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Sample records for integration chapter cis

  1. Chapter 1: Biomedical knowledge integration.

    PubMed

    Payne, Philip R O

    2012-01-01

    The modern biomedical research and healthcare delivery domains have seen an unparalleled increase in the rate of innovation and novel technologies over the past several decades. Catalyzed by paradigm-shifting public and private programs focusing upon the formation and delivery of genomic and personalized medicine, the need for high-throughput and integrative approaches to the collection, management, and analysis of heterogeneous data sets has become imperative. This need is particularly pressing in the translational bioinformatics domain, where many fundamental research questions require the integration of large scale, multi-dimensional clinical phenotype and bio-molecular data sets. Modern biomedical informatics theory and practice has demonstrated the distinct benefits associated with the use of knowledge-based systems in such contexts. A knowledge-based system can be defined as an intelligent agent that employs a computationally tractable knowledge base or repository in order to reason upon data in a targeted domain and reproduce expert performance relative to such reasoning operations. The ultimate goal of the design and use of such agents is to increase the reproducibility, scalability, and accessibility of complex reasoning tasks. Examples of the application of knowledge-based systems in biomedicine span a broad spectrum, from the execution of clinical decision support, to epidemiologic surveillance of public data sets for the purposes of detecting emerging infectious diseases, to the discovery of novel hypotheses in large-scale research data sets. In this chapter, we will review the basic theoretical frameworks that define core knowledge types and reasoning operations with particular emphasis on the applicability of such conceptual models within the biomedical domain, and then go on to introduce a number of prototypical data integration requirements and patterns relevant to the conduct of translational bioinformatics that can be addressed via the design and

  2. Chapter 1: Biomedical Knowledge Integration

    PubMed Central

    Payne, Philip R. O.

    2012-01-01

    The modern biomedical research and healthcare delivery domains have seen an unparalleled increase in the rate of innovation and novel technologies over the past several decades. Catalyzed by paradigm-shifting public and private programs focusing upon the formation and delivery of genomic and personalized medicine, the need for high-throughput and integrative approaches to the collection, management, and analysis of heterogeneous data sets has become imperative. This need is particularly pressing in the translational bioinformatics domain, where many fundamental research questions require the integration of large scale, multi-dimensional clinical phenotype and bio-molecular data sets. Modern biomedical informatics theory and practice has demonstrated the distinct benefits associated with the use of knowledge-based systems in such contexts. A knowledge-based system can be defined as an intelligent agent that employs a computationally tractable knowledge base or repository in order to reason upon data in a targeted domain and reproduce expert performance relative to such reasoning operations. The ultimate goal of the design and use of such agents is to increase the reproducibility, scalability, and accessibility of complex reasoning tasks. Examples of the application of knowledge-based systems in biomedicine span a broad spectrum, from the execution of clinical decision support, to epidemiologic surveillance of public data sets for the purposes of detecting emerging infectious diseases, to the discovery of novel hypotheses in large-scale research data sets. In this chapter, we will review the basic theoretical frameworks that define core knowledge types and reasoning operations with particular emphasis on the applicability of such conceptual models within the biomedical domain, and then go on to introduce a number of prototypical data integration requirements and patterns relevant to the conduct of translational bioinformatics that can be addressed via the design and

  3. Low Thrust, Deep Throttling, US/CIS Integrated NTRE

    NASA Astrophysics Data System (ADS)

    Culver, Donald W.; Kolganov, Vyacheslav; Rochow, Richard F.

    1994-07-01

    In 1993 our international team performed a follow-on ``Nuclear Thermal Rocket Engine (NTRE) Extended Life Feasibility Assessment'' study for the Nuclear Propulsion Office (NPO) at NASAs Lewis Research Center. The main purpose of this study was to complete the 1992 study matrix to assess NTRE designs at thrust levels of 22.5, 11.3, and 6.8 tonnes, using Commonwealth of Independent States (CIS) reactor technology. An additional Aerojet goal was to continue improving the NTRE concept we had generated. Deep throttling, mission performance optimized engine design parametrics, and reliability/cost enhancing engine system simplifications were studied, because they seem to be the last three basic design improvements sorely needed by post-NERVA NTRE. Deep throttling improves engine life by eliminating damaging thermal and mechanical shocks caused by after-cooling with pulsed coolant flow. Alternately, it improves mission performance with steady flow after-cooling by minimizing reactor over-cooling. Deep throttling also provides a practical transition from high pressures and powers of the high thrust power cycle to the low pressures and powers of our electric power generating mode. Two deep throttling designs are discussed; a workable system that was studied and a simplified system that is recommended for future study. Mission-optimized engine thrust/weight (T/W) and Isp predictions are included along with system flow schemes and concept sketches.

  4. i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.

    PubMed

    Herrmann, Carl; Van de Sande, Bram; Potier, Delphine; Aerts, Stein

    2012-08-01

    The field of regulatory genomics today is characterized by the generation of high-throughput data sets that capture genome-wide transcription factor (TF) binding, histone modifications, or DNAseI hypersensitive regions across many cell types and conditions. In this context, a critical question is how to make optimal use of these publicly available datasets when studying transcriptional regulation. Here, we address this question in Drosophila melanogaster for which a large number of high-throughput regulatory datasets are available. We developed i-cisTarget (where the 'i' stands for integrative), for the first time enabling the discovery of different types of enriched 'regulatory features' in a set of co-regulated sequences in one analysis, being either TF motifs or 'in vivo' chromatin features, or combinations thereof. We have validated our approach on 15 co-expressed gene sets, 21 ChIP data sets, 628 curated gene sets and multiple individual case studies, and show that meaningful regulatory features can be confidently discovered; that bona fide enhancers can be identified, both by in vivo events and by TF motifs; and that combinations of in vivo events and TF motifs further increase the performance of enhancer prediction.

  5. Chapter 636, Voluntary Integration in Massachusetts. Successful Programs of Choice.

    ERIC Educational Resources Information Center

    Spier, Adele W.; And Others

    A statewide study was conducted to identify and describe successful voluntary school desegregation programs funded under Chapter 636, a 1974 amendment to Massachussets' Racial Imbalance Law. Programs selected were of four types: (1) school-based (elementary, middle, and high); (2) school system- or district-wide; (3) part-time and full-time…

  6. Haemophilia care in India: innovations and integrations by various chapters of Haemophilia Federation of India (HFI).

    PubMed

    Ghosh, K; Shetty, S; Sahu, D

    2010-01-01

    Care of persons with haemophilia (PWH) in western countries is the responsibility of the government of those countries with or without funding from health insurers. Haemophilia societies in western countries work as pressure groups to ensure better care, and they disseminate information on the disease and some of the societies even support medical research for haemophilia care. In India, Haemophilia Federation of India (HFI) was established in 1982 with few haemophilia families and sympathizers of their cause; subsequently more than 65 chapters involving more than 12 500 PWH came up under HFI. HFI and its constituent chapters are unique in the world in the sense that they are not only trying to involve state and federal government to take responsibility for delivering haemophilia care, but they are also using various innovative and integrative techniques to deliver haemophilia care to PWH themselves, till the time federal and state governments of the country make suitable arrangement for their care. In this study, several of these approaches are discussed with the understanding that 80% of worlds' haemophilia population needs similar help, and the national haemophilia organizations (NMO) of various developing countries will find some of the approaches useful and adaptable to their own circumstances.

  7. Conjugative Transfer and cis-Mobilization of a Genomic Island by an Integrative and Conjugative Element of Streptococcus agalactiae

    PubMed Central

    Puymège, Aurore; Bertin, Stéphane; Chuzeville, Sarah; Guédon, Gérard

    2013-01-01

    Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913–6917, 2008). We investigated here the mobility of the elements integrated into the 3′ end of a tRNALys gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNALys) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3′ end of the tRNALys gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion. PMID:23275243

  8. Conjugative transfer and cis-mobilization of a genomic island by an integrative and conjugative element of Streptococcus agalactiae.

    PubMed

    Puymège, Aurore; Bertin, Stéphane; Chuzeville, Sarah; Guédon, Gérard; Payot, Sophie

    2013-03-01

    Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913-6917, 2008). We investigated here the mobility of the elements integrated into the 3' end of a tRNA(Lys) gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNA(Lys)) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3' end of the tRNA(Lys) gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion.

  9. Digital Systems Validation Handbook. Volume 2. Chapter 18. Avionic Data Bus Integration Technology

    DTIC Science & Technology

    1993-11-01

    U.S. Department of Transportation PFe 1rs Aviation Administration DOT/FAA/CT-88/10 HANDBOOK- VOLUME H DIGITAL SYSTEMS VALIDATION - CHAPTER 18 tw...18-29 improve identification, control, and auditing of software. SCM and SQA methods in RTCA/DO-178A are drawn directly from proven methods of hardware...procedures, and practices; reviews and audits ; configuration management; medium control; testing; supplier control; and appropriate records. A brief

  10. cis-1,2-Dichloroethylene

    Integrated Risk Information System (IRIS)

    EPA / 635 / R - 09 / 006 F www.epa.gov / iris TOXICOLOGICAL REVIEW OF cis - 1,2 - DICHLOROETHYLENE and trans - 1,2 - DICHLOROETHYLENE ( CAS Nos . cis : 156 - 59 - 2 ; trans : 156 - 60 - 5 ; mixture : 540 - 59 - 0 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS )

  11. Designing Adaptive Low-Dissipative High Order Schemes for Long-Time Integrations. Chapter 1

    NASA Technical Reports Server (NTRS)

    Yee, Helen C.; Sjoegreen, B.; Mansour, Nagi N. (Technical Monitor)

    2001-01-01

    A general framework for the design of adaptive low-dissipative high order schemes is presented. It encompasses a rather complete treatment of the numerical approach based on four integrated design criteria: (1) For stability considerations, condition the governing equations before the application of the appropriate numerical scheme whenever it is possible; (2) For consistency, compatible schemes that possess stability properties, including physical and numerical boundary condition treatments, similar to those of the discrete analogue of the continuum are preferred; (3) For the minimization of numerical dissipation contamination, efficient and adaptive numerical dissipation control to further improve nonlinear stability and accuracy should be used; and (4) For practical considerations, the numerical approach should be efficient and applicable to general geometries, and an efficient and reliable dynamic grid adaptation should be used if necessary. These design criteria are, in general, very useful to a wide spectrum of flow simulations. However, the demand on the overall numerical approach for nonlinear stability and accuracy is much more stringent for long-time integration of complex multiscale viscous shock/shear/turbulence/acoustics interactions and numerical combustion. Robust classical numerical methods for less complex flow physics are not suitable or practical for such applications. The present approach is designed expressly to address such flow problems, especially unsteady flows. The minimization of employing very fine grids to overcome the production of spurious numerical solutions and/or instability due to under-resolved grids is also sought. The incremental studies to illustrate the performance of the approach are summarized. Extensive testing and full implementation of the approach is forthcoming. The results shown so far are very encouraging.

  12. Integration of coral reef ecosystem process studies and remote sensing: Chapter 5

    USGS Publications Warehouse

    Brook, John; Yates, Kimberly; Halley, Robert

    2006-01-01

    anthropogenic causes (Brown, 1988). Models of coral reef ecosystems, parameterized by process measurements and scaled in time-space using remote sensing, have the potential to address pressing research questions that are central to devising valid management strategies (Grigg el al., 1984; Hatcher, 1997b). To attain this goal, ecosystem-level models that integrate studies of physical and chemical forcing with observed biological and geological responses are required. This interdisciplinary approach to understanding reef biogeochemical dynamics can allow investigations that integrate the scales of time and space (Hatcher, 1997a), thereby enabling prediction of coral reef change (Andréfouët and Payri, 2001). In turn, prediction of holistic ecosystem function within various environmental focusing scenarios has substantial promise in mitigating future disturbance. Indeed, management of coral reefs at the ecosystem level has been suggested as the only meaningful approach to preserving coral reefs (Bohnsack and Ault, 1996; Christensen et al., 1996).

  13. Author Contribution to the Pu Handbook II: Chapter 37 LLNL Integrated Sample Preparation Glovebox (TEM) Section

    SciTech Connect

    Wall, Mark A.

    2016-10-25

    The development of our Integrated Actinide Sample Preparation Laboratory (IASPL) commenced in 1998 driven by the need to perform transmission electron microscopy studies on naturally aged plutonium and it’s alloys looking for the microstructural effects of the radiological decay process (1). Remodeling and construction of a laboratory within the Chemistry and Materials Science Directorate facilities at LLNL was required to turn a standard radiological laboratory into a Radiological Materials Area (RMA) and Radiological Buffer Area (RBA) containing type I, II and III workplaces. Two inert atmosphere dry-train glove boxes with antechambers and entry/exit fumehoods (Figure 1), having a baseline atmosphere of 1 ppm oxygen and 1 ppm water vapor, a utility fumehood and a portable, and a third double-walled enclosure have been installed and commissioned. These capabilities, along with highly trained technical staff, facilitate the safe operation of sample preparation processes and instrumentation, and sample handling while minimizing oxidation or corrosion of the plutonium. In addition, we are currently developing the capability to safely transfer small metallographically prepared samples to a mini-SEM for microstructural imaging and chemical analysis. The gloveboxes continue to be the most crucial element of the laboratory allowing nearly oxide-free sample preparation for a wide variety of LLNL-based characterization experiments, which includes transmission electron microscopy, electron energy loss spectroscopy, optical microscopy, electrical resistivity, ion implantation, X-ray diffraction and absorption, magnetometry, metrological surface measurements, highpressure diamond anvil cell equation-of-state, phonon dispersion measurements, X-ray absorption and emission spectroscopy, and differential scanning calorimetry. The sample preparation and materials processing capabilities in the IASPL have also facilitated experimentation at world-class facilities such as the

  14. An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data

    PubMed Central

    Ji, Hongkai; Jiang, Hui; Ma, Wenxiu; Johnson, David S.; Myers, Richard M.; Wong, Wing H.

    2008-01-01

    CisGenome is a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. It is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate (FDR) computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP-chip analysis methods, the software contains new statistical methods designed specifically for ChIP-seq data. CisGenome has a modular design so that it supports interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure, conservation, and DNA sequence and motif information. We illustrate the use of these tools by a comparative analysis of ChIP-chip and ChIP-seq data for the transcription factor NRSF/REST, a study of ChIP-seq analysis without negative control sample, and an analysis of a novel motif in Nanog- and Sox2-binding regions. PMID:18978777

  15. Representative Agricultural Pathways and Scenarios for Regional Integrated Assessment of Climate Change Impacts, Vulnerability, and Adaptation. 5; Chapter

    NASA Technical Reports Server (NTRS)

    Valdivia, Roberto O.; Antle, John M.; Rosenzweig, Cynthia; Ruane, Alexander C.; Vervoort, Joost; Ashfaq, Muhammad; Hathie, Ibrahima; Tui, Sabine Homann-Kee; Mulwa, Richard; Nhemachena, Charles; Ponnusamy, Paramasivam; Rasnayaka, Herath; Singh, Harbir

    2015-01-01

    The global change research community has recognized that new pathway and scenario concepts are needed to implement impact and vulnerability assessment where precise prediction is not possible, and also that these scenarios need to be logically consistent across local, regional, and global scales. For global climate models, representative concentration pathways (RCPs) have been developed that provide a range of time-series of atmospheric greenhouse-gas concentrations into the future. For impact and vulnerability assessment, new socio-economic pathway and scenario concepts have also been developed, with leadership from the Integrated Assessment Modeling Consortium (IAMC).This chapter presents concepts and methods for development of regional representative agricultural pathways (RAOs) and scenarios that can be used for agricultural model intercomparison, improvement, and impact assessment in a manner consistent with the new global pathways and scenarios. The development of agriculture-specific pathways and scenarios is motivated by the need for a protocol-based approach to climate impact, vulnerability, and adaptation assessment. Until now, the various global and regional models used for agricultural-impact assessment have been implemented with individualized scenarios using various data and model structures, often without transparent documentation, public availability, and consistency across disciplines. These practices have reduced the credibility of assessments, and also hampered the advancement of the science through model intercomparison, improvement, and synthesis of model results across studies. The recognition of the need for better coordination among the agricultural modeling community, including the development of standard reference scenarios with adequate agriculture-specific detail led to the creation of the Agricultural Model Intercomparison and Improvement Project (AgMIP) in 2010. The development of RAPs is one of the cross-cutting themes in AgMIP's work

  16. Chapter 1: Direct Normal Radiation

    SciTech Connect

    Myer, Daryl R.

    2016-04-15

    This chapter addresses the quantitative and qualitative aspects of the solar resource, the direct solar radiation. It discusses the total or integrated broadband direct beam extraterrestrial radiation (ETR). This total integrated irradiance is comprised of photons of electromagnetic radiation. The chapter also discusses the impact of the atmosphere and its effect upon the direct normal irradiance (DNI) beam radiation. The gases and particulates present in the atmosphere traversed by the direct beam reflect, absorb, and scatter differing spectral regions and proportions of the direct beam, and act as a variable filter. Knowledge of the available broadband DNI beam radiation resource data is essential in designing a concentrating photovoltaic (CPV) system. Spectral variations in the DNI beam radiation affect the performance of a CPV system depending on the solar cell technology used. The chapter describes propagation and scattering processes of circumsolar radiation (CSR), which includes the Mie scattering from large particles.

  17. Materials for Spacecraft. Chapter 6

    NASA Technical Reports Server (NTRS)

    Finckenor, Miria M.

    2016-01-01

    The general knowledge in this chapter is intended for a broad variety of spacecraft: manned or unmanned, low Earth to geosynchronous orbit, cis-lunar, lunar, planetary, or deep space exploration. Materials for launch vehicles are covered in chapter 7. Materials used in the fabrication of spacecraft hardware should be selected by considering the operational requirements for the particular application and the design engineering properties of the candidate materials. The information provided in this chapter is not intended to replace an in-depth materials study but rather to make the spacecraft designer aware of the challenges for various types of materials and some lessons learned from more than 50 years of spaceflight. This chapter discusses the damaging effects of the space environment on various materials and what has been successfully used in the past or what may be used for a more robust design. The material categories covered are structural, thermal control for on-orbit and re-entry, shielding against radiation and meteoroid/space debris impact, optics, solar arrays, lubricants, seals, and adhesives. Spacecraft components not directly exposed to space must still meet certain requirements, particularly for manned spacecraft where toxicity and flammability are concerns. Requirements such as fracture control and contamination control are examined, with additional suggestions for manufacturability. It is important to remember that the actual hardware must be tested to understand the real, "as-built" performance, as it could vary from the design intent. Early material trades can overestimate benefits and underestimate costs. An example of this was using graphite/epoxy composite in the International Space Station science racks to save weight. By the time the requirements for vibration isolation, Space Shuttle frequencies, and experiment operations were included, the weight savings had evaporated.

  18. Tourette Association Chapters

    MedlinePlus

    ... com Arizona Email: info@tsa-az.org Website: http://tsa-az.org/ Arkansas Support Group of Northwest ... California/Hawaii Chapter Email: cbrackett2004@yahoo.com Website: http://www.tsanorcal-hawaii.org Southern California Chapter Phone: ...

  19. Melt inclusions: Chapter 6

    USGS Publications Warehouse

    ,; Lowenstern, J. B.

    2014-01-01

    Melt inclusions are small droplets of silicate melt that are trapped in minerals during their growth in a magma. Once formed, they commonly retain much of their initial composition (with some exceptions) unless they are re-opened at some later stage. Melt inclusions thus offer several key advantages over whole rock samples: (i) they record pristine concentrations of volatiles and metals that are usually lost during magma solidification and degassing, (ii) they are snapshots in time whereas whole rocks are the time-integrated end products, thus allowing a more detailed, time-resolved view into magmatic processes (iii) they are largely unaffected by subsolidus alteration. Due to these characteristics, melt inclusions are an ideal tool to study the evolution of mineralized magma systems. This chapter first discusses general aspects of melt inclusions formation and methods for their investigation, before reviewing studies performed on mineralized magma systems.

  20. Chapter 6: Temperature

    USGS Publications Warehouse

    Jones, Leslie A.; Muhlfeld, Clint C.; Hauer, F. Richard; F. Richard Hauer,; Lamberti, G.A.

    2017-01-01

    Stream temperature has direct and indirect effects on stream ecology and is critical in determining both abiotic and biotic system responses across a hierarchy of spatial and temporal scales. Temperature variation is primarily driven by solar radiation, while landscape topography, geology, and stream reach scale ecosystem processes contribute to local variability. Spatiotemporal heterogeneity in freshwater ecosystems influences habitat distributions, physiological functions, and phenology of all aquatic organisms. In this chapter we provide an overview of methods for monitoring stream temperature, characterization of thermal profiles, and modeling approaches to stream temperature prediction. Recent advances in temperature monitoring allow for more comprehensive studies of the underlying processes influencing annual variation of temperatures and how thermal variability may impact aquatic organisms at individual, population, and community based scales. Likewise, the development of spatially explicit predictive models provide a framework for simulating natural and anthropogenic effects on thermal regimes which is integral for sustainable management of freshwater systems.

  1. Chapter Four: Discursive Resources

    ERIC Educational Resources Information Center

    Young, Richard F.

    2008-01-01

    In this chapter, the focus of attention moves from the contexts described in chapter 3 to the verbal, nonverbal, and interactional resources that participants employ in discursive practices. These resources are discussed within the frame of participation status and participation framework proposed by Goffman. Verbal resources employed by…

  2. Status of flexible CIS research at ISET

    NASA Technical Reports Server (NTRS)

    Basol, B. M.; Kapur, V. K.; Minnick, A.; Halani, A.; Leidholm, C. R.

    1994-01-01

    Polycrystalline thin film solar cells fabricated on light-weight, flexible substrates are very attractive for space applications. In this work CulnSe2 (CIS) based thin film devices were processed on metallic foil substrates using the selenization technique. CIS deposition method involved reaction of electron-bean evaporated Cu-In precursor layers with a selenizing atmosphere at around 400 C. Several metallic foils such as Mo, Ti, Al, Ni, and Cu were evaluated as possible substrates for these devices. Solar cells with AM1.5 efficiencies of 9.0-9.34 percent and good mechanical integrity were demonstrated on Mo and Ti foils. Monolithic integration of these devices was also demonstrated up to 4 in x 4 in size.

  3. Cis-regulatory mutations in human disease

    PubMed Central

    2009-01-01

    Cis-acting regulatory sequences are required for the proper temporal and spatial control of gene expression. Variation in gene expression is highly heritable and a significant determinant of human disease susceptibility. The diversity of human genetic diseases attributed, in whole or in part, to mutations in non-coding regulatory sequences is on the rise. Improvements in genome-wide methods of associating genetic variation with human disease and predicting DNA with cis-regulatory potential are two of the major reasons for these recent advances. This review will highlight select examples from the literature that have successfully integrated genetic and genomic approaches to uncover the molecular basis by which cis-regulatory mutations alter gene expression and contribute to human disease. The fine mapping of disease-causing variants has led to the discovery of novel cis-acting regulatory elements that, in some instances, are located as far away as 1.5 Mb from the target gene. In other cases, the prior knowledge of the regulatory landscape surrounding the gene of interest aided in the selection of enhancers for mutation screening. The success of these studies should provide a framework for following up on the large number of genome-wide association studies that have identified common variants in non-coding regions of the genome that associate with increased risk of human diseases including, diabetes, autism, Crohn's, colorectal cancer, and asthma, to name a few. PMID:19641089

  4. Cis-regulatory mutations in human disease.

    PubMed

    Epstein, Douglas J

    2009-07-01

    Cis-acting regulatory sequences are required for the proper temporal and spatial control of gene expression. Variation in gene expression is highly heritable and a significant determinant of human disease susceptibility. The diversity of human genetic diseases attributed, in whole or in part, to mutations in non-coding regulatory sequences is on the rise. Improvements in genome-wide methods of associating genetic variation with human disease and predicting DNA with cis-regulatory potential are two of the major reasons for these recent advances. This review will highlight select examples from the literature that have successfully integrated genetic and genomic approaches to uncover the molecular basis by which cis-regulatory mutations alter gene expression and contribute to human disease. The fine mapping of disease-causing variants has led to the discovery of novel cis-acting regulatory elements that, in some instances, are located as far away as 1.5 Mb from the target gene. In other cases, the prior knowledge of the regulatory landscape surrounding the gene of interest aided in the selection of enhancers for mutation screening. The success of these studies should provide a framework for following up on the large number of genome-wide association studies that have identified common variants in non-coding regions of the genome that associate with increased risk of human diseases including, diabetes, autism, Crohn's, colorectal cancer, and asthma, to name a few.

  5. Chapter 9: Reliability

    SciTech Connect

    Algora, Carlos; Espinet-Gonzalez, Pilar; Vazquez, Manuel; Bosco, Nick; Miller, David; Kurtz, Sarah; Rubio, Francisca; McConnell,Robert

    2016-04-15

    This chapter describes the accumulated knowledge on CPV reliability with its fundamentals and qualification. It explains the reliability of solar cells, modules (including optics) and plants. The chapter discusses the statistical distributions, namely exponential, normal and Weibull. The reliability of solar cells includes: namely the issues in accelerated aging tests in CPV solar cells, types of failure and failures in real time operation. The chapter explores the accelerated life tests, namely qualitative life tests (mainly HALT) and quantitative accelerated life tests (QALT). It examines other well proven and experienced PV cells and/or semiconductor devices, which share similar semiconductor materials, manufacturing techniques or operating conditions, namely, III-V space solar cells and light emitting diodes (LEDs). It addresses each of the identified reliability issues and presents the current state of the art knowledge for their testing and evaluation. Finally, the chapter summarizes the CPV qualification and reliability standards.

  6. Chapter 9: Electronics

    SciTech Connect

    Grupen, Claus; Shwartz, Boris A.

    2006-12-19

    Sophisticated front-end electronics are a key part of practically all modern radiation detector systems. This chapter introduces the basic principles and their implementation. Topics include signal acquisition, electronic noise, pulse shaping (analog and digital), and data readout techniques.

  7. Chapter on Distributed Computing

    DTIC Science & Technology

    1989-02-01

    MASSACHUSETTS LABORATORY FOR INSTITUTE OF COMPUTER SCIENCE TECHNOLOGY ("D / o O MIT/LCS/TM-384 CHAPTER ON DISTRIBUTED COMPUTING Leslie Lamport Nancy...22217 ELEMENT NO. NO. NO. ACCESSION NO. 11. TITLE (Miude Secuwity Ciaifiation) Chapter on Distributed Computing 12. PERSONAL AUTHOR(S) Lamport... distributed computing , distributed systems models, dis- tributed algorithms, message-passing, shared variables, 19. UBSTRACT (Continue on reverse if

  8. Streamflow data: Chapter 13

    USGS Publications Warehouse

    Wiche, Gregg J.; Holmes, Robert

    2016-01-01

    Streamflow data are vital for a variety of water-resources issues, from flood warning to water supply planning. The collection of streamflow data is usually an involved and complicated process. This chapter serves as an overview of the streamflow data collection process. Readers with the need for the detailed information on the streamflow data collection process are referred to the many references noted in this chapter.

  9. Diagnostic and vaccine chapter.

    PubMed

    Wolfram, J H; Kokanov, S K; Verkhovsky, O A

    2010-10-01

    The first report in this chapter describes the development of a killed composite vaccine. This killed vaccine is non-infectious to humans, other animals, and the environment. The vaccine has low reactivity, is non-abortive, and does not induce pathomorphological alterations to the organs of vaccinated animals. The second report of this chapter describes the diagnostic value of a competitive enzyme-linked immunosorbent assay for detecting Brucella-specific antibodies and its ability to discriminate vaccinated cattle from infected cattle. The results indicated that the competitive enzyme-linked immunosorbent assay is more sensitive than traditional tests for detecting antibodies to Brucella abortus in naturally and experimentally infected cattle.

  10. Chapter 3: Energy Security

    SciTech Connect

    Foust, Thomas D.; Arent, Doug; de Carvalho Macedo, Isaias; Goldemberg, Jose; Hoysala, Chanakya; Filho, Rubens Maciel; Nigro, Francisco E. B.; Richard, Tom L.; Saddler, Jack; Samseth, Jon; Somerville, Chris R.

    2015-04-01

    This chapter considers the energy security implications and impacts of bioenergy. We provide an assessment to answer the following questions: What are the implications for bioenergy and energy security within the broader policy environment that includes food and water security, development, economic productivity, and multiple foreign policy aspects? What are the conditions under which bioenergy contributes positively to energy security?

  11. Chapter Three: Investigating Context

    ERIC Educational Resources Information Center

    Young, Richard F.

    2008-01-01

    This chapter begins with the statement that all talk happens somewhere, somehow, at some time and is produced by somebody for some purpose, and the approach that practice theorists have taken is that talk and its context are inseparable. The challenges that face an analyst of practice are then to describe the context, describe the talk, and…

  12. Hurrah for Chapter Books.

    ERIC Educational Resources Information Center

    Jones, Glenowyn L.

    This annotated bibliography contains a list of 42 recent Chapter Books. The bibliography is divided into the following topics: Adventure-Survival (3 titles); Autobiography-Biography (3 titles); Death (1 title); Easy Readers (8 titles); Good Reading (12 titles); Historical Fiction (10 titles); Mystery (3 titles); Newbery Award Winner, 2000; and…

  13. CisLunar Habitat Internal Architecture Design Criteria

    NASA Technical Reports Server (NTRS)

    Jones, R.; Kennedy, K.; Howard, R.; Whitmore, M.; Martin, C.; Garate, J.

    2017-01-01

    BACKGROUND: In preparation for human exploration to Mars, there is a need to define the development and test program that will validate deep space operations and systems. In that context, a Proving Grounds CisLunar habitat spacecraft is being defined as the next step towards this goal. This spacecraft will operate differently from the ISS or other spacecraft in human history. The performance envelope of this spacecraft (mass, volume, power, specifications, etc.) is being defined by the Future Capabilities Study Team. This team has recognized the need for a human-centered approach for the internal architecture of this spacecraft and has commissioned a CisLunar Phase-1 Habitat Internal Architecture Study Team to develop a NASA reference configuration, providing the Agency with a "smart buyer" approach for future acquisition. THE CISLUNAR HABITAT INTERNAL ARCHITECTURE STUDY: Overall, the CisLunar Habitat Internal Architecture study will address the most significant questions and risks in the current CisLunar architecture, habitation, and operations concept development. This effort is achieved through definition of design criteria, evaluation criteria and process, design of the CisLunar Habitat Phase-1 internal architecture, and the development and fabrication of internal architecture concepts combined with rigorous and methodical Human-in-the-Loop (HITL) evaluations and testing of the conceptual innovations in a controlled test environment. The vision of the CisLunar Habitat Internal Architecture Study is to design, build, and test a CisLunar Phase-1 Habitat Internal Architecture that will be used for habitation (e.g. habitability and human factors) evaluations. The evaluations will mature CisLunar habitat evaluation tools, guidelines, and standards, and will interface with other projects such as the Advanced Exploration Systems (AES) Program integrated Power, Avionics, Software (iPAS), and Logistics for integrated human-in-the-loop testing. The mission of the Cis

  14. Vibrational overtone spectrum of matrix isolated cis, cis-HOONO.

    PubMed

    Zhang, Xu; Nimlos, Mark R; Ellison, G Barney; Varner, Mychel E; Stanton, John F

    2007-05-07

    Cis, cis-peroxynitrous acid is known to be an intermediate in atmospheric reactions between OH and NO2 as well as HOO and NO. The infrared absorption spectra of matrix-isolated cc-HOONO and cc-DOONO in argon have been observed in the range of 500-8000 cm-1. Besides the seven fundamental vibrational modes that have been assigned earlier for this molecule [Zhang et al., J. Chem. Phys. 124, 084305 (2006)], more than 50 of the overtone and combination bands have been observed for cc-HOONO and cc-DOONO. Ab initio CCSD(T)/atomic natural orbital anharmonic force field calculations were used to help guide the assignments. Based on this study of the vibrational overtone transitions of cis, cis-HOONO that go as high as 8000 cm-1 and the earlier paper on the vibrational fundamentals, we conclude that the CCSD(T)/ANO anharmonic frequencies seem to correct to +/-35 cm-1. The success of the theoretically predicted anharmonic frequencies {upsilon} in assigning overtone spectra of HOONO up to 8000 cm-1 suggests that the CCSD(T)/ANO method is producing a reliable potential energy surface for this reactive molecule.

  15. DBMS UTILIZATION: A Corporate Information System (CIS) development approach

    NASA Technical Reports Server (NTRS)

    Rozett, P.

    1983-01-01

    The Corporate Information System (CIS), an integrated information system intended to tie the corporation together as a functioning entity, is described. In addition to being a major upgraded automated data processing system, the CIS is a management philosophy which recognizes data as a valuable corporate resource and which distinguishes between data and selected data, or information. It further recognizes that different users need different kinds of information. Plans for CIS development are discussed. It will offer its users not just after-the-fact data, but timely information in a format that is meaningful and useful to the particular user, so that the information can be applied in planning, controlling, and decision making by all levels of management. In effect, CIS will help the corporation itself to function as a total, integrated system by typing together administrative activities through information exchange. The CIS supports the operational, tactical control, and strategic planning functions of the corporation. Operational functions are the day-to-day processing necessary to support the corporation's work, such as purchasing and payroll.

  16. Nutrient dynamics: Chapter 3

    USGS Publications Warehouse

    Likens, Gene E.; LaBaugh, James W.; Buso, Donald C.; Bade, Darren; Winter, Thomas C.; Likens, Gene E.

    2009-01-01

    This chapter focuses on the variability and trends in chemical concentrations and fluxes at Mirror Lake during the period 1981–2000. It examines the water and chemical budgets of Mirror Lake to identify and understand better long-term trends in the chemical characteristics of the lake. It also identifies the causes of changes in nutrient concentrations and examines the contribution of hydrologic pathways to the contamination of Mirror Lake by road salt. The role of groundwater and precipitation on water and chemical budgets of the lake are also examined.

  17. Polymorphism of linoleic acid (cis-9, cis-12-octadecadienoic acid) and alpha-linolenic acid (cis-9, cis-12, cis-15-octadecatrienoic acid).

