility for multi-institutional use to improve each institution s ability to study outcomes, determine best practices, and support research. The project has demonstrated the feasibility of deploying a federated database environment for research purposes to multiple institutions.« less

Quantification of uncertainties in the performance of smart composite structures

NASA Technical Reports Server (NTRS)

Shiao, Michael C.; Chamis, Christos C.

1993-01-01

A composite wing with spars, bulkheads, and built-in control devices is evaluated using a method for the probabilistic assessment of smart composite structures. Structural responses (such as change in angle of attack, vertical displacements, and stresses in regular plies with traditional materials and in control plies with mixed traditional and actuation materials) are probabilistically assessed to quantify their respective scatter. Probabilistic sensitivity factors are computed to identify those parameters that have a significant influence on a specific structural response. Results show that the uncertainties in the responses of smart composite structures can be quantified. Responses such as structural deformation, ply stresses, frequencies, and buckling loads in the presence of defects can be reliably controlled to satisfy specified design requirements.

Polycomb-Mediated Repression and Sonic Hedgehog Signaling Interact to Regulate Merkel Cell Specification during Skin Development

PubMed Central

Bar, Carmit; Tsai, Pai-Chi; Valdes, Victor J.; Cohen, Idan; Santoriello, Francis J.; Zhao, Dejian; Hsu, Ya-Chieh; Ezhkova, Elena

2016-01-01

An increasing amount of evidence indicates that developmental programs are tightly regulated by the complex interplay between signaling pathways, as well as transcriptional and epigenetic processes. Here, we have uncovered coordination between transcriptional and morphogen cues to specify Merkel cells, poorly understood skin cells that mediate light touch sensations. In murine dorsal skin, Merkel cells are part of touch domes, which are skin structures consisting of specialized keratinocytes, Merkel cells, and afferent neurons, and are located exclusively around primary hair follicles. We show that the developing primary hair follicle functions as a niche required for Merkel cell specification. We find that intraepidermal Sonic hedgehog (Shh) signaling, initiated by the production of Shh ligand in the developing hair follicles, is required for Merkel cell specification. The importance of Shh for Merkel cell formation is further reinforced by the fact that Shh overexpression in embryonic epidermal progenitors leads to ectopic Merkel cells. Interestingly, Shh signaling is common to primary, secondary, and tertiary hair follicles, raising the possibility that there are restrictive mechanisms that regulate Merkel cell specification exclusively around primary hair follicles. Indeed, we find that loss of Polycomb repressive complex 2 (PRC2) in the epidermis results in the formation of ectopic Merkel cells that are associated with all hair types. We show that PRC2 loss expands the field of epidermal cells competent to differentiate into Merkel cells through the upregulation of key Merkel-differentiation genes, which are known PRC2 targets. Importantly, PRC2-mediated repression of the Merkel cell differentiation program requires inductive Shh signaling to form mature Merkel cells. Our study exemplifies how the interplay between epigenetic and morphogen cues regulates the complex patterning and formation of the mammalian skin structures. PMID:27414999

Polycomb-Mediated Repression and Sonic Hedgehog Signaling Interact to Regulate Merkel Cell Specification during Skin Development.

PubMed

Perdigoto, Carolina N; Dauber, Katherine L; Bar, Carmit; Tsai, Pai-Chi; Valdes, Victor J; Cohen, Idan; Santoriello, Francis J; Zhao, Dejian; Zheng, Deyou; Hsu, Ya-Chieh; Ezhkova, Elena

2016-07-01

An increasing amount of evidence indicates that developmental programs are tightly regulated by the complex interplay between signaling pathways, as well as transcriptional and epigenetic processes. Here, we have uncovered coordination between transcriptional and morphogen cues to specify Merkel cells, poorly understood skin cells that mediate light touch sensations. In murine dorsal skin, Merkel cells are part of touch domes, which are skin structures consisting of specialized keratinocytes, Merkel cells, and afferent neurons, and are located exclusively around primary hair follicles. We show that the developing primary hair follicle functions as a niche required for Merkel cell specification. We find that intraepidermal Sonic hedgehog (Shh) signaling, initiated by the production of Shh ligand in the developing hair follicles, is required for Merkel cell specification. The importance of Shh for Merkel cell formation is further reinforced by the fact that Shh overexpression in embryonic epidermal progenitors leads to ectopic Merkel cells. Interestingly, Shh signaling is common to primary, secondary, and tertiary hair follicles, raising the possibility that there are restrictive mechanisms that regulate Merkel cell specification exclusively around primary hair follicles. Indeed, we find that loss of Polycomb repressive complex 2 (PRC2) in the epidermis results in the formation of ectopic Merkel cells that are associated with all hair types. We show that PRC2 loss expands the field of epidermal cells competent to differentiate into Merkel cells through the upregulation of key Merkel-differentiation genes, which are known PRC2 targets. Importantly, PRC2-mediated repression of the Merkel cell differentiation program requires inductive Shh signaling to form mature Merkel cells. Our study exemplifies how the interplay between epigenetic and morphogen cues regulates the complex patterning and formation of the mammalian skin structures.

Modelling and Simulation of the Dynamics of the Antigen-Specific T Cell Response Using Variable Structure Control Theory.

PubMed

Anelone, Anet J N; Spurgeon, Sarah K

2016-01-01

Experimental and mathematical studies in immunology have revealed that the dynamics of the programmed T cell response to vigorous infection can be conveniently modelled using a sigmoidal or a discontinuous immune response function. This paper hypothesizes strong synergies between this existing work and the dynamical behaviour of engineering systems with a variable structure control (VSC) law. These findings motivate the interpretation of the immune system as a variable structure control system. It is shown that dynamical properties as well as conditions to analytically assess the transition from health to disease can be developed for the specific T cell response from the theory of variable structure control. In particular, it is shown that the robustness properties of the specific T cell response as observed in experiments can be explained analytically using a VSC perspective. Further, the predictive capacity of the VSC framework to determine the T cell help required to overcome chronic Lymphocytic Choriomeningitis Virus (LCMV) infection is demonstrated. The findings demonstrate that studying the immune system using variable structure control theory provides a new framework for evaluating immunological dynamics and experimental observations. A modelling and simulation tool results with predictive capacity to determine how to modify the immune response to achieve healthy outcomes which may have application in drug development and vaccine design.

Enzymatic synthesis of structured lipids.

PubMed

Iwasaki, Yugo; Yamane, Tsuneo

2004-01-01

Structured lipids (SLs) are defined as lipids that are modified chemically or enzymatically in order to change their structure. This review deals with structured triacylglycerols (STGs) and structured phospholipids (SPLs). The most typical STGs are MLM-type STGs, having medium chain fatty acids (FAs) at the 1- and 3-positions and a long chain fatty acid at the 2- position. MLM-type STGs are synthesized by: 1) 1,3-position-specific lipase-catalyzed acyl exchange of TG with FA or with FA ethylester (FAEt); 2) 1,3-position-specific lipase-catalyzed acylation of glycerol with FA, giving symmetric 1,3-diacyl-sn-glycerol, followed by chemical acylation at the sn-2 position, and; 3) 1,3-position-specific lipase-catalyzed deacylation of TG, giving 2-monoacylglycerol, followed by reacylation at the 1- and 3-positions with FA or with (FAEt). Enzymatic preparation of SPLs requires: 1) acyl group modification, and 2) head group modification of phospholipids. Acyl group modification is performed using lipases or phospholipase A2-mediated transesterification or ester synthesis to introduce arbitrary fatty acid to phospholipids. Head group modification is carried out by phospholipase D-catalyzed transphosphatidylation. A wide range of compounds can be introduced into the polar head of phospholipids, making it possible to prepare various SPLs.

T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures

PubMed Central

Schaffter, Samuel W; Green, Leopold N; Schneider, Joanna; Subramanian, Hari K K; Schulman, Rebecca

2018-01-01

Abstract The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases. PMID:29718412

T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures.

PubMed

Schaffter, Samuel W; Green, Leopold N; Schneider, Joanna; Subramanian, Hari K K; Schulman, Rebecca; Franco, Elisa

2018-06-01

The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases.

Aortic root segmentation in 4D transesophageal echocardiography

NASA Astrophysics Data System (ADS)

Chechani, Shubham; Suresh, Rahul; Patwardhan, Kedar A.

2018-02-01

The Aortic Valve (AV) is an important anatomical structure which lies on the left side of the human heart. The AV regulates the flow of oxygenated blood from the Left Ventricle (LV) to the rest of the body through aorta. Pathologies associated with the AV manifest themselves in structural and functional abnormalities of the valve. Clinical management of pathologies often requires repair, reconstruction or even replacement of the valve through surgical intervention. Assessment of these pathologies as well as determination of specific intervention procedure requires quantitative evaluation of the valvular anatomy. 4D (3D + t) Transesophageal Echocardiography (TEE) is a widely used imaging technique that clinicians use for quantitative assessment of cardiac structures. However, manual quantification of 3D structures is complex, time consuming and suffers from inter-observer variability. Towards this goal, we present a semiautomated approach for segmentation of the aortic root (AR) structure. Our approach requires user-initialized landmarks in two reference frames to provide AR segmentation for full cardiac cycle. We use `coarse-to-fine' B-spline Explicit Active Surface (BEAS) for AR segmentation and Masked Normalized Cross Correlation (NCC) method for AR tracking. Our method results in approximately 0.51 mm average localization error in comparison with ground truth annotation performed by clinical experts on 10 real patient cases (139 3D volumes).

Cohesin-interacting protein WAPL-1 regulates meiotic chromosome structure and cohesion by antagonizing specific cohesin complexes

PubMed Central

Crawley, Oliver; Barroso, Consuelo; Testori, Sarah; Ferrandiz, Nuria; Silva, Nicola; Castellano-Pozo, Maikel; Jaso-Tamame, Angel Luis; Martinez-Perez, Enrique

2016-01-01

Wapl induces cohesin dissociation from DNA throughout the mitotic cell cycle, modulating sister chromatid cohesion and higher-order chromatin structure. Cohesin complexes containing meiosis-specific kleisin subunits govern most aspects of meiotic chromosome function, but whether Wapl regulates these complexes remains unknown. We show that during C. elegans oogenesis WAPL-1 antagonizes binding of cohesin containing COH-3/4 kleisins, but not REC-8, demonstrating that sensitivity to WAPL-1 is dictated by kleisin identity. By restricting the amount of chromosome-associated COH-3/4 cohesin, WAPL-1 controls chromosome structure throughout meiotic prophase. In the absence of REC-8, WAPL-1 inhibits COH-3/4-mediated cohesion, which requires crossover-fated events formed during meiotic recombination. Thus, WAPL-1 promotes functional specialization of meiotic cohesin: WAPL-1-sensitive COH-3/4 complexes modulate higher-order chromosome structure, while WAPL-1-refractory REC-8 complexes provide stable cohesion. Surprisingly, a WAPL-1-independent mechanism removes cohesin before metaphase I. Our studies provide insight into how meiosis-specific cohesin complexes are regulated to ensure formation of euploid gametes. DOI: http://dx.doi.org/10.7554/eLife.10851.001 PMID:26841696

Digital Cellular Solid Pressure Vessels: A Novel Approach for Human Habitation in Space

NASA Technical Reports Server (NTRS)

Cellucci, Daniel; Jenett, Benjamin; Cheung, Kenneth C.

2017-01-01

It is widely assumed that human exploration beyond Earth's orbit will require vehicles capable of providing long duration habitats that simulate an Earth-like environment - consistent artificial gravity, breathable atmosphere, and sufficient living space- while requiring the minimum possible launch mass. This paper examines how the qualities of digital cellular solids - high-performance, repairability, reconfigurability, tunable mechanical response - allow the accomplishment of long-duration habitat objectives at a fraction of the mass required for traditional structural technologies. To illustrate the impact digital cellular solids could make as a replacement to conventional habitat subsystems, we compare recent proposed deep space habitat structural systems with a digital cellular solids pressure vessel design that consists of a carbon fiber reinforced polymer (CFRP) digital cellular solid cylindrical framework that is lined with an ultra-high molecular weight polyethylene (UHMWPE) skin. We use the analytical treatment of a linear specific modulus scaling cellular solid to find the minimum mass pressure vessel for a structure and find that, for equivalent habitable volume and appropriate safety factors, the use of digital cellular solids provides clear methods for producing structures that are not only repairable and reconfigurable, but also higher performance than their conventionally manufactured counterparts.

Extraction of membrane structure in eyeball from MR volumes

NASA Astrophysics Data System (ADS)

Oda, Masahiro; Kin, Taichi; Mori, Kensaku

2017-03-01

This paper presents an accurate extraction method of spherical shaped membrane structures in the eyeball from MR volumes. In ophthalmic surgery, operation field is limited to a small region. Patient specific surgical simulation is useful to reduce complications. Understanding of tissue structure in the eyeball of a patient is required to achieve patient specific surgical simulations. Previous extraction methods of tissue structure in the eyeball use optical coherence tomography (OCT) images. Although OCT images have high resolution, imaging regions are limited to very small. Global structure extraction of the eyeball is difficult from OCT images. We propose an extraction method of spherical shaped membrane structures including the sclerotic coat, choroid, and retina. This method is applied to a T2 weighted MR volume of the head region. MR volume can capture tissue structure of whole eyeball. Because we use MR volumes, out method extracts whole membrane structures in the eyeball. We roughly extract membrane structures by applying a sheet structure enhancement filter. The rough extraction result includes parts of the membrane structures. Then, we apply the Hough transform to extract a sphere structure from the voxels set of the rough extraction result. The Hough transform finds a sphere structure from the rough extraction result. An experimental result using a T2 weighted MR volume of the head region showed that the proposed method can extract spherical shaped membrane structures accurately.

Thrombin specificity. Requirement for apolar amino acids adjacent to the thrombin cleavage site of polypeptide substrate.

PubMed

Chang, J Y

1985-09-02

alpha-Thrombin cleavage of 30 polypeptide hormones and their derivatives were analysed by quantitative amino-terminal analysis. The polypeptides included secretin, vasoactive intestinal polypeptide, cholecystokinin fragment, dynorphin A, somatostatins, gastrin-releasing peptide, calcitonins and human parathyroid hormone fragment. Most of them were selected mainly on the ground that they contain sequence structures homologous to the well known tripeptide substrates of alpha-thrombin. All selected polypeptides have one single major cleavage site and both Arg-Xaa and Lys-Xaa bonds were found to be selectively cleaved by alpha-thrombin. Under fixed conditions (1 nmol polypeptide/0.5 NIH unit alpha-thrombin in 20 microliters of 50 mM ammonium bicarbonate at 25 degrees C), the time required for 50% cleavage ranges from less than 1 min to longer than 24 h. Heparin invariably enhanced thrombin cleavage on all polypeptide analysed. The optimum cleavage site for alpha-thrombin has the structures of (a) P4-P3-Pro-Arg-P1'-P2', where P3 and P4 are hydrophobic amino acid and P1', P2' are nonacidic amino acids and (b) P2-Arg-P1', where P2 or P1' are Gly. The requirement for hydrophobic P3 and P4 was further demonstrated by the drastic decrease of thrombin cleavage rates in both gastrin-releasing peptide and calcitonins after chemical removal of hydrophobic P3 and P4 residues. The requirement for nonacidic P1' and P2' residues was demonstrated by the drastic increase of thrombin cleavage rates in both calcitonin and parathyroid hormone fragments, after specific chemical modification of acidic P1' and P2' residues. These findings confirm the importance of hydrophobic P2-P4 residues for thrombin specificity and provide new evidence to indicate that apolar P1' and P2' residues are also crucial for thrombin specificity. It is concluded that specific cleavage of polypeptides by alpha-thrombin can be reasonably predicted and that chemical modification can be a useful tool in enhancing thrombin cleavage.

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1

PubMed Central

Sasnauskas, Giedrius; Kauneckaitė, Kotryna; Siksnys, Virginijus

2018-01-01

Abstract Arabidopsis thaliana requires a prolonged period of cold exposure during winter to initiate flowering in a process termed vernalization. Exposure to cold induces epigenetic silencing of the FLOWERING LOCUS C (FLC) gene by Polycomb group (PcG) proteins. A key role in this epigenetic switch is played by transcriptional repressors VAL1 and VAL2, which specifically recognize Sph/RY DNA sequences within FLC via B3 DNA binding domains, and mediate recruitment of PcG silencing machinery. To understand the structural mechanism of site-specific DNA recognition by VAL1, we have solved the crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence 5′-CATGCA-3′/5′-TGCATG-3′. We find that VAL1-B3 makes H-bonds and van der Waals contacts to DNA bases of all six positions of the canonical Sph/RY element. In agreement with the structure, in vitro DNA binding studies show that VAL1-B3 does not tolerate substitutions at any position of the 5′-TGCATG-3′ sequence. The VAL1-B3–DNA structure presented here provides a structural model for understanding the specificity of plant B3 domains interacting with the Sph/RY and other DNA sequences. PMID:29660015

IMCS reflight certification requirements and design specifications

NASA Technical Reports Server (NTRS)

1984-01-01

The requirements for reflight certification are established. Software requirements encompass the software programs that are resident in the PCC, DEP, PDSS, EC, or any related GSE. A design approach for the reflight software packages is recommended. These designs will be of sufficient detail to permit the implementation of reflight software. The PDSS/IMC Reflight Certification system provides the tools and mechanisms for the user to perform the reflight certification test procedures, test data capture, test data display, and test data analysis. The system as defined will be structured to permit maximum automation of reflight certification procedures and test data analysis.

MIL-H-8501B: Application to shipboard terminal operations

NASA Technical Reports Server (NTRS)

Cappetta, A. N.; Johns, J. B.

1993-01-01

The philosophy and structure of the proposed U.S. Military Specification for Handling Qualities Requirements for Military Rotorcraft, MIL-H-8501B, are presented with emphasis on shipboard terminal operations. The impact of current and future naval operational requirements on the selection of appropriate combinations of basic vehicle dynamics and usable cue environments are identified. An example 'walk through' of MIL-H-8501B is conducted from task identification to determination of stability and control requirements. For selected basic vehicle dynamics, criteria as a function of input/response magnitude are presented. Additionally, rotorcraft design development implications are discussed.

A scoping review of assessment tools for laparoscopic suturing.

PubMed

Bilgic, Elif; Endo, Satoshi; Lebedeva, Ekaterina; Takao, Madoka; McKendy, Katherine M; Watanabe, Yusuke; Feldman, Liane S; Vassiliou, Melina C

2018-05-03

A needs assessment identified a gap in teaching and assessment of laparoscopic suturing (LS) skills. The purpose of this review is to identify assessment tools that were used to assess LS skills, to evaluate validity evidence available, and to provide guidance for selecting the right assessment tool for specific assessment conditions. Bibliographic databases were searched till April 2017. Full-text articles were included if they reported on assessment tools used in the operating room/simulation to (1) assess procedures that require LS or (2) specifically assess LS skills. Forty-two tools were identified, of which 26 were used for assessing LS skills specifically and 26 for procedures that require LS. Tools had the most evidence in internal structure and relationship to other variables, and least in consequences. Through identification and evaluation of assessment tools, the results of this review could be used as a guideline when implementing assessment tools into training programs.

Critical role for the chemokine receptor CXCR6 in NK cell-mediated antigen-specific memory of haptens and viruses.

PubMed

Paust, Silke; Gill, Harvinder S; Wang, Bao-Zhong; Flynn, Michael P; Moseman, E Ashley; Senman, Balimkiz; Szczepanik, Marian; Telenti, Amalio; Askenase, Philip W; Compans, Richard W; von Andrian, Ulrich H

2010-12-01

Hepatic natural killer (NK) cells mediate antigen-specific contact hypersensitivity (CHS) in mice deficient in T cells and B cells. We report here that hepatic NK cells, but not splenic or naive NK cells, also developed specific memory of vaccines containing antigens from influenza, vesicular stomatitis virus (VSV) or human immunodeficiency virus type 1 (HIV-1). Adoptive transfer of virus-sensitized NK cells into naive recipient mice enhanced the survival of the mice after lethal challenge with the sensitizing virus but not after lethal challenge with a different virus. NK cell memory of haptens and viruses depended on CXCR6, a chemokine receptor on hepatic NK cells that was required for the persistence of memory NK cells but not for antigen recognition. Thus, hepatic NK cells can develop adaptive immunity to structurally diverse antigens, an activity that requires NK cell-expressed CXCR6.

Developing learning environments which support early algebraic reasoning: a case from a New Zealand primary classroom

NASA Astrophysics Data System (ADS)

Hunter, Jodie

2014-12-01

Current reforms in mathematics education advocate the development of mathematical learning communities in which students have opportunities to engage in mathematical discourse and classroom practices which underlie algebraic reasoning. This article specifically addresses the pedagogical actions teachers take which structure student engagement in dialogical discourse and activity which facilitates early algebraic reasoning. Using videotaped recordings of classroom observations, the teacher and researcher collaboratively examined the classroom practices and modified the participatory practices to develop a learning environment which supported early algebraic reasoning. Facilitating change in the classroom environment was a lengthy process which required consistent and ongoing attention initially to the social norms and then to the socio-mathematical norms. Specific pedagogical actions such as the use of specifically designed tasks, materials and representations and a constant press for justification and generalisation were required to support students to link their numerical understandings to algebraic reasoning.

Histone H4 acetylation required for chromatin decompaction during DNA replication.

PubMed

Ruan, Kun; Yamamoto, Takaharu G; Asakawa, Haruhiko; Chikashige, Yuji; Kimura, Hiroshi; Masukata, Hisao; Haraguchi, Tokuko; Hiraoka, Yasushi

2015-07-30

Faithful DNA replication is a prerequisite for cell proliferation. Several cytological studies have shown that chromosome structures alter in the S-phase of the cell cycle. However, the molecular mechanisms behind the alteration of chromosome structures associated with DNA replication have not been elucidated. Here, we investigated chromatin structures and acetylation of specific histone residues during DNA replication using the meiotic nucleus of the fission yeast Schizosaccharomyces pombe. The S. pombe meiotic nucleus provides a unique opportunity for measuring the levels of compaction of chromatin along the chromosome in a defined orientation. By direct measurement of chromatin compaction in living cells, we demonstrated that decompaction of chromatin occurs during meiotic DNA replication. This chromatin decompaction was suppressed by depletion of histone acetyltransferase Mst1 or by arginine substitution of specific lysine residues (K8 and K12) of histone H4. These results suggest that acetylation of histone H4 residues K8 and K12 plays a critical role in loosening chromatin structures during DNA replication.

Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

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

Koropatkin, Nicole M.; Martens, Eric C.; Gordon, Jeffrey I.

2009-01-12

The human gut microbiota performs functions that are not encoded in our Homo sapiens genome, including the processing of otherwise undigestible dietary polysaccharides. Defining the structures of proteins involved in the import and degradation of specific glycans by saccharolytic bacteria complements genomic analysis of the nutrient-processing capabilities of gut communities. Here, we describe the atomic structure of one such protein, SusD, required for starch binding and utilization by Bacteroides thetaiotaomicron, a prominent adaptive forager of glycans in the distal human gut microbiota. The binding pocket of this unique {alpha}-helical protein contains an arc of aromatic residues that complements the naturalmore » helical structure of starch and imposes this conformation on bound maltoheptaose. Furthermore, SusD binds cyclic oligosaccharides with higher affinity than linear forms. The structures of several SusD/oligosaccharide complexes reveal an inherent ligand recognition plasticity dominated by the three-dimensional conformation of the oligosaccharides rather than specific interactions with the composite sugars.« less

Selected issues of the universal communication environment implementation for CII standard

NASA Astrophysics Data System (ADS)

Zagoździńska, Agnieszka; Poźniak, Krzysztof T.; Drabik, Paweł K.