    PubMed

    Ueno, S; Miyazaki, A; Yano, J; Furukawa, Y; Suzuki, M; Sato, K

    2000-10-01

    Crystallization and polymorphic properties of linoleic acid (cis-9, cis-12-Octadecadienoic acid) (LA) and alpha-linolenic acid (cis-9, cis-12, cis-15-Octadecatrienoic acid) (alpha-LNA) have been studied by optical microscopy, differential scanning calorimetry (DSC) and X-ray diffraction (XRD). The DSC analyses presented three polymorphs in LA, and two polymorphs in alpha-LNA. The XRD patterns of the higher- and lower-temperature forms in LA and alpha-LNA showed orthorhombic O'(//)+O-like and O'(//) subcell, which were similar to those of alpha- and gamma-forms of mono-unsaturated fatty acids, respectively. From the solvent crystallization of LA and alpha-LNA in acetonitrile, single crystals of the higher temperature polymorphs have been obtained. The crystal habits of truncated rhombic shape were also similar to those of alpha-forms of the mono-unsaturated fatty acids. The enthalpy and entropy values of fusion and dissolution of the alpha-forms of LA, alpha-LNA and oleic acid showed that the two values decreased with increasing number of the cis-double bond.

  18. Cis-Lunar Base Camp

    NASA Technical Reports Server (NTRS)

    Merrill, Raymond G.; Goodliff, Kandyce E.; Mazanek, Daniel D.; Reeves, John D., Jr.

    2012-01-01

    Historically, when mounting expeditions into uncharted territories, explorers have established strategically positioned base camps to pre-position required equipment and consumables. These base camps are secure, safe positions from which expeditions can depart when conditions are favorable, at which technology and operations can be tested and validated, and facilitate timely access to more robust facilities in the event of an emergency. For human exploration missions into deep space, cis-lunar space is well suited to serve as such a base camp. The outer regions of cis-lunar space, such as the Earth-Moon Lagrange points, lie near the edge of Earth s gravity well, allowing equipment and consumables to be aggregated with easy access to deep space and to the lunar surface, as well as more distant destinations, such as near-Earth Asteroids (NEAs) and Mars and its moons. Several approaches to utilizing a cis-lunar base camp for sustainable human exploration, as well as some possible future applications are identified. The primary objective of the analysis presented in this paper is to identify options, show the macro trends, and provide information that can be used as a basis for more detailed mission development. Compared within are the high-level performance and cost of 15 preliminary cis-lunar exploration campaigns that establish the capability to conduct crewed missions of up to one year in duration, and then aggregate mass in cis-lunar space to facilitate an expedition from Cis-Lunar Base Camp. Launch vehicles, chemical propulsion stages, and electric propulsion stages are discussed and parametric sizing values are used to create architectures of in-space transportation elements that extend the existing in-space supply chain to cis-lunar space. The transportation options to cis-lunar space assessed vary in efficiency by almost 50%; from 0.16 to 0.68 kg of cargo in cis-lunar space for every kilogram of mass in Low Earth Orbit (LEO). For the 15 cases, 5-year campaign

  19. Chapter 7: Microalgae

    SciTech Connect

    Efroymson, Rebecca; Coleman, Andre; Wigmosta, Mark; Schoenung, Susan; Sokhansanj, Shahab; Langholtz, Matthew; Davis, Ryan

    2016-07-01

    This chapter of the 2016 Billion-Ton Report provides an estimate of biomass potential at given minimum selling prices. This is not a projection of actual measured biomass or a simulation of commercial projects. Biomass potential is estimated based on 30 years of hourly local climate and strain-specific biophysical characteristics using the Biomass Assessment Tool (BAT), assuming sufficient available nutrients (including CO2). As is the case for terrestrial feedstocks, important resource analysis questions for algae include not only how much of the crop may be available but also what price might be needed to procure that supply. Identifying resource co-location opportunities for algal biofuel facilities has the potential to reduce costs, utilize waste resources, and focus attention on appropriate technologies and locations for commercialization.

  20. Chapter 20: Graphite

    SciTech Connect

    Burchell, Timothy D

    2012-01-01

    Graphite is truly a unique material. Its structure, from the nano- to the millimeter scale give it remarkable properties that lead to numerous and diverse applications. Graphite bond anisotropy, with strong in-plane covalent bonds and weak van der Waals type bonding between the planes, gives graphite its unique combination of properties. Easy shear of the crystal, facilitated by weak interplaner bonds allows graphite to be used as a dry lubricant, and is responsible for the substances name! The word graphite is derived from the Greek to write because of graphites ability to mark writing surfaces. Moreover, synthetic graphite contains within its structure, porosity spanning many orders of magnitude in size. The thermal closure of these pores profoundly affects the properties for example, graphite strength increases with temperature to temperatures in excess of 2200 C. Consequently, graphite is utilized in many high temperature applications. The basic physical properties of graphite are reviewed here. Graphite applications include metallurgical; (aluminum and steel production), single crystal silicon production, and metal casting; electrical (motor brushes and commutators); mechanical (seals, bearings and bushings); and nuclear applications, (see Chapter 91, Nuclear Graphite). Here we discuss the structure, manufacture, properties, and applications of Graphite.

  1. Xenobiotics: Chapter 15

    USGS Publications Warehouse

    Bridges, Christine M.; Semlitsch, Raymond D.; Lannoo, Michael

    2005-01-01

    While a number of compounds have been reported as toxic to amphibians, until recently, there have been conspicuously few ecotoxicological studies concerning amphibians. Studies are now focusing on the effects of xenobiotics on amphibians, an interest likely stimulated by widespread reports of amphibian declines. It has been speculated that chemical contamination may be partially to blame for some documented amphibian declines, by disrupting growth, reproduction, and behavior. However, evidence that xenobiotics are directly to blame for population declines is sparse because environmental concentrations are typically not great enough to generate direct mortality. Although the effects of environmental contaminants on the amphibian immune system are currently unknown, it is possible that exposure to stressors such as organic pollutants (which enter ecosystems in the form of pesticides) may depress immune system function, thus allowing greater susceptibility to fungal infections. This chapter discusses toxicity testing for xenobiotics and presents the results of a study that has focused on the subtle effects of sublethal concentrations of the chemical carbaryl on tadpoles.

  2. IRIS Toxicological Review of Cis-& Trans-1,2-Dichloroethylene (External Review Draft)

    EPA Science Inventory

    EPA is conducting a peer review of the scientific basis supporting the human health hazard and dose-response assessment of cis- and trans-1,2-dichloroethylene that will appear in the Integrated Risk Information System (IRIS) database.

  3. Recycling Of Cis Photovoltaic Waste

    DOEpatents

    Drinkard, Jr., William F.; Long, Mark O.; Goozner; Robert E.

    1998-07-14

    A method for extracting and reclaiming metals from scrap CIS photovoltaic cells and associated photovoltaic manufacturing waste by leaching the waste with dilute nitric acid, skimming any plastic material from the top of the leaching solution, separating glass substrate from the leachate, electrolyzing the leachate to plate a copper and selenium metal mixture onto a first cathode, replacing the cathode with a second cathode, re-electrolyzing the leachate to plate cadmium onto the second cathode, separating the copper from selenium, and evaporating the depleted leachate to yield a zinc and indium containing solid.

  4. Collective Intelligence. Chapter 17

    NASA Technical Reports Server (NTRS)

    Wolpert, David H.

    2003-01-01

    Many systems of self-interested agents have an associated performance criterion that rates the dynamic behavior of the overall system. This chapter presents an introduction to the science of such systems. Formally, collectives are defined as any system having the following two characteristics: First, the system must contain one or more agents each of which we view as trying to maximize an associated private utility; second, the system must have an associated world utility function that rates the possible behaviors of that overall system. In practice, collectives are often very large, distributed, and support little, if any, centralized communication and control, although those characteristics are not part of their formal definition. A naturally occurring example of a collective is a human economy. One can identify the agents and their private utilities as the human individuals in the economy and the associated personal rewards they are each trying to maximize. One could then identify the world utility as the time average of the gross domestic product. ("World utility" per se is not a construction internal to a human economy, but rather something defined from the outside.) To achieve high world utility it is necessary to avoid having the agents work at cross-purposes lest phenomena like liquidity traps or the Tragedy of the Commons (TOC) occur, in which agents' individually pursuing their private utilities lowers world utility. The obvious way to avoid such phenomena is by modifying the agents utility functions to be "aligned" with the world utility. This can be done via punitive legislation. A real-world example of an attempt to do this was the creation of antitrust regulations designed to prevent monopolistic practices.

  5. Chapter 59: Web Services

    NASA Astrophysics Data System (ADS)

    Graham, M. J.

    Web services are a cornerstone of the distributed computing infrastructure that the VO is built upon yet to the newcomer, they can appear to be a black art. This perception is not helped by the miasma of technobabble that pervades the subject and the seemingly impenetrable high priesthood of actual users. In truth, however, there is nothing conceptually difficult about web services (unsurprisingly any complexities will lie in the implementation details) nor indeed anything particularly new. A web service is a piece of software available over a network with a formal description of how it is called and what it returns that a computer can understand. Note that entities such as web servers, ftp servers and database servers do not generally qualify as they lack the standardized description of their inputs and outputs. There are prior technologies, such as RMI, CORBA, and DCOM, that have employed a similar approach but the success of web services lies predominantly in its use of standardized XML to provide a language-neutral way for representing data. In fact, the standardization goes further as web services are traditionally (or as traditionally as five years will allow) tied to a specific set of technologies (WSDL and SOAP conveyed using HTTP with an XML serialization). Alternative implementations are becoming increasingly common and we will cover some of these here. One important thing to remember in all of this, though, is that web services are meant for use by computers and not humans (unlike web pages) and this is why so much of it seems incomprehensible gobbledegook. In this chapter, we will start with an overview of the web services current in the VO and present a short guide on how to use and deploy a web service. We will then review the different approaches to web services, particularly REST and SOAP, and alternatives to XML as a data format. We will consider how web services can be formally described and discuss how advanced features such as security, state

  6. Advanced Concepts. Chapter 21

    NASA Technical Reports Server (NTRS)

    Johnson, Les; Mulqueen, Jack

    2013-01-01

    Before there is a funded space mission, there must be a present need for the mission. Space science and exploration are expensive, and without a well-defined and justifiable need, no one is going to commit significant funding for any space endeavor. However, as discussed in Chapter 1, applications of space technology and many and broad, hence there are many ways to determine and establish a mission need. Robotic science missions are justified by their science return. To be selected for flight, questions like these must be addressed: What is the science question that needs answering, and will the proposed mission be the most cost-effective way to answer it? Why does answering the question require an expensive space flight, instead of some ground-based alternative? If the question can only be answered by flying in space, then why is this approach better than other potential approaches? How much will it cost? And is the technology required to answer the question in hand and ready to use? If not, then how much will it cost and how long will it take to mature the technology to a usable level? There are also many ways to justify human exploration missions, including science return, technology advancement, as well as intangible reasons, such as national pride. Nonetheless, many of the questions that need answering, are similar to those for robotic science missions: Where are the people going, why, and will the proposed mission be the most cost-effective way to get there? What is the safest method to achieve the goal? How much will it cost? And is the technology required to get there and keep the crew alive in hand and ready to use? If not, then how much will it cost and how long will it take to mature the technology to a usable level? Another reason for some groups sending spacecraft into space is for profit. Telecommunications, geospatial imaging, and tourism are examples of proven, market-driven space missions and applications. For this specific set of users, the

  7. Advanced research on cis-Neonicotinoids.

    PubMed

    Shao, Xusheng; Ye, Zhejun; Bao, Haibo; Liu, Zewen; Xu, Xiaoyong; Li, Zhong; Qian, Xuhong

    2011-01-01

    cis-Neonicotinoids are a type of neonicotinoid, in which the nitro or the cyano group are in cis-configuration relative to heteroaromatic moiety, which show excellent activities against a range of insect species. This review covers cis-neonicotinoids with commercialization perspectives, structural optimization (phenylazoneonicotinoids and chlorothiazolyl analogues of Paichongding), modes of action studies, radiao-synthesis of Paichongding and Cycloxaprid, and photostability of neonicotinoids.

  8. Chapter 8: Biomass Pyrolysis Oils

    SciTech Connect

    McCormick, Robert L.; Baldwin, Robert M.; Arbogast, Stephen; Bellman, Don; Paynter, Dave; Wykowski, Jim

    2016-09-06

    Fast pyrolysis is heating on the order of 1000 degrees C/s in the absence of oxygen to 40-600 degrees C, which causes decomposition of the biomass. Liquid product yield from biomass can be as much as 80% of starting dry weight and contains up to 75% of the biomass energy content. Other products are gases, primarily carbon monoxide, carbon dioxide, and methane, as well as solid char and ash. Residence time in the reactor is only 0.5-2 s so that relatively small, low-capital-cost reactors can be used. The low capital cost combined with greenhouse gas emission reductions relative to petroleum fuels of 50-95% makes pyrolysis an attractive process. The pyrolysis liquids have been investigated as a refinery feedstock and as stand-alone fuels. Utilization of raw pyrolysis oil has proven challenging. The organic fraction is highly corrosive because of its high organic acid content. High water content lowers the net heating value and can increase corrosivity. It can be poorly soluble in petroleum or petroleum products and can readily absorb water. Distillation residues can be as high as 50%, viscosity can be high, oils can exhibit poor stability in storage, and they can contain suspended solids. The ignition quality of raw pyrolysis oils is poor, with cetane number estimates ranging from 0 to 35, but more likely to be in the lower end of that range. While the use of raw pyrolysis oils in certain specific applications with specialized combustion equipment may be possible, raw oils must be significantly upgraded for use in on-highway spark-ignition (SI) and compression-ignition (CI) engines. Upgrading approaches most often involve catalytic hydrodeoxygenation, one of a class of reactions known as hydrotreating or hydroprocessing. This chapter discusses the properties of raw and upgraded pyrolysis oils, as well as the potential for integrating biomass pyrolysis with a petroleum refinery to significantly reduce the hydroprocessing cost.

  9. cis-Apa: a practical linker for the microwave-assisted preparation of cyclic pseudopeptides via RCM cyclative cleavage.

    PubMed

    Baron, Alice; Verdié, Pascal; Martinez, Jean; Lamaty, Frédéric

    2011-02-04

    A new linker cis-5-aminopent-3-enoic acid (cis-Apa) was prepared for the synthesis of cyclic pseudopeptides by cyclization-cleavage by using ring-closing methatesis (RCM). We developed a new synthetic pathway for the preparation of the cis-Apa linker that was tested in the cyclization-cleavage process of different RGD peptide sequences. Different macrocyclic peptidomimetics were prepared by using this integrated microwave-assisted method, showing that the readily available cis-Apa amino acid is well adapted as a linker in the cyclization-cleavage process.

  10. Methane Hydrates: Chapter 8

    USGS Publications Warehouse

    Boswell, Ray; Yamamoto, Koji; Lee, Sung-Rock; Collett, Timothy S.; Kumar, Pushpendra; Dallimore, Scott

    2008-01-01

    Gas hydrate is a solid, naturally occurring substance consisting predominantly of methane gas and water. Recent scientific drilling programs in Japan, Canada, the United States, Korea and India have demonstrated that gas hydrate occurs broadly and in a variety of forms in shallow sediments of the outer continental shelves and in Arctic regions. Field, laboratory and numerical modelling studies conducted to date indicate that gas can be extracted from gas hydrates with existing production technologies, particularly for those deposits in which the gas hydrate exists as pore-filling grains at high saturation in sand-rich reservoirs. A series of regional resource assessments indicate that substantial volumes of gas hydrate likely exist in sand-rich deposits. Recent field programs in Japan, Canada and in the United States have demonstrated the technical viability of methane extraction from gas-hydrate-bearing sand reservoirs and have investigated a range of potential production scenarios. At present, basic reservoir depressurisation shows the greatest promise and can be conducted using primarily standard industry equipment and procedures. Depressurisation is expected to be the foundation of future production systems; additional processes, such as thermal stimulation, mechanical stimulation and chemical injection, will likely also be integrated as dictated by local geological and other conditions. An innovative carbon dioxide and methane swapping technology is also being studied as a method to produce gas from select gas hydrate deposits. In addition, substantial additional volumes of gas hydrate have been found in dense arrays of grain-displacing veins and nodules in fine-grained, clay-dominated sediments; however, to date, no field tests, and very limited numerical modelling, have been conducted with regard to the production potential of such accumulations. Work remains to further refine: (1) the marine resource volumes within potential accumulations that can be

  11. Characterization of the binding strengths between boronic acids and cis-diol-containing biomolecules by affinity capillary electrophoresis.

    PubMed

    Lü, Chenchen; Liu, Zhen

    2015-01-01

    The affinity of boronic acids toward cis-diol-containing biomolecules has found wide applications in many fields, such as sensing, separation, drug delivery, and functional materials. A sound understanding of the binding interactions will greatly facilitate exquisite applications of this chemistry. Traditional techniques are associated with some apparent drawbacks, so they are only applicable to a limited range of boronic acids and cis-diol-containing biomolecules. This chapter describes an affinity capillary electrophoresis (ACE) method for the characterization of the binding strengths between boronic acids and cis-diol-containing biomolecules. As compared with existing approaches, such as (11)B NMR, the ACE method exhibits several significant advantages: (1) possibility of simultaneous study of multiple interactions, (2) low requirement on the purity of the binding species, (3) widely applicable to almost all types of cis-diol-containing compounds and boronic acids, and (4) high accuracy and precision.

  12. Germinating the 2050 Cis-Lunar Econosphere

    NASA Technical Reports Server (NTRS)

    Scott, David W.; Curreri, Peter A.; Ferguson, Cynthia K.; Nall, Mark E.; Tinker, Michael L.; Wright, Gregory M.

    2015-01-01

    In early 2013, Marshall Space Flight Center's upper management chartered a diverse team for a six-week 'sprint' to speculate (in a disciplined manner) and paint (with broad brush strokes) a picture of how earth, space, and public/private entities might be operating and relating to each other... in the year 2100. Two 12-person groups of civil servants, one with members having 15 years or less of NASA experience and the other with more senior members, worked independently and then compared and integrated their conclusions. In 2014, the 'Space 2100' team, with some new team members and different group boundaries, ran a longer sprint to a) develop more detailed estimates of the operations and economics of space activities in the vicinity of the Earth and Moon in the 2050 time frame, b) identify evolutionary paths, barriers, and opportunities, and c) suggest actions and philosophies to enable and invigorate progress towards the vision. This paper explores Space 2100's first two sprints and their projections of NASA's role in what will likely be a highly networked, international space industry and cis-lunar infrastructure.

  13. Germinating the 2050 Cis-Lunar Econosphere

    NASA Technical Reports Server (NTRS)

    Scott, David W.; Tinker, Michael L.; Nall, Mark E.; Wright, Gregory M.

    2015-01-01

    In early 2013, the Marshall Space Flight Center (MSFC) Director and MSFC's Office of Strategic Analysis and Communications (OSAC) chartered a diverse team for a six-week "sprint" to speculate (in a disciplined manner) and paint (with broad brush strokes) a picture of how earth, space, and public/private entities might be operating and relating to each other...in the year 2100. Two 12-person groups of civil servants, one with members having 15 years or less of NASA experience and the other with more senior members, worked independently and then compared and integrated their conclusions. In 2014, the "Space 2100" team, with some new team members and different group boundaries, ran a longer sprint to a) develop more detailed estimates of the operations and economics of space activities in the vicinity of the Earth and Moon in the 2050 time frame, b) identify evolutionary steps and viable paths needed to make that a reality, and c) recommend actions to enable and invigorate those steps. This paper explores Space 2100's first two sprints and their projections of NASA's role in what will likely be a highly networked international space industry and cis-lunar infrastructure.

  14. Chapter A7. Biological Indicators

    USGS Publications Warehouse

    Myers, Donna N.; Wilde, Franceska D.

    2003-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) provides guidelines and standard procedures for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This chapter of the manual includes procedures for the (1) determination of biochemical oxygen demand using a 5-day bioassay test; (2) collection, identification, and enumeration of fecal indicator bacteria; (3) collection of samples and information on two laboratory methods for fecal indicator viruses (coliphages); and (4) collection of samples for protozoan pathogens. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters are posted on the World Wide Web on the USGS page 'National Field Manual for the Collection of Water-Quality Data.' The URL for this page is http://pubs.water.usgs.gov/twri9A/ (accessed November 25, 2003).

  15. Chapter A6. Field Measurements

    USGS Publications Warehouse

    Wilde, Franceska D.; Radtke, Dean B.

    1998-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) provides guidelines and standard procedures for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. Chapter A6 presents procedures and guidelines for the collection of data on air and water temperature, and on dissolved-oxygen concentrations, specific electrical conductance, pH, reduction-oxidation potential, alkalinity, and turbidity in water. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters are posted on the World Wide Web on the USGS page 'National Field Manual for the Collection of Water-Quality Data.' The URL for this page is http://pubs.water.usgs.gov/twri9A (accessed August 6, 2005).

  16. Plant growth inhibition by cis-cinnamoyl glucosides and cis-cinnamic acid.

    PubMed

    Hiradate, Syuntaro; Morita, Sayaka; Furubayashi, Akihiro; Fujii, Yoshiharu; Harada, Jiro

    2005-03-01

    Spiraea thunbergii Sieb. contains 1-O-cis-cinnamoyl-beta-D-glucopyranose (CG) and 6-O-(4'-hydroxy-2'-methylene-butyroyl)-1-O-cis-cinnamoyl-beta-D-glucopyranose (BCG) as major plant growth inhibiting constituents. In the present study, we determined the inhibitory activity of CG and BCG on root elongation of germinated seedlings of lettuce (Lactuca sativa), pigweed (Amaranthus retroflexus), red clover (Trifolium pratense), timothy (Phleum pratense), and bok choy (Brassica rapa var chinensis) in comparison with that of two well-known growth inhibitors, 2,4-dichlorophenoxyacetic acid (2,4-D) and (+)-2-cis-4-trans-abscisic acid (cis-ABA), as well as two related chemicals of CG and BCG, cis-cinnamic acid (cis-CA) and trans-cinnamic acid (trans-CA). The EC50 values for CG and BCG on lettuce were roughly one-half to one-quarter of the value for cis-ABA. cis-Cinnamic acid, which is a component of CG and BCG, possessed almost the same inhibitory activity of CG and BCG, suggesting that the essential chemical structure responsible for the inhibitory activity of CG and BCG is cis-CA. The cis-stereochemistry of the methylene moiety is apparently needed for high inhibitory activity, as trans-CA had an EC50 value roughly 100 times that of CG, BCG, and cis-CA. Growth inhibition by CG, BCG, and cis-CA was influenced by the nature of the soil in the growing medium: alluvial soil preserved the bioactivity, whereas volcanic ash and calcareous soils inhibited bioactivity. These findings indicate a potential role of cis-CA and its glucosides as allelochemicals for use as plant growth regulators in agricultural fields.

  17. Substrate influences on CIS device performance

    SciTech Connect

    Dawson-Elli, D.F.; Moore, C.B.; Gay, R.R.; Jensen, C.L.

    1994-12-31

    It has been reported that the substrate plays an active role in copper indium diselenide (CIS) devices. The physical properties of the substrate, i.e., thermal expansion coefficient, chemical composition, strain point, surface quality and cleanliness may all play a role in device efficiency and process reproducibility. For example, sodium is known to influence the conductivity of CIS, and that soda lime glass (SLG) introduces sodium into the CIS. In the experiments reported here, the sodium level in the CIS was varied by (a) changing the substrate composition and (b) the use of SiO{sub x}N{sub y} and SiN{sub x} barrier layers. Cells were fabricated on the candidate substrate and barrier layer combinations. V{sub oc} was observed to drop with the addition of barrier layers to sodium containing glasses. The films were also analyzed for sodium by SIMS. The cell performance and SIMS analysis are presented and their significance is discussed.

  18. Chapter 1. Material and methods

    PubMed Central

    Kagan, A. R.; Uemura, K.

    1976-01-01

    This chapter outlines the way in which the problems of obtaining and assessing population-related material and analysing the data were tackled. Some of the limits of the approach used, namely, the examination of nearly all deaths from several demographically defined communities, are discussed. PMID:1087187

  19. Chapter Seven: Prospects for Practice

    ERIC Educational Resources Information Center

    Young, Richard F.

    2008-01-01

    This chapter suggests further ways that Practice Theory can be applied to understanding language teaching and learning. In particular, the author contends that more work is needed to describe the configuration of discursive resources in practices in foreign language communities in order to design effective pedagogies and assessments. In addition,…

  20. What's New in Chapter Books.

    ERIC Educational Resources Information Center

    Jones, Glenowyn

    Listing 81 chapter books for children published between 1996-1999, this annotated bibliography gives interest level ratings, reading level ratings, a brief summary, and theme assignments. The 13 theme categories listed in alphabetical order include Adventure-Survival, Autobiography-Biography, Death, Divorce, Good Reading, Handicaps, Historical…

  1. Secondary School Mathematics. Preliminary Version. Sample Chapters.

    ERIC Educational Resources Information Center

    Bell, Max S.; And Others

    This volume contains preliminary versions of five of the chapters prepared by the SMSG curriculum project for use in grades 7 and 8. The first four chapters and the tenth chapter in the sequence are presented. The sample chapters in this volume illustrate a number of aspects of the curriculum project: (1) association of ideas of number and space…

  2. Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells.

    PubMed

    Freire-Pritchett, Paula; Schoenfelder, Stefan; Várnai, Csilla; Wingett, Steven W; Cairns, Jonathan; Collier, Amanda J; García-Vílchez, Raquel; Furlan-Magaril, Mayra; Osborne, Cameron S; Fraser, Peter J; Rugg-Gunn, Peter J; Spivakov, Mikhail

    2017-03-23

    Long-range cis-regulatory elements such as enhancers coordinate cell-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. Deciphering the interplay between the promoter connectivity and activity of cis-regulatory elements during lineage commitment is crucial for understanding developmental transcriptional control. Here, we use Promoter Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements. We reveal extensive dynamics of cis-regulatory contacts upon lineage commitment, including the acquisition and loss of promoter interactions. This spatial rewiring occurs preferentially with predicted changes in the activity of cis-regulatory elements, and is associated with changes in target gene expression. Our results provide a global and integrated view of promoter interactome dynamics during lineage commitment of human pluripotent cells.

  3. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.

    PubMed

    Sharpe, Richard M; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit

    2016-01-01

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.

  4. CisSERS: Customizable in silico sequence evaluation for restriction sites

    DOE PAGES

    Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus; ...

    2016-04-12

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated tomore » enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.« less

  5. News from the Suncoast Chapter

    NASA Astrophysics Data System (ADS)

    AGU's serenely-named Suncoast Chapter, one of the union's several regional groups, met twice during the 1989-1990 academic year. The fall meeting featured four panelists discussing “An Oil Spill in Tampa Bay—A Disaster Waiting to Happen.” The spring meeting hosted Arthur D. Weissman, chief of the Guidance and Oversight Branch of the Environmental Protection Agency, speaking

  6. Coronavirus cis-Acting RNA Elements.

    PubMed

    Madhugiri, R; Fricke, M; Marz, M; Ziebuhr, J

    2016-01-01

    Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases. Genome replication and transcription is mediated by a multisubunit protein complex comprised of more than a dozen virus-encoded proteins. The protein complex is thought to bind specific cis-acting RNA elements primarily located in the 5'- and 3'-terminal genome regions and upstream of the open reading frames located in the 3'-proximal one-third of the genome. Here, we review our current understanding of coronavirus cis-acting RNA elements, focusing on elements required for genome replication and packaging. Recent bioinformatic, biochemical, and genetic studies suggest a previously unknown level of conservation of cis-acting RNA structures among different coronavirus genera and, in some cases, even beyond genus boundaries. Also, there is increasing evidence to suggest that individual cis-acting elements may be part of higher-order RNA structures involving long-range and dynamic RNA-RNA interactions between RNA structural elements separated by thousands of nucleotides in the viral genome. We discuss the structural and functional features of these cis-acting RNA elements and their specific functions in coronavirus RNA synthesis.

  7. Cis-interactions between Notch and its ligands block ligand-independent Notch activity

    PubMed Central

    Palmer, William Hunt; Jia, Dongyu; Deng, Wu-Min

    2014-01-01

    The Notch pathway is integrated into numerous developmental processes and therefore is fine-tuned on many levels, including receptor production, endocytosis, and degradation. Notch is further characterized by a twofold relationship with its Delta-Serrate (DSL) ligands, as ligands from opposing cells (trans-ligands) activate Notch, whereas ligands expressed in the same cell (cis-ligands) inhibit signaling. We show that cells without both cis- and trans-ligands can mediate Notch-dependent developmental events during Drosophila oogenesis, indicating ligand-independent Notch activity occurs when the receptor is free of cis- and trans-ligands. Furthermore, cis-ligands can reduce Notch activity in endogenous and genetically induced situations of elevated trans-ligand-independent Notch signaling. We conclude that cis-expressed ligands exert their repressive effect on Notch signaling in cases of trans-ligand-independent activation, and propose a new function of cis-inhibition which buffers cells against accidental Notch activity. DOI: http://dx.doi.org/10.7554/eLife.04415.001 PMID:25486593

  8. Cis and Trans Isomers of Cycloalkenes

    NASA Astrophysics Data System (ADS)

    Barrows, Susan E.; Eberlein, Thomas H.

    2005-09-01

    As a rule, a trans disubstituted alkene is more stable than the corresponding cis isomer. For cycloalkenes of fewer than eleven members, cis isomers are more stable than their trans counterparts. Although this exception to the normal rule is occasionally noted in beginning organic chemistry textbooks, it is often done without a careful analysis of the reasons behind it. The purpose of this article is to provide that analysis. In order for a cycloalkene to accommodate a trans double bond one or more of the following nonideal geometries must occur: a twisted π bond; pyramidal sp 2 -carbon atoms; nonideal sp 3 bond angles; or longer than normal C C single and double bonds. This article provides a list of experimentally determined relative energies of the cis and trans isomers within the series cycloheptene cycloundecene, along with computationally derived energies at several levels of theory. It also examines the geometric distortions through which cycloalkenes relieve the strain introduced by a trans double bond.

  9. Advances in the CIS research at NREL

    SciTech Connect

    Ramanathan, K.; Bhattacharya, R.N.; Granata, J.; Webb, J.; Niles, D.; Contreras, M.A.; Wiesner, H.; Hasoon, F.S.; Noufi, R.

    1997-12-31

    This paper summarizes the research of the CIS Team at NREL in three major areas: absorber deposition; understanding the role of chemical bath deposited (CBD) CdS in CIS junctions; and in the development of devices without CdS. Low cost, scaleable processes chosen for absorber fabrication include sputtering, electrodeposition (ED), and close spaced sublimation (CSS). The interaction between the CBD and the CIS has been investigated and the results show that Cd might be instrumental in shaping the interface. The authors have also developed a process to fabricate a 13.5% efficiency ZnO/CuInGaSe{sub 2} device without CdS or other buffer layers.

  10. Chapter A4. Collection of Water Samples

    USGS Publications Warehouse

    Wilde, Franceska D.

    1999-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) describes protocols and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data that are used to assess the quality of the Nation's surface-water and ground-water resources. This chapter addresses preparations and appropriate methods for the collection of surface-water, groundwater, and associated quality-control samples. Among the topics covered are considerations and procedures to prevent sample contamination; establishing site files; instructions for collecting depth-integrated isokinetic and nonisokinetic samples at flowing- and still-water sites; and guidelines for collecting formation water from wells having various types of construction and hydraulic and aquifer characteristics.

  11. Objectives and Overview. Chapter 1

    NASA Technical Reports Server (NTRS)

    Lamar, John E.; Hummel, Dietrich

    2009-01-01

    The RTO Task Group AVT-113 "Understanding and Modeling Vortical Flows to Improve the Technology Readiness Level for Military Aircraft" was established in April 2003. Two facets of the group, "Cranked Arrow Wing Aerodynamic Project International (CAWAPI)" and "Vortex Flow Experiment-2 (VFE-2)", worked closely together. However, because of the different requirements of each part, the CAWAPI facet concluded its work earlier (December 2006) than the VFE-2 facet (December 2007). In this first chapter of the Final Report of the Task Group an overview on its work is given, and the objectives for the Task Group are described.

  12. Fourier Transform Methods. Chapter 4

    NASA Technical Reports Server (NTRS)

    Kaplan, Simon G.; Quijada, Manuel A.

    2015-01-01

    This chapter describes the use of Fourier transform spectrometers (FTS) for accurate spectrophotometry over a wide spectral range. After a brief exposition of the basic concepts of FTS operation, we discuss instrument designs and their advantages and disadvantages relative to dispersive spectrometers. We then examine how common sources of error in spectrophotometry manifest themselves when using an FTS and ways to reduce the magnitude of these errors. Examples are given of applications to both basic and derived spectrophotometric quantities. Finally, we give recommendations for choosing the right instrument for a specific application, and how to ensure the accuracy of the measurement results..

  13. Earthquake ground motion: Chapter 3

    USGS Publications Warehouse

    Luco, Nicolas; Valley, Michael; Crouse, C.B.

    2012-01-01

    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. Section 3.1 describes the basis of the earthquake ground motion maps in the Provisions and in ASCE 7. Section 3.2 has examples for the determination of ground motion parameters and spectra for use in design. Section 3.3 discusses and provides an example for the selection and scaling of ground motion records for use in response history analysis.

  14. Chapter 1 Information Management Program. User's Guide.

    ERIC Educational Resources Information Center

    RMC Research Corp., Denver, CO.

    The first of seven chapters in this guide for users of the Chapter 1 Information Management Program (CHIMP) provides an introduction to the program, which was designed to help school districts maintain data and produce reports used in the evaluation of Chapter 1 programs. It is noted that these reports are useful for meeting state and federal…

  15. Stereoselective synthesis of cis-p-menth-8-ene-1,7-diol, cis-p-menthane-1,7-diol, and cis-p-menthane-1,7,8-triol.

    PubMed

    Kobler, Christoph; Effenberger, Franz

    2005-04-22

    The natural products cis-p-menthane-1,7-diol (cis-IV), cis-p-menth-8-ene-1,7-diol (cis-I) and cis-p-menthane-1,7,8-triol (cis-II) are obtained starting from the corresponding cis-cyanohydrins, cis-2 and cis-7, respectively, by chemical transformation of the cyano into the hydroxymethyl group. The key step of the synthesis is the very high cis-selectivity (> or = 96 %) of the MeHNL-catalyzed HCN addition to 4-alkylcyclohexanones. From 4-isopropylcyclohexanone (1) the cyanohydrin cis-2 and from 4-(1-methylvinyl)cyclohexanone (6) the cyanohydrin cis-7 result almost quantitatively. Regioselective hydroxylation of cis-I affords the triol cis-II. X-ray crystal structure determinations of the final products confirm their cis-configuration.

  16. Chapter 1 and Chapter 1 Migrant. Evaluation Findings, 1990-91. Executive Summary.

    ERIC Educational Resources Information Center

    Christner, Catherine; And Others

    This report describes an evaluation of the Austin (Texas) Independent School District's (AISD) Chapter 1 and Chapter 1 Migrant programs. Chapter 1 is a federally funded compensatory educational program that provided funding in 1990-91 to 25 AISD elementary schools with high concentrations of low-income students. Chapter 1 Migrant is also a…

  17. Advances in CIS devices fabricated by a non-vacuum technique

    SciTech Connect

    Leidholm, C.R.; Norsworthy, G.A.; Roe, R.; Halani, A.; Basol, B.M.; Kapur, V.K.

    1999-03-01

    A novel, non-vacuum technique based on nano-particle deposition has been developed for the formation of CIS-type solar cell absorbers. Solar cells with {gt}12{percent} efficiency were previously demonstrated using this technique. Improvements in module integration processes have recently yielded 8{percent} minimodules of 75 cm{sup 2} area. {copyright} {ital 1999 American Institute of Physics.}

  18. IRIS Toxicological Review of Cis-& Trans-1,2-Dichloroethylene (Final Report)

    EPA Science Inventory

    EPA has finalized the Toxicological Review of cis- & trans-1,2-Dichloroethylene: in support of the Integrated Risk Information System (IRIS). Now final, this assessment may be used by EPA’s program and regional offices to inform decisions to protect human health.

  19. Conclusions and Recommendations. Chapter 37

    NASA Technical Reports Server (NTRS)

    Lamar, John E.; Hummel, Dietrich

    2009-01-01

    This chapter provides a brief wrap-up of the task group report and focuses on the overall conclusions and recommendations for future work for the CAWAPI and VFE-2 facets beyond the task group. The overall conclusion is that the Technology Readiness Level (TRL) of CFD solvers has been improved in predicting the flow-physics of vortex-dominated flows during the work of the task group, by having flight and wind-tunnel data available for comparison. Moreover, like all good scientific studies, this task group has identified flight conditions on the F-16XL airplane or wind-tunnel test conditions for a specific leading-edge radius on the 65 delta-wing model where the TRL still needs to be increased.

  20. Background and introduction: Chapter 1

    USGS Publications Warehouse

    Shafroth, Patrick B.

    2010-01-01

    efforts.In addition to the legislative context described above, this chapter describes the geographic and environmental contexts surrounding the Act, including key terminology used in subsequent chapters of this report. Subsequent chapters synthesize the state-of-the-science on the following topics: distribution and abundance (extent) of saltcedar and Russian olive in the Western United States, potential for water savings associated with control of saltcedar and Russian olive and associated restoration, considerations related to wildlife use of saltcedar and Russian olive habitat or restored habitats, methods to control saltcedar and Russian olive, possible utilization of dead biomass following control, and approaches and challenges associated with revegetation or restoration following control. A concluding chapter includes discussion of possible long-term management strategies, areas for additional study, potentially useful field demonstrations, and a planning process for on-the-ground projects involving removal of saltcedar and Russian olive.

  1. Preparation and characterization of fluorophenylboronic acid-functionalized affinity monolithic columns for the selective enrichment of cis-diol-containing biomolecules.

    PubMed

    Li, Qianjin; Liu, Zhen

    2015-01-01

    Boronate affinity monolithic columns have been developed into an important means for the selective recognition and capture of cis-diol-containing biomolecules, such as glycoproteins, nucleosides and saccharides. The ligands of boronic acids are playing an important role in boronate affinity monolithic columns. Although several boronate affinity monoliths with high affinity toward cis-diol-containing biomolecules have been reported, only few publications are focused on their detailed procedures for preparation and characterization. This chapter describes in detail the preparation and characterization of a boronate affinity monolithic column applying 2,4-difluoro-3-formyl-phenylboronic acid (DFFPBA) as a ligand. The DFFPBA-functionalized monolithic column not only exhibited an ultrahigh boronate affinity toward cis-diol-containing biomolecules, but also showed great potential for the selective enrichment of cis-diol-containing biomolecules in real samples.

  2. cis-Regulatory control circuits in development.

    PubMed

    Howard, Meredith L; Davidson, Eric H

    2004-07-01

    During development, an organism undergoes many rounds of pattern formation, generating ever-greater complexity with each ensuing round of cell division and specification. The instructions for executing this process are encoded in the cis-regulatory modules that direct the expression of developmental transcription factors and signaling molecules. Each transcription factor binding site within a cis-regulatory module contributes information about when, where, or how much a gene is turned on, and by dissecting the modules driving a given gene, all the inputs governing expression of the gene can be accurately identified. Furthermore, by mapping the output of each gene to the inputs of other genes, it is possible to reverse engineer developmental circuits and even whole networks. At this higher level of organization, common bilaterian strategies for specifying progenitor fields, locking down regulatory states, and driving development forward emerge.

  3. Chapter 4: Geological Carbon Sequestration

    SciTech Connect

    Friedmann, J; Herzog, H

    2006-06-14

    Carbon sequestration is the long term isolation of carbon dioxide from the atmosphere through physical, chemical, biological, or engineered processes. The largest potential reservoirs for storing carbon are the deep oceans and geological reservoirs in the earth's upper crust. This chapter focuses on geological sequestration because it appears to be the most promising large-scale approach for the 2050 timeframe. It does not discuss ocean or terrestrial sequestration. In order to achieve substantial GHG reductions, geological storage needs to be deployed at a large scale. For example, 1 Gt C/yr (3.6 Gt CO{sub 2}/yr) abatement, requires carbon capture and storage (CCS) from 600 large pulverized coal plants ({approx}1000 MW each) or 3600 injection projects at the scale of Statoil's Sleipner project. At present, global carbon emissions from coal approximate 2.5 Gt C. However, given reasonable economic and demand growth projections in a business-as-usual context, global coal emissions could account for 9 Gt C. These volumes highlight the need to develop rapidly an understanding of typical crustal response to such large projects, and the magnitude of the effort prompts certain concerns regarding implementation, efficiency, and risk of the enterprise. The key questions of subsurface engineering and surface safety associated with carbon sequestration are: (1) Subsurface issues: (a) Is there enough capacity to store CO{sub 2} where needed? (b) Do we understand storage mechanisms well enough? (c) Could we establish a process to certify injection sites with our current level of understanding? (d) Once injected, can we monitor and verify the movement of subsurface CO{sub 2}? (2) Near surface issues: (a) How might the siting of new coal plants be influenced by the distribution of storage sites? (b) What is the probability of CO{sub 2} escaping from injection sites? What are the attendant risks? Can we detect leakage if it occurs? (3) Will surface leakage negate or reduce the

  4. PDSS/IMC CIS user's guide

    NASA Technical Reports Server (NTRS)

    1984-01-01

    The Spacelab Payload Development Support System PDSS Image Motion Compensator (IMC) computer interface simulation (CIS) user's manual is given. The software provides a real time interface simulation for the following IMC subsystems: the Dry Rotor Reference Unit, the Advanced Star/Target Reference Optical sensor, the Ultra Violet imaging telescope, the Wisconson Ultraviolet Photopolarimetry Experiment, the Cruciform Power distributor, and the Spacelab Experiment Computer Operating System.

  5. Combinatorial Cis-regulation in Saccharomyces Species.

    PubMed

    Spivak, Aaron T; Stormo, Gary D

    2016-01-15

    Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs) controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1) chromatin immunoprecipitation data for colocalization of transcription factors, (2) gene expression data for coexpression of predicted regulatory targets, and (3) gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF) occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1) combinatorial cis-regulation can be inferred by multi-genome analysis and (2) combinatorial cis-regulation can explain differences in gene expression between species.

  6. Combinatorial Cis-regulation in Saccharomyces Species

    PubMed Central

    Spivak, Aaron T.; Stormo, Gary D.

    2016-01-01

    Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs) controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1) chromatin immunoprecipitation data for colocalization of transcription factors, (2) gene expression data for coexpression of predicted regulatory targets, and (3) gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF) occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1) combinatorial cis-regulation can be inferred by multi-genome analysis and (2) combinatorial cis-regulation can explain differences in gene expression between species. PMID:26772747

  7. VUV thin films, chapter 7

    NASA Technical Reports Server (NTRS)

    Zukic, Muamer; Torr, Douglas G.

    1993-01-01

    The application of thin film technology to the vacuum ultraviolet (VUV) wavelength region from 120 nm to 230 nm has not been fully exploited in the past because of absorption effects which complicate the accurate determination of the optical functions of dielectric materials. The problem therefore reduces to that of determining the real and imaginary parts of a complex optical function, namely the frequency dependent refractive index n and extinction coefficient k. We discuss techniques for the inverse retrieval of n and k for dielectric materials at VUV wavelengths from measurements of their reflectance and transmittance. Suitable substrate and film materials are identified for application in the VUV. Such applications include coatings for the fabrication of narrow and broadband filters and beamsplitters. The availability of such devices open the VUV regime to high resolution photometry, interferometry and polarimetry both for space based and laboratory applications. This chapter deals with the optics of absorbing multilayers, the determination of the optical functions for several useful materials, and the design of VUV multilayer stacks as applied to the design of narrow and broadband reflection and transmission filters and beamsplitters. Experimental techniques are discussed briefly, and several examples of the optical functions derived for selected materials are presented.

  8. Inland surface water: Chapter 18

    USGS Publications Warehouse

    Baron, J.S.; Driscoll, C.T.; Stoddard, J.L.

    2011-01-01

    Freshwater aquatic ecosystems include rivers and streams, large and small lakes, reservoirs, and ephemeral ponds. Wetlands are defi ned and discussed in Chapter 17 of this report. It is estimated that there are 123,400 lakes with a surface area greater than 4 ha in the United States. Most lakes, however, are smaller than 4 ha; small lakes account for the majority of lake surface area both globally and in the United States (Table 18.1; Downing et al. 2006). Th e density of lakes varies greatly by region of the country, from 8.4 lakes per 100 km2 in the upper Midwest and 7.8 lakes per 100 km2 in Florida, to much lower values in other areas of the country (e.g., mid-Atlantic, Southeast, and West <1.0 lakes per 100 km2 ) ( Eilers and Selle 1991). Th e cumulative surface area of these lakes is approximately 9.5 million ha. Th e U.S. Geologic Survey's National Hydrographic Dataset (NHD) estimates that there are approximately 1.1 million km of perennial fl owing streams in the United States. Of these about 91 percent are fi rst through fourth order (“wadeable”) (US EPA 2006).

  9. Sediment transport measurements: Chapter 5

    USGS Publications Warehouse

    Diplas, P.; Kuhnle, R.; Gray, J.; Glysson, D.; Edwards, T.; García, Marcelo H.

    2008-01-01

    Sediment erosion, transport, and deposition in fluvial systems are complex processes that are treated in detail in other sections of this book. Development of methods suitable for the collection of data that contribute to understanding these processes is a still-evolving science. Sediment and ancillary data are fundamental requirements for the proper management of river systems, including the design of structures, the determination of aspects of stream behavior, ascertaining the probable effect of removing an existing structure, estimation of bulk erosion, transport, and sediment delivery to the oceans, ascertaining the long-term usefulness of reservoirs and other public works, tracking movement of solid-phase contaminants, restoration of degraded or otherwise modified streams, and assistance in the calibration and validation of numerical models. This chapter presents techniques for measuring bed-material properties and suspended and bed-load discharges. Well-established and relatively recent, yet adequately tested, sampling equipment and methodologies, with designs that are guided by sound physical and statistical principles, are described. Where appropriate, the theory behind the development of the equipment and guidelines for its use are presented.

  10. Volcanism on Mars. Chapter 41

    NASA Technical Reports Server (NTRS)

    Zimbelman, J. R.; Garry, W. B.; Bleacher, J. E.; Crown, D. A.

    2015-01-01

    Spacecraft exploration has revealed abundant evidence that Mars possesses some of the most dramatic volcanic landforms found anywhere within the solar system. How did a planet half the size of Earth produce volcanoes like Olympus Mons, which is several times the size of the largest volcanoes on Earth? This question is an example of the kinds of issues currently being investigated as part of the space-age scientific endeavor called "comparative planetology." This chapter summarizes the basic information currently known about volcanism on Mars. The volcanoes on Mars appear to be broadly similar in overall morphology (although, often quite different in scale) to volcanic features on Earth, which suggests that Martian eruptive processes are not significantly different from the volcanic styles and processes on Earth. Martian volcanoes are found on terrains of different age, and Martian volcanic rocks are estimated to comprise more than 50% of the Martian surface. This is in contrast to volcanism on smaller bodies such as Earth's Moon, where volcanic activity was mainly confined to the first half of lunar history (see "Volcanism on the Moon"). Comparative planetology supports the concept that volcanism is the primary mechanism for a planetary body to get rid of its internal heat; smaller bodies tend to lose their internal heat more rapidly than larger bodies (although, Jupiter's moon Io appears to contradict this trend; Io's intense volcanic activity is powered by unique gravitational tidal forces within the Jovian system; see "Volcanism on Io"), so that volcanic activity on Mars would be expected to differ considerably from that found on Earth and the Moon.

  11. New Directions for Chapter 1. Congressional Testimony.

    ERIC Educational Resources Information Center

    Rotberg, Iris C.

    The RAND Institute on Education and Training conducted an analysis of Federal policy options to improve education in low-income areas. The analysis focuses on Chapter 1 of the Elementary and Secondary Education Act of 1965, the nation's program for assisting educationally disadvantaged students. After a quarter century of Chapter 1 efforts, it is…

  12. National ESEA Chapter 1 Schoolwide Projects Conference.

    ERIC Educational Resources Information Center

    Cleveland Public Schools, OH.

    This document is a collection of schoolwide compensatory education project plans for 22 elementary schools in the Cleveland (Ohio) Public Schools system, with funding provided by Chapter 1 of the Education Consolidation and Improvement Act. Chapter 1 project plans are included for the following schools: (1) Alfred A. Benesch; (2) Andrew J.…

  13. Chapter 6: Selenium Toxicity to Aquatic Organisms

    EPA Science Inventory

    This chapter addresses the characteristics and nature of organic selenium (Se) toxicity to aquatic organisms, based on the most current state of scientific knowledge. As such, the information contained in this chapter relates to the 'toxicity assessment' phase of aquatic ecologi...

  14. Rotational spectroscopy and dipole moment of cis-cis HOONO and DOONO.

    PubMed

    Fry, Juliane L; Drouin, Brian J; Miller, Charles E

    2006-02-28

    The rotational spectrum of cis-cis HOONO has been studied over a broad range of frequencies, 13-840 GHz, using pulsed beam Fourier-transform microwave spectroscopy and room-temperature flow cell submillimeter spectroscopy. The rotational spectrum of the deuterated isotopomer, cis-cis DOONO, has been studied over a subset of this range, 84-640 GHz. Improved spectroscopic constants have been determined for HOONO, and the DOONO spectrum is analyzed for the first time. Weak-field Stark effect measurements in the region of 84-110 GHz have been employed to determine the molecular dipole moments of cis-cis HOONO [mu(a) = 0.542(8) D, mu(b) = 0.918(15) D, mu = 1.07(2) D] and DOONO [mu(a) = 0.517(9) D, mu(b) = 0.930(15) D, mu = 1.06(2) D]. The quadrupole coupling tensor in the principal inertial axis system for the 14N nucleus has been determined to be chi(aa) = 1.4907(25) MHz, chi(bb) = -4.5990(59) MHz, chi(ab) = 3.17(147) MHz, and chi(cc) = 3.1082(59) MHz. Coordinates of the H atom in the center-of-mass frame have been determined with use of the Kraitchman equations, /aH/ = 0.516 A and /bH/ = 1.171 A. The inertial defects of HOONO and DOONO are consistent with a planar equilibrium structure with significant out-of-plane H atom torsional motion. Comparisons of the present results are made to ab initio calculations.

  15. Fire as an ecosystem process: Chapter 3

    USGS Publications Warehouse

    Keeley, Jon E.; Safford, Hugh D.; Mooney, Harold A.; Zavaleta, Erika S.

    2016-01-01

    This long-anticipated reference and sourcebook for California’s remarkable ecological abundance provides an integrated assessment of each major ecosystem type—its distribution, structure, function, and management. A comprehensive synthesis of our knowledge about this biologically diverse state, Ecosystems of California covers the state from oceans to mountaintops using multiple lenses: past and present, flora and fauna, aquatic and terrestrial, natural and managed. Each chapter evaluates natural processes for a specific ecosystem, describes drivers of change, and discusses how that ecosystem may be altered in the future. This book also explores the drivers of California’s ecological patterns and the history of the state’s various ecosystems, outlining how the challenges of climate change and invasive species and opportunities for regulation and stewardship could potentially affect the state’s ecosystems. The text explicitly incorporates both human impacts and conservation and restoration efforts and shows how ecosystems support human well-being. Edited by two esteemed ecosystem ecologists and with overviews by leading experts on each ecosystem, this definitive work will be indispensable for natural resource management and conservation professionals as well as for undergraduate or graduate students of California’s environment and curious naturalists.

  16. Chapter 17: Estimating Net Savings: Common Practices

    SciTech Connect

    Violette, D. M.; Rathbun, P.

    2014-09-01

    This chapter focuses on the methods used to estimate net energy savings in evaluation, measurement, and verification (EM&V) studies for energy efficiency (EE) programs. The chapter provides a definition of net savings, which remains an unsettled topic both within the EE evaluation community and across the broader public policy evaluation community, particularly in the context of attribution of savings to particular program. The chapter differs from the measure-specific Uniform Methods Project (UMP) chapters in both its approach and work product. Unlike other UMP resources that provide recommended protocols for determining gross energy savings, this chapter describes and compares the current industry practices for determining net energy savings, but does not prescribe particular methods.

  17. Chapter 6: CPV Tracking and Trackers

    SciTech Connect

    Luque-Heredia, Ignacio; Magalhaes, Pedro; Muller, Matthew

    2016-04-15

    This chapter explains the functional requirements of a concentrator photovoltaic (CPV) sun tracker. It derives the design specifications of a CPV tracker. The chapter presents taxonomy of trackers describing the most common tracking architectures, based on the number of axes, their relative position, and the foundation and placing of tracking drives. It deals with the structural issues related to tracker design, mainly related to structural flexure and its impact on the system's acceptance angle. The chapter analyzes the auto-calibrated sun tracking control, by describing the state of the art and its development background. It explores the sun tracking accuracy measurement with a practical example. The chapter discusses tracker manufacturing and tracker field works. It reviews survey of different types of tracker designs obtained from different manufacturers. Finally, the chapter deals with IEC62817, the technical standard developed for CPV sun trackers.

  18. CisSERS: Customizable in silico sequence evaluation for restriction sites

    SciTech Connect

    Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit; Prasad, Manoj

    2016-04-12

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.

  19. Environmental testing of CIS based modules

    SciTech Connect

    Willett, D.

    1995-11-01

    This report describes environmental testing of Siemen`s CIS modules. Charts and diagrams are presented on data concerning: temporary power loss of laminated mini-modules; the 50 thermal cycle test; the 10 humidity freeze cycle test; results after 1000 hours of exposure to damp heat; and interconnect test structures in damp heat testing. It is concluded that moisture ingress causes permanent increases in the series resistance of modules, and that improved packaging is needed for better high humidity reliability. Also, dry dark heat caused temporary power losses which were recovered in sunlight.

  20. Structured decision making: Chapter 5

    USGS Publications Warehouse

    Runge, Michael C.; Grand, James B.; Mitchell, Michael S.; Krausman, Paul R.; Cain, James W. III

    2013-01-01

    Wildlife management is a decision-focused discipline. It needs to integrate traditional wildlife science and social science to identify actions that are most likely to achieve the array of desires society has surrounding wildlife populations. Decision science, a vast field with roots in economics, operations research, and psychology, offers a rich set of tools to help wildlife managers frame, decompose, analyze, and synthesize their decisions. The nature of wildlife management as a decision science has been recognized since the inception of the field, but formal methods of decision analysis have been underused. There is tremendous potential for wildlife management to grow further through the use of formal decision analysis. First, the wildlife science and human dimensions of wildlife disciplines can be readily integrated. Second, decisions can become more efficient. Third, decisions makers can communicate more clearly with stakeholders and the public. Fourth, good, intuitive wildlife managers, by explicitly examining how they make decisions, can translate their art into a science that is readily used by the next generation.

  1. A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements.

    PubMed

    Henry, Kelli F; Kawashima, Tomokazu; Goldberg, Robert B

    2015-06-01

    Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean (Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5'-GAAAAGCGAA-3'), the 10 bp-like motif (5'-GAAAAACGAA-3'), and Region 2 motif (partial sequence 5'-TTGGT-3'). Here, we use site-directed mutagenesis experiments in transgenic tobacco globular-stage embryos to identify two additional cis-regulatory elements within the 54-bp cis-regulatory module that are required for G564 suspensor transcription: the Fifth motif (5'-GAGTTA-3') and a third 10-bp-related sequence (5'-GAAAACCACA-3'). Further deletion of the 54-bp fragment revealed that a 47-bp fragment containing the five motifs (the 10-bp, 10-bp-like, 10-bp-related, Region 2 and Fifth motifs) is sufficient for suspensor transcription, and represents a cis-regulatory module. A consensus sequence for each type of motif was determined by comparing motif sequences shown to activate suspensor transcription. Phylogenetic analyses suggest that the regulation of G564 is evolutionarily conserved. A homologous cis-regulatory module was found upstream of the G564 ortholog in the Common Bean (Phaseolus vulgaris), indicating that the regulation of G564 is evolutionarily conserved in closely related bean species.

  2. Uncovering cis Regulatory Codes Using Synthetic Promoter Shuffling

    PubMed Central

    Kinkhabwala, Ali; Guet, Călin C.

    2008-01-01

    Revealing the spectrum of combinatorial regulation of transcription at individual promoters is essential for understanding the complex structure of biological networks. However, the computations represented by the integration of various molecular signals at complex promoters are difficult to decipher in the absence of simple cis regulatory codes. Here we synthetically shuffle the regulatory architecture — operator sequences binding activators and repressors — of a canonical bacterial promoter. The resulting library of complex promoters allows for rapid exploration of promoter encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter encoded logics predominate. A simple transcriptional cis regulatory code determines both logics, establishing a straightforward map between promoter structure and logic phenotype. The regulatory code is determined solely by the type of transcriptional regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a repressor and an activator generate an ANDN: a AND NOT b. Three-input versions of both logics, having an additional repressor as an input, are also present in the library. The resulting complex promoters cover a wide dynamic range of transcriptional strengths. Synthetic promoter shuffling represents a fast and efficient method for exploring the spectrum of complex regulatory functions that can be encoded by complex promoters. From an engineering point of view, synthetic promoter shuffling enables the experimental testing of the functional properties of complex promoters that cannot necessarily be inferred ab initio from the known properties of the individual genetic components. Synthetic promoter shuffling may provide a useful experimental tool for studying naturally occurring promoter shuffling. PMID:18446205

  3. Closeout of CRADA JSA 2012S004: Chapter 5, Integrated Control System, of the document of the ESS Conceptual Design Report, publicly available at https://europeanspallationsource.se/accelerator-documents

    SciTech Connect

    Satogata, Todd

    2013-04-22

    The integrated control system (ICS) is responsible for the whole ESS machine and facility: accelerator, target, neutron scattering instruments and conventional facilities. This unified approach keeps the costs of development, maintenance and support relatively low. ESS has selected a standardised, field-proven controls framework, the Experimental Physics and Industrial Control System (EPICS), which was originally developed jointly by Argonne and Los Alamos National Laboratories. Complementing this selection are best practices and experience from similar facilities regarding platform standardisation, control system development and device integration and commissioning. The components of ICS include the control system core, the control boxes, the BLED database management system, and the human machine interface. The control system core is a set of systems and tools that make it possible for the control system to provide required data, information and services to engineers, operators, physicists and the facility itself. The core components are the timing system that makes possible clock synchronisation across the facility, the machine protection system (MPS) and the personnel protection system (PPS) that prevent damage to the machine and personnel, and a set of control system services. Control boxes are servers that control a collection of equipment (for example a radio frequency cavity). The integrated control system will include many control boxes that can be assigned to one supplier, such as an internal team, a collaborating institute or a commercial vendor. This approach facilitates a clear division of responsibilities and makes integration much easier. A control box is composed of a standardised hardware platform, components, development tools and services. On the top level, it interfaces with the core control system components (timing, MPS, PPS) and with the human-machine interface. At the bottom, it interfaces with the equipment and parts of the facility through

  4. The Role of cis Regulatory Evolution in Maize Domestication

    PubMed Central

    Lemmon, Zachary H.; Bukowski, Robert; Sun, Qi; Doebley, John F.

    2014-01-01

    Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues. PMID:25375861

  5. Chapter 42. Waterborne and Foodborne Parasites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter identifies the most prominent parasites in North America that are acquired through contaminated food and water including protozoa (Acanthamoeba, Naegleria, Entamoeba, Giardia, Cryptosporidium, Cystoisospora, Cyclospora, Toxoplasma, and Balantidium), nematodes (Trichinella, Angiostrongyl...

  6. AMPLIFICATION OF RIBOSOMAL RNA SEQUENCES - Book Chapter

    EPA Science Inventory

    This book chapter contains the following headings and subheadings: Introduction; Experimental Approach - Precautions, Template, Primers, Reaction Conditions, Enhancers, Post Amplification; Procedures - Template DNA, Basic PCR, Thermal Cycle Parameters, Enzyme Addition, Agarose Ge...

  7. How to write a medical book chapter?

    PubMed

    Kendirci, Muammer

    2013-09-01

    Invited medical book chapters are usually requested by editors from experienced authors who have made significant contributions to the literature in certain fields requested by an editor from an experienced. Before the start of the writing process a consensus should be established between the editor and the author with regard to the title, deadline, specific instructions and content of the manuscript. Certain issues concerning a chapter can be negotiated by the parties beforehand, but some issues cannot. As writing a medical book chapter is seen as an honor in its own right, the assignment needs to be treated with sincerity by elucidating the topic in detail, and maximal effort should be made to keep in mind that the chapter will reach a large target audience. The purpose of this review article is to provide guidance to residents and junior specialists in the field of urology to improve their writing skills.

  8. AIR POLLUTION CONTROL TECHNOLOGIES (CHAPTER 65)

    EPA Science Inventory

    The chapter discusses the use of technologies for reducing air pollution emissions from stationary sources, with emphasis on the control of combustion gen-erated air pollution. Major stationary sources include utility power boilers, industrial boilers and heaters, metal smelting ...

  9. Chapter IV - Safety During Payload Ground Processing

    NASA Technical Reports Server (NTRS)

    Kirkpatrick, Paul; Dollberg, John; Trinchero, Jean-Pierre

    2012-01-01

    This chapter describes the typical hazards that can be expected to be encountered when processing payloads on the ground. Also described are some of the more common controls for these hazards. Many of these controls are based on hard requirements but they are also based on specific lessons learned. This chapter uses the term Flight Hardware (F/H) for all payloads regardless of size.

  10. IRIG 106 Chapter 10 Programmers Handbook

    DTIC Science & Technology

    2016-08-16

    recorders. A prior working knowledge of Chapters 9 and 10, as well as applicable sections of Chapter 6 is essential. 1.2 Document Layout This document...are several methods that may be used to find targets. The iSCSI protocol supports the following discovery mechanisms. • Static Configuration...to perform no discovery in this approach. The initiator uses the IP address and the TCP port information to establish a TCP connection, and it

  11. Polarons and bipolarons in cis-polyacetylene

    NASA Astrophysics Data System (ADS)

    Utz, Wolfram; Förner, Wolfgang

    1998-05-01

    We present a parametrization for the Pariser-Parr-Pople Hamiltonian for the description of cis-polyacetylene (cPA). In contrast to trans-polyacetylene, we have to include symmetry breaking between neighboring sites into the Su-Schrieffer-Heeger-type one-electron part of the Hamiltonian. Our parametrization is based on correlated ab initio calculations on cis-hexatriene and on the results of independent calculations found in the literature. For open-shell systems (singly charged polarons) we use the annihilated unrestricted Hartree-Fock method to avoid the artificial spin contaminations inherent in UHF (unrestricted HF) calculations, which lead to the inclusion of fractions of the correlation energy in UHF total energies which cannot be controlled and are different for different systems and even for different geometries of the same system. Thus UHF is useless for the calculation of potential hypersurfaces and thus in turn for dynamical simulations. We find that in cPA singly-charged polarons are formed, while in doubly-charged chains stable bipolarons are found, although of a quite large width. This is in contrast to recent results reported by Shimoi and Abe [Y. Shimoi and S. Abe, Synth. Met. 69, 687 (1995) and Phys. Rev. B 50, 14 781 (1994)] who found that two singly-charged polarons are more stable for realistic parameter values than a doubly-charged bipolaron. We further find that the charged polarons are mobile in the chain and thus we conclude that polarons and bipolarons can serve as charge carriers (the latter ones spinless) in doped cPA.

  12. Prepare dispersed CIS nano-scale particles and spray coating CIS absorber layers using nano-scale precursors

    NASA Astrophysics Data System (ADS)

    Liou, Jian-Chiun; Diao, Chien-Chen; Lin, Jing-Jenn; Chen, Yen-Lin; Yang, Cheng-Fu

    2014-01-01

    In this study, the Mo-electrode thin films were deposited by a two-stepped process, and the high-purity copper indium selenide-based powder (CuInSe2, CIS) was fabricated by hydrothermal process by Nanowin Technology Co. Ltd. From the X-ray pattern of the CIS precursor, the mainly crystalline phase was CIS, and the almost undetectable CuSe phase was observed. Because the CIS powder was aggregated into micro-scale particles and the average particle sizes were approximately 3 to 8 μm, the CIS power was ground into nano-scale particles, then the 6 wt.% CIS particles were dispersed into isopropyl alcohol to get the solution for spray coating method. Then, 0.1 ml CIS solution was sprayed on the 20 mm × 10 mm Mo/glass substrates, and the heat treatment for the nano-scale CIS solution under various parameters was carried out in a selenization furnace. The annealing temperature was set at 550°C, and the annealing time was changed from 5 to 30 min, without extra Se content was added in the furnace. The influences of annealing time on the densification, crystallization, resistivity ( ρ), hall mobility ( μ), and carrier concentration of the CIS absorber layers were well investigated in this study.

  13. CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes

    PubMed Central

    Jegga, Anil G.; Gupta, Ashima; Gowrisankar, Sivakumar; Deshmukh, Mrunal A.; Connolly, Steven; Finley, Kevin; Aronow, Bruce J.

    2005-01-01

    Combinatorial interactions of sequence-specific trans-acting factors with localized genomic cis-element clusters are the principal mechanism for regulating tissue-specific and developmental gene expression. With the emergence of expanding numbers of genome-wide expression analyses, the identification of the cis-elements responsible for specific patterns of transcriptional regulation represents a critical area of investigation. Computational methods for the identification of functional cis-regulatory modules are difficult to devise, principally because of the short length and degenerate nature of individual cis-element binding sites and the inherent complexity that is generated by combinatorial interactions within cis-clusters. Filtering candidate cis-element clusters based on phylogenetic conservation is helpful for an individual ortholog gene pair, but combining data from cis-conservation and coordinate expression across multiple genes is a more difficult problem. To approach this, we have extended an ortholog gene-pair database with additional analytical architecture to allow for the analysis and identification of maximal numbers of compositionally similar and phylogenetically conserved cis-regulatory element clusters from a list of user-selected genes. The system has been successfully tested with a series of functionally related and microarray profile-based co-expressed ortholog pairs of promoters and genes using known regulatory regions as training sets and co-expressed genes in the olfactory and immunohematologic systems as test sets. CisMols Analyzer is accessible via a Web interface at . PMID:15980500

  14. U.S./CIS eye joint nuclear rocket venture

    NASA Technical Reports Server (NTRS)

    Clark, John S.; Mcilwain, Melvin C.; Smetanikov, Vladimir; D'Yakov, Evgenij K.; Pavshuk, Vladimir A.

    1993-01-01

    An account is given of the significance for U.S. spacecraft development of a nuclear thermal rocket (NTR) reactor concept that has been developed in the (formerly Soviet) Commonwealth of Independent States (CIS). The CIS NTR reactor employs a hydrogen-cooled zirconium hydride moderator and ternary carbide fuels; the comparatively cool operating temperatures associated with this design promise overall robustness.

  15. Short asymmetric synthesis of (-)- and (+)-cis-lauthisan.

    PubMed

    Carreño, M Carmen; Des Mazery, Renaud; Urbano, Antonio; Colobert, Françoise; Solladié, Guy

    2005-05-12

    The asymmetric synthesis of both enantiomers of cis-lauthisan (3) is achieved in only six steps from diethyl pimelate (4), the key steps being the diastereodivergent reduction of beta-ketosulfoxide 7 and the highly cis-stereoselective Et(3)SiH/TMSOTf-promoted reductive cyclization of enantiopure hydroxy sulfinyl ketones (S)-14 and (R)-14.

  16. Peptidyl-prolyl cis-trans isomerases: structure and functions.

    PubMed

    Pliyev, B K; Gurvits, B Y

    1999-07-01

    Peptidyl-prolyl cis-trans isomerases (PPI) catalyze cis-trans isomerization of imide bonds in peptides and proteins. This review summarizes the literature on the structure and functions of PPIs, their involvement in protein folding, and organization of PPI-containing receptors and membrane channels. A possible role of several PPIs in distant interactions between cells is discussed.

  17. Probing the cis-arrangement of prototype tight junction proteins claudin-1 and claudin-3.

    PubMed

    Milatz, Susanne; Piontek, Jörg; Schulzke, Jörg-Dieter; Blasig, Ingolf E; Fromm, Michael; Günzel, Dorothee

    2015-06-15

    Claudins form a large family of TJ (tight junction) proteins featuring four transmembrane segments (TM1-TM4), two extracellular loops, one intracellular loop and intracellular N- and C-termini. They form continuous and branched TJ strands by homo- or heterophilic interaction within the same membrane (cis-interaction) and with claudins of the opposing lateral cell membrane (trans-interaction). In order to clarify the molecular organization of TJ strand formation, we investigated the cis-interaction of two abundant prototypic claudins. Human claudin-1 and claudin-3, fused to ECFP or EYFP at the N- or C-terminus, were expressed in the TJ-free cell line HEK (human embryonic kidney)-293. Using FRET analysis, the proximity of claudin N- and C-termini integrated in homopolymeric strands composed of claudin-3 or of heteropolymeric strands composed of claudin-1 and claudin-3 were determined. The main results are that (i) within homo- and heteropolymers, the average distance between the cytoplasmic ends of the TM1s of cis-interacting claudin molecules is shorter than the average distance between their TM4s, and (ii) TM1 segments of neighbouring claudins are oriented towards each other as the cytoplasmic end of TM1 is in close proximity to more other TM1 segments than TM4 is to other TM4 segments. The results indicate at least two different cis-interaction interfaces within claudin-3 homopolymers as well as within claudin-1/claudin-3 heteropolymers. The data provide novel insight into the molecular TJ architecture consistent with a model with an antiparallel double-row cis-arrangement of classic claudin protomers within strands.