2011-10-01

In the contemporary FPGA market there is the wide assortment of structures, integrated development environments, and boards of different producers. The variety allows to fit resources to requirements of the individual designer. There is the need of standardization of the projects to make it useful in research laboratories equipped with different producers tools. Proposed solution is CII standardization of VHDL components. This paper contains specification of the universal communication environment for CII standard. The link can be used in different FPGA structures. Implementation of the link enables object oriented VHDL programming with the use of CII standardization. The whole environment contains FPGA environment and PC software. The paper contains description of the selected issues of FPGA environment. There is description of some specific solutions that enables environment usage in structures of different producers. The flexibility of different size data transmissions with the use of CII is presented. The specified tool gives the opportunity to use FPGA structures variety fully and design faster and more effectively.

Hercules Single-Stage Reusable Vehicle (HSRV) Operating Base

NASA Technical Reports Server (NTRS)

Moon, Michael J.; McCleskey, Carey M.

2017-01-01

Conceptual design for the layout of lunar-planetary surface support systems remains an important area needing further master planning. This paper explores a structured approach to organize the layout of a Mars-based site equipped for routinely flying a human-scale reusable taxi system. The proposed Hercules Transportation System requires a surface support capability to sustain its routine, affordable, and dependable operation. The approach organizes a conceptual Hercules operating base through functional station sets. The station set approach will allow follow-on work to trade design approaches and consider technologies for more efficient flow of material, energy, and information at future Mars bases and settlements. The station set requirements at a Mars site point to specific capabilities needed. By drawing from specific Hercules design characteristics, the technology requirements for surface-based systems will come into greater focus. This paper begins a comprehensive process for documenting functional needs, architectural design methods, and analysis techniques necessary for follow-on concept studies.

An Fgf-Shh signaling hierarchy regulates early specification of the zebrafish skull

PubMed Central

McCarthy, Neil; Sidik, Alfire; Bertrand, Julien Y.; Eberhart, Johann K.

2016-01-01

The neurocranium generates most of the craniofacial skeleton and consists of prechordal and postchordal regions. Although development of the prechordal is well studied, little is known of the postchordal region. Here we characterize a signaling hierarchy necessary for postchordal neurocranial development involving Fibroblast growth factor (Fgf) signaling for early specification of mesodermally-derived progenitor cells. The expression of hyaluron synthetase 2 (has2) in the cephalic mesoderm requires Fgf signaling and Has2 function, in turn, is required for postchordal neurocranial development. While Hedgehog (Hh)-deficient embryos also lack a postchordal neurocranium, this appears primarily due to a later defect in chondrocyte differentiation. Inhibitor studies demonstrate that postchordal neurocranial development requires early Fgf and later Hh signaling. Collectively, our results provide a mechanistic understanding of early postchordal neurocranial development and demonstrate a hierarchy of signaling between Fgf and Hh in the development of this structure. PMID:27060628

Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway.

PubMed

Saxton, Robert A; Knockenhauer, Kevin E; Wolfson, Rachel L; Chantranupong, Lynne; Pacold, Michael E; Wang, Tim; Schwartz, Thomas U; Sabatini, David M

2016-01-01

Eukaryotic cells coordinate growth with the availability of nutrients through the mechanistic target of rapamycin complex 1 (mTORC1), a master growth regulator. Leucine is of particular importance and activates mTORC1 via the Rag guanosine triphosphatases and their regulators GATOR1 and GATOR2. Sestrin2 interacts with GATOR2 and is a leucine sensor. Here we present the 2.7 angstrom crystal structure of Sestrin2 in complex with leucine. Leucine binds through a single pocket that coordinates its charged functional groups and confers specificity for the hydrophobic side chain. A loop encloses leucine and forms a lid-latch mechanism required for binding. A structure-guided mutation in Sestrin2 that decreases its affinity for leucine leads to a concomitant increase in the leucine concentration required for mTORC1 activation in cells. These results provide a structural mechanism of amino acid sensing by the mTORC1 pathway. Copyright © 2016, American Association for the Advancement of Science.

Automatic Debugging Support for UML Designs

NASA Technical Reports Server (NTRS)

Schumann, Johann; Swanson, Keith (Technical Monitor)

2001-01-01

Design of large software systems requires rigorous application of software engineering methods covering all phases of the software process. Debugging during the early design phases is extremely important, because late bug-fixes are expensive. In this paper, we describe an approach which facilitates debugging of UML requirements and designs. The Unified Modeling Language (UML) is a set of notations for object-orient design of a software system. We have developed an algorithm which translates requirement specifications in the form of annotated sequence diagrams into structured statecharts. This algorithm detects conflicts between sequence diagrams and inconsistencies in the domain knowledge. After synthesizing statecharts from sequence diagrams, these statecharts usually are subject to manual modification and refinement. By using the "backward" direction of our synthesis algorithm. we are able to map modifications made to the statechart back into the requirements (sequence diagrams) and check for conflicts there. Fed back to the user conflicts detected by our algorithm are the basis for deductive-based debugging of requirements and domain theory in very early development stages. Our approach allows to generate explanations oil why there is a conflict and which parts of the specifications are affected.

Methodologies for Verification and Validation of Space Launch System (SLS) Structural Dynamic Models: Appendices

NASA Technical Reports Server (NTRS)

Coppolino, Robert N.

2018-01-01

Verification and validation (V&V) is a highly challenging undertaking for SLS structural dynamics models due to the magnitude and complexity of SLS subassemblies and subassemblies. Responses to challenges associated with V&V of Space Launch System (SLS) structural dynamics models are presented in Volume I of this paper. Four methodologies addressing specific requirements for V&V are discussed. (1) Residual Mode Augmentation (RMA). (2) Modified Guyan Reduction (MGR) and Harmonic Reduction (HR, introduced in 1976). (3) Mode Consolidation (MC). Finally, (4) Experimental Mode Verification (EMV). This document contains the appendices to Volume I.

Research requirements to reduce empty weight of helicopters by use of advanced materials

NASA Technical Reports Server (NTRS)

Hoffstedt, D. J.

1976-01-01

Utilization of the new, lightweight, high-strength, aerospace structural-composite (filament/matrix) materials, when specifically designed into a new aircraft, promises reductions in structural empty weight of 12 percent at recurring costs competive with metals. A program of basic and applied research and demonstration is identified with the objective of advancing the state of the art to the point where civil helicopters are confidently designed, produced, certified, and marketed by 1985. A structural empty-weight reduction of 12 percent was shown to significantly reduce energy consumption in modern high-performance helicopters.

Biophotonic ring resonator for ultrasensitive detection of DMMP as a simulant for organophosphorus agents.

PubMed

Bonnot, Karine; Cuesta-Soto, Francisco; Rodrigo, Manuel; Varriale, Antonio; Sanchez, Nuria; D'Auria, Sabato; Spitzer, Denis; Lopez-Royo, Francisco

2014-05-20

Combining photonic integrated circuits with a biologically based sensing approach has the ability to provide a new generation of portable and low-cost sensor devices with a high specificity and sensitivity for a number of applications in environmental monitoring, defense, and homeland security. We report herein on the specific biosensing under continuous air flow of DMMP, which is commonly used as a simulant and a precursor for the synthesis of Sarin. The proposed technology is based on the selective recognition of the targeted DMMP molecule by specifically modified proteins immobilized on photonic structures. The response of the biophotonic structures shows a high stability and accuracy over 3 months, allowing for the detection in diluted air of DMMP at concentration as low as 35 μg/m(3) (6.8 ppb) in less than 15 min. The performance of the developed technology satisfies most current homeland and military security requirements.

Antibody Recognition of a Human Chorionic Gonadotropin Epitope (hCGβ66–80) Depends on Local Structure Retained in the Free Peptide*

PubMed Central

Gregor, Craig R.; Cerasoli, Eleonora; Schouten, James; Ravi, Jascindra; Slootstra, Jerry; Horgan, Adrian; Martyna, Glenn J.; Ryadnov, Maxim G.; Davis, Paul; Crain, Jason

2011-01-01

Human chorionic gonadotropin (hCG) is an important biomarker in pregnancy and oncology, where it is routinely detected and quantified by specific immunoassays. Intelligent epitope selection is essential to achieving the required assay performance. We present binding affinity measurements demonstrating that a typical β3-loop-specific monoclonal antibody (8G5) is highly selective in competitive immunoassays and distinguishes between hCGβ66–80 and the closely related luteinizing hormone (LH) fragment LHβ86–100, which differ only by a single amino acid residue. A combination of optical spectroscopic measurements and atomistic computer simulations on these free peptides reveals differences in turn type stabilized by specific hydrogen bonding motifs. We propose that these structural differences are the basis for the observed selectivity in the full protein. PMID:21592960

Product Structure, the Heart of Product Definition

NASA Technical Reports Server (NTRS)

DeHoog, C., Jr.

1999-01-01

This paper describes the LMMSS Product Definition System (PDS) philosophy and approach were the use of each item parts document or software can be traced to a specific end item (EI) serial/tail number of the product. It explains why a part-oriented approach to data organization and configuration management is required. The definition of part-oriented is that all appropriate product definition data products will be collected. Referenced and managed by their linkage/relationship to parts/items, The paper will touch upon how LMMSS store/controls product definition information under each project's top product designator in a two tiered approach. One tier for each product end item and another tier which contain/controls listings of drawings, documents. Specifications and standards that are required for hardware item definition.

Flight software development for the isothermal dendritic growth experiment

NASA Technical Reports Server (NTRS)

Levinson, Laurie H.; Winsa, Edward A.; Glicksman, Martin E.

1989-01-01

The Isothermal Dendritic Growth Experiment (IDGE) is a microgravity materials science experiment scheduled to fly in the cargo bay of the shuttle on the United States Microgravity Payload (USMP) carrier. The experiment will be operated by real-time control software which will not only monitor and control onboard experiment hardware, but will also communicate, via downlink data and uplink commands, with the Payload Operations Control Center (POCC) at NASA George C. Marshall Space Flight Center (MSFC). The software development approach being used to implement this system began with software functional requirements specification. This was accomplished using the Yourdon/DeMarco methodology as supplemented by the Ward/Mellor real-time extensions. The requirements specification in combination with software prototyping was then used to generate a detailed design consisting of structure charts, module prologues, and Program Design Language (PDL) specifications. This detailed design will next be used to code the software, followed finally by testing against the functional requirements. The result will be a modular real-time control software system with traceability through every phase of the development process.

Flight software development for the isothermal dendritic growth experiment

NASA Technical Reports Server (NTRS)

Levinson, Laurie H.; Winsa, Edward A.; Glicksman, M. E.

1990-01-01

The Isothermal Dendritic Growth Experiment (IDGE) is a microgravity materials science experiment scheduled to fly in the cargo bay of the shuttle on the United States Microgravity Payload (USMP) carrier. The experiment will be operated by real-time control software which will not only monitor and control onboard experiment hardware, but will also communicate, via downlink data and unlink commands, with the Payload Operations Control Center (POCC) at NASA George C. Marshall Space Flight Center (MSFC). The software development approach being used to implement this system began with software functional requirements specification. This was accomplished using the Yourdon/DeMarco methodology as supplemented by the Ward/Mellor real-time extensions. The requirements specification in combination with software prototyping was then used to generate a detailed design consisting of structure charts, module prologues, and Program Design Language (PDL) specifications. This detailed design will next be used to code the software, followed finally by testing against the functional requirements. The result will be a modular real-time control software system with traceability through every phase of the development process.

Multiscale Structure of UXO Site Characterization: Spatial Estimation and Uncertainty Quantification

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

Ostrouchov, George; Doll, William E.; Beard, Les P.

2009-01-01

Unexploded ordnance (UXO) site characterization must consider both how the contamination is generated and how we observe that contamination. Within the generation and observation processes, dependence structures can be exploited at multiple scales. We describe a conceptual site characterization process, the dependence structures available at several scales, and consider their statistical estimation aspects. It is evident that most of the statistical methods that are needed to address the estimation problems are known but their application-specific implementation may not be available. We demonstrate estimation at one scale and propose a representation for site contamination intensity that takes full account of uncertainty,more » is flexible enough to answer regulatory requirements, and is a practical tool for managing detailed spatial site characterization and remediation. The representation is based on point process spatial estimation methods that require modern computational resources for practical application. These methods have provisions for including prior and covariate information.« less

Specifications Physiological Monitoring System

NASA Technical Reports Server (NTRS)

1985-01-01

The operation of a physiological monitoring system (PMS) is described. Specifications were established for performance, design, interface, and test requirements. The PMS is a compact, microprocessor-based system, which can be worn in a pack on the body or may be mounted on a Spacelab rack or other appropriate structure. It consists of two modules, the Data Control Unit (DCU) and the Remote Control/Display Unit (RCDU). Its purpose is to collect and distribute data from physiological experiments in the Spacelab and in the Orbiter.

Evaluation of a Constrained Facet Analysis Efficiency Model for Identifying the Efficiency of Medical Treatment Facilities in the Army Medical Department

DTIC Science & Technology

1990-07-31

examples on their use is available with the PASS User Documentation Manual. 2 The data structure of PASS requires a three- lvel organizational...files, and missing control variables. A specific problem noted involved the absence of 8087 mathematical co-processor on the target IBM-XT 21 machine...System, required an operational understanding of the advanced mathematical technique used in the model. Problems with the original release of the PASS

In Vivo Monitoring Program Manual, PNL-MA-574

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

Lynch, Timothy P.

2010-07-01

An overview of the administration for the In Vivo Monitoring Program (IVMP) for Hanford. This includes organizational structure and program responsibilities; coordination of in vivo measurements; scheduling measurements; performing measurements; reporting results; and quality assurance. Overall responsibility for the management of the IVMP rests with the Program Manager (PM). The PM is responsible for providing the required in vivo counting services for Hanford Site contractor employees in accordance with Department of Energy (DOE) requirements and the specific statements of work.

Progress in modeling hypersonic turbulent boundary layers

NASA Technical Reports Server (NTRS)

Zeman, Otto

1993-01-01

A good knowledge of the turbulence structure, wall heat transfer, and friction in turbulent boundary layers (TBL) at high speeds is required for the design of hypersonic air breathing airplanes and reentry space vehicles. This work reports on recent progress in the modeling of high speed TBL flows. The specific research goal described here is the development of a second order closure model for zero pressure gradient TBL's for the range of Mach numbers up to hypersonic speeds with arbitrary wall cooling requirements.

Further studies on the quaternary structure of yeast casein kinase II.

PubMed

Szyszka, R; Lopaczyński, W; Gałasiński, W; Grankowski, N; Gasior, E

1986-01-01

Casein kinase type II were isolated by the same procedure, from rat liver, human placenta, Querin carcinoma and yeast, and characterized. The mammalian enzymes were composed of three subunits alpha, alpha' and beta, whereas yeast kinase was composed of two subunits alpha and alpha'. It was shown that the catalytic activity, substrate and phosphate donor specificity, sensitivity to heparin and spermine were the same for all the kinases tested. The results give additional support to the suggestion [1] that the beta subunit is not required for optimal activity and specificity of yeast casein kinase II. The quaternary structure of the yeast enzyme of a molecular weight of approximately 150 000 is proposed as alpha2 alpha'2.

Permeability and flammability study of composite sandwich structures for cryogenic applications

NASA Astrophysics Data System (ADS)

Bubacz, Monika

Fiber reinforced plastics offer advantageous specific strength and stiffness compared to metals and has been identified as candidates for the reusable space transportation systems primary structures including cryogenic tanks. A number of carbon and aramid fiber reinforced plastics have been considered for the liquid hydrogen tanks. Materials selection is based upon mechanical properties and containment performance (long and short term) and upon manufacturing considerations. The liquid hydrogen tank carries shear, torque, end load, and bending moment due to gusts, maneuver, take-off, landing, lift, drag, and fuel sloshing. The tank is pressurized to about 1.5 atmosphere (14.6psi or 0.1 MPa) differential pressure and on ascent maintains the liquid hydrogen at a temperature of 20K. The objective of the research effort into lay the foundation for developing the technology required for reliable prediction of the effects of various design, manufacturing, and service parameters on the susceptibility of composite tanks to develop excessive permeability to cryogenic fuels. Efforts will be expended on developing the materials and structural concepts for the cryogenic tanks that can meet the functional requirements. This will include consideration for double wall composite sandwich structures, with inner wall to meet the cryogenic requirements. The structure will incorporate nanoparticles for properties modifications and developing barriers. The main effort will be extended to tank wall's internal skin design. The main requirements for internal composite stack are: (1) introduction of barrier film (e.g. honeycomb material paper sheet) to reduce the wall permeability to hydrogen, (2) introduction of nanoparticles into laminate resin to prevent micro-cracking or crack propagation. There is a need to characterize and analyze composite sandwich structural damage due to burning and explosion. Better understanding of the flammability and blast resistance of the composite structures needs to be evaluated.

Construction typification as the tool for optimizing the functioning of a robotized manufacturing system

NASA Astrophysics Data System (ADS)

Gwiazda, A.; Banas, W.; Sekala, A.; Foit, K.; Hryniewicz, P.; Kost, G.

2015-11-01

Process of workcell designing is limited by different constructional requirements. They are related to technological parameters of manufactured element, to specifications of purchased elements of a workcell and to technical characteristics of a workcell scene. This shows the complexity of the design-constructional process itself. The results of such approach are individually designed workcell suitable to the specific location and specific production cycle. Changing this parameters one must rebuild the whole configuration of a workcell. Taking into consideration this it is important to elaborate the base of typical elements of a robot kinematic chain that could be used as the tool for building Virtual modelling of kinematic chains of industrial robots requires several preparatory phase. Firstly, it is important to create a database element, which will be models of industrial robot arms. These models could be described as functional primitives that represent elements between components of the kinematic pairs and structural members of industrial robots. A database with following elements is created: the base kinematic pairs, the base robot structural elements, the base of the robot work scenes. The first of these databases includes kinematic pairs being the key component of the manipulator actuator modules. Accordingly, as mentioned previously, it includes the first stage rotary pair of fifth stage. This type of kinematic pairs was chosen due to the fact that it occurs most frequently in the structures of industrial robots. Second base consists of structural robot elements therefore it allows for the conversion of schematic structures of kinematic chains in the structural elements of the arm of industrial robots. It contains, inter alia, the structural elements such as base, stiff members - simple or angular units. They allow converting recorded schematic three-dimensional elements. Last database is a database of scenes. It includes elements of both simple and complex: simple models of technological equipment, conveyors models, models of the obstacles and like that. Using these elements it could be formed various production spaces (robotized workcells), in which it is possible to virtually track the operation of an industrial robot arm modelled in the system.

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

Hand, L.N.

Some proposed techniques for using laser beams to accelerate charged particles are reviewed. Two specific ideas for 'grating-type' accelerating structures are discussed. Speculations are presented about how a successful laser accelerator could be used in a 'multi-pass collider', a type of machine which would have characteristics intermediate between those of synchrotrons and linear (single-pass) colliders. No definite conclusions about practical structures for laser accelerators are reached, but it is suggested that a serious effort be made to design a small prototype machine. Achieving a reasonable luminosity demands that the accelerator either be a cw machine or that laser peak powermore » requirements be much higher than those presently available. Use of superconducting gratings requires a wavelength in the sub-millimeter range.« less

The laser accelerator-another unicorn in the garden

NASA Astrophysics Data System (ADS)

Hand, L. N.

1981-07-01

Some proposed techniques for using laser beams to accelerate charged particles was reviewed. Two specific ideas for grating type accelerating structures are discussed. Speculations are presented about how a successful laser accelerator could be used in a multipass collider; a type of machine which would have characteristics intermediate between those of synchrotrons and linear (single pass) colliders. No definite conclusions about practical structures for laser accelerators are reached, but it is suggested that a serious effort be made to design a small prototype machine. Achieving a reasonable luminosity demands that the accelerator either be a cw machine or that laser peak power requirements to be much higher than those presently available. Use of superconducting gratings requires a wavelength in the sub-millimeter range.

Modularity and design principles in the sea urchin embryo gene regulatory network

PubMed Central

Peter, Isabelle S.; Davidson, Eric H.

2010-01-01

The gene regulatory network (GRN) established experimentally for the pre-gastrular sea urchin embryo provides causal explanations of the biological functions required for spatial specification of embryonic regulatory states. Here we focus on the structure of the GRN which controls the progressive increase in complexity of territorial regulatory states during embryogenesis; and on the types of modular subcircuits of which the GRN is composed. Each of these subcircuit topologies executes a particular operation of spatial information processing. The GRN architecture reflects the particular mode of embryogenesis represented by sea urchin development. Network structure not only specifies the linkages constituting the genomic regulatory code for development, but also indicates the various regulatory requirements of regional developmental processes. PMID:19932099

Quantitative nondestructive evaluation: Requirements for tomorrow's reliability

NASA Technical Reports Server (NTRS)

Heyman, Joseph S.

1991-01-01

Quantitative Nondestructive Evaluation (QNDE) is the technology of measurement, analysis, and prediction of the state of material/structural systems for safety, reliability, and mission assurance. QNDE has impact on everyday life from the cars we drive, the planes we fly, the buildings we work or live in, literally to the infrastructure of our world. Here, researchers highlight some of the new sciences and technologies that are part of a safer, cost effective tomorrow. Specific technologies that are discussed are thermal QNDE of aircraft structural integrity, ultrasonic QNDE for materials characterization, and technology spinoffs from aerospace to the medical sector. In each case, examples are given of how new requirements result in enabling measurement technologies, which in turn change the boundaries of design/practice.

Automatically updating predictive modeling workflows support decision-making in drug design.

PubMed

Muegge, Ingo; Bentzien, Jörg; Mukherjee, Prasenjit; Hughes, Robert O

2016-09-01

Using predictive models for early decision-making in drug discovery has become standard practice. We suggest that model building needs to be automated with minimum input and low technical maintenance requirements. Models perform best when tailored to answering specific compound optimization related questions. If qualitative answers are required, 2-bin classification models are preferred. Integrating predictive modeling results with structural information stimulates better decision making. For in silico models supporting rapid structure-activity relationship cycles the performance deteriorates within weeks. Frequent automated updates of predictive models ensure best predictions. Consensus between multiple modeling approaches increases the prediction confidence. Combining qualified and nonqualified data optimally uses all available information. Dose predictions provide a holistic alternative to multiple individual property predictions for reaching complex decisions.