  18. Oxylipin Signaling: A Distinct Role for the Jasmonic Acid Precursor cis-(+)-12-Oxo-Phytodienoic Acid (cis-OPDA)

    PubMed Central

    Dave, Anuja; Graham, Ian A.

    2012-01-01

    Oxylipins are lipid-derived compounds, many of which act as signals in the plant response to biotic and abiotic stress. They include the phytohormone jasmonic acid (JA) and related jasmonate metabolites cis-(+)-12-oxo-phytodienoic acid (cis-OPDA), methyl jasmonate, and jasmonoyl-L-isoleucine (JA-Ile). Besides the defense response, jasmonates are involved in plant growth and development and regulate a range of processes including glandular trichome development, reproduction, root growth, and senescence. cis-OPDA is known to possess a signaling role distinct from JA-Ile. The non-enzymatically derived phytoprostanes are structurally similar to cis-OPDA and induce a common set of genes that are not responsive to JA in Arabidopsis thaliana. A novel role for cis-OPDA in seed germination regulation has recently been uncovered based on evidence from double mutants and feeding experiments showing that cis-OPDA interacts with abscisic acid (ABA), inhibits seed germination, and increases ABA INSENSITIVE5 (ABI5) protein abundance. Large amounts of cis-OPDA are esterified to galactolipids in A. thaliana and the resulting compounds, known as Arabidopsides, are thought to act as a rapidly available source of cis-OPDA. PMID:22645585

  19. [Enzymatic formation of a cis,cis-muconic acid derivative using pyrazon-degrading bacteria (author's transl)].

    PubMed

    Blobel, F; Eberspächer, J; Haug, S; Lingens, F

    1976-01-01

    The cis,cis-muconic acid derivative of pyrazon, which was formerly isolated from the medium of pyrazon-degrading bacteria, was formed enzymatically by incubation of the catechol derivative of pyrazon with partially purified ortho pyrocatechase from pyrazon-degrading bacteria.

  20. Chapter 10: CPV Multijunction Solar Cell Characterization

    SciTech Connect

    Osterwald, Carl R.; Siefer, Gerald

    2016-04-15

    Characterization of solar cells can be divided into two types: the first is measurement of electrooptical semiconductor device parameters, and the second is determination of electrical conversion efficiency. This chapter reviews the multijunction concepts that are necessary for understanding Concentrator photovoltaic (CPV) cell characterization techniques, and describes how CPV efficiency is defined and used. For any I-V measurement of a multijunction cell, the sun simulator spectrum has to be adjusted in a way that all junctions generate the same photocurrent ratios with respect to each other as under reference conditions. The chapter discusses several procedures for spectral irradiance adjustments of solar simulators, essential for multijunction measurements. It overviews the light sources and optics commonly used in simulators for CPV cells under concentration. Finally, the chapter talks about the cell area, quantum efficiency (QE), and current-voltage (I-V) curve measurements that are needed to characterize cells as a function of irradiance.

  1. Marine West Coast Forests, Chapter 9

    USGS Publications Warehouse

    Perakis, Steven S.; Geiser, Linda H.; Lilleskov, Erik A.; Pardo, Linda H.; Robin-Abbott, Molly J.; Driscoll, Charles T.

    2011-01-01

    Human activities have greatly increased nitrogen emissions and deposition across large areas of Earth. Although nitrogen is an essential nutrient for plant growth, too much nitrogen in excess of critical loads leads to losses of biodiversity, soil and stream acidification, nutrient imbalances, and other deleterious effects. In a new report quantifying critical loads of nitrogen deposition across the United States, USGS scientist Steve Perakis and co-authors provided a chapter about responses of marine west coast forests. Much of this region is understudied with respect to nitrogen deposition, and in this chapter the authors identify known adverse effects and estimate critical loads of nitrogen deposition for western Oregon and Washington and southeast Alaska forests. Perakis also contributed to the synthesis chapter, which includes background, objectives, advantages and uncertainties of critical loads, an overview of critical loads across U.S. ecoregions, and other topics.

  2. Chapter A5. Processing of Water Samples

    USGS Publications Warehouse

    Wilde, Franceska D.; Radtke, Dean B.; Gibs, Jacob; Iwatsubo, Rick T.

    1999-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) describes protocols and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This chapter addresses methods to be used in processing water samples to be analyzed for inorganic and organic chemical substances, including the bottling of composite, pumped, and bailed samples and subsamples; sample filtration; solid-phase extraction for pesticide analyses; sample preservation; and sample handling and shipping. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be announced on the USGS Home Page on the World Wide Web under 'New Publications of the U.S. Geological Survey.' The URL for this page is http:/ /water.usgs.gov/lookup/get?newpubs.

  3. Chapter A8. Bottom-Material Samples

    USGS Publications Warehouse

    Radtke, Dean B.

    1998-01-01

    The National Field Manual for the Collection of Water-Quality Data(National Field Manual) describes protocols (requirements and recommendations) and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This release of Chapter A8 provides guidelines for the equipment and procedures needed to collect and process samples of bottom material for the evaluation of surface-water quality. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters are posted on the World Wide Web on the USGS page 'National Field Manual for the Collection of Water-Quality Data.' The URL for this page is http://pubs.water.usgs.gov/twri9A/ (accessed April 2005).

  4. Chapter A1. Preparations for Water Sampling

    USGS Publications Warehouse

    Wilde, Franceska D.; Radtke, Dean B.; Gibs, Jacob; Iwatsubo, Rick T.

    1998-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) provides guidelines and standard procedures for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This chapter addresses field-trip preparations, including selection of sample-collection sites for studies of surface-water quality, site reconnaissance and well selection for studies of groundwater quality, and the establishment of electronic files and field files and folders for a sampling site. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters are posted on the World Wide Web on the USGS page 'National Field Manual for the Collection of Water-Quality Data.' The URL for this page is http://pubs.water.usgs.gov/twri9A/ (accessed Jan. 31, 2005).

  5. 21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 6 2012-04-01 2012-04-01 false Methyl esters of conjugated linoleic acid (cis-9... § 573.637 Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and...

  6. Secondary School Mathematics, Chapter 27, Logic, Chapter 28, Applications of Probability and Statistics. Student's Text.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    One chapter in the fourteenth unit of this SMSG series deals with logic; simple and compound statements, truth tables, logical equivalence, rules of a logical argument, proof, quantifiers, and negations are the topics covered. The second chapter of the unit discusses applications of probability and statistics, including random sampling,…

  7. Secondary School Mathematics, Chapter 13, Perpendiculars and Parallels (I), Chapter 14, Similarity. Student's Text.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    The first chapter of the seventh unit in this SMSG series discusses perpendiculars and parallels; topics covered include the relationship between parallelism and perpendicularity, rectangles, transversals, parallelograms, general triangles, and measurement of the circumference of the earth. The second chapter, on similarity, discusses scale…

  8. [Biennial Survey of Education, 1926-1928. Bulletin, 1930, No. 16. Chapter I - Chapter XX

    ERIC Educational Resources Information Center

    Office of Education, United States Department of the Interior, 1930

    1930-01-01

    This document contains the first twenty chapters of the Biennial Survey of Education document, covering the years 1926-1928. The following chapters are included in this document: (1) Higher education (Arthur J. Klein); (2) Medical education (N. P. Colwell); (3) Legal education (Alfred Z. Reed); (4) Significant movements in city school systems (W.…

  9. Effects of Cd{sup 2+} on cis-dimer structure of E-cadherin in living cells

    SciTech Connect

    Takeda, Hiroshi

    2014-02-21

    Highlights: • The effects of Cd on the dimer of cadherin in living cells was analyzed. • Cd induced cadherin dimer formation was not detected in living cell with low Ca. • Ca mediated structural cooperativity and allostery in the native cadherin. • Ca concentration-dependent competitive displacement of Cd from cadherin is proposed. - Abstract: E-cadherin, a calcium (Ca{sup 2+})-dependent cell–cell adhesion molecule, plays a key role in the maintenance of tissue integrity. We have previously demonstrated that E-cadherin functions in vivo as a cis-dimer through chemical cross-linking reagents. Ca{sup 2+} plays an important role in the cis-dimer formation of cadherin. However, the molecular mechanisms by which Ca{sup 2+} interacts with the binding sites that regulate cis-dimer structures have not been completely elucidated. As expected for a Ca{sup 2+} antagonist, cadmium (Cd{sup 2+}) disrupts cadherin function by displacing Ca{sup 2+} from its binding sites on the cadherin molecules. We used Cd{sup 2+} as a probe for investigating the role of Ca{sup 2+} in the dynamics of the E-cadherin extracellular region that involve cis-dimer formation and adhesion. While cell–cell adhesion assembly was completely disrupted in the presence of Cd{sup 2+}, the amount of cis-dimers of E-cadherin that formed at the cell surface was not affected. In our “Cd{sup 2+}-switch” experiments, we did not find that Cd{sup 2+}-induced E-cadherin cis-dimer formation in EL cells when they were incubated in low-Ca{sup 2+} medium. In the present study, we demonstrated for the first time the effects of Cd{sup 2+} on the cis-dimer structure of E-cadherin in living cells using a chemical cross-link analysis.

  10. Comprehensively Evaluating cis-Regulatory Variation in the Human Prostate Transcriptome by Using Gene-Level Allele-Specific Expression

    PubMed Central

    Larson, Nicholas B.; McDonnell, Shannon; French, Amy J.; Fogarty, Zach; Cheville, John; Middha, Sumit; Riska, Shaun; Baheti, Saurabh; Nair, Asha A.; Wang, Liang; Schaid, Daniel J.; Thibodeau, Stephen N.

    2015-01-01

    The identification of cis-acting regulatory variation in primary tissues has the potential to elucidate the genetic basis of complex traits and further our understanding of transcriptomic diversity across cell types. Expression quantitative trait locus (eQTL) association analysis using RNA sequencing (RNA-seq) data can improve upon the detection of cis-acting regulatory variation by leveraging allele-specific expression (ASE) patterns in association analysis. Here, we present a comprehensive evaluation of cis-acting eQTLs by analyzing RNA-seq gene-expression data and genome-wide high-density genotypes from 471 samples of normal primary prostate tissue. Using statistical models that integrate ASE information, we identified extensive cis-eQTLs across the prostate transcriptome and found that approximately 70% of expressed genes corresponded to a significant eQTL at a gene-level false-discovery rate of 0.05. Overall, cis-eQTLs were heavily concentrated near the transcription start and stop sites of affected genes, and effects were negatively correlated with distance. We identified multiple instances of cis-acting co-regulation by using phased genotype data and discovered 233 SNPs as the most strongly associated eQTLs for more than one gene. We also noted significant enrichment (25/50, p = 2E−5) of previously reported prostate cancer risk SNPs in prostate eQTLs. Our results illustrate the benefit of assessing ASE data in cis-eQTL analyses by showing better reproducibility of prior eQTL findings than of eQTL mapping based on total expression alone. Altogether, our analysis provides extensive functional context of thousands of SNPs in prostate tissue, and these results will be of critical value in guiding studies examining disease of the human prostate. PMID:25983244

  11. Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression.

    PubMed

    Larson, Nicholas B; McDonnell, Shannon; French, Amy J; Fogarty, Zach; Cheville, John; Middha, Sumit; Riska, Shaun; Baheti, Saurabh; Nair, Asha A; Wang, Liang; Schaid, Daniel J; Thibodeau, Stephen N

    2015-06-04

    The identification of cis-acting regulatory variation in primary tissues has the potential to elucidate the genetic basis of complex traits and further our understanding of transcriptomic diversity across cell types. Expression quantitative trait locus (eQTL) association analysis using RNA sequencing (RNA-seq) data can improve upon the detection of cis-acting regulatory variation by leveraging allele-specific expression (ASE) patterns in association analysis. Here, we present a comprehensive evaluation of cis-acting eQTLs by analyzing RNA-seq gene-expression data and genome-wide high-density genotypes from 471 samples of normal primary prostate tissue. Using statistical models that integrate ASE information, we identified extensive cis-eQTLs across the prostate transcriptome and found that approximately 70% of expressed genes corresponded to a significant eQTL at a gene-level false-discovery rate of 0.05. Overall, cis-eQTLs were heavily concentrated near the transcription start and stop sites of affected genes, and effects were negatively correlated with distance. We identified multiple instances of cis-acting co-regulation by using phased genotype data and discovered 233 SNPs as the most strongly associated eQTLs for more than one gene. We also noted significant enrichment (25/50, p = 2E-5) of previously reported prostate cancer risk SNPs in prostate eQTLs. Our results illustrate the benefit of assessing ASE data in cis-eQTL analyses by showing better reproducibility of prior eQTL findings than of eQTL mapping based on total expression alone. Altogether, our analysis provides extensive functional context of thousands of SNPs in prostate tissue, and these results will be of critical value in guiding studies examining disease of the human prostate.

  12. Integration

    ERIC Educational Resources Information Center

    Kalyn, Brenda

    2006-01-01

    Integrated learning is an exciting adventure for both teachers and students. It is not uncommon to observe the integration of academic subjects such as math, science, and language arts. However, educators need to recognize that movement experiences in physical education also can be linked to academic curricula and, may even lead the…

  13. Chapter XX: POLYMODAL SENSORY INTEGRATION IN RETINAL GANGLION CELLS

    PubMed Central

    Križaj, David

    2016-01-01

    An animal's ability to perceive the external world is conditioned by its capacity to extract and encode specific features of the visual image. The output of the vertebrate retina is not a simple representation of the 2D visual map generated by photon absorptions in the photoreceptor layer. Rather, spatial, temporal, direction selectivity and color “dimensions” of the original image are distributed in the form of parallel output channels mediated by distinct retinal ganglion cell (RGC) populations. We propose that visual information transmitted to the brain includes additional, light-independent, inputs that reflect the functional states of the retina, anterior eye and the body. These may include the local ion microenvironment, glial metabolism and systemic parameters such as intraocular pressure, temperature and immune activation which act on ion channels that are intrinsic to RGCs. We particularly focus on light-independent mechanical inputs that are associated with physical impact, cell swelling and intraocular pressure as excessive mechanical stimuli lead to the counterintuitive experience of “pressure phosphenes” and/or debilitating blinding disease such as glaucoma and diabetic retinopathy. We point at recently discovered retinal mechanosensitive ion channels as examples through which molecular physiology brings together Greek phenomenology, modern neuroscience and medicine. Thus, RGC output represents a unified picture of the embodied context within which vision takes place. PMID:26427477

  14. Multi-phase back contacts for CIS solar cells

    DOEpatents

    Rockett, Angus A.; Yang, Li-Chung

    1995-01-01

    Multi-phase, single layer, non-interdiffusing M-Mo back contact metallized films, where M is selected from Cu, Ga, or mixtures thereof, for CIS cells are deposited by a sputtering process on suitable substrates, preferably glass or alumina, to prevent delamination of the CIS from the back contact layer. Typical CIS compositions include CuXSe.sub.2 where X is In or/and Ga. The multi-phase mixture is deposited on the substrate in a manner to provide a columnar microstructure, with micro-vein Cu or/and Ga regions which partially or fully vertically penetrate the entire back contact layer. The CIS semiconductor layer is then deposited by hybrid sputtering and evaporation process. The Cu/Ga-Mo deposition is controlled to produce the single layer two-phase columnar morphology with controllable Cu or Ga vein size less than about 0.01 microns in width. During the subsequent deposition of the CIS layer, the columnar Cu/Ga regions within the molybdenum of the Cu/Ga-Mo back layer tend to partially leach out, and are replaced by columns of CIS. Narrower Cu and/or Ga regions, and those with fewer inner connections between regions, leach out more slowly during the subsequent CIS deposition. This gives a good mechanical and electrical interlock of the CIS layer into the Cu/Ga-Mo back layer. Solar cells employing In-rich CIS semiconductors bonded to the multi-phase columnar microstructure back layer of this invention exhibit vastly improved photo-electrical conversion on the order of 17% greater than Mo alone, improved uniformity of output across the face of the cell, and greater Fill Factor.

  15. Multi-phase back contacts for CIS solar cells

    DOEpatents

    Rockett, A.A.; Yang, L.C.

    1995-12-19

    Multi-phase, single layer, non-interdiffusing M-Mo back contact metallized films, where M is selected from Cu, Ga, or mixtures thereof, for CIS cells are deposited by a sputtering process on suitable substrates, preferably glass or alumina, to prevent delamination of the CIS from the back contact layer. Typical CIS compositions include CuXSe{sub 2} where X is In or/and Ga. The multi-phase mixture is deposited on the substrate in a manner to provide a columnar microstructure, with micro-vein Cu or/and Ga regions which partially or fully vertically penetrate the entire back contact layer. The CIS semiconductor layer is then deposited by hybrid sputtering and evaporation process. The Cu/Ga-Mo deposition is controlled to produce the single layer two-phase columnar morphology with controllable Cu or Ga vein size less than about 0.01 microns in width. During the subsequent deposition of the CIS layer, the columnar Cu/Ga regions within the molybdenum of the Cu/Ga-Mo back layer tend to partially leach out, and are replaced by columns of CIS. Narrower Cu and/or Ga regions, and those with fewer inner connections between regions, leach out more slowly during the subsequent CIS deposition. This gives a good mechanical and electrical interlock of the CIS layer into the Cu/Ga-Mo back layer. Solar cells employing In-rich CIS semiconductors bonded to the multi-phase columnar microstructure back layer of this invention exhibit vastly improved photo-electrical conversion on the order of 17% greater than Mo alone, improved uniformity of output across the face of the cell, and greater Fill Factor. 15 figs.

  16. Chapter 1 Migrant Education Program: Final Report.

    ERIC Educational Resources Information Center

    Kauffman, Thomas B.; And Others

    This report documents the implementation of the migrant education program funded under Chapter 1 of the Education Consolidation Improvement Act in the Houston (Texas) Independent School District and evaluates the program's impact on student achievement, grades, conduct, and attendance. The program offered assistance to eligible migrant children…

  17. Recommended Research on Artificial Gravity. Chapter 13

    NASA Technical Reports Server (NTRS)

    Vernikos, Joan; Paloski, William; Fuller, Charles; Clement, Gilles

    2006-01-01

    Based on the summaries presented in the above sections of what is still to be learned on the effects of artificial gravity on human functions, this chapter will discuss the short- and long-term steps of research required to understand fundamentals and to validate operational aspects of using artificial gravity as an effective countermeasure for long-duration space travel.

  18. Chapter 8: Youth, Technology, and Media Cultures

    ERIC Educational Resources Information Center

    Sefton-Green, Julian

    2006-01-01

    This chapter begins with a scenario contrasting two seemingly different images of child and media from before and after the "digital revolution." The author argues that there is much greater continuity in how this relationship has been conceptualized over the period than is commonly imagined. While not offering a comprehensive study of recent…

  19. Parent Involvement in Local Chapter 1 Programs.

    ERIC Educational Resources Information Center

    Jay, E. Deborah; Shields, Patrick M.

    This report focuses on the involvement of parents in local projects funded under Title I of the Elementary and Secondary Education Act and Chapter 1 of the Education Consolidation and Improvement Act. It researches the kind and extent of involvement, the impact of state and local factors on it, and the effect of the change from Title I to Chapter…

  20. Chapter 1 Schoolwide Project Study. Final Report.

    ERIC Educational Resources Information Center

    Schenck, E. Allen; Beckstrom, Sharon

    Chapter 1 schoolwide projects are intended to serve educationally disadvantaged students by improving the instructional program provided to all students in high-poverty schools. This report provides a comprehensive look at schoolwide projects in the 1991-92 school year, using data from surveys of all schoolwide project schools. The response rate…

  1. Chapter 2. Adolescents' Attitudes toward the Computer

    ERIC Educational Resources Information Center

    Russian Education and Society, 2004

    2004-01-01

    This second chapter focuses on an analysis of the aspects that characterize the typical content of students' attitudes toward the world of computers. In this connection, it attempts to determine what is of the greatest interest to students as they deal with the world of computers, which types of programs they use, and which magazines they read…

  2. Chapter 9. Benefits of International Collaboration

    EPA Science Inventory

    In this chapter, we share what we have learned from working with our Brazilian colleagues on a multi university, multiyear, and multi basin ecological assessment and how those experiences were transmitted more broadly. These lessons (each of which is described in subsequent parag...

  3. Chapter 4. Students' Attitudes toward Computer Games

    ERIC Educational Resources Information Center

    Russian Education and Society, 2004

    2004-01-01

    In this chapter, the authors attempt not only to discern aspects that relate to age, place, and the amount of time devoted to playing computer games in adolescence, but also to study content characteristics of their attitudes such as: the developmental dynamic in the change of their genre preferences in computer games, changes in factors that…

  4. Chapter 7: Materials for Launch Vehicle Structures

    NASA Technical Reports Server (NTRS)

    Henson, Grant; Jone, Clyde S. III

    2017-01-01

    This chapter concerns materials for expendable and reusable launch vehicle (LV) structures. An emphasis is placed on applications and design requirements, and how these requirements are met by the optimum choice of materials. Structural analysis and qualification strategies, which cannot be separated from the materials selection process, are described.

  5. Chapter 6. available lepidopteran insect cell lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter lists the known cell lines from Lepidoptera, largely based on previous compilations of insect cell lines published by W. Fred Hink. More than 320 lines from 65 species are listed. The official designation is given for each cell line as well as the species, tissue source, and, when kno...

  6. Chapter 3. Fresh Meat Texture and Tenderness

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This book chapter summarizes the current state of knowledge of meat tenderness and the antemortem and postmortem strategies that can be used to influence meat tenderness. Tenderness is critical to the consumer acceptance of meat products. Numerous antemortem and postmortem factors can impact tende...

  7. Metrology of Large Parts. Chapter 5

    NASA Technical Reports Server (NTRS)

    Stahl, H. Philip

    2012-01-01

    As discussed in the first chapter of this book, there are many different methods to measure a part using optical technology. Chapter 2 discussed the use of machine vision to measure macroscopic features such as length and position, which was extended to the use of interferometry as a linear measurement tool in chapter 3, and laser or other trackers to find the relation of key points on large parts in chapter 4. This chapter looks at measuring large parts to optical tolerances in the sub-micron range using interferometry, ranging, and optical tools discussed in the previous chapters. The purpose of this chapter is not to discuss specific metrology tools (such as interferometers or gauges), but to describe a systems engineering approach to testing large parts. Issues such as material warpage and temperature drifts that may be insignificant when measuring a part to micron levels under a microscope, as will be discussed in later chapters, can prove to be very important when making the same measurement over a larger part. In this chapter, we will define a set of guiding principles for successfully overcoming these challenges and illustrate the application of these principles with real world examples. While these examples are drawn from specific large optical testing applications, they inform the problems associated with testing any large part to optical tolerances. Manufacturing today relies on micrometer level part performance. Fields such as energy and transportation are demanding higher tolerances to provide increased efficiencies and fuel savings. By looking at how the optics industry approaches sub-micrometer metrology, one can gain a better understanding of the metrology challenges for any larger part specified to micrometer tolerances. Testing large parts, whether optical components or precision structures, to optical tolerances is just like testing small parts, only harder. Identical with what one does for small parts, a metrologist tests large parts and optics

  8. The metabolism of cis- and trans-decalin

    PubMed Central

    Elliott, T. H.; Robertson, J. S.; Williams, R. T.

    1966-01-01

    1. The metabolism of cis- and trans-decalin in the rabbit has been investigated. 2. Both hydrocarbons were oxidized to racemic secondary alcohols and excreted as ether glucuronides in amounts equal to about 60% of the dose administered. The principal glucuronides were isolated as triacetyl methyl esters and as sodium salts. 3. cis-Decalin gave rise mainly to (±)-cis–cis-2-decalol, together with a little cis–trans-2-decalol, and trans-decalin mainly to (±)-trans–cis-2-decalol and a small amount of trans–trans-2-decalol. 4. These results suggest that biological oxidation of the decalins does not occur via a free-radical mechanism. An attempt is made to explain why racemic alcohols are obtained, rather than the more typical optically active products of enzymic reaction, and a mechanism is proposed. It is suggested that enzymes similar to steroid hydroxylases are involved. PMID:5968538

  9. Trans-cis molecular photoswitching in interstellar Space.

    PubMed

    Cuadrado, S; Goicoechea, J R; Roncero, O; Aguado, A; Tercero, B; Cernicharo, J

    2016-12-01

    As many organic molecules, formic acid (HCOOH) has two conformers (trans and cis). The energy barrier to internal conversion from trans to cis is much higher than the thermal energy available in molecular clouds. Thus, only the most stable conformer (trans) is expected to exist in detectable amounts. We report the first interstellar detection of cis-HCOOH. Its presence in ultraviolet (UV) irradiated gas exclusively (the Orion Bar photodissociation region), with a low trans-to-cis abundance ratio of 2.8 ± 1.0, supports a photoswitching mechanism: a given conformer absorbs a stellar photon that radiatively excites the molecule to electronic states above the interconversion barrier. Subsequent fluorescent decay leaves the molecule in a different conformer form. This mechanism, which we specifically study with ab initio quantum calculations, was not considered in Space before but likely induces structural changes of a variety of interstellar molecules submitted to UV radiation.

  10. Trans-cis molecular photoswitching in interstellar Space*

    PubMed Central

    Cuadrado, S.; Goicoechea, J. R.; Roncero, O.; Aguado, A.; Tercero, B.; Cernicharo, J.

    2016-01-01

    As many organic molecules, formic acid (HCOOH) has two conformers (trans and cis). The energy barrier to internal conversion from trans to cis is much higher than the thermal energy available in molecular clouds. Thus, only the most stable conformer (trans) is expected to exist in detectable amounts. We report the first interstellar detection of cis-HCOOH. Its presence in ultraviolet (UV) irradiated gas exclusively (the Orion Bar photodissociation region), with a low trans-to-cis abundance ratio of 2.8 ± 1.0, supports a photoswitching mechanism: a given conformer absorbs a stellar photon that radiatively excites the molecule to electronic states above the interconversion barrier. Subsequent fluorescent decay leaves the molecule in a different conformer form. This mechanism, which we specifically study with ab initio quantum calculations, was not considered in Space before but likely induces structural changes of a variety of interstellar molecules submitted to UV radiation. PMID:28003686

  11. New cis-clerodane diterpenoids from Croton schiedeanus.

    PubMed

    Puebla, Pilar; Correa, Sofía Ximena; Guerrero, Mario; Carron, Rosalía; San Feliciano, Arturo

    2005-03-01

    The acid fraction of extracts from the aerial part of Croton schiedeanus afforded six cis-clerodane type diterpenoids. Two of them (1 and 4) are new natural compounds. Structural elucidation was achieved on the basis of their spectral data.

  12. Workstation Designs for a Cis-Lunar Deep Space Habitat

    NASA Technical Reports Server (NTRS)

    Howe, A. Scott

    2014-01-01

    Using the International Standard Payload Rack (ISPR) system, a suite of workstations required for deep space missions have been proposed to fill out habitation functions in an International Space Station (ISS) derived Cis-lunar Deep Space Habitat. This paper introduces the functional layout of the Cis-lunar habitat design, and describes conceptual designs for modular deployable work surfaces, General Maintenance Workstation (GMWS), In-Space Manufacturing Workstation (ISMW), Intra-Vehicular Activity Telerobotics Work Station (IVA-TRWS), and Galley / Wardroom.

  13. Genetic engineering of Yarrowia lipolytica for enhanced production of trans-10, cis-12 conjugated linoleic acid

    PubMed Central

    2013-01-01

    Background Conjugated linoleic acid (CLA) has been extensively studied for decades because of its health benefits including cancer prevention, anti-atherogenic and anti-obesity effects, and modulation of the immune system. We previously described the production of trans-10, cis-12 CLA in Yarrowia lipolytica by expressing the gene coding for linoleic acid isomerase from Propionibacterium acnes (pai). However the stable strain produced CLA at about 0.08% of dry cell weight (DCW), a level of production which was not high enough for practical applications. The goal of the present study was to enhance production of CLA by genetic engineering of Y. lipolytica strains. Results We have now co-expressed the delta 12-desaturase gene (FADS12, d12) from Mortierella alpina together with the codon-optimized linoleic acid isomerase (opai) gene in Y. lipolytica, expressed under the control of promoter hp16d modified by fusing 12 copies of UAS1B to the original promoter hp4d. A multi-copy integration plasmid was used to further enhance the expression of both genes. Using glucose as the sole carbon source, the genetically-modified Y. lipolytica produced trans-10, cis-12-CLA at a level of up to 10% of total fatty acids and 0.4% of DCW. Furthermore, when the recombinant yeast was grown with soybean oil, trans-10, cis-12-CLA now accumulated at a level of up to 44% of total fatty acids, which represented 30% of DCW after 38.5 h of cultivation. In addition, trans-10, cis-12-CLA was also detected in the growth medium up to 0.9 g/l. Conclusions We have successfully produced trans-10, cis-12-CLA with a titre of 4 g/l of culture (3.1 g/l in cells and 0.9 g/l in culture medium). Our results demonstrate the potential use of Y. lipolytica as a promising microbial cell factory for trans-10, cis-12-CLA production. PMID:23866108

  14. The tomato cis-prenyltransferase gene family.

    PubMed

    Akhtar, Tariq A; Matsuba, Yuki; Schauvinhold, Ines; Yu, Geng; Lees, Hazel A; Klein, Samuel E; Pichersky, Eran

    2013-02-01

    cis-prenyltransferases (CPTs) are predicted to be involved in the synthesis of long-chain polyisoprenoids, all with five or more isoprene (C5) units. Recently, we identified a short-chain CPT, neryl diphosphate synthase (NDPS1), in tomato (Solanum lycopersicum). Here, we searched the tomato genome and identified and characterized its entire CPT gene family, which comprises seven members (SlCPT1-7, with NDPS1 designated as SlCPT1). Six of the SlCPT genes encode proteins with N-terminal targeting sequences, which, when fused to GFP, mediated GFP transport to the plastids of Arabidopsis protoplasts. The SlCPT3-GFP fusion protein was localized to the cytosol. Enzymatic characterization of recombinant SlCPT proteins demonstrated that SlCPT6 produces Z,Z-FPP, and SlCPT2 catalyzes the formation of nerylneryl diphosphate while SlCPT4, SlCPT5 and SlCPT7 synthesize longer-chain products (C25-C55). Although no in vitro activity was demonstrated for SlCPT3, its expression in the Saccharomyces cerevisiae dolichol biosynthesis mutant (rer2) complemented the temperature-sensitive growth defect. Transcripts of SlCPT2, SlCPT4, SlCPT5 and SlCPT7 are present at low levels in multiple tissues, SlCPT6 is exclusively expressed in red fruit and roots, and SlCPT1, SlCPT3 and SlCPT7 are highly expressed in trichomes. RNAi-mediated suppression of NDPS1 led to a large decrease in β-phellandrene (which is produced from neryl diphosphate), with greater reductions achieved with the general 35S promoter compared to the trichome-specific MKS1 promoter. Phylogenetic analysis revealed CPT gene families in both eudicots and monocots, and showed that all the short-chain CPT genes from tomato (SlCPT1, SlCPT2 and SlCPT6) are closely linked to terpene synthase gene clusters.

  15. Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing

    PubMed Central

    Gao, Qingsong; Sun, Wei; Ballegeer, Marlies; Libert, Claude; Chen, Wei

    2015-01-01

    Divergence of alternative splicing represents one of the major driving forces to shape phenotypic diversity during evolution. However, the extent to which these divergences could be explained by the evolving cis-regulatory versus trans-acting factors remains unresolved. To globally investigate the relative contributions of the two factors for the first time in mammals, we measured splicing difference between C57BL/6J and SPRET/EiJ mouse strains and allele-specific splicing pattern in their F1 hybrid. Out of 11,818 alternative splicing events expressed in the cultured fibroblast cells, we identified 796 with significant difference between the parental strains. After integrating allele-specific data from F1 hybrid, we demonstrated that these events could be predominately attributed to cis-regulatory variants, including those residing at and beyond canonical splicing sites. Contrary to previous observations in Drosophila, such predominant contribution was consistently observed across different types of alternative splicing. Further analysis of liver tissues from the same mouse strains and reanalysis of published datasets on other strains showed similar trends, implying in general the predominant contribution of cis-regulatory changes in the evolution of mouse alternative splicing. PMID:26134616

  16. Control of carotenoid biosynthesis through a heme-based cis-trans isomerase

    PubMed Central

    Beltrán, Jesús; Kloss, Brian; Hosler, Jonathan P.; Geng, Jiafeng; Liu, Aimin; Modi, Anuja; Dawson, John H.; Sono, Masanori; Shumskaya, Maria; Ampomah-Dwamena, Charles; Love, James D.; Wurtzel, Eleanore T.

    2015-01-01

    Plants synthesize carotenoids essential for plant development and survival. These metabolites also serve as essential nutrients for human health. The biosynthetic pathway leading to all plant carotenoids occurs in chloroplasts and other plastids and requires 15-cis-ζ-carotene isomerase (Z-ISO). It was not certain whether isomerization was achieved by Z-ISO alone or in combination with other enzymes. Here we show that Z-ISO is a bona fide enzyme and integral membrane protein. Z-ISO independently catalyzes the cis-to-trans isomerization of the 15–15′ C=C bond in 9,15,9′-cis-ζ-carotene to produce the substrate required by the following biosynthetic pathway enzyme. We discovered that isomerization depends upon a ferrous heme b cofactor that undergoes redox-regulated ligand-switching between the heme iron and alternate Z-ISO amino acid residues. Heme b-dependent isomerization of a large, hydrophobic compound in a membrane is unprecedented. As an isomerase, Z-ISO represents a new prototype for heme b proteins and potentially utilizes a novel chemical mechanism. PMID:26075523

  17. Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus

    PubMed Central

    Sundaram, Vasavi; Choudhary, Mayank N. K.; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A.; Wang, Ting

    2017-01-01

    Cis-regulatory modules contain multiple transcription factor (TF)-binding sites and integrate the effects of each TF to control gene expression in specific cellular contexts. Transposable elements (TEs) are uniquely equipped to deposit their regulatory sequences across a genome, which could also contain cis-regulatory modules that coordinate the control of multiple genes with the same regulatory logic. We provide the first evidence of mouse-specific TEs that encode a module of TF-binding sites in mouse embryonic stem cells (ESCs). The majority (77%) of the individual TEs tested exhibited enhancer activity in mouse ESCs. By mutating individual TF-binding sites within the TE, we identified a module of TF-binding motifs that cooperatively enhanced gene expression. Interestingly, we also observed the same motif module in the in silico constructed ancestral TE that also acted cooperatively to enhance gene expression. Our results suggest that ancestral TE insertions might have brought in cis-regulatory modules into the mouse genome. PMID:28348391

  18. Vaccination against bacterial kidney disease: Chapter 22

    USGS Publications Warehouse

    Elliott, Diane G.; Wiens, Gregory D.; Hammell, K. Larry; Rhodes, Linda D.; Edited by Gudding, Roar; Lillehaug, Atle; Evensen, Øystein

    2014-01-01

    Bacterial kidney disease (BKD) of salmonid fishes, caused by Renibacterium salmoninarum, has been recognized as a serious disease in salmonid fishes since the 1930s. This chapter discusses the occurrence and significance, etiology, and pathogenesis of BKD. It then describes the different vaccination procedures and the effects and side-effects of vaccination. Despite years of research, however, only a single vaccine has been licensed for prevention of BKD, and has demonstrated variable efficacy. Therefore, in addition to a presentation of the current status of BKD vaccination, a discussion of potential future directions for BKD vaccine development is included in the chapter. This discussion is focused on the unique characteristics of R. salmoninarum and its biology, as well as aspects of the salmonid immune system that might be explored specifically to develop more effective vaccines for BKD prevention.

  19. Chapter D in Geological Survey research 1964

    USGS Publications Warehouse

    ,

    1964-01-01

    This collection of 43 short papers is the last of the chapters of Geological Survey Research 1964. The papers report on scientific and economic results of current work by members of the Geologic, Conservation, Water Resources, and Topographic Divisions of the U.S. Geological Survey. Some of the papers present results of completed parts of continuing investigations; others announce new discoveries or preliminary results of investigations that will be discussed in greater detail in reports to be published in the future. Still others are. scientific notes of limited scope, and short papers on techniques and instrumentation. Chapter A of this series presents a summary of results of work done during the present fiscal year.

  20. Chapter 1: Physics with Trapped Charged Particles

    NASA Astrophysics Data System (ADS)

    Knoop, Martina; Madsen, Niels; Thompson, Richard C.

    2014-01-01

    Ion traps, which were first introduced in the late 1950s and early 1960s, have established themselves as indispensable tools in many areas of physics, chemistry and technology. This chapter gives a brief survey of the operating principles and development of ion traps, together with a short description of how ions are loaded and detected. This is followed by a brief account of some of the current applications of ion traps.

  1. Dust and human health: Chapter 15

    USGS Publications Warehouse

    Morman, Suzette A.; Plumlee, Geoffrey S.; Knippertz, Peter; Stuut, Jan-Berend W.

    2013-01-01

    It is generally accepted that exposure to fine particulate matter may increase risk for human morbidity and mortality. Until recently, population health related studies examining the effects of particulate matter on human health generally examined anthropogenic (industry and combustion by-products) sources with few studies considering contributions from natural sources. This chapter provides an overview of naturally occurring inorganic mineral dust research and associated human health ailments and some of the challenges in elucidating the etiological mechanisms responsible.

  2. Haramekhala - tantra (the first chapter on medicine).

    PubMed

    Sharma, P V

    1986-01-01

    This translation of Haramekhala - tantra of the author is based on Banaras Hindu University manuscript which seems to be a novel one. The manuscript runs into 133 stanzas in all in the form of dialogue between lord Siva and goddess Parvati. This is only the first chapter (of the great work) dealing with medicine. From stanza 109 onwards some magic spells are described and as such those have not been included in this translation.

  3. Nozomi Cis-Lunar Phase Orbit Determination

    NASA Technical Reports Server (NTRS)

    Ryne, Mark; Criddle, Kevin

    2000-01-01

    Japan's Institute of Space and Astronautical Science (ISAS) launched Nozomi, its first mission to the planet Mars using the newly developed M-V launch vehicle on July 3, 1998. Scientific objectives of the mission are to study the structure and dynamics of the Martian upper atmosphere and its interaction with the solar wind. Nozomi is a cooperative mission between ISAS and the National Aeronautics and Space Administration (NASA). The NASA contribution includes navigation and tracking services provided by the Jet Propulsion Laboratory (JPL). The spacecraft also serves as an engineering demonstration of basic technology for planetary exploration. One of the new technologies was a unique trajectory, developed by ISAS, which used solar gravitational perturbations at the weak stability boundary as an aid to achieve an Earth-Mars transfer orbit. This trajectory saves approximately 120 m/s of Delta V compared to direct hyperbolic insertion and is considered an enabling technology for the mission. Nozomi was the first spacecraft to employ this trajectory and provided on-orbit validation of the technique. The trajectory was achieved by initially placing the spacecraft in a highly elliptical cis-lunar phasing orbit. Six maneuvers were performed during this period to correct injection errors and target an outbound lunar swingby in September 1998. The gravity assist from the lunar swingby raised apogee to the vicinity of the weak stability boundary. After three more targeting maneuvers, Nozomi performed an inbound lunar swingby followed immediately by a powered Earth swingby in late December 1998. A 420 m/s Trans Mars Insertion (TMI) burn at the final Earth periapsis was intended to place the spacecraft on a heliocentric trajectory leading to Mars orbit insertion in October 1999. Orbit determination for Nozomi is performed in parallel by both ISAS and the Multi-Mission Navigation (MMNAV) group at JPL. This was an advantage for the mission because each group would generate

  4. Chapter A9. Safety in Field Activities

    USGS Publications Warehouse

    Lane, Susan L.; Ray, Ronald G.

    1998-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) describes protocols (requirements and recommendations) and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This chapter of the manual addresses topics related to personal safety to be used in the collection of water-quality data, including: policies and general regulations on field safety; transportation of people and equipment; implementation of surface-water and ground-water activities; procedures for handling chemicals; and information on potentially hazardous environmental conditions, animals, and plants. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be announced on the USGS Home Page on the World Wide Web under 'New Publications of the U.S. Geological Survey.' The URL for this page is http://pubs.usgs.gov/publications/ index.html.

  5. Solid Lubrication Fundamentals and Applications. Chapter 6

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa

    2000-01-01

    This chapter focuses attention on the friction and wear properties of selected solid lubricating films to aid users in choosing the best lubricant, deposition conditions, and operational variables. For simplicity, discussion of the tribological properties of concern is separated into two parts. The first part of the chapter discusses the different solid lubricating films selected for study including commercially developed solid film lubricants: (1) bonded molybdenum disulfide (MoS2), (2) magnetron-sputtered MoS2, (3) ion-plated silver, (4) ion-plated lead, (5) magnetron-sputtered diamondlike carbon (MS DLC), and (6) plasma-assisted, chemical-vapor-deposited diamondlike carbon (PACVD DEC) films. Marked differences in the friction and wear properties of the different films resulted from the different environmental conditions (ultrahigh vacuum, humid air, and dry nitrogen) and the solid film lubricant materials. The second part of the chapter discusses the physical and chemical characteristics, friction behavior, and endurance life of the magnetron-sputtered MoS2 films. The role of interface species and the effects of applied load, film thickness, oxygen pressure, environment, and temperature on the friction and wear properties are considered.

  6. A Survey of Geologic Resources. Chapter 11

    NASA Technical Reports Server (NTRS)

    Edmonson, Jennifer; Rickman, Doug

    2012-01-01

    This chapter focuses on the resources available from the Moon itself: regolith, geologically concentrated materials, and lunar physical features that will enable habitation and generation of power on the surface. This chapter briefly covers the formation of the Moon and thus the formation of the crust of the Moon, as well as the evolution of the regolith. The characteristics of the regolith are provided in some detail, including its mineralogy and lithology. The location of high concentrations of specific minerals or rocks is noted. Other ideal locations for in situ resource utilization technology and lunar habitation are presented. This chapter is intended to be a brief review of current knowledge, and to serve as a foundational source for further study. Each concept presented here has a wealth of literature associated with it; the reader is therefore directed to that literature with each discussion. With great interest in possible manned lunar landings and continued study of the Moon by multiple satellites, the available information changes regularly.

  7. Fundamentals of Physics, Part 1 (Chapters 1-11)

    NASA Astrophysics Data System (ADS)

    Halliday, David; Resnick, Robert; Walker, Jearl

    2003-12-01

    Chapter 1.Measurement. How does the appearance of a new type of cloud signal changes in Earth's atmosphere? 1-1 What Is Physics? 1-2 Measuring Things. 1-3 The International System of Units. 1-4 Changing Units. 1-5 Length. 1-6 Time. 1-7 Mass. Review & Summary. Problems. Chapter 2.Motion Along a Straight Line. What causes whiplash injury in rear-end collisions of cars? 2-1 What Is Physics? 2-2 Motion. 2-3 Position and Displacement. 2-4 Average Velocity and Average Speed. 2-5 Instantaneous Velocity and Speed. 2-6 Acceleration. 2-7 Constant Acceleration: A Special Case. 2-8 Another Look at Constant Acceleration. 2-9 Free-Fall Acceleration. 2-10 Graphical Integration in Motion Analysis. Review & Summary. Questions. Problems. Chapter 3.Vectors. How does an ant know the way home with no guiding clues on the deser t plains? 3-2 Vectors and Scalars. 3-3 Adding Vectors Geometrically. 3-4 Components of Vectors. 3-5 Unit Vectors. 3-6 Adding Vectors by Components. 3-7 Vectors and the Laws of Physics. 3-8 Multiplying Vectors. Review & Summary. Questions. Problems. Chapter 4.Motion in Two and Three Dimensions. In a motorcycle jump for record distance, where does the jumper put the second ramp? 4-1 What Is Physics? 4-2 Position and Displacement. 4-3 Average Velocity and Instantaneous Velocity. 4-4 Average Acceleration and Instantaneous Acceleration. 4-5 Projectile Motion. 4-6 Projectile Motion Analyzed. 4-7 Uniform Circular Motion. 4-8 Relative Motion in One Dimension. 4-9 Relative Motion in Two Dimensions. Review & Summary. Questions. Problems. Chapter 5.Force and Motion-I. When a pilot takes off from an aircraft carrier, what causes the compulsion to fly the plane into the ocean? 5-1 What Is Physics? 5-2 Newtonian Mechanics. 5-3 Newton's First Law. 5-4 Force. 5-5 Mass. 5-6 Newton's Second Law. 5-7 Some Particular Forces. 5-8 Newton's Third Law. 5-9 Applying Newton's Laws. Review & Summary. Questions. Problems. Chapter 6.Force and Motion-II. Can a Grand Prix race car be driven

  8. Fundamentals of Physics, Volume 1, (Chapters 1 - 21)

    NASA Astrophysics Data System (ADS)

    Walker, Jearl

    2004-01-01

    Chapter 1. Measurement 1. How does the appearance of a new type of cloud signal changes in Earth's atmosphere? 1-1 What Is Physics? 1-2 Measuring Things. 1-3 The International System of Units. 1-4 Changing Units. 1-5 Length. 1-6 Time. 1-7 Mass. Review & Summary. Problems. Chapter 2. Motion Along a Straight Line. What causes whiplash injury in rear-end collisions of cars? 2-1 What Is Physics? 2-2 Motion. 2-3 Position and Displacement. 2-4 Average Velocity and Average Speed. 2-5 Instantaneous Velocity and Speed. 2-6 Acceleration. 2-7 Constant Acceleration: A Special Case. 2-8 Another Look at Constant Acceleration. 2-9 Free-Fall Acceleration. 2-10 Graphical Integration in Motion Analysis. 2 Review & Summary. Questions. Problems. Chapter 3. Vectors. How does an ant know the way home with no guiding clues on the desert plains? 3-1 What Is Physics? 3-2 Vectors and Scalars. 3-3 Adding Vectors Geometrically. 3-4 Components of Vectors. 3-5 Unit Vectors. 3-6 Adding Vectors by Components. 3-7 Vectors and the Laws of Physics. 3-8 Multiplying Vectors. Review & Summary. Questions. Problems. Chapter 4. Motion in Two and Three Dimensions. In a motorcycle jump for record distance, where does the jumper put the second ramp? 4-1 What Is Physics? 4-2 Position and Displacement. 4-3 Average Velocity and Instantaneous Velocity. 4-4 Average Acceleration and Instantaneous Acceleration. 4-5 Projectile Motion. 4-6 Projectile Motion Analyzed. 4-7 Uniform Circular Motion. 4-8 Relative Motion in One Dimension. 4-9 Relative Motion in Two Dimensions. Review & Summary. Questions. Problems. Chapter 5. Force and Motion--I. When a pilot takes off from an aircraft carrier, what causes the compulsion to .y the plane into the ocean? 5-1 What Is Physics? 5-2 Newtonian Mechanics. 5-3 Newton's First Law. 5-4 Force. 5-5 Mass. 5-6 Newton's Second Law. 5-7 Some Particular Forces. 5-8 Newton's Third Law. 5-9 Applying Newton's Laws. Review & Summary. Questions. Problems. Chapter 6. Force and Motion--II. Can a

  9. Overview of NATO Background on Scramjet Technology. Chapter 1

    NASA Technical Reports Server (NTRS)

    Drummond, J. Philip; Bouchez, Marc; McClinton, Charles R.

    2006-01-01

    The purpose of the present overview is to summarize the current knowledge of the NATO contributors. All the topics will be addressed in this chapter, with references and some examples. This background enhances the level of knowledge of the NATO scramjet community, which will be used for writing the specific chapters of the Report. Some previous overviews have been published on scramjet technology worldwide. NASA, DOD, the U.S. industry and global community have studied scramjet-powered hypersonic vehicles for over 40 years. Within the U.S. alone, NASA, DOD (DARPA, U.S. Navy and USAF), and industry have participated in hypersonic technology development. Over this time NASA Langley Research Center continuously studied hypersonic system design, aerothermodynamics, scramjet propulsion, propulsion-airframe integration, high temperature materials and structural architectures, and associated facilities, instrumentation and test methods. These modestly funded programs were substantially augmented during the National Aero-Space Plane (X-30) Program, which spent more than $3B between 1984 and 1995, and brought the DOD and other NASA Centers, universities and industry back into hypersonics. In addition, significant progress was achieved in all technologies required for hypersonic flight, and much of that technology was transferred into other programs, such as X-33, DC-X, X-37, X-43, etc. In addition, technology transfer impacted numerous other industries, including automotive, medical, sports and aerospace.

  10. Glucose intolerance following cis-platinum treatment in rats.

    PubMed

    Goldstein, R S; Mayor, G H; Rosenbaum, R W; Hook, J B; Santiago, J V; Bond, J T

    1982-01-01

    cis-Dichlorodiammineplatinum (cis-Pt) is a heavy metal complex used in cancer chemotherapy. Since this drug has been shown to induce hyperglycemia in rats, these studies were initiated to elucidate the effects of cis-Pt on carbohydrate tolerance and insulin and glucagon secretion. Two days following i.v. cis-Pt (2.5 or 7.5 mg/kg, 5 ml/kg) or vehicle administration to male F-344 rats, plasma glucose, immunoreactive insulin (IRI) and glucagon (IRG) concentrations were determined in the basal state and serially following a glucose load (2 g/kg, i.p.). Since cis-Pt induces a dose-related anorexia, a pair-fed control group was also studied. Administration of 7.5 mg/kg cis-Pt was associated with plasma glucose concentrations 2.5-5 times greater than ad-libitum and pair-fed controls at every time point during the 2-h glucose tolerance test. Although basal plasma IRI concentrations of the 7.5-mg/kg group were comparable to ad-libitum fed controls, they were significantly greater than those of pair-fed partners. Furthermore, the appropriate IRI response to a glucose stimulus observed in both controls and the 2.5-mg/kg group was absent in the 7.5-mg/kg group. Basal plasma IRG concentrations of the 7.5-mg/kg group were approximately 3-4 times greater than ad-libitum and pair-fed controls and were not suppressed following a glucose load. These results suggest that cis-Pt induces marked glucose intolerance in association with an impaired IRI response and abnormal glucagon response to a glucose stimulus.

  11. Methodology (Chapter A in the Teacher's Manual of the Adult Migrant Education Program, Australia).

    ERIC Educational Resources Information Center

    Ingram, D. E.

    This methodology for teaching English as a second language begins with a discussion of the basis for methodology, which is seen as revolving around the nature of language and the nature of the learner and society. The actual methodological approach is embodied in the following chapters: "Developing an Integrated Programme,""Focus on Use,""Focus on…

  12. Water, water quality and health (Chapter 3 in Book entitled: Environmental Tracking for Public Health Surveillance).

    EPA Science Inventory

    This chapter identifies the role environmental tracking plays in identifying public health water hazard and water quality issues. It outlines public health issues to be examined and provides an integrated overview of water and diseases by combining knowledge of the hydrological ...

  13. Evaluating cis-2,6-dimethylpiperidide (cis-DMP) as a base component in lithium-mediated zincation chemistry.

    PubMed

    Armstrong, David R; Garden, Jennifer A; Kennedy, Alan R; Leenhouts, Sarah M; Mulvey, Robert E; O'Keefe, Philip; O'Hara, Charles T; Steven, Alan

    2013-09-27

    Most recent advances in metallation chemistry have centred on the bulky secondary amide 2,2,6,6-tetramethylpiperidide (TMP) within mixed metal, often ate, compositions. However, the precursor amine TMP(H) is rather expensive so a cheaper substitute would be welcome. Thus this study was aimed towards developing cheaper non-TMP based mixed-metal bases and, as cis-2,6-dimethylpiperidide (cis-DMP) was chosen as the alternative amide, developing cis-DMP zincate chemistry which has received meagre attention compared to that of its methyl-rich counterpart TMP. A new lithium diethylzincate, [(TMEDA)LiZn(cis-DMP)Et2] (TMEDA=N,N,N',N'-tetramethylethylenediamine) has been synthesised by co-complexation of Li(cis-DMP), Et2Zn and TMEDA, and characterised by NMR (including DOSY) spectroscopy and X-ray crystallography, which revealed a dinuclear contact ion pair arrangement. By using N,N-diisopropylbenzamide as a test aromatic substrate, the deprotonative reactivity of [(TMEDA)LiZn(cis-DMP)Et2] has been probed and contrasted with that of the known but previously uninvestigated di-tert-butylzincate, [(TMEDA)LiZn(cis-DMP)tBu2]. The former was found to be the superior base (for example, producing the ortho-deuteriated product in respective yields of 78% and 48% following D2O quenching of zincated benzamide intermediates). An 88% yield of 2-iodo-N,N-diisopropylbenzamide was obtained on reaction of two equivalents of the diethylzincate with the benzamide followed by iodination. Comparisons are also drawn using 1,1,1,3,3,3-hexamethyldisilazide (HMDS), diisopropylamide and TMP as the amide component in the lithium amide, Et2Zn and TMEDA system. Under certain conditions, the cis-DMP base system was found to give improved results in comparison to HMDS and diisopropylamide (DA), and comparable results to a TMP system. Two novel complexes isolated from reactions of the di-tert-butylzincate and crystallographically characterised, namely the pre-metallation complex [{(iPr)2N(Ph)C=O}LiZn(cis

  14. Evaluating cis-2,6-Dimethylpiperidide (cis-DMP) as a Base Component in Lithium-Mediated Zincation Chemistry

    PubMed Central

    Armstrong, David R; Garden, Jennifer A; Kennedy, Alan R; Leenhouts, Sarah M; Mulvey, Robert E; O'Keefe, Philip; O'Hara, Charles T; Steven, Alan

    2013-01-01

    Most recent advances in metallation chemistry have centred on the bulky secondary amide 2,2,6,6-tetramethylpiperidide (TMP) within mixed metal, often ate, compositions. However, the precursor amine TMP(H) is rather expensive so a cheaper substitute would be welcome. Thus this study was aimed towards developing cheaper non-TMP based mixed-metal bases and, as cis-2,6-dimethylpiperidide (cis-DMP) was chosen as the alternative amide, developing cis-DMP zincate chemistry which has received meagre attention compared to that of its methyl-rich counterpart TMP. A new lithium diethylzincate, [(TMEDA)LiZn(cis-DMP)Et2] (TMEDA=N,N,N′,N′-tetramethylethylenediamine) has been synthesised by co-complexation of Li(cis-DMP), Et2Zn and TMEDA, and characterised by NMR (including DOSY) spectroscopy and X-ray crystallography, which revealed a dinuclear contact ion pair arrangement. By using N,N-diisopropylbenzamide as a test aromatic substrate, the deprotonative reactivity of [(TMEDA)LiZn(cis-DMP)Et2] has been probed and contrasted with that of the known but previously uninvestigated di-tert-butylzincate, [(TMEDA)LiZn(cis-DMP)tBu2]. The former was found to be the superior base (for example, producing the ortho-deuteriated product in respective yields of 78 % and 48 % following D2O quenching of zincated benzamide intermediates). An 88 % yield of 2-iodo-N,N-diisopropylbenzamide was obtained on reaction of two equivalents of the diethylzincate with the benzamide followed by iodination. Comparisons are also drawn using 1,1,1,3,3,3-hexamethyldisilazide (HMDS), diisopropylamide and TMP as the amide component in the lithium amide, Et2Zn and TMEDA system. Under certain conditions, the cis-DMP base system was found to give improved results in comparison to HMDS and diisopropylamide (DA), and comparable results to a TMP system. Two novel complexes isolated from reactions of the di-tert-butylzincate and crystallographically characterised, namely the pre-metallation complex [{(iPr)2N(Ph)C=O}LiZn(cis

  15. Multiple Functional Variants in cis Modulate PDYN Expression.

    PubMed

    Babbitt, Courtney C; Silverman, Jesse S; Haygood, Ralph; Reininga, Jennifer M; Rockman, Matthew V; Wray, Gregory A

    2010-02-01

    Understanding genetic variation and its functional consequences within cis-regulatory regions remains an important challenge in human genetics and evolution. Here, we present a fine-scale functional analysis of segregating variation within the cis-regulatory region of prodynorphin, a gene that encodes an endogenous opioid precursor with roles in cognition and disease. In order to characterize the functional consequences of segregating variation in cis in a region under balancing selection in different human populations, we examined associations between specific polymorphisms and gene expression in vivo and in vitro. We identified five polymorphisms within the 5' flanking region that affect transcript abundance: a 68-bp repeat recognized in prior studies, as well as two microsatellites and two single nucleotide polymorphisms not previously implicated as functional variants. The impact of these variants on transcription differs by brain region, sex, and cell type, implying interactions between cis genotype and the differentiated state of cells. The effects of individual variants on expression level are not additive in some combinations, implying epistatic interactions between nearby variants. These data reveal an unexpectedly complex relationship between segregating genetic variation and its expression-trait consequences and highlights the importance of close functional scrutiny of natural genetic variation within even relatively well-studied cis-regulatory regions.

  16. Cis-regulatory mechanisms governing stem and progenitor cell transitions

    PubMed Central

    Johnson, Kirby D.; Kong, Guangyao; Gao, Xin; Chang, Yuan-I; Hewitt, Kyle J.; Sanalkumar, Rajendran; Prathibha, Rajalekshmi; Ranheim, Erik A.; Dewey, Colin N.; Zhang, Jing; Bresnick, Emery H.

    2015-01-01

    Cis-element encyclopedias provide information on phenotypic diversity and disease mechanisms. Although cis-element polymorphisms and mutations are instructive, deciphering function remains challenging. Mutation of an intronic GATA motif (+9.5) in GATA2, encoding a master regulator of hematopoiesis, underlies an immunodeficiency associated with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Whereas an inversion relocalizes another GATA2 cis-element (−77) to the proto-oncogene EVI1, inducing EVI1 expression and AML, whether this reflects ectopic or physiological activity is unknown. We describe a mouse strain that decouples −77 function from proto-oncogene deregulation. The −77−/− mice exhibited a novel phenotypic constellation including late embryonic lethality and anemia. The −77 established a vital sector of the myeloid progenitor transcriptome, conferring multipotentiality. Unlike the +9.5−/− embryos, hematopoietic stem cell genesis was unaffected in −77−/− embryos. These results illustrate a paradigm in which cis-elements in a locus differentially control stem and progenitor cell transitions, and therefore the individual cis-element alterations cause unique and overlapping disease phenotypes. PMID:26601269

  17. 48 CFR Appendixes A-C to Chapter 7 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false A Appendixes A-C to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendixes A-C to Chapter 7...

  18. 48 CFR Appendixes A-C to Chapter 7 - [Reserved

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false A Appendixes A-C to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendixes A-C to Chapter 7...

  19. 48 CFR Appendixes G-H to Chapter 7 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false G Appendixes G-H to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendixes G-H to Chapter 7...

  20. 48 CFR Appendix G to Chapter 2 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false G Appendix G to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendix G to Chapter 2...

  1. 48 CFR Appendix E to Chapter 7 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false E Appendix E to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendix E to Chapter 7...

  2. Anatomy and physiology of plant conductive systems. Book chapter

    SciTech Connect

    McFarlane, C.

    1993-01-01

    Mathematical models considered in the book are representations of the physical features and chemical reactions that define interactions between plants and their environment. By centering attention on equations, it is easy to lose sight of the intricate and complex nature of the problem. The particular chapter describes the anatomy of important plant features and briefly discuss some physiological principles that will help to visualize and perceive the conditions which are represented in the models. Because of the many competing interactions, the fate of chemicals in the soil/plant/air environment is not obvious. Models were thus developed to intelligently integrate available knowledge, to increase understanding of the complex interactions, to aid in presentation of plant functions, and to help make predictions about chemical fate.

  3. Space Applications of Mass Spectrometry. Chapter 31

    NASA Technical Reports Server (NTRS)

    Hoffman, John H.; Griffin, Timothy P.; Limero, Thomas; Arkin, C. Richard

    2010-01-01

    Mass spectrometers have been involved in essentially all aspects of space exploration. This chapter outlines some of these many uses. Mass spectrometers have not only helped to expand our knowledge and understanding of the world and solar system around us, they have helped to put man safely in space and expand our frontier. Mass spectrometry continues to prove to be a very reliable, robust, and flexible analytical instrument, ensuring that its use will continue to help aid our investigation of the universe and this small planet that we call home.

  4. Solid Lubrication Fundamentals and Applications. Chapter 2

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa

    1998-01-01

    This chapter describes powerful analytical techniques capable of sampling tribological surfaces and solid-film lubricants. Some of these techniques may also be used to determine the locus of failure in a bonded structure or coated substrate; such information is important when seeking improved adhesion between a solid-film lubricant and a substrate and when seeking improved performance and long life expectancy of solid lubricants. Many examples are given here and through-out the book on the nature and character of solid surfaces and their significance in lubrication, friction, and wear. The analytical techniques used include the late spectroscopic methods.

  5. Student Chapters: Meeting Expectations and Providing High Quality Experiences

    ERIC Educational Resources Information Center

    Davis, Casey E.; Juengling, Lisa B.; Laurent, Rebekah D.; Pye, Nicole; Williamson, James

    2014-01-01

    Why do students join student chapters? What do they hope to gain from joining them? The Louisiana State University (LSU) chapter of the Society of American Archivists (SAA) conducted a research project that addresses these questions. The SAA-LSU chapter surveyed LIS students and recent graduates from the 61 ALA accredited LIS programs in the…

  6. Using Kolb's Experiential Learning Cycle in Chapter Presentations

    ERIC Educational Resources Information Center

    Stokes-Eley, Stephanie

    2007-01-01

    Student-led chapter presentations provide an excellent opportunity for instructors to evaluate a student's comprehension of the assigned chapter, as well as the student's ability to present and convey information in a public forum. Although several instructors realize the benefits of requiring students to complete chapter presentations either as…

  7. Columbia: The Economic Foundation of Peace. Chapters 21-28.

    ERIC Educational Resources Information Center

    Giugale, Marcelo M., Ed.; Lafourcade, Olivier, Ed.; Luff, Connie, Ed.

    This document contains 8 chapters of a 35-chapter book that presents a comprehensive diagnosis of current economic, social, and educational conditions in Colombia and their importance to development prospects and the quest for peace. The eight chapters covered here are part of a section titled "Sharing the Fruits of Growth with All…

  8. Identification and characterization of promoters and cis-regulatory elements of genes involved in secondary metabolites production in hop (Humulus lupulus. L).

    PubMed

    Duraisamy, Ganesh Selvaraj; Mishra, Ajay Kumar; Kocabek, Tomas; Matoušek, Jaroslav

    2016-10-01

    Molecular and biochemical studies have shown that gene contains single or combination of different cis-acting regulatory elements are actively controlling the transcriptional regulation of associated genes, downstream effects of these result in the modulation of various biological pathways such as biotic/abiotic stress responses, hormonal responses to growth and development processes and secondary metabolite production. Therefore, the identification of promoters and their cis-regulatory elements is one of intriguing area to study the dynamic complex regulatory network of genes activities by integrating computational, comparative, structural and functional genomics. Several bioinformatics servers or database have been established to predict the cis-acting elements present in the promoter region of target gene and their association with the expression profiles in the TFs. The aim of this study is to predict possible cis-acting regulatory elements that have putative role in the transcriptional regulation of a dynamic network of metabolite gene activities controlling prenylflavonoid and bitter acids biosynthesis in hop (Humulus lupulus). Recent release of hop draft genome enabled us to predict the possible cis-acting regulatory elements by extracting 2kbp of 5' regulatory regions of genes important for lupulin metabolome biosynthesis, using Plant CARE, PLACE and Genomatix Matinspector professional databases. The result reveals the plausible role of cis-acting regulatory elements in the regulation of gene expression primarily involved in lupulin metabolome biosynthesis including under various stress conditions.

  9. cisExpress: motif detection in DNA sequences

    PubMed Central

    Triska, Martin; Grocutt, David; Southern, James; Murphy, Denis J.; Tatarinova, Tatiana

    2013-01-01

    Motivation: One of the major challenges for contemporary bioinformatics is the analysis and accurate annotation of genomic datasets to enable extraction of useful information about the functional role of DNA sequences. This article describes a novel genome-wide statistical approach to the detection of specific DNA sequence motifs based on similarities between the promoters of similarly expressed genes. This new tool, cisExpress, is especially designed for use with large datasets, such as those generated by publicly accessible whole genome and transcriptome projects. cisExpress uses a task farming algorithm to exploit all available computational cores within a shared memory node. We demonstrate the robust nature and validity of the proposed method. It is applicable for use with a wide range of genomic databases for any species of interest. Availability: cisExpress is available at www.cisexpress.org. Contact: tatiana.tatarinova@usc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23793750

  10. Methods of assessing responses of trees, stands, and ecosystems to air pollution (Chapter 7). Book chapter

    SciTech Connect

    Stolte, K.W.; Duriscoe, D.M.; Cook, E.R.; Cline, S.P.

    1992-01-01

    The chapter focuses on three main types of assessments of pollution effects used in the case studies chronicled in Chapter 8 through 12 (Regional Studies of conifer forests in the west). These are measures of crown condition of individual trees; impacts on populations and communities; and temporal patterns in radial growth. The concepts behind the development of each approach are introduced with references to previous work, leading to a discussion of the state of science. The importance of quality assurance techniques to the success of any assessment of air pollution effects is also discussed.

  11. Promoting the APS Chapter Program by sharing its history, best practices, and how-to guide for establishing new chapters.

    PubMed

    Hopper, Mari K

    2017-03-01

    Early establishment of physiological societies in Oklahoma and Ohio demonstrated the benefits of networking physiologists and paved the way for establishing the APS Chapter Program. Designed to promote the general objectives of the APS, the Chapter Program was officially launched in 1995, with Ohio being the first recognized chapter. There are 13 active chapters regularly engaged in numerous activities designed to advance physiology education and research. In the hopes that others will recognize the important offerings of state chapters and consider organizing one, the aims for this paper are to 1) share a brief history, 2) provide rationale for chapter initiation, and 3) describe the process involved in establishing a chapter. In light of current changes in American Medical Association and Liaison Committee on Medical Education guidelines, the present time may be critical in promoting chapters, as they play a vital role in sustaining recognition and support for the discipline.

  12. Conditional gene vectors regulated in cis.

    PubMed

    Pich, Dagmar; Humme, Sibille; Spindler, Mark-Peter; Schepers, Aloys; Hammerschmidt, Wolfgang

    2008-08-01

    Non-integrating gene vectors, which are stably and extrachromosomally maintained in transduced cells would be perfect tools to support long-term expression of therapeutic genes but preserve the genomic integrity of the cellular host. Small extrachromosomal plasmids share some of these ideal characteristics but are primarily based on virus blueprints. These plasmids are dependent on viral trans-acting factors but they can replicate their DNA molecules in synchrony with the chromosome of the cellular host and segregate to daughter cells in an autonomous fashion. On the basis of the concept of the latent origin of DNA replication of Epstein-Barr virus, oriP, we devised novel derivatives, which exclusively rely on an artificial replication factor for both nuclear retention and replication of plasmid DNA. In addition, an allosteric switch regulates the fate of the plasmid molecules, which are rapidly lost upon addition of doxycycline. Conditional maintenance of these novel plasmid vectors allows the reversible transfer of genetic information into target cells for the first time.

  13. The role of cis-carotenoids in abscisic acid biosynthesis.

    PubMed

    Parry, A D; Babiano, M J; Horgan, R

    1990-08-01

    Evidence has been obtained which is consistent with 9'-cis-neoxanthin being a major precursor of abscisic acid (ABA) in higher plants. A mild, rapid procedure was developed for the extraction and analysis of carotenoids from a range of tissues. Once purified the carotenoids were identified from their light-absorbance properties, reactions with dilute acid, high-performance liquid chromatography Rts, mass spectra and the quasiequilibria resulting from iodine-catalysed or chlorophyllsensitised photoisomerisation. Two possible ABA precursors, 9'-cis-neoxanthin and 9-cis-violaxanthin, were identified in extracts of light-grown and etiolated leaves (of Lycopersicon esculentum, Phaseolus vulgaris, Vicia faba, Pisum sativum, Cicer arietinum, Zea mays, Nicotiana plumbaginifolia, Plantago lanceolata and Digitalis purpurea), and roots of light-grown and etiolated plants (Lycopersicon, Phaseolus and Zea). The 9,9'-di-cisisomer of violaxanthin was synthesised but its presence was not detected in any extracts. Levels of 9'-cis-neoxanthin and all-trans-violaxanthin were between 20- to 100-fold greater than those of ABA in light-grown leaves. The levels of 9-cis-violaxanthin were similar to those of ABA but unaffected by water stress. Etiolated Phaseolus leaves contained reduced amounts of carotenoids (15-20% compared with light-grown leaves) but retained the ability to synthesise large amounts of ABA. The amounts of ABA synthesised, measured as increases in ABA and its metabolites phaseic acid and dihydrophaseic acid, were closely matched by decreases in the levels of 9'-cis-neoxanthin and all-trans-violaxanthin. In etiolated seedlings grown on 50% D2O, deuterium incorporation into ABA was similar to that into the xanthophylls. Relative levels of carotenoids in roots and light-grown and etiolated leaves of the ABA-deficient mutants, notabilis, flacca and sitiens were the same as those found in wild-type tomato tissues.