Structured Innovation of High-Performance Wave Energy Converter Technology: Preprint

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

Weber, Jochem W.; Laird, Daniel

Wave energy converter (WEC) technology development has not yet delivered the desired commercial maturity nor, and more importantly, the techno-economic performance. The reasons for this have been recognized and fundamental requirements for successful WEC technology development have been identified. This paper describes a multi-year project pursued in collaboration by the National Renewable Energy Laboratory and Sandia National Laboratories to innovate and develop new WEC technology. It specifies the project strategy, shows how this differs from the state-of-the-art approach and presents some early project results. Based on the specification of fundamental functional requirements of WEC technology, structured innovation and systemic problemmore » solving methodologies are applied to invent and identify new WEC technology concepts. Using Technology Performance Levels (TPL) as an assessment metric of the techno-economic performance potential, high performance technology concepts are identified and selected for further development. System performance is numerically modelled and optimized and key performance aspects are empirically validated. The project deliverables are WEC technology specifications of high techno-economic performance technologies of TPL 7 or higher at TRL 3 with some key technology challenges investigated at higher TRL. These wave energy converter technology specifications will be made available to industry for further, full development and commercialisation (TRL 4 - TRL 9).« less

Protein-based hydrogels for tissue engineering

PubMed Central

Schloss, Ashley C.; Williams, Danielle M.; Regan, Lynne J.

2017-01-01

The tunable mechanical and structural properties of protein-based hydrogels make them excellent scaffolds for tissue engineering and repair. Moreover, using protein-based components provides the option to insert sequences associated with the promoting both cellular adhesion to the substrate and overall cell growth. Protein-based hydrogel components are appealing for their structural designability, specific biological functionality, and stimuli-responsiveness. Here we present highlights in the field of protein-based hydrogels for tissue engineering applications including design requirements, components, and gel types. PMID:27677513

Lean Middleware

NASA Technical Reports Server (NTRS)

Maluf, David A.; Bell, David g.; Ashish, Naveen

2005-01-01

This paper describes an approach to achieving data integration across multiple sources in an enterprise, in a manner that is cost efficient and economically scalable. We present an approach that does not rely on major investment in structured, heavy-weight database systems for data storage or heavy-weight middleware responsible for integrated access. The approach is centered around pushing any required data structure and semantics functionality (schema) to application clients, as well as pushing integration specification and functionality to clients where integration can be performed on-the-fly .

Modeling and Design Analysis Methodology for Tailoring of Aircraft Structures with Composites

NASA Technical Reports Server (NTRS)

Rehfield, Lawrence W.

2004-01-01

Composite materials provide design flexibility in that fiber placement and orientation can be specified and a variety of material forms and manufacturing processes are available. It is possible, therefore, to 'tailor' the structure to a high degree in order to meet specific design requirements in an optimum manner. Common industrial practices, however, have limited the choices designers make. One of the reasons for this is that there is a dearth of conceptual/preliminary design analysis tools specifically devoted to identifying structural concepts for composite airframe structures. Large scale finite element simulations are not suitable for such purposes. The present project has been devoted to creating modeling and design analysis methodology for use in the tailoring process of aircraft structures. Emphasis has been given to creating bend-twist elastic coupling in high aspect ratio wings or other lifting surfaces. The direction of our work was in concert with the overall NASA effort Twenty- First Century Aircraft Technology (TCAT). A multi-disciplinary team was assembled by Dr. Damodar Ambur to work on wing technology, which included our project.

Unzippers, Resolvers and Sensors: A Structural and Functional Biochemistry Tale of RNA Helicases

PubMed Central

Leitão, Ana Lúcia; Costa, Marina C.; Enguita, Francisco J.

2015-01-01

The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes. PMID:25622248

Exploring for the optimal structural design for the 3D-printing technology for cranial reconstruction: a biomechanical and histological study comparison of solid vs. porous structure.

PubMed

Lim, Jun Young; Kim, Namhyun; Park, Jong-Chul; Yoo, Sun K; Shin, Dong Ah; Shim, Kyu-Won

2017-09-01

Cranioplasty for recovering skull defects carries the risk for a number of complications. Various materials are used, including autologous bone graft, metallic materials, and non-metallic materials, each of which has advantages and disadvantages. If the use of autologous bone is not feasible, those artificial materials also have constraints in the case of complex anatomy and/or irregular defects. This study used metal 3D-printing technology to overcome these existing drawbacks and analyze the clinical and mechanical performance requirements. To find an optimal structure that satisfied the structural and mechanical stability requirements, we evaluated biomechanical stability using finite element analysis (FEA) and mechanical testing. To ensure clinical applicability, the model was subjected to histological evaluation. Each specimen was implanted in the femur of a rabbit and was evaluated using histological measurements and push-out test. We believe that our data will provide the basis for future applications of a variety of unit structures and further clinical trials and research, as well as the direction for the study of other patient-specific implants.

Rapid time-resolved diffraction studies of protein structures using synchrotron radiation

NASA Astrophysics Data System (ADS)

Bartunik, Hans D.; Bartunik, Lesley J.

1992-07-01

The crystal structure of intermediate states in biological reactions of proteins of multi-protein complexes may be studied by time-resolved X-ray diffraction techniques which make use of the high spectral brilliance, continuous wavelength distribution and pulsed time structure of synchrotron radiation. Laue diffraction methods provide a means of investigating intermediate structures with lifetimes in the millisecond time range at presently operational facilities. Third-generation storage rings which are under construction may permit one to reach a time resolution of one microsecond for non-cyclic and one nanosecond for cyclic reactions. The number of individual exposures required for exploring reciprocal space and hence the total time scale strongly depend on the lattice order that may be affected, e.g., by conformational changes. Time-resolved experiments require high population of a specific intermediate which has to be homogeneous over the crystal volume. A number of external excitation techniques have been developed including in situ liberation of active metabolites by laser pulse photolysis of photolabile inactive precursors. First applications to crystal structure analysis of catalytic intermediates of enzymes demonstrate the potential of time-resolved protein crystallography.

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

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

Wang, Yeming; Opperman, Laura; Wickens, Marvin

2011-11-02

Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4-6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short regionmore » of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.« less

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

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

Wang, Yeming; Opperman, Laura; Wickens, Marvin

2010-08-19

Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4-6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short regionmore » of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.« less

Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove

PubMed Central

Ivanova, Marina E.; Fletcher, Georgina C.; O’Reilly, Nicola; Purkiss, Andrew G.; Thompson, Barry J.; McDonald, Neil Q.

2015-01-01

Many components of epithelial polarity protein complexes possess PDZ domains that are required for protein interaction and recruitment to the apical plasma membrane. Apical localization of the Crumbs (Crb) transmembrane protein requires a PDZ-mediated interaction with Pals1 (protein-associated with Lin7, Stardust, MPP5), a member of the p55 family of membrane-associated guanylate kinases (MAGUKs). This study describes the molecular interaction between the Crb carboxy-terminal motif (ERLI), which is required for Drosophila cell polarity, and the Pals1 PDZ domain using crystallography and fluorescence polarization. Only the last four Crb residues contribute to Pals1 PDZ-domain binding affinity, with specificity contributed by conserved charged interactions. Comparison of the Crb-bound Pals1 PDZ structure with an apo Pals1 structure reveals a key Phe side chain that gates access to the PDZ peptide-binding groove. Removal of this side chain enhances the binding affinity by more than fivefold, suggesting that access of Crb to Pals1 may be regulated by intradomain contacts or by protein–protein interaction. PMID:25760605

The Origins of Transmembrane Ion Channels

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.

2012-01-01

Even though membrane proteins that mediate transport of ions and small molecules across cell walls are among the largest and least understood biopolymers in contemporary cells, it is still possible to shed light on their origins and early evolution. The central observation is that transmembrane portions of most ion channels are simply bundles of -helices. By combining results of experimental and computer simulation studies on synthetic models and natural channels, mostly of non-genomic origin, we show that the emergence of -helical channels was protobiologically plausible, and did not require highly specific amino acid sequences. Despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. Specifically, we explain how the antiamoebin channels, which are made of identical helices, 16 amino acids in length, achieve efficiency comparable to that of highly evolved channels. We further show that antiamoebin channels are extremely flexible, compared to modern, genetically coded channels. On the basis of our results, we propose that channels evolved further towards high structural complexity because they needed to acquire stable rigid structures and mechanisms for precise regulation rather than improve efficiency. In general, even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.

X-PAT: a multiplatform patient referral data management system for small healthcare institution requirements.

PubMed

Masseroli, Marco; Marchente, Mario

2008-07-01

We present X-PAT, a platform-independent software prototype that is able to manage patient referral multimedia data in an intranet network scenario according to the specific control procedures of a healthcare institution. It is a self-developed storage framework based on a file system, implemented in eXtensible Markup Language (XML) and PHP Hypertext Preprocessor Language, and addressed to the requirements of limited-dimension healthcare entities (small hospitals, private medical centers, outpatient clinics, and laboratories). In X-PAT, healthcare data descriptions, stored in a novel Referral Base Management System (RBMS) according to Health Level 7 Clinical Document Architecture Release 2 (CDA R2) standard, can be easily applied to the specific data and organizational procedures of a particular healthcare working environment thanks also to the use of standard clinical terminology. Managed data, centralized on a server, are structured in the RBMS schema using a flexible patient record and CDA healthcare referral document structures based on XML technology. A novel search engine allows defining and performing queries on stored data, whose rapid execution is ensured by expandable RBMS indexing structures. Healthcare personnel can interface the X-PAT system, according to applied state-of-the-art privacy and security measures, through friendly and intuitive Web pages that facilitate user acceptance.

Accessible cell phone design: development and application of a needs analysis framework.

PubMed

Smith-Jackson, Tonya; Nussbaum, Maury; Mooney, Aaron

2003-05-20

This research describes the development and use of the Needs Analysis and Requirements Acquisition (NARA) framework to elicit and construct user requirements for the design of cell phones (which are a type of assistive technology) that are both usable and accessible to persons with disabilities. Semi-structured interviews and a focus group were used to elicit information and a systematic approach was used to translation information into requirements (construct). Elicitation and construction are the first two stages of NARA. Requirements for general and feature-specific phone attributes were identified, and several requirements were found to match six of the seven universal design principles. The study demonstrated that NARA is both a straight-forward and cost-effective method to develop user requirements and can be used throughout the development cycle.

Enhancing requirements engineering for patient registry software systems with evidence-based components.

PubMed

Lindoerfer, Doris; Mansmann, Ulrich

2017-07-01

Patient registries are instrumental for medical research. Often their structures are complex and their implementations use composite software systems to meet the wide spectrum of challenges. Commercial and open-source systems are available for registry implementation, but many research groups develop their own systems. Methodological approaches in the selection of software as well as the construction of proprietary systems are needed. We propose an evidence-based checklist, summarizing essential items for patient registry software systems (CIPROS), to accelerate the requirements engineering process. Requirements engineering activities for software systems follow traditional software requirements elicitation methods, general software requirements specification (SRS) templates, and standards. We performed a multistep procedure to develop a specific evidence-based CIPROS checklist: (1) A systematic literature review to build a comprehensive collection of technical concepts, (2) a qualitative content analysis to define a catalogue of relevant criteria, and (3) a checklist to construct a minimal appraisal standard. CIPROS is based on 64 publications and covers twelve sections with a total of 72 items. CIPROS also defines software requirements. Comparing CIPROS with traditional software requirements elicitation methods, SRS templates and standards show a broad consensus but differences in issues regarding registry-specific aspects. Using an evidence-based approach to requirements engineering for registry software adds aspects to the traditional methods and accelerates the software engineering process for registry software. The method we used to construct CIPROS serves as a potential template for creating evidence-based checklists in other fields. The CIPROS list supports developers in assessing requirements for existing systems and formulating requirements for their own systems, while strengthening the reporting of patient registry software system descriptions. It may be a first step to create standards for patient registry software system assessments. Copyright © 2017 Elsevier Inc. All rights reserved.

Coded Statutory Data Sets for Evaluation of Public Health Law

ERIC Educational Resources Information Center

Costich, Julia Field

2012-01-01

Background and objectives: The evaluation of public health law requires reliable accounts of underlying statutes and regulations. States often enact public health-related statutes with nonuniform provisions, and variation in the structure of state legal codes can foster inaccuracy in evaluating the impact of specific categories of law. The optimal…

Teaching social justice using a pedagogy of engagement.

PubMed

Belknap, Ruth Ann

2008-01-01

Teaching an undergraduate level diversity course with a health focus requires specific teaching methods. A pedagogy of engagement provides an effective strategy for exploring issues of race, class, gender, and structural inequalities that underlie health disparities. Engagement learning enhances understanding of theories of oppression and liberation presented in the course and highlights social justice issues.

Identification of Proteins Required for Repair of Double-Strand Chromosome Breaks, a Predisposing Factor in Breast Cancer

DTIC Science & Technology

2001-06-01

enzymatic apparatus needed to initiate DNA replication on recombination intermediates. Escherichia coli PriA protein was found to play a critical function in...the transition from recombination to DNA replication . PriA specifically binds to forked DNA structures created by recombination or replication fork

21 CFR 201.300 - Notice to manufacturers, packers, and distributors of glandular preparations.

Code of Federal Regulations, 2014 CFR

2014-04-01

... function of the human body that they are intended to affect. Since any such representations offering these..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL LABELING Specific Labeling Requirements... structure or any function of the body. (b) Manufacturers have heretofore taken advantage of § 201.100...

21 CFR 201.300 - Notice to manufacturers, packers, and distributors of glandular preparations.

Code of Federal Regulations, 2013 CFR

2013-04-01

... function of the human body that they are intended to affect. Since any such representations offering these..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL LABELING Specific Labeling Requirements... structure or any function of the body. (b) Manufacturers have heretofore taken advantage of § 201.100...

Guide for Occupational Exploration: Activities in Career and Self-Assessment. Counselor Edition.

ERIC Educational Resources Information Center

Ryan, Thomas P.

The self- and career-assessment activities contained in this booklet, together with the summary sheet (score card) which each student will produce, provide a structured process for students to examine their preferences, aptitudes, and value systems and compare them with the requirements and attributes of thirty-five specific careers. Aimed…

Stereoscopic Projection in Organic Chemistry: Bridging the Gap between Two and Three Dimensions.

ERIC Educational Resources Information Center

Rozzelle, Arlene A.; Rosenfeld, Stuart M.

1985-01-01

Shows how to make stereo slides of three-dimensional molecular models. The slides have been used to teach chirality, conformational isomerism, how models and two-dimensional representations embody selected aspects of structure, and fundamentals of using the specific model set required in a particular organic chemistry course. (JN)

Neural Correlates of Dutch Verb Second in Speech Production

ERIC Educational Resources Information Center

den Ouden, Dirk-Bart; Hoogduin, Hans; Stowe, Laurie A.; Bastiaanse, Roelien

2008-01-01

Dutch speakers with agrammatic Broca's aphasia are known to have problems with the production of finite verbs in main clauses. This performance pattern has been accounted for in terms of the specific syntactic complexity of the Dutch main clause structure, which requires an extra syntactic operation (Verb Second), relative to the basic…

21 CFR 201.300 - Notice to manufacturers, packers, and distributors of glandular preparations.

Code of Federal Regulations, 2010 CFR

2010-04-01

... function of the human body that they are intended to affect. Since any such representations offering these..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL LABELING Specific Labeling Requirements... structure or any function of the body. (b) Manufacturers have heretofore taken advantage of § 201.100...

21 CFR 201.300 - Notice to manufacturers, packers, and distributors of glandular preparations.

Code of Federal Regulations, 2011 CFR

2011-04-01

... function of the human body that they are intended to affect. Since any such representations offering these..., DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL LABELING Specific Labeling Requirements... structure or any function of the body. (b) Manufacturers have heretofore taken advantage of § 201.100...

Teaching through Interactive Pictures: Computer, Video and Human Realities.

ERIC Educational Resources Information Center

Strauss, Andre

A technique designed to make the classroom use of videotapes for second language teaching for specific purposes more efficient is described. The technique begins with a classroom review of basic vocabulary and structures, which is then tested with a computer exercise. A second stage requires discussion and memorization of vocabulary and phrases…

Canopy gap dynamics of second-growth red spruce-northern hardwood stands in West Virginia

Treesearch

James S. Rentch; Thomas M. Schuler; Gregory J. Nowacki; Nathan R. Beane; W. Mark Ford

2010-01-01

Forest restoration requires an understanding of the natural disturbance regime of the target community and estimates of the historic range of variability of ecosystem components (composition, structure, and disturbance processes). Management prescriptions that support specific restoration activities should be consistent with these parameters. In this study, we describe...

Family-Centered Early Intervention for Communication Disorders: Prevention and Treatment. Excellence in Practice Series.

ERIC Educational Resources Information Center

Donahue-Kilburg, Gail

This book is designed to provide a broad range of information on family structure and function in an increasingly multicultural society, family system characteristics and the implications for intervention, communication development in the family context, the nature and delivery of family centered-services, specific requirements of Public Law…

46 CFR 160.032-5 - Inspection and testing of davits.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Inspection and testing of davits. (a) Material testing. (1) Where davit arms and frames are fabricated of steel castings, an inspector shall be present at the foundry where such castings are made to witness the... affidavit stating that the structural steel complies with the requirements of the specification noted in...

46 CFR 160.032-5 - Inspection and testing of davits.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Inspection and testing of davits. (a) Material testing. (1) Where davit arms and frames are fabricated of steel castings, an inspector shall be present at the foundry where such castings are made to witness the... affidavit stating that the structural steel complies with the requirements of the specification noted in...

Management Information System for ESD Program Offices.

DTIC Science & Technology

1978-03-01

Management Information System (MIS) functional requirements for the ESD Program Office are defined in terms of the Computer-Aided Design and Specification Tool. The development of the computer data base and a description of the MIS structure is included in the report. This report addresses management areas such as cost/budgeting, scheduling, tracking capabilities, and ECP

Evaluation in the Older Blind Independent Living Program: Advantages of a Structural Equation Modeling Approach. Research Report

ERIC Educational Resources Information Center

Giesen, Martin J.; Cavenaugh, Brenda S.

2006-01-01

Rehabilitation Services Administration (RSA) requires that independent living programs annually report demographic information on consumers receiving services and the numbers receiving specific types of services. Although some states collect information on consumer outcomes (for example, improvement in daily living skills), RSA does not request…

33 CFR 154.1035 - Specific requirements for facilities that could reasonably be expected to cause significant and...

Code of Federal Regulations, 2010 CFR

2010-07-01

... spill management team member within the organizational structure described in paragraph (b)(3)(iii) of... discharge, potential discharge, or emergency involving the following equipment and scenarios: (A) Failure of manifold, mechanical loading arm, other transfer equipment, or hoses, as appropriate; (B) Tank overfill; (C...

46 CFR 164.007-6 - Test report.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 6 2011-10-01 2011-10-01 false Test report. 164.007-6 Section 164.007-6 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND MATERIALS: SPECIFICATIONS AND APPROVAL MATERIALS Structural Insulations § 164.007-6 Test report. (a) The test report required shall contain at least the following: (1)...

33 CFR 320.4 - General policies for evaluating permit applications.

Code of Federal Regulations, 2012 CFR

2012-07-01

... specific factor may be given great weight on one proposal, while it may not be present or as important on... will ask the Governor to express his views or to designate one state agency to represent the official... are designed for safety, non-Federal applicants may be required to demonstrate that the structures...

33 CFR 320.4 - General policies for evaluating permit applications.

Code of Federal Regulations, 2013 CFR

2013-07-01

... specific factor may be given great weight on one proposal, while it may not be present or as important on... will ask the Governor to express his views or to designate one state agency to represent the official... are designed for safety, non-Federal applicants may be required to demonstrate that the structures...

33 CFR 320.4 - General policies for evaluating permit applications.

Code of Federal Regulations, 2011 CFR

2011-07-01

... specific factor may be given great weight on one proposal, while it may not be present or as important on... will ask the Governor to express his views or to designate one state agency to represent the official... are designed for safety, non-Federal applicants may be required to demonstrate that the structures...

21st Century Manufacturing Supervisors and Their Historical Roots

ERIC Educational Resources Information Center

Hotek, Douglas R.

2003-01-01

This article provides a perspective of the past and present roles of the manufacturing supervisor with a specific focus on new skills requirements. Within the structure of manufacturing management, the supervisor plays a key role in implementing today's complex automated manufacturing technologies. The supervisor is at the bottom of the management…

46 CFR 164.007-6 - Test report.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 6 2014-10-01 2014-10-01 false Test report. 164.007-6 Section 164.007-6 Shipping COAST...: SPECIFICATIONS AND APPROVAL MATERIALS Structural Insulations § 164.007-6 Test report. (a) The test report required shall contain at least the following: (1) Name of manufacturer. (2) Purpose of test. (3) Test...

Classroom Management, Social Participation Structures and Required Social Competence in Kindergarten.

ERIC Educational Resources Information Center

Verhaeghe, Jean Pierre; Vanobbergen, Bruno

Noting that becoming familiar with the work system of the kindergarten classroom (a functional system with its own rules and procedures for activities and transition) is important for students' development and well-being, this study examined the work systems in two kindergarten classrooms and children's associated context-specific social…

Lifelong Learning: Attitudes of Slovenian Higher Educators toward Accreditation of Prior Learning Experiences

ERIC Educational Resources Information Center

Omerzel, Doris Gomezelj; Sirca, Nada Trunk; Shapiro, Arthur; Brejc, Mateja; Permuth, Steve

2008-01-01

This article focuses first on fundamental trends weakening the European--specifically, the Slovenian--economy and social structure, which are creating a two-class system consisting of an undereducated/uneducated population unable to compete for employment in an economy increasingly requiring more education to update employees' skills. Learning and…

Eukaryotic Elongation Factor 1A Interacts with the Upstream Pseudoknot Domain in the 3′ Untranslated Region of Tobacco Mosaic Virus RNA

PubMed Central

Zeenko, Vladimir V.; Ryabova, Lyubov A.; Spirin, Alexander S.; Rothnie, Helen M.; Hess, Daniel; Browning, Karen S.; Hohn, Thomas

2002-01-01

The genomic RNA of tobacco mosaic virus (TMV), like that of other positive-strand RNA viruses, acts as a template for both translation and replication. The highly structured 3′ untranslated region (UTR) of TMV RNAs plays an important role in both processes; it is not polyadenylated but ends with a tRNA-like structure (TLS) preceded by a conserved upstream pseudoknot domain (UPD). The TLS of tobamoviral RNAs can be specifically aminoacylated and, in this state, can interact with eukaryotic elongation factor 1A (eEF1A)/GTP with high affinity. Using a UV cross-linking assay, we detected another specific binding site for eEF1A/GTP, within the UPDs of TMV and crucifer-infecting tobamovirus (crTMV), that does not require aminoacylation. A mutational analysis revealed that UPD pseudoknot conformation and some conserved primary sequence elements are required for this interaction. Its possible role in the regulation of tobamovirus gene expression and replication is discussed. PMID:11991996

An SRY mutation causing human sex reversal resolves a general mechanism of structure-specific DNA recognition: application to the four-way DNA junction.