  14. Universal Sensor and Actuator Requirements. Chapter 5

    NASA Technical Reports Server (NTRS)

    Rosenfeld, Taylor; Webster, John; Garg, Sanjay

    2009-01-01

    The previous chapters have focused on the requirements for sensors and actuators for "More Intelligent Gas Turbine Engines" from the perspective of performance and operating environment. Even if a technology is available, which meets these performance requirements, there are still various hurdles to be overcome for the technology to transition into a real engine. Such requirements relate to TRL (Technology Readiness Level), durability, reliability, volume, weight, cost, etc. This chapter provides an overview of such universal requirements which any sensor or actuator technology will have to meet before it can be implemented on a product. The objective here is to help educate the researchers or technology developers on the extensive process that the technology has to go through beyond just meeting performance requirements. The hope is that such knowledge will help the technology developers as well as decision makers to prevent wasteful investment in developing solutions to performance requirements, which have no potential to meet the "universal" requirements. These "universal" requirements can be divided into 2 broad areas: 1) Technology value proposition; and 2) Technology maturation. These requirements are briefly discussed in the following.

  15. Volatile hydrocarbons and fuel oxygenates: Chapter 12

    USGS Publications Warehouse

    Cozzarelli, Isabelle M.

    2014-01-01

    Petroleum hydrocarbons and fuel oxygenates are among the most commonly occurring and widely distributed contaminants in the environment. This chapter presents a summary of the sources, transport, fate, and remediation of volatile fuel hydrocarbons and fuel additives in the environment. Much research has focused on the transport and transformation processes of petroleum hydrocarbons and fuel oxygenates, such as benzene, toluene, ethylbenzene, and xylenes and methyl tert‐butyl ether, in groundwater following release from underground storage tanks. Natural attenuation from biodegradation limits the movement of these contaminants and has received considerable attention as an environmental restoration option. This chapter summarizes approaches to environmental restoration, including those that rely on natural attenuation, and also engineered or enhanced remediation. Researchers are increasingly combining several microbial and molecular-based methods to give a complete picture of biodegradation potential and occurrence at contaminated field sites. New insights into the fate of petroleum hydrocarbons and fuel additives have been gained by recent advances in analytical tools and approaches, including stable isotope fractionation, analysis of metabolic intermediates, and direct microbial evidence. However, development of long-term detailed monitoring programs is required to further develop conceptual models of natural attenuation and increase our understanding of the behavior of contaminant mixtures in the subsurface.

  16. Chapter 44: history of neurology in Italy.

    PubMed

    Bentivoglio, Marina; Mazzarello, Paolo

    2010-01-01

    The chapter starts from the Renaissance (although the origins of Italian neurology can be traced back to the Middle Ages), when treatises of nervous system physiopathology still followed Hippocratic and Galenic "humoral" theories. In Italy, as elsewhere in Europe, the concepts of humoral pathology were abandoned in the 18th century, when neurology was influenced by novel trends. Neurology acquired the status of clinical discipline (as "clinic of mental diseases") after national reunification (declared in 1861 but completed much later). At the end of the 19th and first decades of the 20th century, eminent Italian "neuropsychiatrists" (including, among many others, Ugo Cerletti, who introduced electroconvulsive shock therapy in 1938) stimulated novel knowledge and approaches, "centers of excellence" flourished, and "Neurological Institutes" were founded. In the first half of the 20th century, the history of Italian neurology was dominated by World Wars I and II (which stimulated studies on the wounded) and the fascist regime in-between the Wars (when the flow of information was instead very limited). Italy became a republic in 1946, and modern neurology and its distinction from psychiatry were finally promoted. The chapter also provides detailed accounts of scientific societies and journals dedicated to the neurological sciences in Italy.

  17. Chapter 9. Benefits of International Collaboration | Science ...

    EPA Pesticide Factsheets

    In this chapter, we share what we have learned from working with our Brazilian colleagues on a multi university, multiyear, and multi basin ecological assessment and how those experiences were transmitted more broadly. These lessons (each of which is described in subsequent paragraphs) included 1) learning about markedly different ecosystems; 2) values to the U.S. Environmental Protection Agency (USEPA) of testing monitoring protocols in those ecosystems; 3) applying lessons from the CEMIG (Companhia Energética de Minas Gerais) project to research on other continents and elsewhere in Brazil; 4) advantages of academic team research; 5) benefits of corporate-sponsored research and federal student scholarships; 6) communicating with the general public; 7) the research web that has developed out of our work in Brazil; and 8) experiencing Brazilian culture. The USEPA’s NARS survey designs and field methods are being applied in large basin stream surveys in countries outside of the U.S. These applications not only provide valuable tests of the NARS approaches, but enhance International cooperation and generate new understandings of natural and anthropogenic controls on biota and physical habitat in streams. These understandings not only aid interpretation of the condition of streams in the regions surveyed, but also refine approaches for interpreting aquatic resource surveys elsewhere. In this book chapter, Robert Hughes and Philip Kaufmann describe th

  18. Promoting the APS Chapter Program by Sharing Its History, Best Practices, and How-to Guide for Establishing New Chapters

    ERIC Educational Resources Information Center

    Hopper, Mari K.

    2017-01-01

    Early establishment of physiological societies in Oklahoma and Ohio demonstrated the benefits of networking physiologists and paved the way for establishing the APS Chapter Program. Designed to promote the general objectives of the APS, the Chapter Program was officially launched in 1995, with Ohio being the first recognized chapter. There are 13…

  19. Materials for Liquid Propulsion Systems. Chapter 12

    NASA Technical Reports Server (NTRS)

    Halchak, John A.; Cannon, James L.; Brown, Corey

    2016-01-01

    Earth to orbit launch vehicles are propelled by rocket engines and motors, both liquid and solid. This chapter will discuss liquid engines. The heart of a launch vehicle is its engine. The remainder of the vehicle (with the notable exceptions of the payload and guidance system) is an aero structure to support the propellant tanks which provide the fuel and oxidizer to feed the engine or engines. The basic principle behind a rocket engine is straightforward. The engine is a means to convert potential thermochemical energy of one or more propellants into exhaust jet kinetic energy. Fuel and oxidizer are burned in a combustion chamber where they create hot gases under high pressure. These hot gases are allowed to expand through a nozzle. The molecules of hot gas are first constricted by the throat of the nozzle (de-Laval nozzle) which forces them to accelerate; then as the nozzle flares outwards, they expand and further accelerate. It is the mass of the combustion gases times their velocity, reacting against the walls of the combustion chamber and nozzle, which produce thrust according to Newton's third law: for every action there is an equal and opposite reaction. Solid rocket motors are cheaper to manufacture and offer good values for their cost. Liquid propellant engines offer higher performance, that is, they deliver greater thrust per unit weight of propellant burned. They also have a considerably higher thrust to weigh ratio. Since liquid rocket engines can be tested several times before flight, they have the capability to be more reliable, and their ability to shut down once started provides an extra margin of safety. Liquid propellant engines also can be designed with restart capability to provide orbital maneuvering capability. In some instances, liquid engines also can be designed to be reusable. On the solid side, hybrid solid motors also have been developed with the capability to stop and restart. Solid motors are covered in detail in chapter 11. Liquid

  20. History of Artificial Gravity. Chapter 3

    NASA Technical Reports Server (NTRS)

    Clement, Gilles; Bukley, Angie; Paloski, William

    2006-01-01

    This chapter reviews the past and current projects on artificial gravity during space missions. The idea of a rotating wheel-like space station providing artificial gravity goes back in the writings of Tsiolkovsky, Noordung, and Wernher von Braun. Its most famous fictional representation is in the film 2001: A Space Odyssey, which also depicts spin-generated artificial gravity aboard a space station and a spaceship bound for Jupiter. The O Neill-type space colony provides another classic illustration of this technique. A more realistic approach to rotating the space station is to provide astronauts with a smaller centrifuge contained within a spacecraft. The astronauts would go into it for a workout, and get their gravity therapeutic dose for a certain period of time, daily or a few times a week. This simpler concept is current being tested during ground-based studies in several laboratories around the world.

  1. Tamarix, hydrology and fluvial geomorphology: Chapter 7

    USGS Publications Warehouse

    Auerbach, Daniel A.; Merritt, David M.; Shafroth, Patrick B.; Sher, Anna A; Quigley, Martin F.

    2013-01-01

    This chapter explores the impact of hydrology and fluvial geomorphology on the distribution and abundance of Tamarix as well as the reciprocal effects of Tamarix on hydrologic and geomorphic conditions. It examines whether flow-regime alteration favors Tamarix establishment over native species, and how Tamarix stands modify processes involved in the narrowing of river channels and the formation of floodplains. It begins with an overview of the basic geomorphic and hydrologic character of rivers in the western United States before analyzing how this setting has contributed to the regional success of Tamarix. It then considers the influence of Tamarix on the hydrogeomorphic form and function of rivers and concludes by discussing how a changing climate, vegetation management, and continued water-resource development affect the future role of Tamarix in these ecosystems.

  2. Mercury and halogens in coal: Chapter 2

    USGS Publications Warehouse

    Kolker, Allan; Quick, Jeffrey C.; Granite, Evan J.; Pennline, Henry W.; Senior, Constance L.

    2014-01-01

    Apart from mercury itself, coal rank and halogen content are among the most important factors inherent in coal that determine the proportion of mercury captured by conventional controls during coal combustion. This chapter reviews how mercury in coal occurs, gives available concentration data for mercury in U.S. and international commercial coals, and provides an overview of the natural variation in halogens that influence mercury capture. Three databases, the U.S. Geological Survey coal quality (USGS COALQUAL) database for in-ground coals, and the 1999 and 2010 U.S. Environmental Protection Agency (EPA) Information Collection Request (ICR) databases for coals delivered to power stations, provide extensive results for mercury and other parameters that are compared in this chapter. In addition to the United States, detailed characterization of mercury is available on a nationwide basis for China, whose mean values in recent compilations are very similar to the United States in-ground mean of 0.17 ppm mercury. Available data for the next five largest producers (India, Australia, South Africa, the Russian Federation, and Indonesia) are more limited and with the possible exceptions of Australia and the Russian Federation, do not allow nationwide means for mercury in coal to be calculated. Chlorine in coal varies as a function of rank and correspondingly, depth of burial. As discussed elsewhere in this volume, on a proportional basis, bromine is more effective than chlorine in promoting mercury oxidation in flue gas and capture by conventional controls. The ratio of bromine to chlorine in coal is indicative of the proportion of halogens present in formation waters within a coal basin. This ratio is relatively constant except in coals that have interacted with deep-basin brines that have reached halite saturation, enriching residual fluids in bromine. Results presented here help optimize mercury capture by conventional controls and provide a starting point for

  3. Commercial Off-the-Shelf (COTS) Components and Enterprise Component Information System (eCIS)

    SciTech Connect

    John Minihan; Ed Schmidt; Greg Enserro; Melissa Thompson

    2008-06-30

    The purpose of the project was to develop the processes for using commercial off-the-shelf (COTS) parts for WR production and to put in place a system for implementing the data management tools required to disseminate, store, track procurement, and qualify vendors. Much of the effort was devoted to determining if the use of COTS parts was possible. A basic question: How does the Nuclear Weapons Complex (NWC) begin to use COTS in the weapon Stockpile Life Extension Programs with high reliability, affordability, while managing risk at acceptable levels? In FY00, it was determined that a certain weapon refurbishment program could not be accomplished without the use of COTS components. The elements driving the use of COTS components included decreased cost, greater availability, and shorter delivery time. Key factors that required implementation included identifying the best suppliers and components, defining life cycles and predictions of obsolescence, testing the feasibility of using COTS components with a test contractor to ensure capability, as well as quality and reliability, and implementing the data management tools required to disseminate, store, track procurement, and qualify vendors. The primary effort of this project then was to concentrate on the risks involved in the use of COTS and address the issues of part and vendor selection, procurement and acceptance processes, and qualification of the parts via part and sample testing. The Enterprise Component Information System (eCIS) was used to manage the information generated by the COTS process. eCIS is a common interface for both the design and production of NWC components and systems integrating information between SNL National Laboratory (SNL) and the Kansas City Plant (KCP). The implementation of COTS components utilizes eCIS from part selection through qualification release. All part related data is linked across an unclassified network for access by both SNL and KCP personnel. The system includes not

  4. Efficient direct ZnO/CIS solar cells

    SciTech Connect

    Olsen, L.C.; William Addis, F.; Lei, W.; Li, J.

    1996-01-01

    This paper describes investigations of CIS solar cells with ZnO window layers deposited by MOCVD. These studies have been conducted with graded absorber CIS substrates obtained from Siemens Solar. Cell fabrication involves surface preparation of the Siemens substrate, growth of 200 to 400 A of undoped ZnO by MOCVD, deposition of a highly conducting ZnO top contact layer and deposition of a Ni/Ag collector grid. MOCVD growth of ZnO is accomplished in a SPIRE 500XT reactor by reacting a zinc adduct and tetrahydrofuran. Processing development has been conducted by forming test cells on ZnO/CIS structures by depositing thin, transparent Al contacts 2.8 mm in diameter on top of the ZnO window layer to serve as contacts. Several cells have been completed with a total area efficiency {ge}11.0{percent}, with the best result being 11.3{percent}. The best active area efficiency is approximately 12{percent}. Other topics discussed include current-voltage characteristics of direct ZnO/CIS cells. {copyright} {ital 1996 American Institute of Physics.}

  5. Trans-cis molecular photoswitching in interstellar space

    NASA Astrophysics Data System (ADS)

    Cuadrado, S.; Goicoechea, J. R.; Roncero, O.; Aguado, A.; Tercero, B.; Cernicharo, J.

    2016-11-01

    As many organic molecules, formic acid (HCOOH) has two conformers (trans and cis). The energy barrier to internal conversion from trans to cis is much higher than the thermal energy available in molecular clouds. Thus, only the most stable conformer (trans) is expected to exist in detectable amounts. We report the first interstellar detection of cis-HCOOH. Its presence in ultraviolet (UV) irradiated gas exclusively (the Orion Bar photodissociation region), with a low trans-to-cis abundance ratio of 2.8 ± 1.0, supports a photoswitching mechanism: a given conformer absorbs a stellar photon that radiatively excites the molecule to electronic states above the interconversion barrier. Subsequent fluorescent decay leaves the molecule in a different conformer form. This mechanism, which we specifically study with ab initio quantum calculations, was not considered in Space before but likely induces structural changes of a variety of interstellar molecules submitted to UV radiation. This paper makes use of observations obtained with the IRAM-30 m telescope. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain).

  6. Creating a Collaborative Learning Community in the CIS Sandbox

    ERIC Educational Resources Information Center

    Frydenberg, Mark

    2013-01-01

    Purpose: The purpose of this paper is to investigate the impact of transforming a traditional university computer lab to create a collaborative learning community known as the CIS Sandbox, by remodeling a physical space and supporting it with a virtual presence through the use of social media tools. The discussion applies Selander's "designs for…

  7. cis- and trans-Stilbenes: Chromatographic Separation and Photochemical Isomerization.

    ERIC Educational Resources Information Center

    Levine, Samuel G.; And Others

    1988-01-01

    Describes an experiment that is to be performed midway in the first semester of an undergraduate organic chemistry laboratory coinciding with the students' introduction to cis-trans isomerism in the study of alkenes. Discusses the apparatus, materials, experimental procedure, historical significance, and results. (CW)

  8. Epistatic Interactions in the Arabinose Cis-Regulatory Element.

    PubMed

    Lagator, Mato; Igler, Claudia; Moreno, Anaísa B; Guet, Călin C; Bollback, Jonathan P

    2016-03-01

    Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner.

  9. 7 CFR 272.10 - ADP/CIS Model Plan.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Regulations of the Department of Agriculture (Continued) FOOD AND NUTRITION SERVICE, DEPARTMENT OF AGRICULTURE FOOD STAMP AND FOOD DISTRIBUTION PROGRAM REQUIREMENTS FOR PARTICIPATING STATE AGENCIES § 272.10 ADP/CIS... automate their food stamp program operations and computerize their systems for obtaining,...

  10. A cis-Regulatory Signature for Chordate Anterior Neuroectodermal Genes

    PubMed Central

    Christiaen, Lionel; Joly, Jean-Stéphane

    2010-01-01

    One of the striking findings of comparative developmental genetics was that expression patterns of core transcription factors are extraordinarily conserved in bilaterians. However, it remains unclear whether cis-regulatory elements of their target genes also exhibit common signatures associated with conserved embryonic fields. To address this question, we focused on genes that are active in the anterior neuroectoderm and non-neural ectoderm of the ascidian Ciona intestinalis. Following the dissection of a prototypic anterior placodal enhancer, we searched all genomic conserved non-coding elements for duplicated motifs around genes showing anterior neuroectodermal expression. Strikingly, we identified an over-represented pentamer motif corresponding to the binding site of the homeodomain protein OTX, which plays a pivotal role in the anterior development of all bilaterian species. Using an in vivo reporter gene assay, we observed that 10 of 23 candidate cis-regulatory elements containing duplicated OTX motifs are active in the anterior neuroectoderm, thus showing that this cis-regulatory signature is predictive of neuroectodermal enhancers. These results show that a common cis-regulatory signature corresponding to K50-Paired homeodomain transcription factors is found in non-coding sequences flanking anterior neuroectodermal genes in chordate embryos. Thus, field-specific selector genes impose architectural constraints in the form of combinations of short tags on their target enhancers. This could account for the strong evolutionary conservation of the regulatory elements controlling field-specific selector genes responsible for body plan formation. PMID:20419150

  11. Abundant raw material for cis-regulatory evolution in humans.

    PubMed

    Rockman, Matthew V; Wray, Gregory A

    2002-11-01

    Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (<13,000), in part because of an overrepresentation among the former in multiallelic tandem repeat variation, especially (AC)(n) dinucleotide microsatellites. The role of microsatellites in gene expression variation may provide a larger store of heritable phenotypic variation, and a more rapid mutational input of such variation, than has been realized. Finally, we outline the distinctive consequences of cis-regulatory variation for the genotype-phenotype relationship, including ubiquitous epistasis and genotype-by-environment interactions, as well as underappreciated modes of pleiotropy and overdominance. Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.

  12. Abundant raw material for cis-regulatory evolution in humans

    NASA Technical Reports Server (NTRS)

    Rockman, Matthew V.; Wray, Gregory A.

    2002-01-01

    Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (<13,000), in part because of an overrepresentation among the former in multiallelic tandem repeat variation, especially (AC)(n) dinucleotide microsatellites. The role of microsatellites in gene expression variation may provide a larger store of heritable phenotypic variation, and a more rapid mutational input of such variation, than has been realized. Finally, we outline the distinctive consequences of cis-regulatory variation for the genotype-phenotype relationship, including ubiquitous epistasis and genotype-by-environment interactions, as well as underappreciated modes of pleiotropy and overdominance. Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.

  13. Structural Brain Network Characteristics Can Differentiate CIS from Early RRMS

    PubMed Central

    Muthuraman, Muthuraman; Fleischer, Vinzenz; Kolber, Pierre; Luessi, Felix; Zipp, Frauke; Groppa, Sergiu

    2016-01-01

    Focal demyelinated lesions, diffuse white matter (WM) damage, and gray matter (GM) atrophy influence directly the disease progression in patients with multiple sclerosis. The aim of this study was to identify specific characteristics of GM and WM structural networks in subjects with clinically isolated syndrome (CIS) in comparison to patients with early relapsing-remitting multiple sclerosis (RRMS). Twenty patients with CIS, 33 with RRMS, and 40 healthy subjects were investigated using 3 T-MRI. Diffusion tensor imaging was applied, together with probabilistic tractography and fractional anisotropy (FA) maps for WM and cortical thickness correlation analysis for GM, to determine the structural connectivity patterns. A network topology analysis with the aid of graph theoretical approaches was used to characterize the network at different community levels (modularity, clustering coefficient, global, and local efficiencies). Finally, we applied support vector machines (SVM) to automatically discriminate the two groups. In comparison to CIS subjects, patients with RRMS were found to have increased modular connectivity and higher local clustering, highlighting increased local processing in both GM and WM. Both groups presented increased modularity and clustering coefficients in comparison to healthy controls. SVM algorithms achieved 97% accuracy using the clustering coefficient as classifier derived from GM and 65% using WM from probabilistic tractography and 67% from modularity of FA maps to differentiate between CIS and RRMS patients. We demonstrate a clear increase of modular and local connectivity in patients with early RRMS in comparison to CIS and healthy subjects. Based only on a single anatomic scan and without a priori information, we developed an automated and investigator-independent paradigm that can accurately discriminate between patients with these clinically similar disease entities, and could thus complement the current dissemination-in-time criteria for

  14. Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

    PubMed Central

    Brody, Thomas; Yavatkar, Amarendra S; Kuzin, Alexander; Kundu, Mukta; Tyson, Leonard J; Ross, Jermaine; Lin, Tzu-Yang; Lee, Chi-Hon; Awasaki, Takeshi; Lee, Tzumin; Odenwald, Ward F

    2012-01-01

    Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc. Key findings A genome-wide catalog of Drosophila conserved DNA sequence clusters. cis-Decoder discovers functionally related enhancers. Functionally related enhancers share balanced sequence element copy numbers. Many enhancers function during multiple phases of development. PMID:22174086

  15. Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells

    PubMed Central

    Gisselbrecht, Stephen S; He, Fangxue Sherry; Estrada, Beatriz; Michelson, Alan M; Bulyk, Martha L

    2006-01-01

    While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need for computational methods that can evaluate hypothesized cis regulatory codes before the difficult task of experimental verification is undertaken. We have developed a novel computational framework (termed “CodeFinder”) that integrates transcription factor binding site and gene expression information to evaluate whether a hypothesized transcriptional regulatory model (TRM; i.e., a set of co-regulating transcription factors) is likely to target a given set of co-expressed genes. Our basic approach is to simultaneously predict cis regulatory modules (CRMs) associated with a given gene set and quantify the enrichment for combinatorial subsets of transcription factor binding site motifs comprising the hypothesized TRM within these predicted CRMs. As a model system, we have examined a TRM experimentally demonstrated to drive the expression of two genes in a sub-population of cells in the developing Drosophila mesoderm, the somatic muscle founder cells. This TRM was previously hypothesized to be a general mode of regulation for genes expressed in this cell population. In contrast, the present analyses suggest that a modified form of this cis regulatory code applies to only a subset of founder cell genes, those whose gene expression responds to specific genetic perturbations in a similar manner to the gene on which the original model was based. We have confirmed this hypothesis by experimentally discovering six (out of 12 tested) new CRMs driving expression in the embryonic mesoderm, four of which drive expression in founder cells. PMID:16733548

  16. Cis-trans isomerization in the S1 state of acetylene: identification of cis-well vibrational levels.

    PubMed

    Merer, Anthony J; Steeves, Adam H; Baraban, Joshua H; Bechtel, Hans A; Field, Robert W

    2011-06-28

    A systematic analysis of the S(1)-trans (Ã(1)A(u)) state of acetylene, using IR-UV double resonance along with one-photon fluorescence excitation spectra, has allowed assignment of at least part of every single vibrational state or polyad up to a vibrational energy of 4200 cm(-1). Four observed vibrational levels remain unassigned, for which no place can be found in the level structure of the trans-well. The most prominent of these lies at 46 175 cm(-1). Its (13)C isotope shift, exceptionally long radiative lifetime, unexpected rotational selection rules, and lack of significant Zeeman effect, combined with the fact that no other singlet electronic states are expected at this energy, indicate that it is a vibrational level of the S(1)-cis isomer (Ã(1)A(2)). Guided by ab initio calculations [J. H. Baraban, A. R. Beck, A. H. Steeves, J. F. Stanton, and R. W. Field, J. Chem. Phys. 134, 244311 (2011)] of the cis-well vibrational frequencies, the vibrational assignments of these four levels can be established from their vibrational symmetries together with the (13)C isotope shift of the 46 175 cm(-1) level (assigned here as cis-3(1)6(1)). The S(1)-cis zero-point level is deduced to lie near 44 900 cm(-1), and the ν(6) vibrational frequency of the S(1)-cis well is found to be roughly 565 cm(-1); these values are in remarkably good agreement with the results of recent ab initio calculations. The 46 175 cm(-1) vibrational level is found to have a 3.9 cm(-1) staggering of its K-rotational structure as a result of quantum mechanical tunneling through the isomerization barrier. Such tunneling does not give rise to ammonia-type inversion doubling, because the cis and trans isomers are not equivalent; instead the odd-K rotational levels of a given vibrational level are systematically shifted relative to the even-K rotational levels, leading to a staggering of the K-structure. These various observations represent the first definite assignment of an isomer of

  17. Numerical Prediction of Dust. Chapter 10

    NASA Technical Reports Server (NTRS)

    Benedetti, Angela; Baldasano, J. M.; Basart, S.; Benincasa, F.; Boucher, O.; Brooks, M.; Chen, J. P.; Colarco, P. R.; Gong, S.; Huneeus, N.; Jones, L; Lu, S.; Menut, L.; Mulcahy, J.; Nickovic, S.; Morcrette, J.-J.; Perez, C.; Reid, J. S.; Sekiyama, T. T.; Tanaka, T.; Terradellas, E.; Westphal, D. L.; Zhang, X.-Y.; Zhou, C.-H.

    2013-01-01

    Covers the whole breadth of mineral dust research, from a scientific perspective Presents interdisciplinary work including results from field campaigns, satellite observations, laboratory studies, computer modelling and theoretical studies Explores the role of dust as a player and recorder of environmental change This volume presents state-of-the-art research about mineral dust, including results from field campaigns, satellite observations, laboratory studies, computer modelling and theoretical studies. Dust research is a new, dynamic and fast-growing area of science and due to its multiple roles in the Earth system, dust has become a fascinating topic for many scientific disciplines. Aspects of dust research covered in this book reach from timescales of minutes (as with dust devils, cloud processes, and radiation) to millennia (as with loess formation and oceanic sediments), making dust both a player and recorder of environmental change. The book is structured in four main parts that explore characteristics of dust, the global dust cycle, impacts of dust on the Earth system, and dust as a climate indicator. The chapters in these parts provide a comprehensive, detailed overview of this highly interdisciplinary subject. The contributions presented here cover dust from source to sink and describe all the processes dust particles undergo while travelling through the atmosphere. Chapters explore how dust is lifted and transported, how it affects radiation, clouds, regional circulations, precipitation and chemical processes in the atmosphere, and how it deteriorates air quality. The book explores how dust is removed from the atmosphere by gravitational settling, turbulence or precipitation, how iron contained in dust fertilizes terrestrial and marine ecosystems, and about the role that dust plays in human health. We learn how dust is observed, simulated using computer models and forecast. The book also details the role of dust deposits for climate reconstructions

  18. Chapter 24: Programmatic Interfaces - IDL VOlib

    NASA Astrophysics Data System (ADS)

    Miller, C. J.

    In this chapter, we describe a library for working with the VO using IDL (the Interactive Data Language). IDL is a software environment for data analysis, visualization, and cross-platform application development. It has wide-usage in astronomy, including NASA (e.g. http://seadas.gsfc.nasa.gov/), the Sloan Digital Sky Survey (http://www.sdss.org), and the Spitzer Infrared Spectrograph Instrument (http://ssc.spitzer.caltech.edu/archanaly/contributed/smart/). David Stern, the founder of Research Systems, Inc. (RSI), began the development of IDL while working with NASA's Mars Mariner 7 and 9 data at the Laboratory for Atmospheric and Space Physics at the University of Colorado. In 1981, IDL was rewritten in assembly language and FORTRAN for VAX/VMS. IDL's usage has expanded over the last decade into the fields of medical imaging and engineering, among many others. IDL's programming style carries over much of this FORTRAN-legacy, and has a familiar feel to many astronomers who learned their trade using FORTRAN. The spread of IDL-usage amongst astronomers can in part be attributed to the wealth of publicly astronomical libraries. The Goddard Space Flight Center (GSFC) maintains a list of astronomy-related IDL libraries, including the well known Astronomy User's Library (hereafter ASTROLIB2). We will use some of these GSFC IDL libraries. We note that while IDL is a licensed-software product, the source code of user-written procedures are typically freely available to the community. To make the most out of this section as a reader, it is important that many of the data discovery, access, and analysis protocols are understood before reading this chapter. In the next section, we provide an overview of some of the NVO terminology with which the reader should be familiar. The IDL library discussed here is specifically for use with the Virtual Observatory and is named VOlib. IDL's VOlib is available at http://nvo.noao.edu and is included with the software distrubution for this

  19. Carbon cycling in terrestrial environments: Chapter 17

    USGS Publications Warehouse

    Wang, Yang; Huntington, Thomas G.; Osher, Laurie J.; Wassenaar, Leonard I; Trumbore, Susan E.; Amundson, Ronald; Harden, Jennifer W.; McKnight, Diane M.; Schiff, Sherry L.; Aiken, George R.; Lyons, W. Berry; Aravena, Ramon O.; Baron, Jill S.

    1998-01-01

    This chapter reviews a number of applications of isotopic techniques for the investigation of carbon cycling processes. Carbon dioxide (C02) is an important greenhouse gas. Its concentration in the atmosphere has increased from an estimated 270 ppm at the beginning of the industrial revolution to ∼ 360 ppm at present. Climatic conditions and atmospheric C02 concentration also influence isotopic discrimination during photosynthesis. Natural and anthropogenically induced variations in the carbon isotopic abundance can be exploited to investigate carbon transformations between pools on various time scales. It also discusses one of the isotopes of carbon, the 14C, that is produced in the atmosphere by interactions of cosmic-ray produced neutrons with stable isotopes of nitrogen (N), oxygen (O), and carbon (C), and has a natural abundance in the atmosphere of ∼1 atom 14 C per 1012 atoms 12C. The most important factor affecting the measured 14C ages of soil organic matter is the rate of organic carbon cycling in soils. Differences in the dynamics of soil carbon among different soils or soil horizons will result in different soil organic 14C signatures. As a result, the deviation of the measured 14C age from the true age could differ significantly among different soils or soil horizons.

  20. Microscopic functional anatomy: Integumentary system: Chapter 17

    USGS Publications Warehouse

    Elliott, Diane G.; Ostrander, Gary K.

    2000-01-01

    Many of the features of the fish integument can only be observed microscopically. Because there are over 20,000 living fishes, mostly higher bony fishes (teleosts), a great diversity exists in the microscopic anatomy of the integument. This chapter presents several examples from varied taxonomic groups to illustrate the variation in morphological features. As in all vertebrate epidermis, the fundamental structural unit is the epithelial cell. This is the only constant feature, as a great diversity of cell types exists in the various fish taxa. Some of these include apocrine mucous cells and a variety of other secretory cells, ionocytes, sensory cells, and wandering cells such as leukocytes. The dermis consists essentially of two sets of collagen fibers arranged in opposing geodesic spirals around the body. The dermis of most fishes is divided into two major layers. The upper (outer) layer, the stratum spongiosum or stratum laxum, is a loose network of connective tissue, whereas the lower layer, the stratum compactum, is a dense layer consisting primarily of orthogonal collagen bands. There are also specialized dermal elements such as chromatophores scales, and fin rays.

  1. Variations in pesticide tolerance: Chapter 16

    USGS Publications Warehouse

    Bridges, Christine M.; Semlitsch, Raymond D.; Lannoo, Michael

    2005-01-01

    A growing body of evidence suggests that a number of amphibian populations have declined in recent years. The cause of these population declines has been difficult to establish because in some instances only a single species is declining while sympatric species are thriving. This chapter discusses the results of research that has been conducted to determine the degree of variation present in amphibians with respect to their response to insecticide exposure. The study assessed the degree of variation in response to an anthropogenic stressor among and within species of frogs in the family Ranidae, focusing on the variation in tolerance of tadpoles to the insecticide carbaryl. Carbaryl acts by inhibiting nervous system acetylcholinesterase, which is a common mode of action among insecticides; thus, carbaryl can serve as a model chemical with which to examine amphibian responses. The study also analyzed variation in a hierarchical fashion to identify where variation was the greatest: among nine ranid species, among populations within a single species, and within populations of southern leopard frogs.

  2. Three-Dimensional Imaging. Chapter 10

    NASA Technical Reports Server (NTRS)

    Kelso, R. M.; Delo, C.

    1999-01-01

    This chapter is concerned with three-dimensional imaging of fluid flows. Although relatively young, this field of research has already yielded an enormous range of techniques. These vary widely in cost and complexity, with the cheapest light sheet systems being within the budgets of most laboratories, and the most expensive Magnetic Resonance Imaging systems available to a select few. Taking the view that the most likely systems to be developed are those using light sheets, the authors will relate their knowledge and experience of such systems. Other systems will be described briefly and references provided. Flows are inherently three-dimensional in structure; even those generated around nominally 2-D surface geometry. It is becoming increasingly apparent to scientists and engineers that the three-dimensionalities, both large and small scale, are important in terms of overall flow structure and species, momentum, and energy transport. Furthermore, we are accustomed to seeing the world in three dimensions, so it is natural that we should wish to view, measure and interpret flows in three-dimensions. Unfortunately, 3-D images do not lend themselves to convenient presentation on the printed page, and this task is one of the challenges facing us.

  3. Pesticide Registration Manual: Chapter 10 - Data Compensation Requirements

    EPA Pesticide Factsheets

    This chapter provides information about data compensation requirements, procedures, and obligations when submitting an application for registration, amended registration, reregistration or registration review.

  4. Dealing with Processing Chapter 10 Files from Multiple Vendors

    NASA Technical Reports Server (NTRS)

    Knudtson, Kevin Mark

    2011-01-01

    This presentation discusses the experiences of the NASA Dryden Flight Research Center's (DFRC) Western Aeronautical Test Range (WATR) in dealing with the problems encountered while performing post flight data processing using the WATR's data collection/processing system on Chapter 10 files from different Chapter 10 recorders. The transition to Chapter 10 recorders has brought Vvith it an assortment of issues that must be addressed: the ambiguities of language in the Chapter 10 standard, the unrealistic near-term expectations of the Chapter 10 standard, the incompatibility of data products generated from Chapter 10 recorders, and the unavailability of mature Chapter 10 applications. Some of these issues properly belong to the users of Chapter 10 recorders, some to the manufacturers, and some to the flight test community at large. The goal of this presentation is to share the WATR's lesson learned in processing data products from various Chapter 10 recorder vendors. The WATR could benefit greatly in the open forum Vvith lessons learned discussions with other members of the flight test community.

  5. Quantitative functional interrelations within the cis-regulatory system of the S. purpuratus Endo16 gene.

    PubMed

    Yuh, C H; Moore, J G; Davidson, E H

    1996-12-01

    similar approach to analyze the repressive activity of the three Endo16 cis-regulatory modules that act negatively in controlling spatial expression. The evidence obtained confirms that the repressive modules act only by affecting the output of module A (C.-H. Yuh and E. Davidson (1996) Development 122, 1069-1082). A new hierarchical model of the cis-regulatory system was formulated in which module A plays a central integrating role, and which also implies specific functions for certain DNA-binding sites within the basal promoter fragment of the gene. Additional kinetic experiments were then carried out, and key aspects of the model were confirmed.

  6. Near-UV absorption cross sections and trans/cis equilibrium of nitrous acid

    SciTech Connect

    Bongartz, A.; Kames, J.; Welter, F.; Schurath, U. )

    1991-02-07

    The A {sup 1}A{double prime} {l arrow} X {sup 1}A{prime} absorption spectrum of gaseous nitrous acid has been measured in the 300-400-nm range. Absolute cross sections were determined by a combination of gas-phase and wet chemical analysis. The cross sections of prominent bands are 25% larger than the recommended values of Stockwell and Calvert. The influence of spectral resolution on absolute and differential absorption cross sections was also investigated. The integrated band area of the n{pi}* transition yields an oscillator strength f = (8.90 {plus minus} 0.36) {times} 10{sup {minus}4}, less than the reported liquid phase value of 2 {times} 10{sup {minus}3}. The equilibrium constant K = p{sub trans}/p{sub cis}, based on the assumption that the oscillator strength of the n{pi}* transition is the same for both rotamers, was found to be 3.25 {plus minus} 0.30 at 277 K. This yields an energy difference {Delta}E between trans- and cis-HONO of -2,700 J mol{sup {minus}1} in the electronic ground state, and -6,000 J mol{sup {minus}1} in the excited state.

  7. Cis and Trans Cooperativity of E-Cadherin Mediates Adhesion in Biomimetic Lipid Droplets

    PubMed Central

    Pontani, Lea-Laetitia; Jorjadze, Ivane; Brujic, Jasna

    2016-01-01

    The regulation of cell-cell adhesion is important in cell motility, tissue growth, and for the mechanical integrity of tissues. Although the role of active cytoskeleton dynamics in regulating cadherin interactions is crucial in vivo, here we present a biomimetic emulsion system to characterize the passive E-cadherin-mediated adhesion between droplets. The visualization of a three-dimensional assembly of lipid droplets, functionalized with extracellular E-cadherin domains, reveals a hierarchy of homophilic interactions. First, the high interfacial tension of droplets facilitates trans cadherin-cadherin adhesion, which is strong enough to stabilize looser than random close packing configurations. Second, fluorescence enhancement shows that adding clustering agents, such as calcium or chelating ligands, favor the lateral cis adhesion of the already bound cadherin pairs over the clustering of monomer cadherin on the surface. Finally, above a threshold cadherin and calcium concentration, the cis and trans protein interactions become strong enough to trigger and promote droplet fusion. While E-cadherin is not known to participate in cellular fusion, this mechanism is general because replacing calcium with cholesterol to cluster the cadherin-carrying lipids also promotes fusion. These results suggest that passive clustering, via calcium-induced dimerization or membrane ordering, may contribute to the reinforcement of cell-cell contacts. Alternatively, a molecular switch for fusion offers a route to mixing droplet contents and controlling their size in situ. PMID:26789762

  8. Absorption of CIS Immigrants into Israeli Schools: A Semipermeable Enclave Model.

    ERIC Educational Resources Information Center

    Resnik, Julia; Sabar, Naama; Shoham, Edna; Shapira, Rina

    2001-01-01

    Examined how immigrants from the Commonwealth of Independent States (CIS) assimilated into Israeli society and schools. Data from observations, interviews, and surveys indicated that educational policies and school arrangements, and CIS immigrants' high self-esteem, produced a semipermeable enclave. CIS students acquired the Hebrew language and…

  9. Cis-Selective Ring-Opening Metathesis Polymerization with Ruthenium Catalysts

    PubMed Central

    Keitz, Benjamin K.; Fedorov, Alexey; Grubbs, Robert H.

    2012-01-01

    Using a C-H activated, ruthenium-based metathesis catalyst, the cis selective ROMP of several monocyclic alkenes, as well as norbornene and oxanorbornene-type monomers is reported. The cis content of the isolated polymers depended heavily on monomer structure and temperature. By lowering the temperature, cis content as high as 96% could be obtained. PMID:22239675

  10. Cluster Ion Spectrometry (CIS) Data Archiving in the CAA

    NASA Astrophysics Data System (ADS)

    Dandouras, I. S.; Barthe, A.; Penou, E.; Brunato, S.; Reme, H.; Kistler, L. M.; Blagau, A.; Facsko, G.; Kronberg, E.; Laakso, H. E.

    2009-12-01

    The Cluster Active Archive (CAA) aims at preserving the four Cluster spacecraft data, so that they are usable in the long-term by the scientific community as well as by the instrument team PIs and Co-Is. This implies that the data are filed together with the descriptive and documentary elements making it possible to select and interpret them. The CIS (Cluster Ion Spectrometry) experiment is a comprehensive ionic plasma spectrometry package onboard the four Cluster spacecraft, capable of obtaining full three-dimensional ion distributions (about 0 to 40 keV/e) with a time resolution of one spacecraft spin (4 sec) and with mass-per-charge composition determination. The CIS package consists of two different instruments, a Hot Ion Analyser (HIA) and a time-of-flight ion Composition Distribution Function (CODIF) analyser. For the archival of the CIS data a multi-level approach has been adopted. The CAA archival includes processed raw data (Level 1 data), moments of the ion distribution functions (Level 2 data), and calibrated high-resolution data in a variety of physical units (Level 3 data). The latter are 3-D ion distribution functions and 2-D pitch-angle distributions. In addition, a software package has been developed to allow the CAA user to interactively calculate partial or total moments of the ion distributions. Instrument cross-calibration has been an important activity in preparing the data for archival. The CIS data archive includes also experiment documentation, graphical products for browsing through the data, and data caveats. In addition, data quality indexes are under preparation, to help the user. Given the complexity of an ion spectrometer, and the variety of its operational modes, each one being optimised for a different magnetospheric region or measurement objective, consultation of the data caveats by the end user will always be a necessary step in the data analysis.

  11. Thermodynamic state ensemble models of cis-regulation.

    PubMed

    Sherman, Marc S; Cohen, Barak A

    2012-01-01

    A major goal in computational biology is to develop models that accurately predict a gene's expression from its surrounding regulatory DNA. Here we present one class of such models, thermodynamic state ensemble models. We describe the biochemical derivation of the thermodynamic framework in simple terms, and lay out the mathematical components that comprise each model. These components include (1) the possible states of a promoter, where a state is defined as a particular arrangement of transcription factors bound to a DNA promoter, (2) the binding constants that describe the affinity of the protein-protein and protein-DNA interactions that occur in each state, and (3) whether each state is capable of transcribing. Using these components, we demonstrate how to compute a cis-regulatory function that encodes the probability of a promoter being active. Our intention is to provide enough detail so that readers with little background in thermodynamics can compose their own cis-regulatory functions. To facilitate this goal, we also describe a matrix form of the model that can be easily coded in any programming language. This formalism has great flexibility, which we show by illustrating how phenomena such as competition between transcription factors and cooperativity are readily incorporated into these models. Using this framework, we also demonstrate that Michaelis-like functions, another class of cis-regulatory models, are a subset of the thermodynamic framework with specific assumptions. By recasting Michaelis-like functions as thermodynamic functions, we emphasize the relationship between these models and delineate the specific circumstances representable by each approach. Application of thermodynamic state ensemble models is likely to be an important tool in unraveling the physical basis of combinatorial cis-regulation and in generating formalisms that accurately predict gene expression from DNA sequence.

  12. Proton irradiation of the CIS115 for the JUICE mission

    NASA Astrophysics Data System (ADS)

    Soman, M. R.; Allanwood, E. A. H.; Holland, A. D.; Winstone, G. P.; Gow, J. P. D.; Stefanov, K.; Leese, M.

    2015-09-01

    The CIS115 is one of the latest CMOS Imaging Sensors designed by e2v technologies, with 1504x2000 pixels on a 7 μm pitch. Each pixel in the array is a pinned photodiode with a 4T architecture, achieving an average dark current of 22 electrons pixel-1 s-1 at 21°C measured in a front-faced device. The sensor aims for high optical sensitivity by utilising e2v's back-thinning and processing capabilities, providing a sensitive silicon thickness approximately 9 μm to 12 μm thick with a tuned anti-reflective coating. The sensor operates in a rolling shutter mode incorporating reset level subtraction resulting in a mean pixel readout noise of 4.25 electrons rms. The full well has been measured to be 34000 electrons in a previous study, resulting in a dynamic range of up to 8000. These performance characteristics have led to the CIS115 being chosen for JANUS, the high-resolution and wide-angle optical camera on the JUpiter ICy moon Explorer (JUICE). The three year science phase of JUICE is in the harsh radiation environment of the Jovian magnetosphere, primarily studying Jupiter and its icy moons. Analysis of the expected radiation environment and shielding levels from the spacecraft and instrument design predict the End Of Life (EOL) displacement and ionising damage for the CIS115 to be equivalent to 1010 10 MeV protons cm-2 and 100 krad(Si) respectively. Dark current and image lag characterisation results following initial proton irradiations are presented, detailing the initial phase of space qualification of the CIS115. Results are compared to the pre-irradiation performance and the instrument specifications and further qualification plans are outlined.

  13. History and Status of the CIS Customs Union

    SciTech Connect

    Lawson, T.M.; Erickson, S.A.

    1999-08-31

    This report explores the history of the CIS Customs Union and the major obstacles the Union faces in its implementation. Investigation of the Customs Union is necessary as its implementation could effect the Second Line of Defense (SLD) Program. Russian Customs contends that radiation detectors should not be installed along the Customs Union members borders of as the borders will be dissolved when the Union is implemented.

  14. City of Troitsk and Sooty Snow, Chelyabinsk, CIS

    NASA Technical Reports Server (NTRS)

    1992-01-01

    This view shows the industrial pollution around the Siberian city of Troitsk (54.0N, 61.0E). Troitsk is the smallest of a group of three heavy industrial cities east of the Urals, the others being Magnitogorsk and Chelyabinsk. All have been cited as being some of the worst industrial polluted cities in the CIS. Despite being the smallest of the three, Troitsk has the largest area of soot blackened snow. Respiratory diseases among the citizens are chronic.

  15. Cis-elements governing trinucleotide repeat instability in Saccharomyces cerevisiae.

    PubMed Central

    Rolfsmeier, M L; Dixon, M J; Pessoa-Brandão, L; Pelletier, R; Miret, J J; Lahue, R S

    2001-01-01

    Trinucleotide repeat (TNR) instability in humans is governed by unique cis-elements. One element is a threshold, or minimal repeat length, conferring frequent mutations. Since thresholds have not been directly demonstrated in model systems, their molecular nature remains uncertain. Another element is sequence specificity. Unstable TNR sequences are almost always CNG, whose hairpin-forming ability is thought to promote instability by inhibiting DNA repair. To understand these cis-elements further, TNR expansions and contractions were monitored by yeast genetic assays. A threshold of approximately 15--17 repeats was observed for CTG expansions and contractions, indicating that thresholds function in organisms besides humans. Mutants lacking the flap endonuclease Rad27p showed little change in the expansion threshold, suggesting that this element is not altered by the presence or absence of flap processing. CNG or GNC sequences yielded frequent mutations, whereas A-T rich sequences were substantially more stable. This sequence analysis further supports a hairpin-mediated mechanism of TNR instability. Expansions and contractions occurred at comparable rates for CTG tract lengths between 15 and 25 repeats, indicating that expansions can comprise a significant fraction of mutations in yeast. These results indicate that several unique cis-elements of human TNR instability are functional in yeast. PMID:11290713

  16. Cis and trans interactions between atlastin molecules during membrane fusion

    PubMed Central

    Liu, Tina Y.; Bian, Xin; Romano, Fabian B.; Shemesh, Tom; Rapoport, Tom A.; Hu, Junjie

    2015-01-01

    Atlastin (ATL), a membrane-anchored GTPase that mediates homotypic fusion of endoplasmic reticulum (ER) membranes, is required for formation of the tubular network of the peripheral ER. How exactly ATL mediates membrane fusion is only poorly understood. Here we show that fusion is preceded by the transient tethering of ATL-containing vesicles caused by the dimerization of ATL molecules in opposing membranes. Tethering requires GTP hydrolysis, not just GTP binding, because the two ATL molecules are pulled together most strongly in the transition state of GTP hydrolysis. Most tethering events are futile, so that multiple rounds of GTP hydrolysis are required for successful fusion. Supported lipid bilayer experiments show that ATL molecules sitting on the same (cis) membrane can also undergo nucleotide-dependent dimerization. These results suggest that GTP hydrolysis is required to dissociate cis dimers, generating a pool of ATL monomers that can dimerize with molecules on a different (trans) membrane. In addition, tethering and fusion require the cooperation of multiple ATL molecules in each membrane. We propose a comprehensive model for ATL-mediated fusion that takes into account futile tethering and competition between cis and trans interactions. PMID:25825753

  17. Cis-Active RNA Elements (CREs) and Picornavirus RNA Replication

    PubMed Central

    Steil, Benjamin P.; Barton, David J.

    2009-01-01

    Our understanding of picornavirus RNA replication has improved over the past 10 years, due in large part to the discovery of cis-active RNA elements (CREs) within picornavirus RNA genomes. CREs function as templates for the conversion of VPg, the Viral Protein of the genome, into VPgpUpUOH. These so called CREs are different from the previously recognized cis-active RNA sequences and structures within the 5′ and 3′ NTRs of picornavirus genomes. Two adenosine residues in the loop of the CRE RNA structures allow the viral RNA-dependent RNA polymerase 3DPol to add two uridine residues to the tyrosine residue of VPg. Because VPg and/or VPgpUpUOH prime the initiation of viral RNA replication, the asymmetric replication of viral RNA could not be explained without an understanding of the viral RNA template involved in the conversion of VPg into VPgpUpUOH primers. We review the growing body of knowledge regarding picornavirus CREs and discuss how CRE RNAs work coordinately with viral replication proteins and other cis-active RNAs in the 5′ and 3′ NTRs during RNA replication. PMID:18773930

  18. Introduction to MODIS Cloud Products. Chapter 5

    NASA Technical Reports Server (NTRS)

    Baum, Bryan A.; Platnick, Steven

    2006-01-01

    derived from heritage instruments. This chapter provides an overview of the MODIS Level-2 and -3 operational cloud products.

  19. Ecological consequences of manipulative parasites: chapter 9

    USGS Publications Warehouse

    Lafferty, Kevin D.; Kuris, A. M.

    2012-01-01

    phrases such as “may ultimately infl uence community structure” (Kiesecker and Blaustein 1999), yet few demonstrate ecological effects. Here, we consider the conditions under which manipulative parasites might have a substantial ecological effect in nature and highlight those for which evidence exists (see also Chapter 10).

  20. Chapter 2 Formula: Evaluation Report 1990-91.

    ERIC Educational Resources Information Center

    Bliss, Kristen M.

    Chapter 2 Formula provides federal funds to the states through the Elementary and Secondary Education Act of 1965 (ESEA) as amended by P.L. 100-297 in 1988. Chapter 2 funds can support one or more programs that do the following: meet the educational needs of students with special needs (at-risk and high-cost students); acquire curricular…

  1. Grand-Slam Strategies: Winning Tips for Cutting Chapter Costs.

    ERIC Educational Resources Information Center

    Burdette, Melinda

    1992-01-01

    Techniques for more cost-effective college alumni chapter administration include better marketing and communications, regionally tailored periodicals, planning ahead, coordinating spring volunteer training with admissions travel, encouraging faculty participation, using mentors for program development, letting chapters pay expenses, and better use…

  2. 41 CFR Appendix D to Chapter 301 - Glossary of Acronyms

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 41 Public Contracts and Property Management 4 2011-07-01 2011-07-01 false Glossary of Acronyms D Appendix D to Chapter 301 Public Contracts and Property Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES Ch. 301, App. D Appendix D to Chapter 301—Glossary of Acronyms...

  3. 41 CFR Appendix D to Chapter 301 - Glossary of Acronyms

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 41 Public Contracts and Property Management 4 2013-07-01 2012-07-01 true Glossary of Acronyms D Appendix D to Chapter 301 Public Contracts and Property Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES Ch. 301, App. D Appendix D to Chapter 301—Glossary of Acronyms...

  4. Results of a Process for Improving Chapter 1 Programs.

    ERIC Educational Resources Information Center

    Billig, Shelley H.; And Others

    Between 1985 and 1988, the Northwest Regional Educational Laboratory Chapter 1 Technical Assistance Center developed, refined, and disseminated a research-based process for improving local compensatory education programs. Known as the Chapter 1 Improvement Process (CHIP), the effort combined knowledge from five research areas into a year-long,…

  5. IRIG 106-07 Chapter 10 Programming Handbook

    DTIC Science & Technology

    2009-03-01

    in the Chapter 10 header. Format 0 video data can be readily decoded with commonly available MPEG libraries such as the open source ffmpeg library...106 Chapter 10 releases. MPEG decoder libraries such as ffmpeg commonly take as input a 188 byte array of TS data. Due to the use of 16-bit words

  6. 48 CFR Appendixes B-E to Chapter 2 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false B Appendixes B-E to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendixes B-E to Chapter 2...

  7. 48 CFR Appendixes B-E to Chapter 2 - [Reserved

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 3 2012-10-01 2012-10-01 false B Appendixes B-E to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendixes B-E to Chapter 2...

  8. 48 CFR Appendixes B-E to Chapter 2 - [Reserved

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 3 2014-10-01 2014-10-01 false B Appendixes B-E to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendixes B-E to Chapter 2...

  9. 48 CFR Appendixes B-E to Chapter 2 - [Reserved

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 3 2011-10-01 2011-10-01 false B Appendixes B-E to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendixes B-E to Chapter 2...

  10. 41 CFR Appendix D to Chapter 301 - Glossary of Acronyms

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 41 Public Contracts and Property Management 4 2010-07-01 2010-07-01 false Glossary of Acronyms D Appendix D to Chapter 301 Public Contracts and Property Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES Ch. 301, App. D Appendix D to Chapter 301—Glossary of Acronyms...

  11. Chapter 1 Support for Instructional Development, 1986-87.

    ERIC Educational Resources Information Center

    Kaemper, Jack; Morse, Kathy

    Six of the 39 Albuquerque (New Mexico) Public Schools' Chapter 1 participating schools, as part of the school-based budgeting process, allocated a portion of their Chapter 1 resource allocation for on-site intensive staff development activities. Three schools--Alamosa, Chaparral, and Duranes--agreed to utilize the time of a Support for…

  12. Biological effects: Marine mammals and sea turtles (chapter 14). Book chapter

    SciTech Connect

    Haebler, R.

    1994-01-01

    All spills are different, varying in type and amount of oil spilled, species exposed, and geographic and atmospheric conditions. It is important to understand as much as possible about both the natural history and characteristics of various species and the specific effects oil has on wildlife. Doing so improves the ability to extrapolate from one spill to another and improves prediction of types and severity of effects to wildlife. This chapter presents an overview of the biological effects of oil on marine mammals and sea turtles.

  13. PreCisIon: PREdiction of CIS-regulatory elements improved by gene’s positION

    PubMed Central

    Elati, Mohamed; Nicolle, Rémy; Junier, Ivan; Fernández, David; Fekih, Rim; Font, Julio; Képès, François

    2013-01-01

    Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices, which may match large numbers of sites and produce an unreliable list of target genes. To improve the prediction of binding sites, we propose to additionally use the unrelated knowledge of the genome layout. Indeed, it has been shown that co-regulated genes tend to be either neighbors or periodically spaced along the whole chromosome. This study demonstrates that respective gene positioning carries significant information. This novel type of information is combined with traditional sequence information by a machine learning algorithm called PreCisIon. To optimize this combination, PreCisIon builds a strong gene target classifier by adaptively combining weak classifiers based on either local binding sequence or global gene position. This strategy generically paves the way to the optimized incorporation of any future advances in gene target prediction based on local sequence, genome layout or on novel criteria. With the current state of the art, PreCisIon consistently improves methods based on sequence information only. This is shown by implementing a cross-validation analysis of the 20 major TFs from two phylogenetically remote model organisms. For Bacillus subtilis and Escherichia coli, respectively, PreCisIon achieves on average an area under the receiver operating characteristic curve of 70 and 60%, a sensitivity of 80 and 70% and a specificity of 60 and 56%. The newly predicted gene targets are demonstrated to be functionally consistent with previously known targets, as assessed by analysis of Gene Ontology enrichment or of the relevant literature and databases. PMID:23241390

  14. Integrated Modeling Systems

    DTIC Science & Technology

    1989-01-01

    Summer 1979). WMSI Working Paper No. 291A. 173 Dyer , J. and R. Sarin. "Measurable Multiattribute Value Functions," Operations Research. 27:4 (July...J. McCall. "Expected Utility Maximizing Job Search," Chapter 7 of Studies in the Economics of Search, 1979, North-Holland. WMSI Working Paper No. 274...model integration, solver integration, and integration of various utilities . Model integration is further divided into four subtypes based on a four-level

  15. Chapter A3. Cleaning of Equipment for Water Sampling

    USGS Publications Warehouse

    Wilde, Franceska D.; Radtke, Dean B.; Gibs, Jacob; Iwatsubo, Rick T.

    1998-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) describes protocols and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. Chapter A3 describes procedures for cleaning the equipment used to collect and process samples of surface water and ground water and procedures for assessing the efficacy of the equipment-cleaning process. This chapter is designed for use with the other chapters of this field manual. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be posted on the USGS page 'National Field Manual for the Collection of Water-Quality Data.' The URL for this page is http://pubs.water.usgs.gov/twri9A/ (accessed September 20, 2004).

  16. Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

    PubMed Central

    Hughes, Jim R.; Cheng, Jan-Fang; Ventress, Nicki; Prabhakar, Shyam; Clark, Kevin; Anguita, Eduardo; De Gobbi, Marco; de Jong, Pieter; Rubin, Eddy; Higgs, Douglas R.

    2005-01-01

    An important step toward improving the annotation of the human genome is to identify cis-acting regulatory elements from primary DNA sequence. One approach is to compare sequences from multiple, divergent species. This approach distinguishes multispecies conserved sequences (MCS) in noncoding regions from more rapidly evolving neutral DNA. Here, we have analyzed a region of ≈238kb containing the human α globin cluster that was sequenced and/or annotated across the syntenic region in 22 species spanning 500 million years of evolution. Using a variety of bioinformatic approaches and correlating the results with many aspects of chromosome structure and function in this region, we were able to identify and evaluate the importance of 24 individual MCSs. This approach sensitively and accurately identified previously characterized regulatory elements but also discovered unidentified promoters, exons, splicing, and transcriptional regulatory elements. Together, these studies demonstrate an integrated approach by which to identify, subclassify, and predict the potential importance of MCSs. PMID:15998734

  17. Nanoporous Materials in Atmosphere Revitalization. Chapter 1

    NASA Technical Reports Server (NTRS)

    Hernandez-Maldonado, J.; Ishikawa, Yasuyuki; Luna, Bernadette; Junaedi, Christian; Mulloth, Lila; Perry, Jay L.; Raptis, Raphael G.; Roychoudhury, Subir

    2012-01-01

    lowering cabin levels of CO2 and NH3 as well as reducing power requirements and increasing reliability. This chapter summarizes the challenges faced by ECLS system engineers in pursuing these goals, and the promising materials developments that may be part of the technical solution for challenges of crewed space exploration beyond LEO.

  18. Integrity in Student Development

    ERIC Educational Resources Information Center

    Roberts, Dennis C.; Banta, Trudy W.

    2011-01-01

    The quest for integrity in practice and theory has been part of the evolution of student personnel work all the way back to the turn of the 20th century. This chapter seeks to take stock of the question of integrity in relation to one of the core knowledge bases used by those engaged in student affairs work today--student development. The authors…

  19. Secondary School Mathematics, Chapter 15, The Real Number System, Chapter 16, Area, Volume, and Computation. Student's Text.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    Topics covered in the first chapter of Unit 8 of this SMSG series include square roots, operations with radicals, operations with real numbers, and the structure of the real number system. The second chapter deals with measurement of area (for rectangular regions, other polygons, and circles), volume and surface area, computation involving…

  20. Getting the Most from Pi Sigma Alpha Chapters: Exploring the Chapter Activity Grant Program and Its Multiplier Effects

    ERIC Educational Resources Information Center

    Alexander, Robert M.

    2009-01-01

    The political science honor society, Pi Sigma Alpha, has chapters in nearly 700 institutions across the United States. The organization sponsors many programs that can contribute a great deal to students of political science; however, many students are unaware of these opportunities. This article encourages chapter advisors to make use of these…

  1. Reinventing Chapter 1: Annual National Conference of State Chapter 1 Coordinators. Conference Presentations (September 20-23, 1993).

    ERIC Educational Resources Information Center

    Office of Elementary and Secondary Education (ED), Washington, DC. Compensatory Education Programs.

    This document provides the individual and panel presentations for the Annual National Conference of State Chapter 1 Coordinators concerning Compensatory Education Programs. Presentations and their authors are as follows: (1) "Chapter 1 and School Reform: An Overview" (Richard W. Riley); (2) "Systemic Reform and Educational…

  2. Enantioselective disruption of the endocrine system by Cis-Bifenthrin in the male mice.

    PubMed

    Jin, Yuanxiang; Wang, Jiangcong; Pan, Xiuhong; Miao, Wenyu; Lin, Xiaojian; Wang, Linggang; Fu, Zhengwei

    2015-07-01

    Bifenthrin (BF), as a chiral pyrethroid, is widely used to control field and household pests in China. At present, the commercial BF is a mixed compound containing cis isomers (cis-BF) including two enantiomers of 1R-cis-BF and 1S-cis-BF. In the present study, the two individual cis-BF enantiomers were separated by a preparative supercritical fluid chromatography. Then, four week-old adolescent male ICR mice were orally administered 1R-cis-BF and 1S-cis-BF separately daily for 3 weeks at doses of 0, 7.5 and 15 mg/kg/day, respectively. Results showed that the transcription status of some genes involved in cholesterol synthesis and transport as well as testosterone (T) synthesis in the testes were influenced by cis-BF enantiomers. Especially, we observed that the transcription status of key genes on the pathway of T synthesis including cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc) and cytochrome P450 17α-hydroxysteroid dehydrogenase (P45017α)) were selectively altered in the testis of mice when treated with 1S-cis-BF, suggesting that it is the possible reason to explain why the lower serum T concentration in 1S-cis-BF treated group. Taken together, it concluded that both of the cis-BF enantiomers have the endocrine disruption activities, while 1S-cis-BF was higher than 1R-cis-BF in mice when exposed during the puberty. The data was helpful to understand the toxicity of cis-BF in mammals under enantiomeric level.

  3. Metal-organic frameworks from copper dimers with cis- and trans-1,4-cyclohexanedicarboxylate and cis,cis-1,3,5-cyclohexanetricarboxylate.

    PubMed

    Kumagai, Hitoshi; Akita-Tanaka, Motoko; Inoue, Katsuya; Takahashi, Kazuyuki; Kobayashi, Hayao; Vilminot, Serge; Kurmoo, Mohamedally

    2007-07-23

    Single crystals of three coordination networks containing the Cu(2)(COO)(4) core bridged by cyclohexane have been hydrothermally prepared by the reaction of 1,4-cyclohexanedicarboxylic (1,4-H(2)chdc) or 1,3,5-cyclohexanetricarboxylic (1,3,5-H(3)chtc) acid and Cu(NO(3))(2) x 6H(2)O. We report their characterizations by single-crystal X-ray structure determinations, IR spectroscopy, thermal analyses, and their magnetic properties. [Cu(2)(trans-1,4-chdc)(2)] (1) consists of 4 x 4 grids with the dimeric nodes connected by the trans-1,4-chdc, and these grids are then connected to each other by Cu-O bonds, resulting in a porous network (void volume of 130 Angstrom(3) per cell or 25%) with no solvent in its cavities. [Cu(2)(cis-1,4-chdc)(2)(H(2)O)(2)] (2) consists of two-legged ladders where the dimer nodes are bridged by pairs of cis-1,4-chdc and the water molecules cap the ends of the Cu dimers. [Cu(2)(1,3,5-Hchtc)(2)] (3) displays 4 x 4 grids, but each dimeric node is connected to its neighbors within the same grid by Cu-O bonds to form a layered network which further makes hydrogen-bond interactions with its neighbors. 2 and 3 have compact structures without any space for solvents. IR and DT-TGA confirm the absence of water in the empty channels of 1, while IR shows the presence of both protonated and deprotonated carboxyl groups for 3. The magnetic properties of all three compounds are dominated by the strong Cu-Cu antiferromagnetic interaction resulting in singlet-triplet gaps of 450-500 K.

  4. Alchornea cordifolia seed oil: A rich source of a new C20 epoxide, (+)cis-14,15-epoxy-cis-11-eicosenoic acid.

    PubMed

    Kleiman, R; Plattner, R D; Spencer, G F

    1977-07-01

    A C20 homolog of vernolic acid has been found at the 50% level inAlchornea cordifolia, Euphorbiaceae, seed oil. This new acid, (+)cis-14,15-epoxy-cis-11-eicosenoic (alchornoic) acid, was isolated by high-pressure liquid chromotography and characterized by mass spectrometry, nuclear magnetic resonance and infrared spectroscopy, optical rotary dispersion, and ozonolysis-gas-chromotography.

  5. 21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... contain not less than 35 percent of other fatty acid esters composed of oleic acid, palmitic acid, stearic... 21 Food and Drugs 6 2013-04-01 2013-04-01 false Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic acids). 573.637 Section 573.637 Food and Drugs FOOD...

  6. Children's Art Carnival Creative Reading Program, 1988-89. E.C.I.A. Chapter 1. Evaluation Section Report.

    ERIC Educational Resources Information Center

    Guerrero, Frank; And Others

    The Chapter One Children's Art Carnival (C.A.C.) Creative Reading Program was designed to improve students' literacy skills through participation in creative arts activities integrated with instruction in reading and writing. Operating at sites in Manhattan, Queens, and the Bronx, the 1988-89 program served 334 students in second through fifth…

  7. BMC{trademark}: Baseline report; Greenbook (chapter)

    SciTech Connect

    1997-07-31

    Barrier Membrane Containment (BMC){trademark} is a high-density polyethylene membrane (HDPE) groundwater barrier and pass-through system, with applications ranging from plume control and containment to groundwater manipulation coupled with in-site treatment. BMC{trademark} system can function as a permeable or impermeable reaction wall, a cut-off wall, interceptor trenches, a barrier with collection and/or monitoring system, and a pass-through in a funnel and gate configuration. BMC{trademark} can be inspected with a down-hole video camera, producing a permanent VHS format tape, insuring the integrity of the wall and the interlocking joints.

  8. Genomic approaches to finding cis-regulatory modules in animals

    PubMed Central

    Hardison, Ross C.; Taylor, James

    2012-01-01

    Differential gene expression is the fundamental mechanism underlying animal development and cell differentiation. However, it is a challenge to identify comprehensively and accurately the DNA sequences required to regulate gene expression, called cis-regulatory modules (CRMs). Three major features (singly or in combination) are used to predict CRMs: clusters of transcription-factor binding-site motifs, noncoding DNA under evolutionary constraint, and biochemical marks associated with CRMs, such as histone modifications and protein occupancy. The validation rates for predictions indicate that identifying diagnostic biochemical marks is the most reliable method, and understanding is enhanced by analysis of motifs and conservation patterns within those predicted CRMs. PMID:22705667

  9. cis-clerodane diterpenes from the liverwort Scapania ciliata.

    PubMed

    Liu, Na; Zhu, Rong-Xiu; Wang, Song; Zhang, Jiao-Zhen; Lin, Zhao-Min; Li, Rui-Juan; Lou, Hong-Xiang

    2013-09-01

    Chemical investigation of the Chinese liverwort Scapania ciliata led to the isolation of four new cis-clerodane lactones, named ciliatolides A-D (1-4, resp.), among which compound 1 was found to be a tetranorclerodanoid. Their structures were determined by extensive analysis of spectroscopic data, and, in the case of compound 1, together with a single-crystal X-ray diffraction analysis. The absolute configurations were established by analysis of the CD spectra and by quantum-chemical CD calculations. The cytotoxicities of compounds 1-4 were preliminarily tested against the PC3 and MCF-7 cell lines.

  10. Chapter 2: Development of the peripheral nerve.

    PubMed

    Kaplan, Suleyman; Odaci, Ersan; Unal, Bunyami; Sahin, Bunyamin; Fornaro, Michele

    2009-01-01

    Normal function of the peripheral nerve (PN) is based on morphological integrity and relationship between axons, Schwann cells, and connective sheaths, which depends on the correct development of all these components. Most of the relevant studies in this field were carried out using animal models, since reports on the development of the human PNs from the time of prenatal formation to postnatal development are limited as it is quite difficult to find many nerves in fetuses. In this review paper, we will address the main developmental stages of axons, Schwann cells, and connective tissue sheaths in PNs. Knowledge on the development of PNs and their main components is important for the study of nerve repair and regeneration. This knowledge can be helpful for designing innovative treatment strategies since, like with other organs, the development and regeneration processes share many biological features.