PubMed

Peters, R; King, C Y; Ukiyama, E; Falsafi, S; Donahoe, P K; Weiss, M A

1995-04-11

SRY, a genetic "master switch" for male development in mammals, exhibits two biochemical activities: sequence-specific recognition of duplex DNA and sequence-independent binding to the sharp angles of four-way DNA junctions. Here, we distinguish between these activities by analysis of a mutant SRY associated with human sex reversal (46, XY female with pure gonadal dysgenesis). The substitution (168T in human SRY) alters a nonpolar side chain in the minor-groove DNA recognition alpha-helix of the HMG box [Haqq, C.M., King, C.-Y., Ukiyama, E., Haqq, T.N., Falsalfi, S., Donahoe, P.K., & Weiss, M.A. (1994) Science 266, 1494-1500]. The native (but not mutant) side chain inserts between specific base pairs in duplex DNA, interrupting base stacking at a site of induced DNA bending. Isotope-aided 1H-NMR spectroscopy demonstrates that analogous side-chain insertion occurs on binding of SRY to a four-way junction, establishing a shared mechanism of sequence- and structure-specific DNA binding. Although the mutant DNA-binding domain exhibits > 50-fold reduction in sequence-specific DNA recognition, near wild-type affinity for four-way junctions is retained. Our results (i) identify a shared SRY-DNA contact at a site of either induced or intrinsic DNA bending, (ii) demonstrate that this contact is not required to bind an intrinsically bent DNA target, and (iii) rationalize patterns of sequence conservation or diversity among HMG boxes. Clinical association of the I68T mutation with human sex reversal supports the hypothesis that specific DNA recognition by SRY is required for male sex determination.

In-space fabrication of thin-film structures

NASA Technical Reports Server (NTRS)

Lippman, M. E.

1972-01-01

A conceptual study of physical vapor-deposition processes for in-space fabrication of thin-film structures is presented. Potential advantages of in-space fabrication are improved structural integrity and surface reflectivity of free-standing ultra-thin films and coatings. Free-standing thin-film structures can find use as photon propulsion devices (solar sails). Other applications of the concept involve free-standing shadow shields, or thermal control coatings of spacecraft surfaces. Use of expendables (such as booster and interstage structures) as source material for the physical vapor deposition process is considered. The practicability of producing thin, textured, aluminum films by physical vapor deposition and subsequent separation from a revolving substrate is demonstrated by laboratory experiments. Heating power requirement for the evaporation process is estimated for a specific mission.

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

PubMed Central

Theobald, Douglas L.; Wuttke, Deborah S.

2008-01-01

Summary THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. PMID:16777907

Interpreting "Personality" Taxonomies: Why Previous Models Cannot Capture Individual-Specific Experiencing, Behaviour, Functioning and Development. Major Taxonomic Tasks Still Lay Ahead.

PubMed

Uher, Jana

2015-12-01

As science seeks to make generalisations, a science of individual peculiarities encounters intricate challenges. This article explores these challenges by applying the Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals (TPS-Paradigm) and by exploring taxonomic "personality" research as an example. Analyses of researchers' interpretations of the taxonomic "personality" models, constructs and data that have been generated in the field reveal widespread erroneous assumptions about the abilities of previous methodologies to appropriately represent individual-specificity in the targeted phenomena. These assumptions, rooted in everyday thinking, fail to consider that individual-specificity and others' minds cannot be directly perceived, that abstract descriptions cannot serve as causal explanations, that between-individual structures cannot be isomorphic to within-individual structures, and that knowledge of compositional structures cannot explain the process structures of their functioning and development. These erroneous assumptions and serious methodological deficiencies in widely used standardised questionnaires have effectively prevented psychologists from establishing taxonomies that can comprehensively model individual-specificity in most of the kinds of phenomena explored as "personality", especially in experiencing and behaviour and in individuals' functioning and development. Contrary to previous assumptions, it is not universal models but rather different kinds of taxonomic models that are required for each of the different kinds of phenomena, variations and structures that are commonly conceived of as "personality". Consequently, to comprehensively explore individual-specificity, researchers have to apply a portfolio of complementary methodologies and develop different kinds of taxonomies, most of which have yet to be developed. Closing, the article derives some meta-desiderata for future research on individuals' "personality".

Requirements analysis notebook for the flight data systems definition in the Real-Time Systems Engineering Laboratory (RSEL)

NASA Astrophysics Data System (ADS)

Wray, Richard B.

1991-12-01

A hybrid requirements analysis methodology was developed, based on the practices actually used in developing a Space Generic Open Avionics Architecture. During the development of this avionics architecture, a method of analysis able to effectively define the requirements for this space avionics architecture was developed. In this methodology, external interfaces and relationships are defined, a static analysis resulting in a static avionics model was developed, operating concepts for simulating the requirements were put together, and a dynamic analysis of the execution needs for the dynamic model operation was planned. The systems engineering approach was used to perform a top down modified structured analysis of a generic space avionics system and to convert actual program results into generic requirements. CASE tools were used to model the analyzed system and automatically generate specifications describing the model's requirements. Lessons learned in the use of CASE tools, the architecture, and the design of the Space Generic Avionics model were established, and a methodology notebook was prepared for NASA. The weaknesses of standard real-time methodologies for practicing systems engineering, such as Structured Analysis and Object Oriented Analysis, were identified.

Requirements analysis notebook for the flight data systems definition in the Real-Time Systems Engineering Laboratory (RSEL)

NASA Technical Reports Server (NTRS)

Wray, Richard B.

1991-01-01

A hybrid requirements analysis methodology was developed, based on the practices actually used in developing a Space Generic Open Avionics Architecture. During the development of this avionics architecture, a method of analysis able to effectively define the requirements for this space avionics architecture was developed. In this methodology, external interfaces and relationships are defined, a static analysis resulting in a static avionics model was developed, operating concepts for simulating the requirements were put together, and a dynamic analysis of the execution needs for the dynamic model operation was planned. The systems engineering approach was used to perform a top down modified structured analysis of a generic space avionics system and to convert actual program results into generic requirements. CASE tools were used to model the analyzed system and automatically generate specifications describing the model's requirements. Lessons learned in the use of CASE tools, the architecture, and the design of the Space Generic Avionics model were established, and a methodology notebook was prepared for NASA. The weaknesses of standard real-time methodologies for practicing systems engineering, such as Structured Analysis and Object Oriented Analysis, were identified.

Mechanical attachments for flexible blanket TPS

NASA Astrophysics Data System (ADS)

Newquist, Charles W.; Anderson, David M.; Shorey, Mark W.; Preedy, Kristina S.

1998-01-01

The operability of a flexible blanket thermal protection system for a reusable launch vehicle can be improved by using mechanical attachments instead of adhesive bonding to fasten the thermal protection system to the vehicle structure. Mechanical attachments offer specific benefits by (1) permitting the use of composite or metal structures at or near their maximum temperatures (above the adhesive temperature limit) thereby reducing the required TPS thickness and weight, (2) significantly reducing both the frequency and time for TPS replacement, (3) providing easy access to hatches and the underlying structure, and (4) allowing the attachment of flexible TPS to integral cryotanks, where the TPS/structure interface temperature may fall below the lower temperature of the silicone adhesives.

Using Symmetry to Design Self-Assembling Protein Cages and Nanomaterials on the Mid-Nanometer Scale

NASA Astrophysics Data System (ADS)

Yeates, Todd

Self-assembling molecular structures having diverse cellular functions are widespread in nature. Some of the largest and most sophisticated types are built from many copies of the same or similar protein molecules arranged following principles of symmetry. A long-standing engineering goal has been to design novel protein molecules to self-assemble into geometrically specific structures similar to the extraordinary structures that have evolved in Nature. Practical routes to this goal have been developed by using ideas in symmetry to articulate the minimum design requirements for achieving various types of symmetric architectures, including cages, extended two-dimensional layers, and three-dimensional crystalline materials. The key requirement is that two distinct self-associating interfaces, each conferring one element of rotational symmetry, have to be engineered into the protein molecule (or molecules), following particular geometric specifications. The main principle is that combining two separate symmetry elements into a single molecular entity produces a molecule that necessarily assembles into an architecture dictated by a symmetry group that is the product of the two simpler contributing symmetries. Recent experiments have demonstrated success using a variety of symmetry-based strategies. Strategic variations are emerging that differ from each other with respect to biophysical features such as flexibility vs rigidity in the assembled structures, and with respect to design aspects such as whether the protein interfaces are inherited from natural oligomeric proteins or are designed de novo by advanced computational methods. The success of these strategies has been proven by determining crystal structures of several giant, self-assembling protein cages and clusters (10-25 nm in diameter), created by design. The ability to create sophisticated supramolecular structures from designed protein subunits opens the way to broad applications in synthetic biology and nanotechnology.

Requirements for Medical Modeling Languages

PubMed Central

van der Maas, Arnoud A.F.; Ter Hofstede, Arthur H.M.; Ten Hoopen, A. Johannes

2001-01-01

Objective: The development of tailor-made domain-specific modeling languages is sometimes desirable in medical informatics. Naturally, the development of such languages should be guided. The purpose of this article is to introduce a set of requirements for such languages and show their application in analyzing and comparing existing modeling languages. Design: The requirements arise from the practical experience of the authors and others in the development of modeling languages in both general informatics and medical informatics. The requirements initially emerged from the analysis of information modeling techniques. The requirements are designed to be orthogonal, i.e., one requirement can be violated without violation of the others. Results: The proposed requirements for any modeling language are that it be “formal” with regard to syntax and semantics, “conceptual,” “expressive,” “comprehensible,” “suitable,” and “executable.” The requirements are illustrated using both the medical logic modules of the Arden Syntax as a running example and selected examples from other modeling languages. Conclusion: Activity diagrams of the Unified Modeling Language, task structures for work flows, and Petri nets are discussed with regard to the list of requirements, and various tradeoffs are thus made explicit. It is concluded that this set of requirements has the potential to play a vital role in both the evaluation of existing domain-specific languages and the development of new ones. PMID:11230383

In Vivo Characterization of Traumatic Brain Injury Neuropathology with Structural and Functional Neuroimaging

PubMed Central

LEVINE, BRIAN; FUJIWARA, ESTHER; O’CONNOR, CHARLENE; RICHARD, NADINE; KOVACEVIC, NATASA; MANDIC, MARINA; RESTAGNO, ADRIANA; EASDON, CRAIG; ROBERTSON, IAN H.; GRAHAM, SIMON J.; CHEUNG, GORDON; GAO, FUQIANG; SCHWARTZ, MICHAEL L.; BLACK, SANDRA E.

2007-01-01

Quantitative neuroimaging is increasingly used to study the effects of traumatic brain injury (TBI) on brain structure and function. This paper reviews quantitative structural and functional neuroimaging studies of patients with TBI, with an emphasis on the effects of diffuse axonal injury (DAI), the primary neuropathology in TBI. Quantitative structural neuroimaging has evolved from simple planometric measurements through targeted region-of-interest analyses to whole-brain analysis of quantified tissue compartments. Recent studies converge to indicate widespread volume loss of both gray and white matter in patients with moderate-to-severe TBI. These changes can be documented even when patients with focal lesions are excluded. Broadly speaking, performance on standard neuropsychological tests of speeded information processing are related to these changes, but demonstration of specific brain-behavior relationships requires more refined experimental behavioral measures. The functional consequences of these structural changes can be imaged with activation functional neuroimaging. Although this line of research is at an early stage, results indicate that TBI causes a more widely dispersed activation in frontal and posterior cortices. Further progress in analysis of the consequences of TBI on neural structure and function will require control of variability in neuropathology and behavior. PMID:17020478

An operating system for future aerospace vehicle computer systems

NASA Technical Reports Server (NTRS)

Foudriat, E. C.; Berman, W. J.; Will, R. W.; Bynum, W. L.

1984-01-01

The requirements for future aerospace vehicle computer operating systems are examined in this paper. The computer architecture is assumed to be distributed with a local area network connecting the nodes. Each node is assumed to provide a specific functionality. The network provides for communication so that the overall tasks of the vehicle are accomplished. The O/S structure is based upon the concept of objects. The mechanisms for integrating node unique objects with node common objects in order to implement both the autonomy and the cooperation between nodes is developed. The requirements for time critical performance and reliability and recovery are discussed. Time critical performance impacts all parts of the distributed operating system; e.g., its structure, the functional design of its objects, the language structure, etc. Throughout the paper the tradeoffs - concurrency, language structure, object recovery, binding, file structure, communication protocol, programmer freedom, etc. - are considered to arrive at a feasible, maximum performance design. Reliability of the network system is considered. A parallel multipath bus structure is proposed for the control of delivery time for time critical messages. The architecture also supports immediate recovery for the time critical message system after a communication failure.

Functional Specificity of Extracellular Nucleases of Shewanella oneidensis MR-1

PubMed Central

Heun, Magnus; Binnenkade, Lucas; Kreienbaum, Maximilian

2012-01-01

Bacterial species such as Shewanella oneidensis MR-1 require extracellular nucleolytic activity for the utilization of extracellular DNA (eDNA) as a source of nutrients and for the turnover of eDNA as a structural matrix component during biofilm formation. We have previously characterized two extracellular nucleases of S. oneidensis MR-1, ExeM and ExeS. Although both are involved in biofilm formation, they are not specifically required for the utilization of eDNA as a nutrient. Here we identified and characterized EndA, a third extracellular nuclease of Shewanella. The heterologously overproduced and purified protein was highly active and rapidly degraded linear and supercoiled DNAs of various origins. Divalent metal ions (Mg2+ or Mn2+) were required for function. endA is cotranscribed with phoA, an extracellular phosphatase, and is not upregulated upon phosphostarvation. Deletion of endA abolished both extracellular degradation of DNA by S. oneidensis MR-1 and the ability to use eDNA as a sole source of phosphorus. PhoA is not strictly required for the exploitation of eDNA as a nutrient. The activity of EndA prevents the formation of large cell aggregates during planktonic growth. However, in contrast to the findings for ExeM, endA deletion had only minor effects on biofilm formation. The findings strongly suggest that the extracellular nucleases of S. oneidensis exert specific functions required under different conditions. PMID:22492434

A machine learning methodology for the selection and classification of spontaneous spinal cord dorsum potentials allows disclosure of structured (non-random) changes in neuronal connectivity induced by nociceptive stimulation

PubMed Central

Martin, Mario; Contreras-Hernández, Enrique; Béjar, Javier; Esposito, Gennaro; Chávez, Diógenes; Glusman, Silvio; Cortés, Ulises; Rudomin, Pablo

2015-01-01

Previous studies aimed to disclose the functional organization of the neuronal networks involved in the generation of the spontaneous cord dorsum potentials (CDPs) generated in the lumbosacral spinal segments used predetermined templates to select specific classes of spontaneous CDPs. Since this procedure was time consuming and required continuous supervision, it was limited to the analysis of two specific types of CDPs (negative CDPs and negative positive CDPs), thus excluding potentials that may reflect activation of other neuronal networks of presumed functional relevance. We now present a novel procedure based in machine learning that allows the efficient and unbiased selection of a variety of spontaneous CDPs with different shapes and amplitudes. The reliability and performance of the present method is evaluated by analyzing the effects on the probabilities of generation of different classes of spontaneous CDPs induced by the intradermic injection of small amounts of capsaicin in the anesthetized cat, a procedure known to induce a state of central sensitization leading to allodynia and hyperalgesia. The results obtained with the selection method presently described allowed detection of spontaneous CDPs with specific shapes and amplitudes that are assumed to represent the activation of functionally coupled sets of dorsal horn neurones that acquire different, structured configurations in response to nociceptive stimuli. These changes are considered as responses tending to adequate transmission of sensory information to specific functional requirements as part of homeostatic adjustments. PMID:26379540

Sisters Unbound Is Required for Meiotic Centromeric Cohesion in Drosophila melanogaster

PubMed Central

Krishnan, Badri; Thomas, Sharon E.; Yan, Rihui; Yamada, Hirotsugu; Zhulin, Igor B.; McKee, Bruce D.

2014-01-01

Regular meiotic chromosome segregation requires sister centromeres to mono-orient (orient to the same pole) during the first meiotic division (meiosis I) when homologous chromosomes segregate, and to bi-orient (orient to opposite poles) during the second meiotic division (meiosis II) when sister chromatids segregate. Both orientation patterns require cohesion between sister centromeres, which is established during meiotic DNA replication and persists until anaphase of meiosis II. Meiotic cohesion is mediated by a conserved four-protein complex called cohesin that includes two structural maintenance of chromosomes (SMC) subunits (SMC1 and SMC3) and two non-SMC subunits. In Drosophila melanogaster, however, the meiotic cohesion apparatus has not been fully characterized and the non-SMC subunits have not been identified. We have identified a novel Drosophila gene called sisters unbound (sunn), which is required for stable sister chromatid cohesion throughout meiosis. sunn mutations disrupt centromere cohesion during prophase I and cause high frequencies of non-disjunction (NDJ) at both meiotic divisions in both sexes. SUNN co-localizes at centromeres with the cohesion proteins SMC1 and SOLO in both sexes and is necessary for the recruitment of both proteins to centromeres. Although SUNN lacks sequence homology to cohesins, bioinformatic analysis indicates that SUNN may be a structural homolog of the non-SMC cohesin subunit stromalin (SA), suggesting that SUNN may serve as a meiosis-specific cohesin subunit. In conclusion, our data show that SUNN is an essential meiosis-specific Drosophila cohesion protein. PMID:25194162

Rubella virus: first calcium-requiring viral fusion protein.

PubMed

Dubé, Mathieu; Rey, Felix A; Kielian, Margaret

2014-12-01

Rubella virus (RuV) infection of pregnant women can cause fetal death, miscarriage, or severe fetal malformations, and remains a significant health problem in much of the underdeveloped world. RuV is a small enveloped RNA virus that infects target cells by receptor-mediated endocytosis and low pH-dependent membrane fusion. The structure of the RuV E1 fusion protein was recently solved in its postfusion conformation. RuV E1 is a member of the class II fusion proteins and is structurally related to the alphavirus and flavivirus fusion proteins. Unlike the other known class II fusion proteins, however, RuV E1 contains two fusion loops, with a metal ion complexed between them by the polar residues N88 and D136. Here we demonstrated that RuV infection specifically requires Ca(2+) during virus entry. Other tested cations did not substitute. Ca(2+) was not required for virus binding to cell surface receptors, endocytic uptake, or formation of the low pH-dependent E1 homotrimer. However, Ca(2+) was required for low pH-triggered E1 liposome insertion, virus fusion and infection. Alanine substitution of N88 or D136 was lethal. While the mutant viruses were efficiently assembled and endocytosed by host cells, E1-membrane insertion and fusion were specifically blocked. Together our data indicate that RuV E1 is the first example of a Ca(2+)-dependent viral fusion protein and has a unique membrane interaction mechanism.

Constitutive formulations for the mechanical investigation of colonic tissues.

PubMed

Carniel, Emanuele Luigi; Gramigna, Vera; Fontanella, Chiara Giulia; Stefanini, Cesare; Natali, Arturo N

2014-05-01

A constitutive framework is provided for the characterization of the mechanical behavior of colonic tissues, as a fundamental tool for the development of numerical models of the colonic structures. The constitutive analysis is performed by a multidisciplinary approach that requires the cooperation between experimental and computational competences. The preliminary investigation pertains to the review of the tissues histology. The complex structural configuration of the tissues and the specific distributions of fibrous elements entail the nonlinear mechanical behavior and the anisotropic response. The identification of the mechanical properties requires to perform mechanical tests according to different loading situations, as different loading directions. Because of the typical functionality of colon structures, the tissues mechanics is investigated by tensile tests, which are performed on taenia coli and haustra specimens from fresh pig colons. Accounting for the histological investigation and the results from the mechanical tests, a specific hyperelastic framework is provided within the theory of fiber-reinforced composite materials. Preliminary analytical formulations are defined to identify the constitutive parameters by the inverse analysis of the experimental tests. Finite element models of the specimens are developed accounting for the actual configuration of the colon structures to verify the quality of the results. The good agreement between experimental and numerical model results suggests the reliability of the constitutive formulations and parameters. Finally, the developed constitutive analysis makes it possible to identify the mechanical behavior and properties of the different colonic tissues. Copyright © 2013 Wiley Periodicals, Inc.

Review of Special Standards in Quality Management Systems Audits in Automotive Production

NASA Astrophysics Data System (ADS)

Šurinová, Yulia

2013-12-01

Quality management systems (QMS) in automotive industry generally have several differences in comparison with other industrial branches. Different customers have their own specific requirements, including requirements for quality audits. Audits are one of the coretools of quality management to make the PDCA (Plan - Do - Check - Act) cycle work. As a matter of fact, compliance with ISO/TS 16949:2009 requirements is a condition for supplying the automotive industry. However, there are some standards which co-exist together with the ISO 9001 based management systems and technical specification for QMS in automotive ISO/TS16949. Which are those specific standards in automotive industry and what standard to use and why - those are the questions to be answered in this paper. The aim of the paper is to review what standards are used for audits implementation in automotive industry in the Slovak Republic, and why the organizations keep following those "extra" standards even if certification for ISO/TS 16949 is required by all the car makers. The paper is structured as follows: after short introduction to the topic and related terms, presented is our methodology. . In the third section, the achieved results are discussed. And finally, the principal findings of the paper, limitations and conclusions are presented.

Crystal structure of the Melampsora lini effector AvrP reveals insights into a possible nuclear function and recognition by the flax disease resistance protein P.

PubMed

Zhang, Xiaoxiao; Farah, Nadya; Rolston, Laura; Ericsson, Daniel J; Catanzariti, Ann-Maree; Bernoux, Maud; Ve, Thomas; Bendak, Katerina; Chen, Chunhong; Mackay, Joel P; Lawrence, Gregory J; Hardham, Adrienne; Ellis, Jeffrey G; Williams, Simon J; Dodds, Peter N; Jones, David A; Kobe, Bostjan

2018-05-01

The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector-triggered immunity. To investigate the biological function of this effector and the mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc-finger-like structure with a novel interleaved zinc-binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in a loss of P-mediated recognition. The first zinc-coordinating region of the structure displays a positively charged surface and shows some limited similarities to nucleic acid-binding and chromatin-associated proteins. We show that the majority of the AvrP protein accumulates in the plant nucleus when transiently expressed in Nicotiana benthamiana cells, suggesting a nuclear pathogenic function. Polymorphic residues in AvrP and its allelic variants map to the protein surface and could be associated with differences in recognition specificity. Several point mutations of residues on the non-conserved surface patch result in a loss of recognition by P, suggesting that these residues are required for recognition. © 2017 BSPP AND JOHN WILEY & SONS LTD.

Inositol Pentakisphosphate Isomers Bind PH Domains with Varying Specificity and Inhibit Phosphoinositide Interactions

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

S Jackson; S Al-Saigh; C Schultz

2011-12-31

PH domains represent one of the most common domains in the human proteome. These domains are recognized as important mediators of protein-phosphoinositide and protein-protein interactions. Phosphoinositides are lipid components of the membrane that function as signaling molecules by targeting proteins to their sites of action. Phosphoinositide based signaling pathways govern a diverse range of important cellular processes including membrane remodeling, differentiation, proliferation and survival. Myo-Inositol phosphates are soluble signaling molecules that are structurally similar to the head groups of phosphoinositides. These molecules have been proposed to function, at least in part, by regulating PH domain-phosphoinositide interactions. Given the structural similaritymore » of inositol phosphates we were interested in examining the specificity of PH domains towards the family of myo-inositol pentakisphosphate isomers. In work reported here we demonstrate that the C-terminal PH domain of pleckstrin possesses the specificity required to discriminate between different myo-inositol pentakisphosphate isomers. The structural basis for this specificity was determined using high-resolution crystal structures. Moreover, we show that while the PH domain of Grp1 does not possess this high degree of specificity, the PH domain of protein kinase B does. These results demonstrate that some PH domains possess enough specificity to discriminate between myo-inositol pentakisphosphate isomers allowing for these molecules to differentially regulate interactions with phosphoinositides. Furthermore, this work contributes to the growing body of evidence supporting myo-inositol phosphates as regulators of important PH domain-phosphoinositide interactions. Finally, in addition to expanding our knowledge of cellular signaling, these results provide a basis for developing tools to probe biological pathway.« less

Prevention of cross-talk in conserved regulatory systems: identification of specificity determinants in RNA-binding anti-termination proteins of the BglG family

PubMed Central

Hübner, Sebastian; Declerck, Nathalie; Diethmaier, Christine; Le Coq, Dominique; Aymerich, Stephane; Stülke, Jörg

2011-01-01

Each family of signal transduction systems requires specificity determinants that link individual signals to the correct regulatory output. In Bacillus subtilis, a family of four anti-terminator proteins controls the expression of genes for the utilisation of alternative sugars. These regulatory systems contain the anti-terminator proteins and a RNA structure, the RNA anti-terminator (RAT) that is bound by the anti-terminator proteins. We have studied three of these proteins (SacT, SacY, and LicT) to understand how they can transmit a specific signal in spite of their strong structural homology. A screen for random mutations that render SacT capable to bind a RNA structure recognized by LicT only revealed a substitution (P26S) at one of the few non-conserved residues that are in contact with the RNA. We have randomly modified this position in SacT together with another non-conserved RNA-contacting residue (Q31). Surprisingly, the mutant proteins could bind all RAT structures that are present in B. subtilis. In a complementary approach, reciprocal amino acid exchanges have been introduced in LicT and SacY at non-conserved positions of the RNA-binding site. This analysis revealed the key role of an arginine side-chain for both the high affinity and specificity of LicT for its cognate RAT. Introduction of this Arg at the equivalent position of SacY (A26) increased the RNA binding in vitro but also resulted in a relaxed specificity. Altogether our results suggest that this family of anti-termination proteins has evolved to reach a compromise between RNA binding efficacy and specific interaction with individual target sequences. PMID:21278164

RPLP1 and RPLP2 Are Essential Flavivirus Host Factors That Promote Early Viral Protein Accumulation

PubMed Central

Campos, Rafael K.; Wong, Benjamin; Lu, Yi-Fan; Shi, Pei-Yong; Pompon, Julien

2016-01-01

ABSTRACT The Flavivirus genus contains several arthropod-borne viruses that pose global health threats, including dengue viruses (DENV), yellow fever virus (YFV), and Zika virus (ZIKV). In order to understand how these viruses replicate in human cells, we previously conducted genome-scale RNA interference screens to identify candidate host factors. In these screens, we identified ribosomal proteins RPLP1 and RPLP2 (RPLP1/2) to be among the most crucial putative host factors required for DENV and YFV infection. RPLP1/2 are phosphoproteins that bind the ribosome through interaction with another ribosomal protein, RPLP0, to form a structure termed the ribosomal stalk. RPLP1/2 were validated as essential host factors for DENV, YFV, and ZIKV infection in two human cell lines: A549 lung adenocarcinoma and HuH-7 hepatoma cells, and for productive DENV infection of Aedes aegypti mosquitoes. Depletion of RPLP1/2 caused moderate cell-line-specific effects on global protein synthesis, as determined by metabolic labeling. In A549 cells, global translation was increased, while in HuH-7 cells it was reduced, albeit both of these effects were modest. In contrast, RPLP1/2 knockdown strongly reduced early DENV protein accumulation, suggesting a requirement for RPLP1/2 in viral translation. Furthermore, knockdown of RPLP1/2 reduced levels of DENV structural proteins expressed from an exogenous transgene. We postulate that these ribosomal proteins are required for efficient translation elongation through the viral open reading frame. In summary, this work identifies RPLP1/2 as critical flaviviral host factors required for translation. IMPORTANCE Flaviviruses cause important diseases in humans. Examples of mosquito-transmitted flaviviruses include dengue, yellow fever and Zika viruses. Viruses require a plethora of cellular factors to infect cells, and the ribosome plays an essential role in all viral infections. The ribosome is a complex macromolecular machine composed of RNA and proteins and it is responsible for protein synthesis. We identified two specific ribosomal proteins that are strictly required for flavivirus infection of human cells and mosquitoes: RPLP1 and RPLP2 (RPLP1/2). These proteins are part of a structure known as the ribosomal stalk and help orchestrate the elongation phase of translation. We show that flaviviruses are particularly dependent on the function of RPLP1/2. Our findings suggest that ribosome composition is an important factor for virus translation and may represent a regulatory layer for translation of specific cellular mRNAs. PMID:27974556

Formulation of advanced consumables management models: Environmental control and electrical power system performance models requirements

NASA Technical Reports Server (NTRS)

Daly, J. K.; Torian, J. G.

1979-01-01

Software design specifications for developing environmental control and life support system (ECLSS) and electrical power system (EPS) programs into interactive computer programs are presented. Specifications for the ECLSS program are at the detail design level with respect to modification of an existing batch mode program. The FORTRAN environmental analysis routines (FEAR) are the subject batch mode program. The characteristics of the FEAR program are included for use in modifying batch mode programs to form interactive programs. The EPS program specifications are at the preliminary design level. Emphasis is on top-down structuring in the development of an interactive program.

Low-thrust chemical propulsion system pump technology

NASA Technical Reports Server (NTRS)

Sabiers, R. L.; Siebenhaar, A.

1981-01-01

Candidate pump and driver systems for low thrust cargo orbit transfer vehicle engines which deliver large space structures to geosynchronous equatorial orbit and beyond are evaluated. The pumps operate to 68 atmospheres (1000 psi) discharge pressure and flowrates suited to cryogenic engines using either LOX/methane or LOX/hydrogen propellants in thrust ranges from 445 to 8900 N (100 to 2000 lb F). Analysis of the various pumps and drivers indicate that the low specific speed requirement will make high fluid efficiencies difficult to achieve. As such, multiple stages are required. In addition, all pumps require inducer stages. The most attractive main pumps are the multistage centrifugal pumps.

SNAP 19 Pioneer F and G. Final Report

DOE R&D Accomplishments Database

1973-06-01

The generator developed for the Pioneer mission evolved from the SNAP 19 RTG`s launched aboard the NIMBUS III spacecraft. In order to satisfy the power requirements and environment of earth escape trajectory, significant modifications were made to the thermoelectric converter, heat source, and structural configuration. Specifically, a TAGS 2N thermoelectric couple was designed to provide higher efficiency and improved long term power performance, and the electrical circuitry was modified to yield very low magnetic field from current flow in the RTG. A new heat source was employed to satisfy operational requirements and its integration with the generator required alteration to the method of providing support to the fuel capsule.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.

PubMed

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R

2013-10-01

Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. Copyright © 2013 Wiley Periodicals, Inc.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids

PubMed Central

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C.; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R.

2013-01-01

Lignin comprises 15.25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP.binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute.binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. PMID:23606130

Tertiary model of a plant cellulose synthase

PubMed Central

Sethaphong, Latsavongsakda; Haigler, Candace H.; Kubicki, James D.; Zimmer, Jochen; Bonetta, Dario; DeBolt, Seth; Yingling, Yaroslava G.

2013-01-01

A 3D atomistic model of a plant cellulose synthase (CESA) has remained elusive despite over forty years of experimental effort. Here, we report a computationally predicted 3D structure of 506 amino acids of cotton CESA within the cytosolic region. Comparison of the predicted plant CESA structure with the solved structure of a bacterial cellulose-synthesizing protein validates the overall fold of the modeled glycosyltransferase (GT) domain. The coaligned plant and bacterial GT domains share a six-stranded β-sheet, five α-helices, and conserved motifs similar to those required for catalysis in other GT-2 glycosyltransferases. Extending beyond the cross-kingdom similarities related to cellulose polymerization, the predicted structure of cotton CESA reveals that plant-specific modules (plant-conserved region and class-specific region) fold into distinct subdomains on the periphery of the catalytic region. Computational results support the importance of the plant-conserved region and/or class-specific region in CESA oligomerization to form the multimeric cellulose–synthesis complexes that are characteristic of plants. Relatively high sequence conservation between plant CESAs allowed mapping of known mutations and two previously undescribed mutations that perturb cellulose synthesis in Arabidopsis thaliana to their analogous positions in the modeled structure. Most of these mutation sites are near the predicted catalytic region, and the confluence of other mutation sites supports the existence of previously undefined functional nodes within the catalytic core of CESA. Overall, the predicted tertiary structure provides a platform for the biochemical engineering of plant CESAs. PMID:23592721

Lithium ion batteries and their manufacturing challenges

DOE PAGES

Daniel, Claus

2015-03-01

There is no single lithium ion battery. With the variety of materials and electrochemical couples available, it is possible to design battery cells specific to their applications in terms of voltage, state of charge use, lifetime needs, and safety. Selection of specific electrochemical couples also facilitates the design of power and energy ratios and available energy. Integration in a large format cell requires optimized roll-to-roll electrode manufacturing and use of active materials. Electrodes are coated on a metal current collector foil in a composite structure of active material, binders, and conductive additives, requiring careful control of colloidal chemistry, adhesion, andmore » solidification. But the added inactive materials and the cell packaging reduce energy density. Furthermore, degree of porosity and compaction in the electrode can affect battery performance.« less

Hepatitis Delta Antigen Requires a Flexible Quasi-Double-Stranded RNA Structure To Bind and Condense Hepatitis Delta Virus RNA in a Ribonucleoprotein Complex

PubMed Central

Griffin, Brittany L.; Chasovskikh, Sergey; Dritschilo, Anatoly

2014-01-01

ABSTRACT The circular genome and antigenome RNAs of hepatitis delta virus (HDV) form characteristic unbranched, quasi-double-stranded RNA secondary structures in which short double-stranded helical segments are interspersed with internal loops and bulges. The ribonucleoprotein complexes (RNPs) formed by these RNAs with the virus-encoded protein hepatitis delta antigen (HDAg) perform essential roles in the viral life cycle, including viral replication and virion formation. Little is understood about the formation and structure of these complexes and how they function in these key processes. Here, the specific RNA features required for HDAg binding and the topology of the complexes formed were investigated. Selective 2′OH acylation analyzed by primer extension (SHAPE) applied to free and HDAg-bound HDV RNAs indicated that the characteristic secondary structure of the RNA is preserved when bound to HDAg. Notably, the analysis indicated that predicted unpaired positions in the RNA remained dynamic in the RNP. Analysis of the in vitro binding activity of RNAs in which internal loops and bulges were mutated and of synthetically designed RNAs demonstrated that the distinctive secondary structure, not the primary RNA sequence, is the major determinant of HDAg RNA binding specificity. Atomic force microscopy analysis of RNPs formed in vitro revealed complexes in which the HDV RNA is substantially condensed by bending or wrapping. Our results support a model in which the internal loops and bulges in HDV RNA contribute flexibility to the quasi-double-stranded structure that allows RNA bending and condensing by HDAg. IMPORTANCE RNA-protein complexes (RNPs) formed by the hepatitis delta virus RNAs and protein, HDAg, perform critical roles in virus replication. Neither the structures of these RNPs nor the RNA features required to form them have been characterized. HDV RNA is unusual in that it forms an unbranched quasi-double-stranded structure in which short base-paired segments are interspersed with internal loops and bulges. We analyzed the role of the HDV RNA sequence and secondary structure in the formation of a minimal RNP and visualized the structure of this RNP using atomic force microscopy. Our results indicate that HDAg does not recognize the primary sequence of the RNA; rather, the principle contribution of unpaired bases in HDV RNA to HDAg binding is to allow flexibility in the unbranched quasi-double-stranded RNA structure. Visualization of RNPs by atomic force microscopy indicated that the RNA is significantly bent or condensed in the complex. PMID:24741096

Identifying context-specific competencies required by community Australian Football sports trainers.

PubMed

Donaldson, Alex; Finch, Caroline F

2012-08-01

First-aid is a recommended injury prevention and risk management strategy in community sport; however, little is known about the sport-specific competencies required by first-aid providers. To achieve expert consensus on the competencies required by community Australian Football (community-AF) sports trainers. A three-round online Delphi process. Community-AF. 16 Australian sports first-aid and community-AF experts. Rating of competencies as either 'essential', 'expected', 'ideal' or 'not required'. Results After Round 3, 47 of the 77 (61%) competencies were endorsed as 'essential' or 'expected' for a sports trainer to effectively perform the activities required to the standards expected at a community-AF club by ≥75% of experts. These competencies covered: the role of the sports trainer; the responsibilities of the sports trainer; emergency management; injury and illness assessment and immediate management; taping; and injury prevention and risk management. Four competencies (5%) were endorsed as 'ideal' or 'not required' by ≥85% of experts and were excluded from further consideration. The 26 competencies where consensus was not reached were retained as second-tier, optional competencies. Sports trainers are important members of on-field first-aid teams, providing support to both injured players and other sports medicine professionals. The competencies identified in this study provide the basis of a proposed two-tiered community-AF-specific sports trainer education structure that can be implemented by the peak sports body. This includes six mandatory modules, relating to the 'required' competencies, and a further six optional modules covering competencies on which consensus was not reached.

A multi-scale controlled tissue engineering scaffold prepared by 3D printing and NFES technology

NASA Astrophysics Data System (ADS)

Yan, Feifei; Liu, Yuanyuan; Chen, Haiping; Zhang, Fuhua; Zheng, Lulu; Hu, Qingxi

2014-03-01

The current focus in the field of life science is the use of tissue engineering scaffolds to repair human organs, which has shown great potential in clinical applications. Extracellular matrix morphology and the performance and internal structure of natural organs are required to meet certain requirements. Therefore, integrating multiple processes can effectively overcome the limitations of the individual processes and can take into account the needs of scaffolds for the material, structure, mechanical properties and many other aspects. This study combined the biological 3D printing technology and the near-field electro-spinning (NFES) process to prepare a multi-scale controlled tissue engineering scaffold. While using 3D printing technology to directly prepare the macro-scaffold, the compositing NFES process to build tissue micro-morphology ultimately formed a tissue engineering scaffold which has the specific extracellular matrix structure. This scaffold not only takes into account the material, structure, performance and many other requirements, but also focuses on resolving the controllability problems in macro- and micro-forming which further aim to induce cell directed differentiation, reproduction and, ultimately, the formation of target tissue organs. It has in-depth immeasurable significance to build ideal scaffolds and further promote the application of tissue engineering.

Fully-Coupled Fluid/Structure Vibration Analysis Using MSC/NASTRAN

NASA Technical Reports Server (NTRS)

Fernholz, Christian M.; Robinson, Jay H.

1996-01-01

MSC/NASTRAN's performance in the solution of fully-coupled fluid/structure problems is evaluated. NASTRAN is used to perform normal modes (SOL 103) and forced-response analyses (SOL 108, 111) on cylindrical and cubic fluid/structure models. Bulk data file cards unique to the specification of a fluid element are discussed and analytic partially-coupled solutions are derived for each type of problem. These solutions are used to evaluate NASTRAN's solutions for accuracy. Appendices to this work include NASTRAN data presented in fringe plot form, FORTRAN source code listings written in support of this work, and NASTRAN data file usage requirements for each analysis.

From structure to mechanism—understanding initiation of DNA replication

PubMed Central

Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L. Maximilian; Schneider, Sarah; Speck, Christian

2017-01-01

DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2–7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. PMID:28717046

Critical Review of NOAA's Observation Requirements Process

NASA Astrophysics Data System (ADS)

LaJoie, M.; Yapur, M.; Vo, T.; Templeton, A.; Bludis, D.

2017-12-01

NOAA's Observing Systems Council (NOSC) maintains a comprehensive database of user observation requirements. The requirements collection process engages NOAA subject matter experts to document and effectively communicate the specific environmental observation measurements (parameters and attributes) needed to produce operational products and pursue research objectives. User observation requirements documented using a structured and standardized manner and framework enables NOAA to assess its needs across organizational lines in an impartial, objective, and transparent manner. This structure provides the foundation for: selecting, designing, developing, acquiring observing technologies, systems and architectures; budget and contract formulation and decision-making; and assessing in a repeatable fashion the productivity, efficiency and optimization of NOAA's observing system enterprise. User observation requirements are captured independently from observing technologies. Therefore, they can be addressed by a variety of current or expected observing capabilities and allow flexibility to be remapped to new and evolving technologies. NOAA's current inventory of user observation requirements were collected over a ten-year period, and there have been many changes in policies, mission priorities, and funding levels during this time. In light of these changes, the NOSC initiated a critical, in-depth review to examine all aspects of user observation requirements and associated processes during 2017. This presentation provides background on the NOAA requirements process, major milestones and outcomes of the critical review, and plans for evolving and connecting observing requirements processes in the next year.

Preliminary study for a numerical aerodynamic simulation facility. Phase 1: Extension

NASA Technical Reports Server (NTRS)

Lincoln, N. R.

1978-01-01

Functional requirements and preliminary design data were identified for use in the design of all system components and in the construction of a facility to perform aerodynamic simulation for airframe design. A skeleton structure of specifications for the flow model processor and monitor, the operating system, and the language and its compiler is presented.

Molecular and functional analyses of a maize autoactive NB-LRR protein identify precise structural requirements for activity

USDA-ARS?s Scientific Manuscript database

Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat (NB-LRR or NLR) proteins, which trigger a hypersensitive response (HR), a rapid, localized cell death upon recognition of specific pathogens. The maize NLR-encoding Rp1-D21 gene is the result of an intergenic recomb...

Assessing Traumatic Event Exposure: Comparing the Traumatic Life Events Questionnaire to the Structured Clinical Interview for "DSM-IV"

ERIC Educational Resources Information Center

Peirce, Jessica M.; Burke, Christopher K.; Stoller, Kenneth B.; Neufeld, Karin J.; Brooner, Robert K.

2009-01-01

Post-traumatic stress disorder (PTSD) diagnosis requires first identifying a traumatic event, but very few studies have evaluated methods of potential traumatic event assessment and their impact on PTSD diagnosis. The authors compared a behaviorally specific comprehensive multiple-item traumatic event measure with a single-item measure to…

Patent protection for structural genomics-related inventions.

PubMed

Vinarov, Sara D

2003-01-01

Recently there have been some important developments with respect to the patentability of inventions in the field of structural genomics. The leaders of the European Patent Office (EPO), Japan Patent Office (JPO) and the United States Patent Office (USPTO) came together for a trilateral meeting to conduct a comparative study on protein 3-dimensional (3-D) structure related claims in an effort to come to a mutual understanding about the examination of such inventions. The three patent offices were presented with eight different cases: 1) 3-D structural data of a protein per se; 2) computer-readable storage medium encoded with structural data of a protein; 3) protein defined by its tertiary structure; 4) crystals of known proteins; 5) binding pockets and protein domains; 6) and 7) are both directed to in silico screening methods directed to a specific protein; and 8) pharmacophores. The preliminary conclusions reached at the trilateral meeting provide clarity regarding the types of inventions that may be patentable given a specific set of scientific facts in a patent application. Therefore, the guidance provided by this study will help inventors, attorneys and other patent practitioners who file for patent protection on structural genomics-based inventions both here and abroad comply with the patentability requirements of each office.

Autonomous Assembly of Modular Structures in Space and on Extraterrestrial Locations

NASA Technical Reports Server (NTRS)

Alhorn, Dean C.

2005-01-01

The fulfillment of the new US. National Vision for Space Exploration requires many new enabling technologies to accomplish the goal of utilizing space for commercial activities and for returning humans to the moon and extraterrestrial environments. Traditionally, flight structures are manufactured as complete systems and require humans to complete the integration and assembly in orbit. These structures are bulky and require the use of heavy launch vehicles to send the units to the desired location, e.g. International Space Station (ISS). This method requires a high degree of safety, numerous space walks and significant cost for the humans to perform the assembly in orbit. For example, for assembly and maintenance of the ISS, 52 Extravehicular Activities (EVA's) have been performed so far with a total EVA time of approximately 322 hours. Sixteen (16) shuttle flights haw been to the ISS to perform these activities with an approximate cost of $450M per mission. For future space missions, costs have to be reduced to reasonably achieve the exploration goals. One concept that has been proposed is the autonomous assembly of space structures. This concept is an affordable, reliable solution to in-space and extraterrestrial assembly operations. Assembly is autonomously performed when two components containing onboard electronics join after recognizing that the joint is appropriate and in the precise position and orientation required for assembly. The mechanism only activates when the specifications are correct and m a nominal range. After assembly, local sensors and electronics monitor the integrity of the joint for feedback to a master controller. To achieve this concept will require a shift in the methods for designing space structures. In addition, innovative techniques will be required to perform the assembly autonomously. Monitoring of the assembled joint will be necessary for safety and structural integrity. If a very large structure is to be assembled in orbit, then the number of integrity sensors will be significant. Thus simple, low cost sensors are integral to the success of this concept. This paper will address these issues and will propose a novel concept for assembling space structures autonomously. The paper will present Several autonomous assembly methods. Core technologies required to achieve in space assembly will be discussed and novel techniques for communicating, sensing, docking and assembly will be detailed. These core technologies are critical to the goal of utilizing space in a cost efficient and safe manner. Finally, these technologies can also be applied to other systems both on earth and extraterrestrial environments.

Dispersion of Lamb waves in a honeycomb composite sandwich panel.

PubMed

Baid, Harsh; Schaal, Christoph; Samajder, Himadri; Mal, Ajit

2015-02-01

Composite materials are increasingly being used in advanced aircraft and aerospace structures. Despite their many advantages, composites are often susceptible to hidden damages that may occur during manufacturing and/or service of the structure. Therefore, safe operation of composite structures requires careful monitoring of the initiation and growth of such defects. Ultrasonic methods using guided waves offer a reliable and cost effective method for defects monitoring in advanced structures due to their long propagation range and their sensitivity to defects in their propagation path. In this paper, some of the useful properties of guided Lamb type waves are investigated, using analytical, numerical and experimental methods, in an effort to provide the knowledge base required for the development of viable structural health monitoring systems for composite structures. The laboratory experiments involve a pitch-catch method in which a pair of movable transducers is placed on the outside surface of the structure for generating and recording the wave signals. The specific cases considered include an aluminum plate, a woven composite laminate and an aluminum honeycomb sandwich panel. The agreement between experimental, numerical and theoretical results are shown to be excellent in certain frequency ranges, providing a guidance for the design of effective inspection systems. Copyright © 2014 Elsevier B.V. All rights reserved.

Evaluating Security Controls Based on Key Performance Indicators and Stakeholder Mission

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

Sheldon, Frederick T; Abercrombie, Robert K; Mili, Ali

2008-01-01

Good security metrics are required to make good decisions about how to design security countermeasures, to choose between alternative security architectures, and to improve security during operations. Therefore, in essence, measurement can be viewed as a decision aid. The lack of sound practical security metrics is severely hampering progress in the development of secure systems. The Cyberspace Security Econometrics System (CSES) offers the following advantages over traditional measurement systems: (1) CSES reflects the variances that exist amongst different stakeholders of the same system. Different stakeholders will typically attach different stakes to the same requirement or service (e.g., a service maymore » be provided by an information technology system or process control system, etc.). (2) For a given stakeholder, CSES reflects the variance that may exist among the stakes she/he attaches to meeting each requirement. The same stakeholder may attach different stakes to satisfying different requirements within the overall system specification. (3) For a given compound specification (e.g., combination(s) of commercial off the shelf software and/or hardware), CSES reflects the variance that may exist amongst the levels of verification and validation (i.e., certification) performed on components of the specification. The certification activity may produce higher levels of assurance across different components of the specification than others. Consequently, this paper introduces the basis, objectives and capabilities for the CSES including inputs/outputs and the basic structural and mathematical underpinnings.« less

ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.

PubMed

Park, Jungkap; Saitou, Kazuhiro

2014-09-18

Multibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The main challenge in the development of such potentials is to find relevant structural features that characterize the tightly folded proteins. Also, the side-chains of residues adopt several specific, staggered conformations, known as rotamers within protein structures. Different molecular conformations result in different dipole moments and induce charge reorientations. However, until now modeling of the rotameric state of residues had not been incorporated into the development of multibody potentials for modeling non-bonded interactions in protein structures. In this study, we develop a new multibody statistical potential which can account for the influence of rotameric states on the specificity of atomic interactions. In this potential, named "rotamer-dependent atomic statistical potential" (ROTAS), the interaction between two atoms is specified by not only the distance and relative orientation but also by two state parameters concerning the rotameric state of the residues to which the interacting atoms belong. It was clearly found that the rotameric state is correlated to the specificity of atomic interactions. Such rotamer-dependencies are not limited to specific type or certain range of interactions. The performance of ROTAS was tested using 13 sets of decoys and was compared to those of existing atomic-level statistical potentials which incorporate orientation-dependent energy terms. The results show that ROTAS performs better than other competing potentials not only in native structure recognition, but also in best model selection and correlation coefficients between energy and model quality. A new multibody statistical potential, ROTAS accounting for the influence of rotameric states on the specificity of atomic interactions was developed and tested on decoy sets. The results show that ROTAS has improved ability to recognize native structure from decoy models compared to other potentials. The effectiveness of ROTAS may provide insightful information for the development of many applications which require accurate side-chain modeling such as protein design, mutation analysis, and docking simulation.

Software Requirements Specification for Lunar IceCube

NASA Astrophysics Data System (ADS)

Glaser-Garbrick, Michael R.

Lunar IceCube is a 6U satellite that will orbit the moon to measure water volatiles as a function of position, altitude, and time, and measure in its various phases. Lunar IceCube, is a collaboration between Morehead State University, Vermont Technical University, Busek, and NASA. The Software Requirements Specification will serve as contract between the overall team and the developers of the flight software. It will provide a system's overview of the software that will be developed for Lunar IceCube, in that it will detail all of the interconnects and protocols for each subsystem's that Lunar IceCube will utilize. The flight software will be written in SPARK to the fullest extent, due to SPARK's unique ability to make software free of any errors. The LIC flight software does make use of a general purpose, reusable application framework called CubedOS. This framework imposes some structuring requirements on the architecture and design of the flight software, but it does not impose any high level requirements. It will also detail the tools that we will be using for Lunar IceCube, such as why we will be utilizing VxWorks.

An Automated, High-Throughput Method for Interpreting the Tandem Mass Spectra of Glycosaminoglycans

NASA Astrophysics Data System (ADS)

Duan, Jiana; Jonathan Amster, I.

2018-05-01

The biological interactions between glycosaminoglycans (GAGs) and other biomolecules are heavily influenced by structural features of the glycan. The structure of GAGs can be assigned using tandem mass spectrometry (MS2), but analysis of these data, to date, requires manually interpretation, a slow process that presents a bottleneck to the broader deployment of this approach to solving biologically relevant problems. Automated interpretation remains a challenge, as GAG biosynthesis is not template-driven, and therefore, one cannot predict structures from genomic data, as is done with proteins. The lack of a structure database, a consequence of the non-template biosynthesis, requires a de novo approach to interpretation of the mass spectral data. We propose a model for rapid, high-throughput GAG analysis by using an approach in which candidate structures are scored for the likelihood that they would produce the features observed in the mass spectrum. To make this approach tractable, a genetic algorithm is used to greatly reduce the search-space of isomeric structures that are considered. The time required for analysis is significantly reduced compared to an approach in which every possible isomer is considered and scored. The model is coded in a software package using the MATLAB environment. This approach was tested on tandem mass spectrometry data for long-chain, moderately sulfated chondroitin sulfate oligomers that were derived from the proteoglycan bikunin. The bikunin data was previously interpreted manually. Our approach examines glycosidic fragments to localize SO3 modifications to specific residues and yields the same structures reported in literature, only much more quickly.

Applications for the MATILDA robotic platform

NASA Astrophysics Data System (ADS)

Munkeby, Steve H.; Jones, Don; Bugg, George; Smith, Kathryn

2002-07-01

Most robotic platforms have, up to this point, been designed with emphasis placed on improving mobility technologies. Minimal emphasis has been placed on payloads and mission execution. Using a top-down approach, Mesa Associates, Inc. identified specific UGV mission applications and structured its MATILDA platform using these applications for vehicle mobility and motion control requirements. Specific applications identified for the MATILDA platform include: Target surveillance, explosive device neutralization, material pickup and transport, weapon transport and firing, and law enforcement. Current performance results, lessons-learned, technical hurdles, and future applications are examined.

Applications Technology Satellite ATS-6 in orbit checkout report

NASA Technical Reports Server (NTRS)

Moore, W.; Prensky, W. (Editor)

1974-01-01

The activities of the ATS-6 spacecraft for the checkout period of approximately four weeks beginning May 30, 1974 are described, along with the results of a performance evaluation of its subsystems and components. The following specific items are discussed: (1) subsystem requirements/specifications and in-orbit performance summary; (2) flight chronology; (3) spacecraft description; (4) structural/deployment subsystems; (5) electrical power subsystem; (6) thermal control subsystem; (7) telemetry and command subsystems; (8) attitude control subsystem; (9) spacecraft propulsion subsystem; (10) communication subsystem; and (12) experiment subsystem.

Improving Performance in Constructing specific Web Directory using Focused Crawler: An Experiment on Botany Domain

NASA Astrophysics Data System (ADS)

Khalilian, Madjid; Boroujeni, Farsad Zamani; Mustapha, Norwati

Nowadays the growth of the web causes some difficulties to search and browse useful information especially in specific domains. However, some portion of the web remains largely underdeveloped, as shown in lack of high quality contents. An example is the botany specific web directory, in which lack of well-structured web directories have limited user's ability to browse required information. In this research we propose an improved framework for constructing a specific web directory. In this framework we use an anchor directory as a foundation for primary web directory. This web directory is completed by information which is gathered with automatic component and filtered by experts. We conduct an experiment for evaluating effectiveness, efficiency and satisfaction.

Handling Qualities Specifications for U.S. Military Helicopters

NASA Technical Reports Server (NTRS)

Key, David L.

1982-01-01

Inadequacies in the military specification for helicopter handling qualities, MIL-H-8501A, have long been recognized, and the latest procurements by the U.S. Army used special Prime Item Development Specifications (PIDS). This paper assesses the efficacy of these PIDS and suggests that changes should be made. In particular, the structure developed in MIL-F-8785B (ASG) (the specification for flying qualities of piloted airplanes) should be incorporated. Improved requirements must be based on a systematic data base and concentrated on topics most important in preliminary design: static and dynamic stability, control power and sensitivity, and interaction with controllers and displays. Emphasis should be on current military helicopter missions and helicopter idiosyncrasies such as cross-coupling, nonlinearities, and higher-order dynamics.

Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

PubMed Central

Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J. Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V.; Craig, Timothy K.; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C.; van Raaij, Mark J.; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten

2014-01-01

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, over 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this paper, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict trans-membrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin IL-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fibre protein gp17 from bacteriophage T7; the Bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins. PMID:24318984

An early glimpse at long-term subsonic commercial turbofan technology requirements. [fuel conservation

NASA Technical Reports Server (NTRS)

Gray, D. E.; Dugan, J. F.

1975-01-01

This paper reports on the exploratory investigation and initial findings of the study of future turbofan concepts to conserve fuel. To date, these studies have indicated a potential reduction in cruise thrust specific fuel consumption in 1990 turbofans of approximately 15% relative to present day new engines through advances in internal aerodynamics, structure-mechanics, and materials. Advanced materials also offer the potential for fuel savings through engine weight reduction. Further studies are required to balance fuel consumption reduction with sound airlines operational economics.

Structural Basis for the Catalytic Activity of Human SER/THR Protein Phosphatase-5

NASA Technical Reports Server (NTRS)

Swingle, M. R.; Honkanen, R.; Ciszak, E.

2004-01-01

Serinekhreonine protein phosphatase-5 (PP5) affects many signaling networks that regulate cell growth. Here we report the 1.6 Angstrom resolution crystal structure of PP5 catalytic domain with metal and phosphate ions in the active site. The structure reveals a mechanism for PPS-mediated catalysis that requires the precise positioning of two metal ions within a conserved Asp(sup 271)-M(sub 1),-M(sub 2)-His(sup 427)-W(sup 2)-His(sup 304)-Asp(sup 274) catalytic motif, and provides a structural basis for the exceptional catalytic proficiency of protein phosphatases placing them among the most powerful catalysts. Resolution of the entire C-terminus revealed a novel subdomain, and the structure of PP5 should aid development of specific inhibitors.

Antibody modeling using the prediction of immunoglobulin structure (PIGS) web server [corrected].

PubMed

Marcatili, Paolo; Olimpieri, Pier Paolo; Chailyan, Anna; Tramontano, Anna

2014-12-01

Antibodies (or immunoglobulins) are crucial for defending organisms from pathogens, but they are also key players in many medical, diagnostic and biotechnological applications. The ability to predict their structure and the specific residues involved in antigen recognition has several useful applications in all of these areas. Over the years, we have developed or collaborated in developing a strategy that enables researchers to predict the 3D structure of antibodies with a very satisfactory accuracy. The strategy is completely automated and extremely fast, requiring only a few minutes (∼10 min on average) to build a structural model of an antibody. It is based on the concept of canonical structures of antibody loops and on our understanding of the way light and heavy chains pack together.

Space assembly fixtures and aids

NASA Technical Reports Server (NTRS)

Bloom, K. A.; Lillenas, A. N.

1980-01-01

Concepts and requirements for assembly fixtures and aids necessary for the assembly and maintenance of spare platforms were studied. Emphasis was placed on erectable and deployable type structures with the shuttle orbiter as the assembly base. Both single and multiple orbiter flight cases for the platform assembly were considered. Applicable space platform assembly studies were reviewed to provide a data base for establishing the assembly fixture and aids design requirements, assembly constraints, and the development of representative design concepts. Conclusions indicated that fixture requirements will vary with platform size. Larger platforms will require translation relative to the orbiter RMS working volume. The installation of platform payloads and subsystems (e.g., utility distribution) must also be considered in the specification of assembly fixtures and aids.

Testing Strategies for Model-Based Development

NASA Technical Reports Server (NTRS)

Heimdahl, Mats P. E.; Whalen, Mike; Rajan, Ajitha; Miller, Steven P.

2006-01-01

This report presents an approach for testing artifacts generated in a model-based development process. This approach divides the traditional testing process into two parts: requirements-based testing (validation testing) which determines whether the model implements the high-level requirements and model-based testing (conformance testing) which determines whether the code generated from a model is behaviorally equivalent to the model. The goals of the two processes differ significantly and this report explores suitable testing metrics and automation strategies for each. To support requirements-based testing, we define novel objective requirements coverage metrics similar to existing specification and code coverage metrics. For model-based testing, we briefly describe automation strategies and examine the fault-finding capability of different structural coverage metrics using tests automatically generated from the model.

Structure-guided mutational analysis reveals the functional requirements for product specificity of DOT1 enzymes.

PubMed

Dindar, Gülcin; Anger, Andreas M; Mehlhorn, Christine; Hake, Sandra B; Janzen, Christian J

2014-11-12

DOT1 enzymes are conserved methyltransferases that catalyse the methylation of lysine 79 on histone H3 (H3K79). Most eukaryotes contain one DOT1 enzyme, whereas African trypanosomes have two homologues, DOT1A and DOT1B, with different enzymatic activities. DOT1A mediates mono- and dimethylation of H3K76, the homologue of H3K79 in other organisms, whereas DOT1B additionally catalyses H3K76 trimethylation. However, it is unclear how these different enzymatic activities are achieved. Here we employ a trypanosomal nucleosome reconstitution system and structure-guided homology modelling to identify critical residues within and outside the catalytic centre that modulate product specificity. Exchange of these residues transfers the product specificity from one enzyme to the other, and reveals the existence of distinct regulatory domains adjacent to the catalytic centre. Our study provides the first evidence that a few crucial residues in DOT1 enzymes are sufficient to catalyse methyl-state-specific reactions. These results might also have far-reaching consequences for the functional understanding of homologous enzymes in higher eukaryotes.

Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2

PubMed Central

Xie, Xingqiao; Li, Faxiang; Wang, Yuanyuan; Wang, Yingli; Lin, Zhijie; Cheng, Xiaofang; Liu, Jianping; Chen, Changbin; Pan, Lifeng

2015-01-01

The autophagy receptor CALCOCO2/NDP52 functions as a bridging adaptor and plays an essential role in the selective autophagic degradation of invading pathogens by specifically recognizing ubiquitin-coated intracellular pathogens and subsequently targeting them to the autophagic machinery; thereby it is required for innate immune defense against a range of infectious pathogens in mammals. However, the mechanistic basis underlying CALCOCO2-mediated specific recognition of ubiqutinated pathogens is still unknown. Here, using biochemical and structural analyses, we demonstrated that the cargo-binding region of CALCOCO2 contains a dynamic unconventional zinc finger as well as a C2H2-type zinc-finger, and only the C2H2-type zinc finger specifically recognizes mono-ubiquitin or poly-ubiquitin chains. In addition to elucidating the specific ubiquitin recognition mechanism of CALCOCO2, the structure of the CALCOCO2 C2H2-type zinc finger in complex with mono-ubiquitin also uncovers a unique zinc finger-binding mode for ubiquitin. Our findings provide mechanistic insight into how CALCOCO2 targets ubiquitin-decorated pathogens for autophagic degradations. PMID:26506893

E-ELT requirements management

NASA Astrophysics Data System (ADS)

Schneller, D.

2014-08-01

The E-ELT has completed its design phase and is now entering construction. ESO is acting as prime contractor and usually procures subsystems, including their design, from industry. This, in turn, leads to a large number of requirements, whose validity, consistency and conformity with user needs requires extensive management. Therefore E-ELT Systems Engineering has chosen to follow a systematic approach, based on a reasoned requirement architecture that follows the product breakdown structure of the observatory. The challenge ahead is the controlled flow-down of science user needs into engineering requirements, requirement specifications and system design documents. This paper shows how the E-ELT project manages this. The project has adopted IBM DOORTM as a supporting requirements management tool. This paper deals with emerging problems and pictures potential solutions. It shows trade-offs made to reach a proper balance between the effort put in this activity and potential overheads, and the benefit for the project.

MyPMFs: a simple tool for creating statistical potentials to assess protein structural models.

PubMed

Postic, Guillaume; Hamelryck, Thomas; Chomilier, Jacques; Stratmann, Dirk

2018-05-29

Evaluating the model quality of protein structures that evolve in environments with particular physicochemical properties requires scoring functions that are adapted to their specific residue compositions and/or structural characteristics. Thus, computational methods developed for structures from the cytosol cannot work properly on membrane or secreted proteins. Here, we present MyPMFs, an easy-to-use tool that allows users to train statistical potentials of mean force (PMFs) on the protein structures of their choice, with all parameters being adjustable. We demonstrate its use by creating an accurate statistical potential for transmembrane protein domains. We also show its usefulness to study the influence of the physical environment on residue interactions within protein structures. Our open-source software is freely available for download at https://github.com/bibip-impmc/mypmfs. Copyright © 2018. Published by Elsevier B.V.

Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries.

PubMed

Ma, Xiao H; Jia, Jia; Zhu, Feng; Xue, Ying; Li, Ze R; Chen, Yu Z

2009-05-01

Machine learning methods have been explored as ligand-based virtual screening tools for facilitating drug lead discovery. These methods predict compounds of specific pharmacodynamic, pharmacokinetic or toxicological properties based on their structure-derived structural and physicochemical properties. Increasing attention has been directed at these methods because of their capability in predicting compounds of diverse structures and complex structure-activity relationships without requiring the knowledge of target 3D structure. This article reviews current progresses in using machine learning methods for virtual screening of pharmacodynamically active compounds from large compound libraries, and analyzes and compares the reported performances of machine learning tools with those of structure-based and other ligand-based (such as pharmacophore and clustering) virtual screening methods. The feasibility to improve the performance of machine learning methods in screening large libraries is discussed.

NADPH oxidase: an enzyme for multicellularity?

PubMed

Lalucque, Hervé; Silar, Philippe

2003-01-01

Multicellularity has evolved several times during the evolution of eukaryotes. One evolutionary pressure that permits multicellularity relates to the division of work, where one group of cells functions as nutrient providers and the other in specialized roles such as defence or reproduction. This requires signalling systems to ensure harmonious development of multicellular structures. Here, we show that NADPH oxidases are specifically present in organisms that differentiate multicellular structures during their life cycle and are absent from unicellular life forms. The biochemical properties of these enzymes make them ideal candidates for a role in intercellular signalling.

Numerical analysis of stiffened shells of revolution. Volume 4: Engineer's program manual for STARS-2S shell theory automated for rotational structures - 2 (statics) digital computer program

NASA Technical Reports Server (NTRS)

Svalbonas, V.; Ogilvie, P.

1973-01-01

The engineering programming information for the digital computer program for analyzing shell structures is presented. The program is designed to permit small changes such as altering the geometry or a table size to fit the specific requirements. Each major subroutine is discussed and the following subjects are included: (1) subroutine description, (2) pertinent engineering symbols and the FORTRAN coded counterparts, (3) subroutine flow chart, and (4) subroutine FORTRAN listing.

Magnetic field generator

DOEpatents

Krienin, Frank

1990-01-01

A magnetic field generating device provides a useful magnetic field within a specific retgion, while keeping nearby surrounding regions virtually field free. By placing an appropriate current density along a flux line of the source, the stray field effects of the generator may be contained. One current carrying structure may support a truncated cosine distribution, and it may be surrounded by a current structure which follows a flux line that would occur in a full coaxial double cosine distribution. Strong magnetic fields may be generated and contained using superconducting cables to approximate required current surfaces.

[Structure and functional organization of integrated cardiac intensive care].

PubMed

Scherillo, Marino; Miceli, Domenico; Tubaro, Marco; Guiducci, Umberto

2007-05-01

The early invasive strategy for the treatment of acute coronary syndromes and the increasing number of older and sicker patients requiring prolonged and more complex intensive care have induced many changes in the function of the intensive care units. These changes include the statement that specially trained cardiologists and cardiac nurses who can manage patients with acute cardiac conditions should staff the intensive care units. This document indicates the structure of the units and specific recommendations for the number of beds, monitoring system, respirators, pacemaker/defibrillators and additional equipment.

Potential of Organic Matrix Composites for Liquid Oxygen Tank

NASA Technical Reports Server (NTRS)

Davis, Samuel E.; Herald, Stephen D.; Stolzfus, Joel M.; Engel, Carl D.; Bohlen, James W.; Palm, Tod; Robinson, Michael J.

2005-01-01

Composite materials are being considered for the tankage of cryogenic propellants in access to space because of potentially lower structural weights. A major hurdle for composites is an inherent concern about the safety of using flammable structural materials in contact with liquid and gaseous oxygen. A hazards analysis approach addresses a series of specific concerns that must be addressed based upon test data. Under the 2nd Generation Reusable Launch Vehicle contracts, testing was begun for a variety of organic matrix composite materials both to aid in the selection of materials and to provide needed test data to support hazards analyses. The work has continued at NASA MSFC and the NASA WSTF to provide information on the potential for using composite materials in oxygen systems. Appropriate methods for oxygen compatibility testing of structural materials and data for a range of composite materials from impact, friction, flammability and electrostatic discharge testing are presented. Remaining concerns and conclusions about composite tank structures, and recommendations for additional testing are discussed. Requirements for system specific hazards analysis are identified.

Human Pif1 helicase unwinds synthetic DNA structures resembling stalled DNA replication forks

PubMed Central

George, Tresa; Wen, Qin; Griffiths, Richard; Ganesh, Anil; Meuth, Mark; Sanders, Cyril M.

2009-01-01

Pif-1 proteins are 5′→3′ superfamily 1 (SF1) helicases that in yeast have roles in the maintenance of mitochondrial and nuclear genome stability. The functions and activities of the human enzyme (hPif1) are unclear, but here we describe its DNA binding and DNA remodeling activities. We demonstrate that hPif1 specifically recognizes and unwinds DNA structures resembling putative stalled replication forks. Notably, the enzyme requires both arms of the replication fork-like structure to initiate efficient unwinding of the putative leading replication strand of such substrates. This DNA structure-specific mode of initiation of unwinding is intrinsic to the conserved core helicase domain (hPifHD) that also possesses a strand annealing activity as has been demonstrated for the RecQ family of helicases. The result of hPif1 helicase action at stalled DNA replication forks would generate free 3′ ends and ssDNA that could potentially be used to assist replication restart in conjunction with its strand annealing activity. PMID:19700773

Investigation of advancing front method for generating unstructured grid

NASA Technical Reports Server (NTRS)

Thomas, A. M.; Tiwari, S. N.

1992-01-01

The advancing front technique is used to generate an unstructured grid about simple aerodynamic geometries. Unstructured grids are generated using VGRID2D and VGRID3D software. Specific problems considered are a NACA 0012 airfoil, a bi-plane consisting of two NACA 0012 airfoil, a four element airfoil in its landing configuration, and an ONERA M6 wing. Inviscid time dependent solutions are computed on these geometries using USM3D and the results are compared with standard test results obtained by other investigators. A grid convergence study is conducted for the NACA 0012 airfoil and compared with a structured grid. A structured grid is generated using GRIDGEN software and inviscid solutions computed using CFL3D flow solver. The results obtained by unstructured grid for NACA 0012 airfoil showed an asymmetric distribution of flow quantities, and a fine distribution of grid was required to remove this asymmetry. On the other hand, the structured grid predicted a very symmetric distribution, but when the total number of points were compared to obtain the same results it was seen that structured grid required more grid points.

Genetic Interactions Between the Meiosis-Specific Cohesin Components, STAG3, REC8, and RAD21L.

PubMed

Ward, Ayobami; Hopkins, Jessica; Mckay, Matthew; Murray, Steve; Jordan, Philip W

2016-06-01

Cohesin is an essential structural component of chromosomes that ensures accurate chromosome segregation during mitosis and meiosis. Previous studies have shown that there are cohesin complexes specific to meiosis, required to mediate homologous chromosome pairing, synapsis, recombination, and segregation. Meiosis-specific cohesin complexes consist of two structural maintenance of chromosomes proteins (SMC1α/SMC1β and SMC3), an α-kleisin protein (RAD21, RAD21L, or REC8), and a stromal antigen protein (STAG1, 2, or 3). STAG3 is exclusively expressed during meiosis, and is the predominant STAG protein component of cohesin complexes in primary spermatocytes from mouse, interacting directly with each α-kleisin subunit. REC8 and RAD21L are also meiosis-specific cohesin components. Stag3 mutant spermatocytes arrest in early prophase ("zygotene-like" stage), displaying failed homolog synapsis and persistent DNA damage, as a result of unstable loading of cohesin onto the chromosome axes. Interestingly, Rec8, Rad21L double mutants resulted in an earlier "leptotene-like" arrest, accompanied by complete absence of STAG3 loading. To assess genetic interactions between STAG3 and α-kleisin subunits RAD21L and REC8, our lab generated Stag3, Rad21L, and Stag3, Rec8 double knockout mice, and compared them to the Rec8, Rad21L double mutant. These double mutants are phenotypically distinct from one another, and more severe than each single knockout mutant with regards to chromosome axis formation, cohesin loading, and sister chromatid cohesion. The Stag3, Rad21L, and Stag3, Rec8 double mutants both progress further into prophase I than the Rec8, Rad21L double mutant. Our genetic analysis demonstrates that cohesins containing STAG3 and REC8 are the main complex required for centromeric cohesion, and RAD21L cohesins are required for normal clustering of pericentromeric heterochromatin. Furthermore, the STAG3/REC8 and STAG3/RAD21L cohesins are the primary cohesins required for axis formation. Copyright © 2016 Ward et al.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

Downstream approaches to phosphorus management in agricultural landscapes: regional applicability and use.

PubMed

Kröger, R; Dunne, E J; Novak, J; King, K W; McLellan, E; Smith, D R; Strock, J; Boomer, K; Tomer, M; Noe, G B

2013-01-01

This review provides a critical overview of conservation practices that are aimed at improving water quality by retaining phosphorus (P) downstream of runoff genesis. The review is structured around specific downstream practices that are prevalent in various parts of the United States. Specific practices that we discuss include the use of controlled drainage, chemical treatment of waters and soils, receiving ditch management, and wetlands. The review also focuses on the specific hydrology and biogeochemistry associated with each of those practices. The practices are structured sequentially along flowpaths as you move through the landscape, from the edge-of-field, to adjacent aquatic systems, and ultimately to downstream P retention. Often practices are region specific based on geology, cropping practices, and specific P related problems and thus require a right practice, and right place mentality to management. Each practice has fundamental P transport and retention processes by systems that can be optimized by management with the goal of reducing downstream P loading after P has left agricultural fields. The management of P requires a system-wide assessment of the stability of P in different biogeochemical forms (particulate vs. dissolved, organic vs. inorganic), in different storage pools (soil, sediment, streams etc.), and under varying biogeochemical and hydrological conditions that act to convert P from one form to another and promote its retention in or transport out of different landscape components. There is significant potential of hierarchically placing practices in the agricultural landscape and enhancing the associated P mitigation. But an understanding is needed of short- and long-term P retention mechanisms within a certain practice and incorporating maintenance schedules if necessary to improve P retention times and minimize exceeding retention capacity. Copyright © 2012 Elsevier B.V. All rights reserved.

Use of a structured template to facilitate practice-based learning and improvement projects.

PubMed

McClain, Elizabeth K; Babbott, Stewart F; Tsue, Terance T; Girod, Douglas A; Clements, Debora; Gilmer, Lisa; Persons, Diane; Unruh, Greg

2012-06-01

The Accreditation Council for Graduate Medical Education (ACGME) requires residency programs to meet and demonstrate outcomes across 6 competencies. Measuring residents' competency in practice-based learning and improvement (PBLI) is particularly challenging. We developed an educational tool to meet ACGME requirements for PBLI. The PBLI template helped programs document quality improvement (QI) projects and supported increased scholarly activity surrounding PBLI learning. We reviewed program requirements for 43 residency and fellowship programs and identified specific PBLI requirements for QI activities. We also examined ACGME Program Information Form responses on PBLI core competency questions surrounding QI projects for program sites visited in 2008-2009. Data were integrated by a multidisciplinary committee to develop a peer-protected PBLI template guiding programs through process, documentation, and evaluation of QI projects. All steps were reviewed and approved through our GME Committee structure. An electronic template, companion checklist, and evaluation form were developed using identified project characteristics to guide programs through the PBLI process and facilitate documentation and evaluation of the process. During a 24 month period, 27 programs have completed PBLI projects, and 15 have reviewed the template with their education committees, but have not initiated projects using the template. The development of the tool generated program leaders' support because the tool enhanced the ability to meet program-specific objectives. The peer-protected status of this document for confidentiality and from discovery has been beneficial for program usage. The document aggregates data on PBLI and QI initiatives, offers opportunities to increase scholarship in QI, and meets the ACGME goal of linking measures to outcomes important to meeting accreditation requirements at the program and institutional level.

Use of a Structured Template to Facilitate Practice-Based Learning and Improvement Projects

PubMed Central

McClain, Elizabeth K.; Babbott, Stewart F.; Tsue, Terance T.; Girod, Douglas A.; Clements, Debora; Gilmer, Lisa; Persons, Diane; Unruh, Greg

2012-01-01

Background The Accreditation Council for Graduate Medical Education (ACGME) requires residency programs to meet and demonstrate outcomes across 6 competencies. Measuring residents' competency in practice-based learning and improvement (PBLI) is particularly challenging. Purpose We developed an educational tool to meet ACGME requirements for PBLI. The PBLI template helped programs document quality improvement (QI) projects and supported increased scholarly activity surrounding PBLI learning. Methods We reviewed program requirements for 43 residency and fellowship programs and identified specific PBLI requirements for QI activities. We also examined ACGME Program Information Form responses on PBLI core competency questions surrounding QI projects for program sites visited in 2008–2009. Data were integrated by a multidisciplinary committee to develop a peer-protected PBLI template guiding programs through process, documentation, and evaluation of QI projects. All steps were reviewed and approved through our GME Committee structure. Results An electronic template, companion checklist, and evaluation form were developed using identified project characteristics to guide programs through the PBLI process and facilitate documentation and evaluation of the process. During a 24 month period, 27 programs have completed PBLI projects, and 15 have reviewed the template with their education committees, but have not initiated projects using the template. Discussion The development of the tool generated program leaders' support because the tool enhanced the ability to meet program-specific objectives. The peer-protected status of this document for confidentiality and from discovery has been beneficial for program usage. The document aggregates data on PBLI and QI initiatives, offers opportunities to increase scholarship in QI, and meets the ACGME goal of linking measures to outcomes important to meeting accreditation requirements at the program and institutional level. PMID:23730444

Application of Ultrasonic Bone Curette in Endoscopic Endonasal Skull Base Surgery: Technical Note

PubMed Central

Rastelli, Milton M.; Pinheiro-Neto, Carlos D.; Fernandez-Miranda, Juan C.; Wang, Eric W.; Snyderman, Carl H.; Gardner, Paul A.

2014-01-01

Background Endoscopic endonasal surgery (EES) of the skull base often requires extensive bone work in proximity to critical neurovascular structures. Objective To demonstrate the application of an ultrasonic bone curette during EES. Methods Ten patients with skull base lesions underwent EES from September 2011 to April 2012 at the University of Pittsburgh Medical Center. Most of the bone work was done with high-speed drill and rongeurs. The ultrasonic curette was used to remove specific structures. Results All the patients were submitted to fully endoscopic endonasal procedures and had critical bony structures removed with the ultrasonic bone curette. Two patients with degenerative spine diseases underwent odontoid process removal. Five patients with clival and petroclival tumors underwent posterior clinoid removal. Two patients with anterior fossa tumors underwent crista galli removal. One patient underwent unilateral optic nerve decompression. No mechanical or heat injury resulted from the ultrasonic curette. The surrounding neurovascular structures and soft tissue were preserved in all cases. Conclusion In selected EES, the ultrasonic bone curette was successfully used to remove loose pieces of bone in narrow corridors, adjacent to neurovascular structures, and it has advantages to high-speed drills in these specific situations. PMID:24719795

Radial super-resolution in digital holographic microscopy using structured illumination with circular symmetry

NASA Astrophysics Data System (ADS)

Yin, Yujian; Su, Ping; Ma, Jianshe

2018-01-01

A method to improve the radial resolution using special structured light is proposed in the field of digital holographic microscopy (DHM). A specimen is illuminated with circular symmetrical structured light that makes the spectrum have radial movement, so that high frequency components of the specimen are moved into the passband of the receiver to overcome the diffraction limit. In the DHM imaging system, Computer Generated Hologram (CGH) technology is used to generate the required structured light grating. Then the grating is loaded into a spatial light modulator (SLM) to obtain specific structured illumination. After recording the hologram, digital reconstruction, for the microstructure of a binary optical element that needs to observe radial distribution, the radial resolution of the specimen is improved experimentally compare it with the result of one-dimensional sinusoidal structured light imaging. And a method of designing structured light is presented.

MyDas, an Extensible Java DAS Server

PubMed Central

Jimenez, Rafael C.; Quinn, Antony F.; Jenkinson, Andrew M.; Mulder, Nicola; Martin, Maria; Hunter, Sarah; Hermjakob, Henning

2012-01-01

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users. We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details. PMID:23028496

MyDas, an extensible Java DAS server.

PubMed

Salazar, Gustavo A; García, Leyla J; Jones, Philip; Jimenez, Rafael C; Quinn, Antony F; Jenkinson, Andrew M; Mulder, Nicola; Martin, Maria; Hunter, Sarah; Hermjakob, Henning

2012-01-01

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.

Physical interactions between bacteriophage and Escherichia coli proteins required for initiation of lambda DNA replication.

PubMed

Liberek, K; Osipiuk, J; Zylicz, M; Ang, D; Skorko, J; Georgopoulos, C

1990-02-25

The process of initiation of lambda DNA replication requires the assembly of the proper nucleoprotein complex at the origin of replication, ori lambda. The complex is composed of both phage and host-coded proteins. The lambda O initiator protein binds specifically to ori lambda. The lambda P initiator protein binds to both lambda O and the host-coded dnaB helicase, giving rise to an ori lambda DNA.lambda O.lambda P.dnaB structure. The dnaK and dnaJ heat shock proteins have been shown capable of dissociating this complex. The thus freed dnaB helicase unwinds the duplex DNA template at the replication fork. In this report, through cross-linking, size chromatography, and protein affinity chromatography, we document some of the protein-protein interactions occurring at ori lambda. Our results show that the dnaK protein specifically interacts with both lambda O and lambda P, and that the dnaJ protein specifically interacts with the dnaB helicase.

Peptide interfaces with graphene: an emerging intersection of analytical chemistry, theory, and materials.

PubMed

Russell, Shane R; Claridge, Shelley A

2016-04-01

Because noncovalent interface functionalization is frequently required in graphene-based devices, biomolecular self-assembly has begun to emerge as a route for controlling substrate electronic structure or binding specificity for soluble analytes. The remarkable diversity of structures that arise in biological self-assembly hints at the possibility of equally diverse and well-controlled surface chemistry at graphene interfaces. However, predicting and analyzing adsorbed monolayer structures at such interfaces raises substantial experimental and theoretical challenges. In contrast with the relatively well-developed monolayer chemistry and characterization methods applied at coinage metal surfaces, monolayers on graphene are both less robust and more structurally complex, levying more stringent requirements on characterization techniques. Theory presents opportunities to understand early binding events that lay the groundwork for full monolayer structure. However, predicting interactions between complex biomolecules, solvent, and substrate is necessitating a suite of new force fields and algorithms to assess likely binding configurations, solvent effects, and modulations to substrate electronic properties. This article briefly discusses emerging analytical and theoretical methods used to develop a rigorous chemical understanding of the self-assembly of peptide-graphene interfaces and prospects for future advances in the field.

Managing Complex IT Security Processes with Value Based Measures

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

Abercrombie, Robert K; Sheldon, Frederick T; Mili, Ali

2009-01-01

Current trends indicate that IT security measures will need to greatly expand to counter the ever increasingly sophisticated, well-funded and/or economically motivated threat space. Traditional risk management approaches provide an effective method for guiding courses of action for assessment, and mitigation investments. However, such approaches no matter how popular demand very detailed knowledge about the IT security domain and the enterprise/cyber architectural context. Typically, the critical nature and/or high stakes require careful consideration and adaptation of a balanced approach that provides reliable and consistent methods for rating vulnerabilities. As reported in earlier works, the Cyberspace Security Econometrics System provides amore » comprehensive measure of reliability, security and safety of a system that accounts for the criticality of each requirement as a function of one or more stakeholders interests in that requirement. This paper advocates a dependability measure that acknowledges the aggregate structure of complex system specifications, and accounts for variations by stakeholder, by specification components, and by verification and validation impact.« less

Intelligent Sampling of Hazardous Particle Populations in Resource-Constrained Environments

NASA Astrophysics Data System (ADS)

McCollough, J. P.; Quinn, J. M.; Starks, M. J.; Johnston, W. R.

2017-10-01

Sampling of anomaly-causing space environment drivers is necessary for both real-time operations and satellite design efforts, and optimizing measurement sampling helps minimize resource demands. Relating these measurements to spacecraft anomalies requires the ability to resolve spatial and temporal variability in the energetic charged particle hazard of interest. Here we describe a method for sampling particle fluxes informed by magnetospheric phenomenology so that, along a given trajectory, the variations from both temporal dynamics and spatial structure are adequately captured while minimizing oversampling. We describe the coordinates, sampling method, and specific regions and parameters employed. We compare resulting sampling cadences with data from spacecraft spanning the regions of interest during a geomagnetically active period, showing that the algorithm retains the gross features necessary to characterize environmental impacts on space systems in diverse orbital regimes while greatly reducing the amount of sampling required. This enables sufficient environmental specification within a resource-constrained context, such as limited telemetry bandwidth, processing requirements, and timeliness.

PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing.

PubMed

Ivanov, Alexey V; Peng, Hongzhuang; Yurchenko, Vyacheslav; Yap, Kyoko L; Negorev, Dmitri G; Schultz, David C; Psulkowski, Elyse; Fredericks, William J; White, David E; Maul, Gerd G; Sadofsky, Moshe J; Zhou, Ming-Ming; Rauscher, Frank J

2007-12-14

Tandem PHD and bromodomains are often found in chromatin-associated proteins and have been shown to cooperate in gene silencing. Each domain can bind specifically modified histones: the mechanisms of cooperation between these domains are unknown. We show that the PHD domain of the KAP1 corepressor functions as an intramolecular E3 ligase for sumoylation of the adjacent bromodomain. The RING finger-like structure of the PHD domain is required for both Ubc9 binding and sumoylation and directs modification to specific lysine residues in the bromodomain. Sumoylation is required for KAP1-mediated gene silencing and functions by directly recruiting the SETDB1 histone methyltransferase and the CHD3/Mi2 component of the NuRD complex via SUMO-interacting motifs. Sumoylated KAP1 stimulates the histone methyltransferase activity of SETDB1. These data provide a mechanistic explanation for the cooperation of PHD and bromodomains in gene regulation and describe a function of the PHD domain as an intramolecular E3 SUMO ligase.

The zebrafish dorsal axis is apparent at the four-cell stage.

PubMed

Gore, Aniket V; Maegawa, Shingo; Cheong, Albert; Gilligan, Patrick C; Weinberg, Eric S; Sampath, Karuna

2005-12-15

A central question in the development of multicellular organisms pertains to the timing and mechanisms of specification of the embryonic axes. In many organisms, specification of the dorsoventral axis requires signalling by proteins of the Transforming growth factor-beta and Wnt families. Here we show that maternal transcripts of the zebrafish Nodal-related morphogen, Squint (Sqt), can localize to two blastomeres at the four-cell stage and predict the dorsal axis. Removal of cells containing sqt transcripts from four-to-eight-cell embryos or injection of antisense morpholino oligonucleotides targeting sqt into oocytes can cause a loss of dorsal structures. Localization of sqt transcripts is independent of maternal Wnt pathway function and requires a highly conserved sequence in the 3' untranslated region. Thus, the dorsoventral axis is apparent by early cleavage stages and may require the maternally encoded morphogen Sqt and its associated factors. Because the 3' untranslated region of the human nodal gene can also localize exogenous sequences to dorsal cells, this mechanism may be evolutionarily conserved.

Fixed Wing Project: Technologies for Advanced Air Transports

NASA Technical Reports Server (NTRS)

Del Rosario, Ruben; Koudelka, John M.; Wahls, Richard A.; Madavan, Nateri

2014-01-01

The NASA Fundamental Aeronautics Fixed Wing (FW) Project addresses the comprehensive challenge of enabling revolutionary energy efficiency improvements in subsonic transport aircraft combined with dramatic reductions in harmful emissions and perceived noise to facilitate sustained growth of the air transportation system. Advanced technologies and the development of unconventional aircraft systems offer the potential to achieve these improvements. Multidisciplinary advances are required in aerodynamic efficiency to reduce drag, structural efficiency to reduce aircraft empty weight, and propulsive and thermal efficiency to reduce thrust-specific energy consumption (TSEC) for overall system benefit. Additionally, advances are required to reduce perceived noise without adversely affecting drag, weight, or TSEC, and to reduce harmful emissions without adversely affecting energy efficiency or noise.The presentation will highlight the Fixed Wing project vision of revolutionary systems and technologies needed to achieve these challenging goals. Specifically, the primary focus of the FW Project is on the N+3 generation; that is, vehicles that are three generations beyond the current state of the art, requiring mature technology solutions in the 2025-30 timeframe.

Advanced Platform Systems Technology study. Volume 2: Trade study and technology selection

NASA Technical Reports Server (NTRS)

1983-01-01

Three primary tasks were identified which include task 1-trade studies, task 2-trade study comparison and technology selection, and task 3-technology definition. Task 1 general objectives were to identify candidate technology trade areas, determine which areas have the highest potential payoff, define specific trades within the high payoff areas, and perform the trade studies. In order to satisfy these objectives, a structured, organized approach was employed. Candidate technology areas and specific trades were screened using consistent selection criteria and considering possible interrelationships. A data base comprising both manned and unmanned space platform documentation was used as a source of system and subsystem requirements. When requirements were not stated in the data base documentation, assumptions were made and recorded where necessary to characterize a particular spacecraft system. The requirements and assumptions were used together with the selection criteria to establish technology advancement goals and select trade studies. While both manned and unmanned platform data were used, the study was focused on the concept of an early manned space station.

An Fgf-Shh signaling hierarchy regulates early specification of the zebrafish skull.

PubMed

McCarthy, Neil; Sidik, Alfire; Bertrand, Julien Y; Eberhart, Johann K

2016-07-15

The neurocranium generates most of the craniofacial skeleton and consists of prechordal and postchordal regions. Although development of the prechordal is well studied, little is known of the postchordal region. Here we characterize a signaling hierarchy necessary for postchordal neurocranial development involving Fibroblast growth factor (Fgf) signaling for early specification of mesodermally-derived progenitor cells. The expression of hyaluron synthetase 2 (has2) in the cephalic mesoderm requires Fgf signaling and Has2 function, in turn, is required for postchordal neurocranial development. While Hedgehog (Hh)-deficient embryos also lack a postchordal neurocranium, this appears primarily due to a later defect in chondrocyte differentiation. Inhibitor studies demonstrate that postchordal neurocranial development requires early Fgf and later Hh signaling. Collectively, our results provide a mechanistic understanding of early postchordal neurocranial development and demonstrate a hierarchy of signaling between Fgf and Hh in the development of this structure. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Development of a cyber physical apparatus for investigating fluid structure interaction on leading edge vortex evolution

NASA Astrophysics Data System (ADS)

Raghu Gowda, Belagumba Venkatachalaiah

This dissertation examines how simple structural compliance impacts a specific transient vortex phenomenon that occurs on high angle of attack lifting surfaces termed dynamic stall. In many Fluid structure interaction (FSI) research efforts, a purely physical or purely computational approach is taken. In this work a low cost cyber-physical (CPFD) system is designed and developed for representing the FSI in the leading edge vortex (LEV) development problem. The leading edge compliance appears to be favorable in a specific spring constant range for a given wing. When the leading edge compliance prescribed via CPFD system is too low compared with the moment due to dynamic pressure or fluid unsteady effect, the LEV behavior is similar to that of a rigid wing system. When the leading edge compliance is too high, excessive compliance is introduced into the wing system and the leading edge vortex evolution is affected by the large change in wing angle. At moderate leading edge compliance, a balance appears to be achieved in which the leading edge vorticity shedding rate supports the long term evolution of the leading edge vortex. Further investigation is required to determine specific parameters governing these leading edge compliance ranges.

Flexible DNA bending in HU–DNA cocrystal structures

PubMed Central

Swinger, Kerren K.; Lemberg, Kathryn M.; Zhang, Ying; Rice, Phoebe A.

2003-01-01

HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence-specific (IHF) or non-specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation, transcription regulation and site-specific recombination, and is associated with bacterial nucleoids. Cocrystal structures of Anabaena HU bound to DNA (1P71, 1P78, 1P51) reveal that while underlying proline intercalation and asymmetric charge neutralization mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles (∼105–140°). The two bend angles within a single HU complex are not coplanar, and the resulting dihedral angle is consistent with negative supercoiling. Comparison of HU–DNA and IHF–DNA structures suggests that sharper bending is correlated with longer DNA binding sites and smaller dihedral angles. An HU-induced bend may be better modeled as a hinge, not a rigid bend. The ability to induce or stabilize varying bend angles is consistent with HU’s role as an architectural cofactor in many different systems that may require differing geometries. PMID:12853489

Inference of Expanded Lrp-Like Feast/Famine Transcription Factor Targets in a Non-Model Organism Using Protein Structure-Based Prediction

PubMed Central

Ashworth, Justin; Plaisier, Christopher L.; Lo, Fang Yin; Reiss, David J.; Baliga, Nitin S.

2014-01-01

Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of non-model organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB) involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer. PMID:25255272

Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.

PubMed

Ashworth, Justin; Plaisier, Christopher L; Lo, Fang Yin; Reiss, David J; Baliga, Nitin S

2014-01-01

Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of non-model organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB) involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer.

Final acceptance testing of the LSST monolithic primary/tertiary mirror

NASA Astrophysics Data System (ADS)

Tuell, Michael T.; Burge, James H.; Cuerden, Brian; Gressler, William; Martin, Hubert M.; West, Steven C.; Zhao, Chunyu

2014-07-01

The Large Synoptic Survey Telescope (LSST) is a three-mirror wide-field survey telescope with the primary and tertiary mirrors on one monolithic substrate1. This substrate is made of Ohara E6 borosilicate glass in a honeycomb sandwich, spin cast at the Steward Observatory Mirror Lab at The University of Arizona2. Each surface is aspheric, with the specification in terms of conic constant error, maximum active bending forces and finally a structure function specification on the residual errors3. There are high-order deformation terms, but with no tolerance, any error is considered as a surface error and is included in the structure function. The radii of curvature are very different, requiring two independent test stations, each with instantaneous phase-shifting interferometers with null correctors. The primary null corrector is a standard two-element Offner null lens. The tertiary null corrector is a phase-etched computer-generated hologram (CGH). This paper details the two optical systems and their tolerances, showing that the uncertainty in measuring the figure is a small fraction of the structure function specification. Additional metrology includes the radii of curvature, optical axis locations, and relative surface tilts. The methods for measuring these will also be described along with their tolerances.

The riches of the cyclopean paradigm

NASA Astrophysics Data System (ADS)

Tyler, Christopher W.

2005-03-01

The cyclopean paradigm introduced by Bela Julesz remains one of the richest probes into the neural organization of sensory processing, by virtue of both its specificity for purely stereoscopic form and the sophistication of the processing required to retrieve it. The introduction of the sinusoidal stereograting showed that the perceptual limitations of human depth processing are very different from those for monocular form. Their use has also revealed the existence of hypercyclopean form channels selective for specific aspects of the monocularly invisible depth form. The natural extension of stereogratings to patches of stereoGabor ripple has allowed the measurement of the summation properties for depth structure, which is specific for narrow horizontal bars in depth. Consideration of the apparent motion between two cyclopean depth structures reveals the existence of a novel surface correspondence problem operating for cyclopean surfaces over time after the binocular correspondence has been solved. Such concepts imply that remains to be discovered about cyclopean stereopsis and its relationship to 3D form perception from other depth cues.

Structure of the Human FANCL RING-Ube2T Complex Reveals Determinants of Cognate E3-E2 Selection

PubMed Central

Hodson, Charlotte; Purkiss, Andrew; Miles, Jennifer Anne; Walden, Helen

2014-01-01

Summary The combination of an E2 ubiquitin-conjugating enzyme with an E3 ubiquitin-ligase is essential for ubiquitin modification of a substrate. Moreover, the pairing dictates both the substrate choice and the modification type. The molecular details of generic E3-E2 interactions are well established. Nevertheless, the determinants of selective, specific E3-E2 recognition are not understood. There are ∼40 E2s and ∼600 E3s giving rise to a possible ∼24,000 E3-E2 pairs. Using the Fanconi Anemia pathway exclusive E3-E2 pair, FANCL-Ube2T, we report the atomic structure of the FANCL RING-Ube2T complex, revealing a specific and extensive network of additional electrostatic and hydrophobic interactions. Furthermore, we show that these specific interactions are required for selection of Ube2T over other E2s by FANCL. PMID:24389026

The Chemically Elegant Proton Pump Inhibitors

PubMed Central

Roche, Victoria F.

2006-01-01

Medicinal chemistry instruction at Creighton University is designed to provide an in-depth scientifically grounded and clinically relevant learning experience for pharmacy students. Each topic covered in the 2-semester required course sequence is selected based on the general utility of the compounds in question and/or the therapeutic importance of the drugs in treating life-threatening diseases. All lessons provided to campus- and Web-based students by the author are in the form of a descriptive and conversational narrative and course requirements are in place to assure that students read the lesson prior to the class period in which it is discussed. Learning tools and aids are provided to help students more readily discern the most critical aspects of each lesson, to practice required critical thinking and structure analysis skills, and to self-assess competency in meeting specific learning objectives. This manuscript illustrates this approach by sharing a lesson on the chemistry and clinically relevant structure-activity relationships of proton pump inhibitors. PMID:17149430

Rhizobium meliloti lipooligosaccharide nodulation factors: different structural requirements for bacterial entry into target root hair cells and induction of plant symbiotic developmental responses.

PubMed

Ardourel, M; Demont, N; Debellé, F; Maillet, F; de Billy, F; Promé, J C; Dénarié, J; Truchet, G

1994-10-01

Rhizobium meliloti produces lipochitooligosaccharide nodulation NodRm factors that are required for nodulation of legume hosts. NodRm factors are O-acetylated and N-acylated by specific C16-unsaturated fatty acids. nodL mutants produce non-O-acetylated factors, and nodFE mutants produce factors with modified acyl substituents. Both mutants exhibited a significantly reduced capacity to elicit infection thread (IT) formation in alfalfa. However, once initiated, ITs developed and allowed the formation of nitrogen-fixing nodules. In contrast, double nodF/nodL mutants were unable to penetrate into legume hosts and to form ITs. Nevertheless, these mutants induced widespread cell wall tip growth in trichoblasts and other epidermal cells and were also able to elicit cortical cell activation at a distance. NodRm factor structural requirements are thus clearly more stringent for bacterial entry than for the elicitation of developmental plant responses.

Approach to the E-ELT dome and main structure challenges

NASA Astrophysics Data System (ADS)

Bilbao, Armando; Murga, Gaizka; Gómez, Celia; Llarena, Javier

2014-07-01

The E-ELT as a whole could be classified as an extremely challenging project. More precisely, it should be defined as an array of many different sub-challenges, which comprise technical, logistical and managerial matters. This paper reviews some of these critical challenges, in particular those related to the Dome and the Main Structure, suggesting ways to face them in the most pragmatic way possible. Technical challenges for the Dome and the Main Structure are mainly related to the need to upscale current design standards to an order of magnitude larger design. Trying a direct design escalation is not feasible; it would not work. A design effort is needed to cross hybridize current design standards with technologies coming from other different applications. Innovative design is therefore not a wish but a must. And innovative design comes along with design risk. Design risk needs to be tackled from two angles: on the one hand through thorough design validation analysis and on the other hand through extensive pre-assembly and testing. And, once again, full scale integrated pre-assembly and testing of extremely large subsystems is not always possible. Therefore, defining a comprehensive test plan for critical components, critical subsystems and critical subassemblies becomes essential. Logistical challenges are linked to the erection site. Cerro Armazones is a remote site and this needs to be considered when evaluating transport and erection requirements. But it is not only the remoteness of the site that needs to be considered. The size of both Dome and Main Structure require large construction cranes and a well defined erection plan taking into account pre-assembly strategies, limited plan area utilization, erection sequence, erection stability during intermediate stages and, very specifically, efficient coordination between the Dome and the Main Structure erection processes. Managerial issues pose another set of challenges in this project. Both the size of the project and its special technical characteristics require specific managerial skills. Due to the size of the project it becomes essential to effectively manage and integrate a large number of suppliers and fabricators, of very different nature and geographically distributed. Project management plans need to cope with this situation. Also, extensive on site activities require intensive on site organization in line with large construction management strategies. Finally, the technical edge of the project requires deep technical understanding at management level in order to be able to take sound strategic decisions throughout the project in terms of the overall project quality, cost and schedule.

Architecture of the 99 bp DNA-six-protein regulatory complex of the lambda att site.

PubMed

Sun, Xingmin; Mierke, Dale F; Biswas, Tapan; Lee, Sang Yeol; Landy, Arthur; Radman-Livaja, Marta

2006-11-17

The highly directional and tightly regulated recombination reaction used to site-specifically excise the bacteriophage lambda chromosome out of its E. coli host chromosome requires the binding of six sequence-specific proteins to a 99 bp segment of the phage att site. To gain structural insights into this recombination pathway, we measured 27 FRET distances between eight points on the 99 bp regulatory DNA bound with all six proteins. Triangulation of these distances using a metric matrix distance-geometry algorithm provided coordinates for these eight points. The resulting path for the protein-bound regulatory DNA, which fits well with the genetics, biochemistry, and X-ray crystal structures describing the individual proteins and their interactions with DNA, provides a new structural perspective into the molecular mechanism and regulation of the recombination reaction and illustrates a design by which different families of higher-order complexes can be assembled from different numbers and combinations of the same few proteins.

Revealing the planar chemistry of two-dimensional heterostructures at the atomic level.

PubMed

Chou, Harry; Ismach, Ariel; Ghosh, Rudresh; Ruoff, Rodney S; Dolocan, Andrei

2015-06-23

Two-dimensional (2D) atomic crystals and their heterostructures are an intense area of study owing to their unique properties that result from structural planar confinement. Intrinsically, the performance of a planar vertical device is linked to the quality of its 2D components and their interfaces, therefore requiring characterization tools that can reveal both its planar chemistry and morphology. Here, we propose a characterization methodology combining (micro-) Raman spectroscopy, atomic force microscopy and time-of-flight secondary ion mass spectrometry to provide structural information, morphology and planar chemical composition at virtually the atomic level, aimed specifically at studying 2D vertical heterostructures. As an example system, a graphene-on-h-BN heterostructure is analysed to reveal, with an unprecedented level of detail, the subtle chemistry and interactions within its layer structure that can be assigned to specific fabrication steps. Such detailed chemical information is of crucial importance for the complete integration of 2D heterostructures into functional devices.

A Mobile Robot for Locomotion Through a 3D Periodic Lattice Environment

NASA Technical Reports Server (NTRS)

Jenett, Benjamin; Cellucci, Daniel; Cheung, Kenneth

2017-01-01

This paper describes a novel class of robots specifically adapted to climb periodic lattices, which we call 'Relative Robots'. These robots use the regularity of the structure to simplify the path planning, align with minimal feedback, and reduce the number of degrees of freedom (DOF) required to locomote. They can perform vital inspection and repair tasks within the structure that larger truss construction robots could not perform without modifying the structure. We detail a specific type of relative robot designed to traverse a cuboctahedral (CubOct) cellular solids lattice, show how the symmetries of the lattice simplify the design, and test these design methodologies with a CubOct relative robot that traverses a 76.2 mm (3 in.) pitch lattice, MOJO (Multi-Objective JOurneying robot). We perform three locomotion tasks with MOJO: vertical climbing, horizontal climbing, and turning, and find that, due to changes in the orientation of the robot relative to the gravity vector, the success rate of vertical and horizontal climbing is significantly different.

Structures, Material and Processes Technology in the Future Launchers Preparatory Program

NASA Astrophysics Data System (ADS)

Baiocco, P.; Ramusat, G.; Breteau, J.; Bouilly, Th.; Lavelle, Fl.; Cardone, T.; Fischer, H.; Appel, S.; Block, U.

2014-06-01

In the frame of the technology / demonstration activity for European launchers developments and evolutions, a top-down / bottom-up approach has been employed to identify promising technologies and alternative conception. The top-down approach consists in looking for system-driven design solutions and the bottom-up approach features design solutions leading to substantial advantages for the system. The main investigations have been devoted to structures, material and process technology.Preliminary specifications have been used in order to permit sub-system design with the goal to find the major benefit for the overall launch system. In this respect competitiveness factors have been defined to down- select the technology and the corresponding optimized design. The development cost, non-recurring cost, industrialization and operational aspects have been considered for the identification of the most interesting solutions. The TRL/IRL has been assessed depending on the manufacturing company and a preliminary development plan has been issued for some technology.The reference launch systems for the technology and demonstration programs are mainly Ariane 6 with its evolutions, VEGA C/E and others possible longer term systems. Requirements and reference structures architectures have been considered in order to state requirements for representative subscale or full scale demonstrators. The major sub-systems and structures analyzed are for instance the upper stage structures, the engine thrust frame (ETF), the inter stage structures (ISS), the cryogenic propellant tanks, the feeding lines and their attachments, the pressurization systems, the payload adapters and fairings. A specific analysis has been devoted to the efficiency of production processes associated to technologies and design features.The paper provides an overview of the main results of the technology and demonstration activities with the associated system benefits. The materials used for the main structures are metallic and composite owing to sub-systems or sub-assemblies proposed for the European launch systems in development and their evolutions.

Environmental site assessments and audits: Building inspection requirements

NASA Astrophysics Data System (ADS)

Lange, John H.; Kaiser, Genevieve; Thomulka, Kenneth W.

1994-01-01

Environmental site assessment criteria were originally developed by organizations that focused, almost exclusively, on surface, subsurface, and pollution source contamination. Many of the hazards associated with indoor environments and building structures were traditionally not considered when evaluating sources and entities of environmental pollution. Since a large number of building materials are potentially hazardous, careful evaluation is necessary. Until recently, little information on building inspection requirements of environmental problems has been published. Traditionally, asbestos has been the main component of concern. The ever-changing environmental standards have dramatically expanded the scope of building surveys. Indoor environmental concerns, for example, currently include formaldehyde, lead-based paint, polychlorinated biphenyls, radon, and indoor air pollution. Environmental regulations are being expanded and developed that specifically include building structures. These regulatory standards are being triggered by an increased awareness of health effects from indoor exposure, fires, spills, and other accidents that have resulted in injury, death, and financial loss. This article discusses various aspects of assessments for building structures.

Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

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

Silvian,L.; Jin, P.; Carmillo, P.

2006-01-01

Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangementmore » characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.« less

Line-scan Raman microscopy complements optical coherence tomography for tumor boundary detection

NASA Astrophysics Data System (ADS)

Sudheendran, Narendran; Qi, Ji; Young, Eric D.; Lazar, Alexander J.; Lev, Dina C.; Pollock, Raphael E.; Larin, Kirill V.; Shih, Wei-Chuan

2014-10-01

Current technique for tumor resection requires biopsy of the tumor region and histological confirmation before the surgeon can be certain that the entire tumor has been resected. This confirmation process is time consuming both for the surgeon and the patient and also requires sacrifice of healthy tissue, motivating the development of novel technologies which can enable real-time detection of tumor-healthy tissue boundary for faster and more efficient surgeries. In this study, the potential of combining structural information from optical coherence tomography (OCT) and molecular information from line-scan Raman microscopy (LSRM) for such an application is presented. The results show a clear presence of boundary between myxoid liposarcoma and normal fat which is easily identifiable both from structural and molecular information. In cases where structural images are indistinguishable, for example, in normal fat and well differentiated liposarcoma (WDLS) or gastrointestinal sarcoma tumor (GIST) and myxoma, distinct molecular spectra have been obtained. The results suggest LSRM can effectively complement OCT to tumor boundary demarcation with high specificity.

Structure and substrate recruitment of the human spindle checkpoint kinase Bub1.

PubMed

Kang, Jungseog; Yang, Maojun; Li, Bing; Qi, Wei; Zhang, Chao; Shokat, Kevan M; Tomchick, Diana R; Machius, Mischa; Yu, Hongtao

2008-11-07

In mitosis, the spindle checkpoint detects a single unattached kinetochore, inhibits the anaphase-promoting complex or cyclosome (APC/C), and prevents premature sister chromatid separation. The checkpoint kinase Bub1 contributes to checkpoint sensitivity through phosphorylating the APC/C activator, Cdc20, and inhibiting APC/C catalytically. We report here the crystal structure of the kinase domain of Bub1, revealing the requirement of an N-terminal extension for its kinase activity. Though the activation segment of Bub1 is ordered and has structural features indicative of active kinases, the C-terminal portion of this segment sterically restricts substrate access to the active site. Bub1 uses docking motifs, so-called KEN boxes, outside its kinase domain to recruit Cdc20, one of two known KEN box receptors. The KEN boxes of Bub1 are required for the spindle checkpoint in human cells. Therefore, its unusual active-site conformation and mode of substrate recruitment suggest that Bub1 has an exquisitely tuned specificity for Cdc20.

Initial planetary base construction techniques and machine implementation

NASA Technical Reports Server (NTRS)

Crockford, William W.

1987-01-01

Conceptual designs of (1) initial planetary base structures, and (2) an unmanned machine to perform the construction of these structures using materials local to the planet are presented. Rock melting is suggested as a possible technique to be used by the machine in fabricating roads, platforms, and interlocking bricks. Identification of problem areas in machine design and materials processing is accomplished. The feasibility of the designs is contingent upon favorable results of an analysis of the engineering behavior of the product materials. The analysis requires knowledge of several parameters for solution of the constitutive equations of the theory of elasticity. An initial collection of these parameters is presented which helps to define research needed to perform a realistic feasibility study. A qualitative approach to estimating power and mass lift requirements for the proposed machine is used which employs specifications of currently available equipment. An initial, unmanned mission scenario is discussed with emphasis on identifying uncompleted tasks and suggesting design considerations for vehicles and primitive structures which use the products of the machine processing.

13. Operational planning for a specific intervention.

PubMed

2014-05-01

Every intervention must follow an operational plan. Operational plans delineate actions required to meet an objective that is part of the strategic plan (overarching goal). Operational plans dictate the critical pathways for the interventions that will be followed during and following the implementation of the intervention. Operational plans include: (1) an introduction and brief situation report; (2) an overview of the task(s), objectives, and the overarching goal to be addressed; (3) the methods that will be employed; (4) planning factors; (5) the resources that will be required including personnel, equipment, and supplies; (6) timelines, benchmarks, and milestones including their respective indicators, startup time, end point, and estimates of the time required for completion; (7) the administrative structure to be employed; (8) an operating budget; (9) the strategy for acquiring the funding required; (10) roles and responsibilities of the personnel including position descriptions and the competencies required of the personnel (skill sets); (11) mechanisms for monitoring the progress including the indicators that will be employed, (12) safety, including health of the personnel, required immunisations, accommodations, and reporting structure; (13) self-sufficiency; and (14) reporting and accounting. There are many generic items in an operational plan that can be used in successive plans. Without a detailed operational plan, interventions are doomed to probable failure and can profoundly negatively impact other projects operational in the area.

Diversity in Requirement of Genetic and Epigenetic Factors for Centromere Function in Fungi ▿

PubMed Central

Roy, Babhrubahan; Sanyal, Kaustuv

2011-01-01

A centromere is a chromosomal region on which several proteins assemble to form the kinetochore. The centromere-kinetochore complex helps in the attachment of chromosomes to spindle microtubules to mediate segregation of chromosomes to daughter cells during mitosis and meiosis. In several budding yeast species, the centromere forms in a DNA sequence-dependent manner, whereas in most other fungi, factors other than the DNA sequence also determine the centromere location, as centromeres were able to form on nonnative sequences (neocentromeres) when native centromeres were deleted in engineered strains. Thus, in the absence of a common DNA sequence, the cues that have facilitated centromere formation on a specific DNA sequence for millions of years remain a mystery. Kinetochore formation is facilitated by binding of a centromere-specific histone protein member of the centromeric protein A (CENP-A) family that replaces a canonical histone H3 to form a specialized centromeric chromatin structure. However, the process of kinetochore formation on the rapidly evolving and seemingly diverse centromere DNAs in different fungal species is largely unknown. More interestingly, studies in various yeasts suggest that the factors required for de novo centromere formation (establishment) may be different from those required for maintenance (propagation) of an already established centromere. Apart from the DNA sequence and CENP-A, many other factors, such as posttranslational modification (PTM) of histones at centric and pericentric chromatin, RNA interference, and DNA methylation, are also involved in centromere formation, albeit in a species-specific manner. In this review, we discuss how several genetic and epigenetic factors influence the evolution of structure and function of centromeres in fungal species. PMID:21908596

Unique Dynamic Properties of DNA Duplexes Containing Interstrand Crosslinks†

PubMed Central

Friedman, Joshua I.; Jiang, Yu Lin; Miller, Paul S.; Stivers, James T.

2010-01-01

Bifunctional DNA alkylating agents form a diverse assortment of covalent DNA interstrand crosslinked (ICL) structures that are potent cytotoxins. Since it is implausible that cells could possess distinct DNA repair systems for each individual ICL, it is believed that common structural and dynamic features of ICL damage are recognized, rather than specific structural characteristics of each cross-linking agent. Investigation of the structural and dynamic properties of ICLs that might be important for recognition has been complicated by heterogeneous incorporation of these lesions into DNA. To address this problem we have synthesized and characterized several homogenous ICL-DNAs containing site–specific staggered N4-cytosine-ethyl-N4-cytosine crosslinks. Staggered crosslinks were introduced in two ways: in a manner that preserves the overall structure of B-form duplex DNA, and in a manner that highly distorts the DNA structure, with the goal of understanding how structural and dynamic properties of diverse ICL duplexes might flag these sites for repair. Measurements of base pair opening dynamics in the B-form ICL duplex by 1H NMR linewidth or imino proton solvent exchange showed that the guanine base opposite to the crosslinked cytosine opened at least an order of magnitude more slowly than when in a control matched normal duplex. To a lesser degree, the B-form ICL also induced a decrease in base pair opening dynamics that extended from the site of the crosslink to adjacent base pairs. In contrast, the non-B-form ICL showed extensive conformational dynamics at the site of the cross link, which extended over the entire DNA sequence. Since DNA duplexes containing the B-form and non-B-form ICL crosslinks have both been shown to be incised when incubated in mammalian whole cell extracts, while a matched normal duplex is not, we conclude that intrinsic DNA dynamics is not a requirement for specific damage incision of these ICLs. Instead, we propose a general model where destabilized ICL-duplexes serve to energetically facilitate binding of DNA repair factors that must induce bubbles or other distortions in the duplex. However, the essential requirement for incision is an immobile Y-junction where the repair factors are stably bound at the site of the ICL, and the two DNA strands are unpaired. PMID:21174443

Receptor binding proteins of Listeria monocytogenes bacteriophages A118 and P35 recognize serovar-specific teichoic acids

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

Bielmann, Regula; Habann, Matthias; Eugster, Marcel R.

Adsorption of a bacteriophage to the host requires recognition of a cell wall-associated receptor by a receptor binding protein (RBP). This recognition is specific, and high affinity binding is essential for efficient virus attachment. The molecular details of phage adsorption to the Gram-positive cell are poorly understood. We present the first description of receptor binding proteins and a tail tip structure for the siphovirus group infecting Listeria monocytogenes. The host-range determining factors in two phages, A118 and P35 specific for L. monocytogenes serovar 1/2 have been determined. Two proteins were identified as RBPs in phage A118. Rhamnose residues in wallmore » teichoic acids represent the binding ligands for both proteins. In phage P35, protein gp16 could be identified as RBP and the role of both rhamnose and N-acetylglucosamine in phage adsorption was confirmed. Immunogold-labeling and transmission electron microscopy allowed the creation of a topological model of the A118 phage tail. - Highlights: • We present the first description of receptor binding proteins and a tail tip structure for the Siphovirus group infecting Listeria monocytogenes. • The host-range determining factors in two phages, A118 and P35 specific for L. monocytogenes serovar 1/2 have been determined. • Rhamnose residues in wall teichoic acids represent the binding ligands for both receptor binding proteins in phage A118. • Rhamnose and N-acetylglucosamine are required for adsorption of phage P35. • We preset a topological model of the A118 phage tail.« less

Comments on the use of network structures to analyse commercial companies’ evolution and their impact on economic behaviour

NASA Astrophysics Data System (ADS)

Costea, Carmen

2006-10-01

Network analysis studies the development of the social structure of relationships around a group or an institutional body, and how it affects beliefs and behaviours. Causal constraints require a special and deeper attention to the social structure. The purpose of this paper is to give a new approach to the idea that this reality should be primarily conceived and investigated from the perspective of the properties of relations between and within units, instead of the properties of these units themselves. The relationship may refer to the exchange of products, labour, information and money. By mapping these relationships, network analysis can help to uncover the emergent and informal communication patterns of commercial companies that may be compared to the formal communication structures. These emergent patterns can be used to explain institutional and individuals’ behaviours. Network analysis techniques focus on the communication structure of an organization that can be subdivided and handled with different approaches. Structural features that can be analysed through the use of network analysis techniques are, for example, the (formal and informal) communication patterns in an organization or the identification of specific groups within an organization. Special attention may be given to specific aspects of communication patterns.