  11. Latex Clearing Protein—an Oxygenase Cleaving Poly(cis-1,4-Isoprene) Rubber at the cis Double Bonds

    PubMed Central

    Hiessl, Sebastian; Böse, Dietrich; Oetermann, Sylvia; Eggers, Jessica; Pietruszka, Jörg

    2014-01-01

    Gordonia polyisoprenivorans strain VH2, a potent rubber-degrading actinomycete, harbors two latex clearing proteins (Lcps), which are known to be essential for the microbial degradation of rubber. However, biochemical information on the exact role of this protein in the degradation of polyisoprene was lacking. In this study, the gene encoding Lcp1VH2 was heterologously expressed in strains of Escherichia coli, the corresponding protein was purified, and its role in rubber degradation was examined by measurement of oxygen consumption as well as by chromatographic and spectroscopic methods. It turned out that active Lcp1VH2 is a monomer and is responsible for the oxidative cleavage of poly(cis-1,4-isoprene) in synthetic as well as in natural rubber by the addition of oxygen (O2) to the cis double bonds. The resulting oligomers possess repetitive isoprene units with aldehyde (CHO-CH2—) and ketone (—CH2-CO-CH3) functional groups at the termini. Two fractions with average isoprene contents of 18 and 10, respectively, were isolated, thus indicating an endocleavage mechanism. The activity of Lcp1VH2 was determined by applying a polarographic assay. Alkenes, acyclic terpenes, or other rubber-like polymers, such as poly(cis-1,4-butadiene) or poly(trans-1,4-isoprene), are not oxidatively cleaved by Lcp1VH2. The pH and temperature optima of the enzyme are at pH 7 and 30°C, respectively. Furthermore, it was demonstrated that active Lcp1VH2 is a Cu(II)-containing oxygenase that exhibits a conserved domain of unknown function which cannot be detected in any other hitherto-characterized enzyme. The results presented here indicate that this domain might represent a new protein family of oxygenases. PMID:24928880

  12. Latex clearing protein-an oxygenase cleaving poly(cis-1,4-isoprene) rubber at the cis double bonds.

    PubMed

    Hiessl, Sebastian; Böse, Dietrich; Oetermann, Sylvia; Eggers, Jessica; Pietruszka, Jörg; Steinbüchel, Alexander

    2014-09-01

    Gordonia polyisoprenivorans strain VH2, a potent rubber-degrading actinomycete, harbors two latex clearing proteins (Lcps), which are known to be essential for the microbial degradation of rubber. However, biochemical information on the exact role of this protein in the degradation of polyisoprene was lacking. In this study, the gene encoding Lcp1VH2 was heterologously expressed in strains of Escherichia coli, the corresponding protein was purified, and its role in rubber degradation was examined by measurement of oxygen consumption as well as by chromatographic and spectroscopic methods. It turned out that active Lcp1VH2 is a monomer and is responsible for the oxidative cleavage of poly(cis-1,4-isoprene) in synthetic as well as in natural rubber by the addition of oxygen (O2) to the cis double bonds. The resulting oligomers possess repetitive isoprene units with aldehyde (CHO-CH2-) and ketone (-CH2-CO-CH3) functional groups at the termini. Two fractions with average isoprene contents of 18 and 10, respectively, were isolated, thus indicating an endocleavage mechanism. The activity of Lcp1VH2 was determined by applying a polarographic assay. Alkenes, acyclic terpenes, or other rubber-like polymers, such as poly(cis-1,4-butadiene) or poly(trans-1,4-isoprene), are not oxidatively cleaved by Lcp1VH2. The pH and temperature optima of the enzyme are at pH 7 and 30°C, respectively. Furthermore, it was demonstrated that active Lcp1VH2 is a Cu(II)-containing oxygenase that exhibits a conserved domain of unknown function which cannot be detected in any other hitherto-characterized enzyme. The results presented here indicate that this domain might represent a new protein family of oxygenases.

  13. Pesticide Registration Manual: Chapter 17 - State Regulatory Authority

    EPA Pesticide Factsheets

    FIFRA authorizes states to issue Experimental Use Permits, Special Local Needs registrations, and to apply for Emergency Exemptions under specific conditions. This chapter provides detailed information relevant to state actions under FIFRA.

  14. General RMP Guidance - Chapter 4: Offsite Consequence Analysis

    EPA Pesticide Factsheets

    This chapter provides basic compliance information, not modeling methodologies, for people who plan to do their own air dispersion modeling. OCA is a required part of the risk management program, and involves worst-case and alternative release scenarios.

  15. United States Parmacopeia Chapter <797> timeline: 1989 to 2013.

    PubMed

    Newton, David W

    2013-01-01

    This article features a tabular chronology of events deemed relevant to the creation and revision of United States Pharmacopeia General Chapter <797> Pharmaceutical Compounding--Sterile Preparations, which premiered in 2004.

  16. Solid Lubrication Fundamentals and Applications. Chapter 1; Introduction and Background

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa

    1996-01-01

    This chapter presents an introduction and historical background to the field of tribology, especially solid lubrication and lubricants and sets them in the perspective of techniques and materials in lubrication. Also, solid and liquid lubrication films are defined and described.

  17. Transverse section through the Grand Lodge and Grand Chapter rooms ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Transverse section through the Grand Lodge and Grand Chapter rooms of James H. Windrim and George Summers’s neoclassical competition design for the New Masonic Temple, Philadelphia, 1867 - Masonic Temple, 1 North Broad Street, Philadelphia, Philadelphia County, PA

  18. Legislative engagement at the chapter level: tips for getting involved.

    PubMed

    Montgomery, Tiffany M

    2012-01-01

    Legislative and advocacy efforts of locally organized groups of nurses can affect local, state and national health care issues. Ways to get involved include participating in AWHONN chapter and section meetings, local health fairs and letter-writing campaigns.

  19. FDA Bacteriological Analytical Manual, Chapter 10, 2003: Listeria monocytogenes

    EPA Pesticide Factsheets

    FDA Bacteriological Analytical Manual, Chapter 10 describes procedures for analysis of food samples and may be adapted for assessment of solid, particulate, aerosol, liquid and water samples containing Listeria monocytogenes.

  20. Row erupts over axed chapter from Newt Gingrich book

    NASA Astrophysics Data System (ADS)

    Gwynne, Peter

    2012-02-01

    A chapter written by a respected climate scientist for a book co-edited by Republican presidential candidate Newt Gingrich has been canned because its author asserts that humans are responsible for climate change.

  1. Standardizing electrofishing power for boat electrofishing: chapter 14

    USGS Publications Warehouse

    Miranda, L.E. (Steve); Bonar, Scott A.; Hubert, Wayne A.; Willis, David W.

    2009-01-01

    Standardizing boat electrofishing entails achieving an accepted level of collection consistency by managing various brand factors, including (1) the temporal and spatial distribution of sampling effort, (2) boat operation, (3) equipment configuration, (4) characteristics of the waveform and energized field, and (5) power transferred to fish. This chapter focuses exclusively on factor 5:L factors 1-4 have been addressed in earlier chapters. Additionally, while the concepts covered in this chapter address boat electrofishing in general, the power settings discussed were developed from tests with primarily warmwater fish communities. Others (see Chapter 9) recommend lower power settings for communities consisting of primarily coldwater fishes. For reviews of basic concepts of electricity, electrofishing theory and systems, fish behavior relative to diverse waveforms, and injury matter, the reader is referred to Novotny (1990), Reynold (1996), and Snyder (2003).

  2. Crystal structure of 1,6-di-thia-cyclo-deca-cis-3,cis-8-diene (DTCDD).

    PubMed

    Baughman, Russell G; Delanty, Molly C; Ortwerth, Michael F

    2014-11-01

    The title compound, C8H12S2 (trivial name DTCDD), was obtained as a side product of the reaction between cis-1,4-di-chloro-but-2-ene and sodium sulfide. The asymmetric unit consists of one-quarter of the mol-ecule (S site symmetry 2) and the complete mol-ecule has 2/m (C 2h ) point symmetry with the C=C bond in an E conformation. The geometry of the title compound is compared to those of a chloro derivative and a mercury complex.

  3. Randomized Subspace Learning for Proline Cis-Trans Isomerization Prediction.

    PubMed

    Al-Jarrah, Omar Y; Yoo, Paul D; Taha, Kamal; Muhaidat, Sami; Shami, Abdallah; Zaki, Nazar

    2015-01-01

    Proline residues are common source of kinetic complications during folding. The X-Pro peptide bond is the only peptide bond for which the stability of the cis and trans conformations is comparable. The cis-trans isomerization (CTI) of X-Pro peptide bonds is a widely recognized rate-limiting factor, which can not only induces additional slow phases in protein folding but also modifies the millisecond and sub-millisecond dynamics of the protein. An accurate computational prediction of proline CTI is of great importance for the understanding of protein folding, splicing, cell signaling, and transmembrane active transport in both the human body and animals. In our earlier work, we successfully developed a biophysically motivated proline CTI predictor utilizing a novel tree-based consensus model with a powerful metalearning technique and achieved 86.58 percent Q2 accuracy and 0.74 Mcc, which is a better result than the results (70-73 percent Q2 accuracies) reported in the literature on the well-referenced benchmark dataset. In this paper, we describe experiments with novel randomized subspace learning and bootstrap seeding techniques as an extension to our earlier work, the consensus models as well as entropy-based learning methods, to obtain better accuracy through a precise and robust learning scheme for proline CTI prediction.

  4. Phase transitions in chlorobenzene-cis-decalin mixtures

    NASA Astrophysics Data System (ADS)

    Mansingh, Abhai; Agarwal, C. B.; Singh, Ramadhar

    1980-01-01

    The dielectric constant ɛ' and loss tangent tan δ of chlorobenzene-cis-decalin mixtures have been measured in the temperature range 77 K to 330 K and frequency range 0.1 to 100 kHz. On cooling, ɛ' increases with decreasing temperature upto about 135 K, after which it drops rapidly with decreasing T followed by a slow decrease. This indicates that the liquid mixture goes to an amorphous phase which transforms to a glass phase of restricted dipole rotation below T g; however, the peak in ɛ' is due to relaxation in the amorphous phase (α relaxation) and does not give an exact T g. On heating, the behaviour of the cooling curve is retraced upto 160 K, after which ɛ' drops suddenly to a value lower than that at 77 K in the glass phase. This indicates the transition to a crystalline phase in which dipole rotational freedom is completely lost. The crystalline phase changes to a eutectic liquid phase of high ɛ' at a temperature (200 K) lower than the melting point of chlorobenzene and cis-decalin. Dielectric dispersion is observed only in the glass and amorphous phases. The dielectric relaxation time is independent of the concentration of chlorobenzene.

  5. Theoretical study of trans-cis photoisomerism in polymethine cyanines

    NASA Astrophysics Data System (ADS)

    Momicchioli, Fabio; Baraldi, Ivan; Berthier, Gaston

    1988-06-01

    The trans-cis photoisomerism of polymethine dyes has been interpreted so far using different and rather inconsistent models of the potential energy surfaces. In order to search for a unified electronic model, we tackled the problem again from an intramolecular point of view. Our study consisted in qualitative MO considerations followed by explicit (CS INDO) calculations of the S 0, T 1 and S 1 potential energy curves for a proper model system: pentamethine cyanine isomerizing around the 2-3 and 3-4 bonds. Torsional energy levels for the calculated potential curves were also obtained. The main conclusions are: (i) the photoreaction proceeds through a "non-spectroscopic" (perp) S 1 minimum which exists also in the isolated molecule, (ii) this twisted excited species has charge transfer character (TICT), as opposed to the biradicaloid character of the "non-spectroscopic" S 1 minimum involved in the trans→cis photoisomerization of olefines (e.g., stilbene). The possible consequences on the dynamics of the excited state relaxation in non-polar solvents are envisaged.

  6. [Synthesis and crystalline structure of cis-monochloro(dimenthylsulfoxide)].

    PubMed

    Bentefrit, F; Viossat, B; Tomas, A; Nguyen Huy, D; Morgant, G

    2002-03-01

    The synthesis of cis-monochloro(dimethylsulfoxide)(metforminuro) platine(II) was investigated. It crystallizes in the monoclinic system, space group P 2(1)/c with Z=4. The cell parameters are: a=9.173(2); b=11.286( 2); c=12.556( 3) (A); b=99.69(2) degrees. The structure of this compound was refined to R=0.031 and wR=0.038 using 1461 independent reflexions with I>3 s(I). The platinum coordination is square planar, built up from one Cl, one O from the dimethylsulfoxide, and one bidentate chelating ligand (metforminure anion) via the two imine nitrogen atoms in cis position. The negative charge of the metforminure ligand ensures the electric neutrality in the complex. The crystal packing is characterized by four hydrogen bonds, one of which is bifurcated (involving Cl atom (intramolecular bonding) and O(i) (intermolecular bonding; symmetry code i: x, 3/2-y; 1/2+z).

  7. A primer on regression methods for decoding cis-regulatory logic

    SciTech Connect

    Das, Debopriya; Pellegrini, Matteo; Gray, Joe W.

    2009-03-03

    The rapidly emerging field of systems biology is helping us to understand the molecular determinants of phenotype on a genomic scale [1]. Cis-regulatory elements are major sequence-based determinants of biological processes in cells and tissues [2]. For instance, during transcriptional regulation, transcription factors (TFs) bind to very specific regions on the promoter DNA [2,3] and recruit the basal transcriptional machinery, which ultimately initiates mRNA transcription (Figure 1A). Learning cis-Regulatory Elements from Omics Data A vast amount of work over the past decade has shown that omics data can be used to learn cis-regulatory logic on a genome-wide scale [4-6]--in particular, by integrating sequence data with mRNA expression profiles. The most popular approach has been to identify over-represented motifs in promoters of genes that are coexpressed [4,7,8]. Though widely used, such an approach can be limiting for a variety of reasons. First, the combinatorial nature of gene regulation is difficult to explicitly model in this framework. Moreover, in many applications of this approach, expression data from multiple conditions are necessary to obtain reliable predictions. This can potentially limit the use of this method to only large data sets [9]. Although these methods can be adapted to analyze mRNA expression data from a pair of biological conditions, such comparisons are often confounded by the fact that primary and secondary response genes are clustered together--whereas only the primary response genes are expected to contain the functional motifs [10]. A set of approaches based on regression has been developed to overcome the above limitations [11-32]. These approaches have their foundations in certain biophysical aspects of gene regulation [26,33-35]. That is, the models are motivated by the expected transcriptional response of genes due to the binding of TFs to their promoters. While such methods have gathered popularity in the computational domain

  8. Implications of climate and land use change: Chapter 4

    USGS Publications Warehouse

    Hall, Jefferson S.; Murgueitio, Enrique; Calle, Zoraida; Raudsepp-Hearne, Ciara; Stallard, Robert F.; Balvanera, Patricia; Hall, Jefferson S.; Kirn, Vanessa; Yanguas-Fernandez, Estrella

    2015-01-01

    This chapter relates ecosystem services to climate change and land use. The bulk of the chapter focuses on ecosystem services and steepland land use in the humid Neotropics – what is lost with land-cover changed, and what is gained with various types of restoration that are sustainable given private ownership. Many case studies are presented later in the white paper. The USGS contribution relates to climate change and the role of extreme weather events in land-use planning.

  9. Chapter 16: Magnetic manipulation for force measurements in cell biology.

    PubMed

    Tim O'Brien, E; Cribb, Jeremy; Marshburn, David; Taylor, Russell M; Superfine, Richard

    2008-01-01

    Life is a mechanical process. Cells, tissues, and bodies must act within their environments to grow, divide, move, communicate, and defend themselves. The stiffness and viscosity of cells and biologic materials will vary depending upon a wide variety of variables including for example environmental conditions, activation of signaling pathways, stage of development, gene expression. By pushing and pulling cells or materials such as mucus or extracellular matrix, one can learn about their mechanical properties. By varying the conditions, signaling pathways or genetic background, one can also assess how the response of the cell or material is modulated by that pathway. Magnetic particles are available commercially in many useful sizes, magnetic contents, and surface chemistries. The variety of surface chemistries allow forces to be applied to a specimen through specific linkages such as receptors or particular proteins, allowing the biologist to ask fundamental questions about the role of those linkages in the transduction of force or motion. In this chapter, we discuss the use of a magnetic system designed to apply a wide range of forces and force patterns fully integrated into a high numerical aperture inverted fluorescence microscope. Fine, thin and flat magnetic poles allow the use of high magnification microscope objectives, and flexible software to control the direction and pattern of applied forces supports a variety of experimental situations. The system can be coupled with simple video acquisition for medium-bandwidth, two-dimensional particle tracking. Alternatively, the system can be coupled with a laser tracking and position feedback system for higher resolution, high bandwidth, three-dimensional tracking.

  10. Chapter 3: Plasma Control in ASDEX Upgrade

    SciTech Connect

    Mertens, Vitus; Raupp, Gerhard; Treutterer, Wolfgang

    2003-11-15

    In modern tokamak machines, exploration and successful development of improved plasma regimes is impossible without adequate control systems. In ASDEX Upgrade, the control tasks are performed by two systems, the continuously operating machine control and the plasma control active as long as a plasma discharge lasts. Machine control based on programmable logic controllers operates on a relatively slow timescale of {tau} = 100 ms to configure and monitor the machine's technical systems. Real-time plasma controllers run on faster cycle times of a few milliseconds to feedback (FB) control plasma shape and performance quantities. During the burn of a discharge, a real-time supervisor monitors the full technical and physical system state ({tau} = 10 ms) and applies alternate discharge program segments to optimize discharge performance or react to failures. The supervisor is fully integrated with a layered machine protection system.Plasma position and shape control in ASDEX Upgrade is particularly difficult: Since the poloidal magnetic field (PF) coils are located reactor relevant outside the toroidal magnetic field coil system and distant from the plasma, each PF coil has a global effect on all shape quantities. This makes simultaneous control of shape parameters a multivariable problem. The feedback control algorithm is based on a matrix proportional-integral-derivative method, adapted to handle saturation of coil currents, excess of coil forces, or to balance loads among coils. Control cycle time is {approx}3 ms.In parallel, the plasma performance control (sometimes called kinetic control ) acts on particle fueling and auxiliary heating systems. It consists mainly of FB loops each controlling a single variable. These circuits can be freely combined to simultaneously control a number of different plasma quantities. A clear hierarchy in the control processes allows special real-time processes to override the programmed plasma discharge feedback action: The set of

  11. The Cis-regulatory Logic of the Mammalian Photoreceptor Transcriptional Network

    PubMed Central

    Hsiau, Timothy H.-C.; Diaconu, Claudiu; Myers, Connie A.; Lee, Jongwoo; Cepko, Constance L.; Corbo, Joseph C.

    2007-01-01

    The photoreceptor cells of the retina are subject to a greater number of genetic diseases than any other cell type in the human body. The majority of more than 120 cloned human blindness genes are highly expressed in photoreceptors. In order to establish an integrative framework in which to understand these diseases, we have undertaken an experimental and computational analysis of the network controlled by the mammalian photoreceptor transcription factors, Crx, Nrl, and Nr2e3. Using microarray and in situ hybridization datasets we have produced a model of this network which contains over 600 genes, including numerous retinal disease loci as well as previously uncharacterized photoreceptor transcription factors. To elucidate the connectivity of this network, we devised a computational algorithm to identify the photoreceptor-specific cis-regulatory elements (CREs) mediating the interactions between these transcription factors and their target genes. In vivo validation of our computational predictions resulted in the discovery of 19 novel photoreceptor-specific CREs near retinal disease genes. Examination of these CREs permitted the definition of a simple cis-regulatory grammar rule associated with high-level expression. To test the generality of this rule, we used an expanded form of it as a selection filter to evolve photoreceptor CREs from random DNA sequences in silico. When fused to fluorescent reporters, these evolved CREs drove strong, photoreceptor-specific expression in vivo. This study represents the first systematic identification and in vivo validation of CREs in a mammalian neuronal cell type and lays the groundwork for a systems biology of photoreceptor transcriptional regulation. PMID:17653270

  12. Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora

    PubMed Central

    Steige, Kim A.; Laenen, Benjamin; Reimegård, Johan; Slotte, Tanja

    2017-01-01

    Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species. PMID:28096395

  13. Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora.

    PubMed

    Steige, Kim A; Laenen, Benjamin; Reimegård, Johan; Scofield, Douglas G; Slotte, Tanja

    2017-01-31

    Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species.

  14. Evaluation of 9-cis retinoic acid and mitotane as antitumoral agents in an adrenocortical xenograft model.

    PubMed

    Nagy, Zoltán; Baghy, Kornélia; Hunyadi-Gulyás, Éva; Micsik, Tamás; Nyírő, Gábor; Rácz, Gergely; Butz, Henriett; Perge, Pál; Kovalszky, Ilona; Medzihradszky, Katalin F; Rácz, Károly; Patócs, Attila; Igaz, Peter

    2015-01-01

    The available drug treatment options for adrenocortical carcinoma (ACC) are limited. In our previous studies, the in vitro activity of 9-cis retinoic acid (9-cisRA) on adrenocortical NCI-H295R cells was shown along with its antitumoral effects in a small pilot xenograft study. Our aim was to dissect the antitumoral effects of 9-cisRA on ACC in a large-scale xenograft study involving mitotane, 9-cisRA and their combination. 43 male SCID mice inoculated with NCI-H295R cells were treated in four groups (i. control, ii. 9-cisRA, iii. mitotane, iv. 9-cisRA + mitotane) for 28 days. Tumor size follow-up, histological and immunohistochemical (Ki-67) analysis, tissue gene expression microarray, quantitative real-time-PCR for the validation of microarray results and to detect circulating microRNAs were performed. Protein expression was studied by proteomics and Western-blot validation. Only mitotane alone and the combination of 9-cisRA and mitotane resulted in significant tumor size reduction. The Ki-67 index was significantly reduced in both 9-cisRA and 9-cisRA+mitotane groups. Only modest changes at the mRNA level were found: the 9-cisRA-induced overexpression of apolipoprotein A4 and down-regulation of phosphodiesterase 4A was validated. The expression of circulating hsa-miR-483-5p was significantly reduced in the combined treatment group. The SET protein was validated as being significantly down-regulated in the combined mitotane+9-cisRA group. 9-cisRA might be a helpful additive agent in the treatment of ACC in combination with mitotane. Circulating hsa-miR-483-5p could be utilized for monitoring the treatment efficacy in ACC patients, and the treatment-induced reduction in protein SET expression might raise its relevance in ACC biology.

  15. Evaluation of 9-cis retinoic acid and mitotane as antitumoral agents in an adrenocortical xenograft model

    PubMed Central

    Nagy, Zoltán; Baghy, Kornélia; Hunyadi-Gulyás, Éva; Micsik, Tamás; Nyírő, Gábor; Rácz, Gergely; Butz, Henriett; Perge, Pál; Kovalszky, Ilona; Medzihradszky, Katalin F; Rácz, Károly; Patócs, Attila; Igaz, Peter

    2015-01-01

    The available drug treatment options for adrenocortical carcinoma (ACC) are limited. In our previous studies, the in vitro activity of 9-cis retinoic acid (9-cisRA) on adrenocortical NCI-H295R cells was shown along with its antitumoral effects in a small pilot xenograft study. Our aim was to dissect the antitumoral effects of 9-cisRA on ACC in a large-scale xenograft study involving mitotane, 9-cisRA and their combination. 43 male SCID mice inoculated with NCI-H295R cells were treated in four groups (i. control, ii. 9-cisRA, iii. mitotane, iv. 9-cisRA + mitotane) for 28 days. Tumor size follow-up, histological and immunohistochemical (Ki-67) analysis, tissue gene expression microarray, quantitative real-time-PCR for the validation of microarray results and to detect circulating microRNAs were performed. Protein expression was studied by proteomics and Western-blot validation. Only mitotane alone and the combination of 9-cisRA and mitotane resulted in significant tumor size reduction. The Ki-67 index was significantly reduced in both 9-cisRA and 9-cisRA+mitotane groups. Only modest changes at the mRNA level were found: the 9-cisRA-induced overexpression of apolipoprotein A4 and down-regulation of phosphodiesterase 4A was validated. The expression of circulating hsa-miR-483-5p was significantly reduced in the combined treatment group. The SET protein was validated as being significantly down-regulated in the combined mitotane+9-cisRA group. 9-cisRA might be a helpful additive agent in the treatment of ACC in combination with mitotane. Circulating hsa-miR-483-5p could be utilized for monitoring the treatment efficacy in ACC patients, and the treatment-induced reduction in protein SET expression might raise its relevance in ACC biology. PMID:26885453

  16. Anti-tumor Properties of cis-Resveratrol Methylated Analogues in Metastatic Mouse Melanoma Cells

    PubMed Central

    Morris, Valery L.; Toseef, Tayyaba; Nazumudeen, Fathima B.; Rivoira, Christian; Spatafora, Carmela; Tringali, Corrado; Rotenberg, Susan A.

    2015-01-01

    Resveratrol (E-3,5,4’-trihydroxystilbene) is a polyphenol found in red wine that has been shown to have multiple anti-cancer properties. Although cis (Z) and trans (E) isomers of resveratrol occur in nature, the cis form is not biologically active. However, methylation at key positions of the cis form results in more potent anti-cancer properties. This study determined that synthetic cis-polymethoxystilbenes (methylated analogues of cis-resveratrol) inhibited cancer-related phenotypes of metastatic B16 F10 and non-metastatic B16 F1 mouse melanoma cells. In contrast with cis or trans-resveratrol and trans-polymethoxystilbene which were ineffective at 10 μM, cis-polymethoxystilbenes inhibited motility and proliferation of melanoma cells with low micromolar specificity (IC50 <10 μM). Inhibitory effects by cis-polymethoxystilbenes were significantly stronger with B16 F10 cells and were accompanied by decreased expression of β-tubulin and pleckstrin homology domain-interacting protein, a marker of metastatic B16 cells. Thus, cis-polymethoxystilbenes have potential as chemotherapeutic agents for metastatic melanoma. PMID:25567208

  17. Formation of cis-coniferin in cell-free extracts of Fagus grandifolia Ehrh bark

    NASA Technical Reports Server (NTRS)

    Yamamoto, E.; Inciong, E. J.; Davin, L. B.; Lewis, N. G.

    1990-01-01

    American beech (Fagus grandifolia Ehrh) bark exclusively accumulates cis-monolignols and their glucosidic conjugates; no evidence for the accumulation of trans-monolignols has been found. The glucosyltransferase from this source exhibits a very unusual substrate specificity for cis, and not trans, monolignols. This is further evidence that cis monolignols are involved in lignin formation in these plant tissues. Preliminary evidence for the existence of a novel trans-cis monolignol isomerase was obtained, in agreement with our contention that this isomerization is not photochemically mediated.

  18. Enantioselective synthesis of cis-decalins using organocatalysis and sulfonyl Nazarov reagents.

    PubMed

    Peña, Javier; Silveira-Dorta, Gastón; Moro, Rosalina F; Garrido, Narciso M; Marcos, Isidro S; Sanz, Francisca; Díez, David

    2015-04-10

    The first organocatalytic synthesis of cis-decalins using sulfonyl Nazarov reagents is reported. The Jørgensen's catalyst directs this highly enantioselective synthesis using different cyclohexenal derivatives.

  19. Enthalpy of ligand substitution in cis organopalladium complexes with monodentate ligands.

    PubMed

    Salas, Gorka; Casares, Juan A; Espinet, Pablo

    2009-10-21

    The enthalpy for the substitution reaction cis-[PdRf(2)(THF)(2)] + 2 L -->cis-[PdRf(2)L(2)] + 2THF (THF = tetrahydrofuran) has been measured in THF by calorimetric methods for Rf = 3,5-dichloro-2,4,6-trifluorophenyl, L = PPh(3), AsPh(3), SbPh(3), PMePh(2), PCyPh(2), PMe(3), AsMePh(2), or L(2) = dppe (1,2-bis(diphenylphosphino)ethane), dppf (1,1'-bis(diphenylphosphino)ferrocene). The values determined show that the substitution enthalpy has a strong dependence on the electronic and steric properties of the ligand. The study of the consecutive substitution reactions cis-[PdRf(2)(THF)(2)] + L -->cis-[PdRf(2)L(THF)] + THF, and cis-[PdRf(2)L(THF)] + L -->cis-[PdRf(2)L(2)] + THF has been carried our for L = PPh(3) and L = PCyPh(2). The first substitution is clearly more favorable for the bulkier leaving ligand, but the second gives practically the same DeltaH value for both cases, indicating that the differences in steric hindrance happen to compensate the electronic differences for both ligands. The X-ray structures of cis-[PdRf(2)(PMePh(2))(2)], cis-[PdRf(2)(dppe)] and cis-[PdRf(2)(dppf)] are reported.

  20. Annual Report of the Integrated Status and Effectiveness Monitoring Program: Fiscal Year 2008

    SciTech Connect

    Terraqua, Inc.

    2009-07-20

    This document was created as an annual report detailing the accomplishments of the Integrated Status and Effectiveness Monitoring Program (ISEMP) in the Upper Columbia Basin in fiscal year 2008. The report consists of sub-chapters that reflect the various components of the program. Chapter 1 presents a report on programmatic coordination and accomplishments, and Chapters 2 through 4 provide a review of how ISEMP has progressed during the 2008 fiscal year in each of the pilot project subbasins: the John Day (Chapter 2), Wenatchee/Entiat (Chapter 3) and Salmon River (Chapter 4). Chapter 5 presents a report on the data management accomplishments in 2008.

  1. Au nanoparticle scaffolds modulating intermolecular interactions among the conjugated azobenzenes chemisorbed on curved surfaces: tuning the kinetics of cis-trans isomerisation

    NASA Astrophysics Data System (ADS)

    Raimondo, Corinna; Kenens, Bart; Reinders, Federica; Mayor, Marcel; Uji-I, Hiroshi; Samorì, Paolo

    2015-08-01

    π-π Intermolecular interactions among adjacent conjugated azobenzenes chemisorbed on (non-)flat Au surfaces can be tuned by varying the curvature of the Au nanoparticles. Here we show that such interactions rule the thermal cis-trans isomerization kinetics, towards a better control on the azobenzene bistability for its optimal integration as a responsive material.π-π Intermolecular interactions among adjacent conjugated azobenzenes chemisorbed on (non-)flat Au surfaces can be tuned by varying the curvature of the Au nanoparticles. Here we show that such interactions rule the thermal cis-trans isomerization kinetics, towards a better control on the azobenzene bistability for its optimal integration as a responsive material. Electronic supplementary information (ESI) available: Physico-chemical characterization of the different sizes of nanoparticles, UV-Vis, Surface Enhanced Raman Spectroscopy (SERS), materials and methods. See DOI: 10.1039/c5nr03688g

  2. Air cleaners for indoor-air-pollution control (Chapter 10). Book chapter, Feb 89-Jul 90

    SciTech Connect

    Viner, A.S.; Ramanathan, K.; Hanley, J.T.; Smith, D.D.; Ensor, D.S.

    1991-01-01

    The chapter describes an experimental study to evaluate performance characteristics of currently available controls for indoor air pollutants, including both particles and gases. The study evaluated the particle-size-dependent collection efficiency of seven commercially available devices for particulate control: a common furnace filter, four industrial filters, and two electronic air cleaners (EACs). The furnance filter had negligible effect on particles with diameters between 0.1 and 1 micrometer. The industrial filters, with ASHRAE ratings of 95, 85, 65, and 40% showed minimum efficiency at about 0.1 micrometer, which was substantially less than the ASHRAE efficiency. One EAC, essentially a furnance filter with a high-voltage electrode, reached a maximum efficiency of 30% at low flowrates (7 cu m/min); however, it had a negligible effect at higher flowrates. The other EAC, similar to an industrial ESP, showed efficiencies of 80-90% over the entire size range at low to moderate flowrates. At the highest flowrate, a minimum efficiency was detected at 0.35 micrometer. The study also evaluated the suitability of commerically available carbon-based sorbents (wood, coal, and coconut) for removing low concentrations of volatile organic compounds (benzene, acetaldehyde, and 1,1,1-trichloroethane).

  3. Distant cis Regulatory Elements in Human Skeletal Muscle Differentiation

    PubMed Central

    McCord, Rachel Patton; Zhou, Vicky W.; Yuh, Tiffany; Bulyk, Martha L.

    2011-01-01

    Identifying gene regulatory elements and their target genes in human cells remains a significant challenge. Despite increasing evidence of physical interactions between distant regulatory elements and gene promoters in mammalian cells, many studies consider only promoter-proximal regulatory regions. We identify putative cis-regulatory modules (CRMs) in human skeletal muscle differentiation by combining myogenic TF binding data before and after differentiation with histone modification data in myoblasts. CRMs that are distant (>20 kb) from muscle gene promoters are common and are more likely than proximal promoter regions to show differentiation-specific changes in myogenic TF binding. We find that two of these distant CRMs, known to activate transcription in differentiating myoblasts, interact physically with gene promoters (PDLIM3 and ACTA1) during differentiation. Our results highlight the importance of considering distal CRMs in investigations of mammalian gene regulation and support the hypothesis that distant CRM-promoter looping contacts are a general mechanism of gene regulation. PMID:21907276

  4. Fungal regulatory evolution: cis and trans in the balance

    PubMed Central

    Thompson, Dawn Anne; Regev, Aviv

    2009-01-01

    Regulatory divergence is likely a major driving force in evolution. Comparative genomics is being increasingly used to infer the evolution of gene regulation. Ascomycota fungi are uniquely suited among eukaryotes for regulatory evolution studies, due to broad phylogenetic scope, many sequenced genomes, and tractability of genomic analysis. Here we review recent advances in the identification of the contribution of cis and trans factors to expression divergence. Whereas current strategies have led to the discovery of surprising signatures and mechanisms, we still understand very little about the adaptive role of regulatory evolution. Empirical studies including experimental evolution, comparative functional genomics and hybrid and engineered strains are showing early promise toward deciphering the contribution of regulatory divergence to adaptation. PMID:19914250

  5. Mechanism of cis-prenyltransferase reaction probed by substrate analogues.

    PubMed

    Lu, Yen-Pin; Liu, Hon-Ge; Teng, Kuo-Hsun; Liang, Po-Huang

    2010-10-01

    Undecaprenyl pyrophosphate synthase (UPPS) is a cis-type prenyltransferases which catalyzes condensation reactions of farnesyl diphosphate (FPP) with eight isopentenyl pyrophosphate (IPP) units to generate C(55) product. In this study, we used two analogues of FPP, 2-fluoro-FPP and [1,1-(2)H(2)]FPP, to probe the reaction mechanism of Escherichia coli UPPS. The reaction rate of 2-fluoro-FPP with IPP under single-turnover condition is similar to that of FPP, consistent with the mechanism without forming a farnesyl carbocation intermediate. Moreover, the deuterium secondary KIE of 0.985±0.022 measured for UPPS reaction using [1,1-(2)H(2)]FPP supports the associative transition state. Unlike the sequential mechanism used by trans-prenyltransferases, our data demonstrate E. coli UPPS utilizes the concerted mechanism.

  6. TFM-Explorer: mining cis-regulatory regions in genomes

    PubMed Central

    Tonon, Laurie; Varré, Jean-Stéphane

    2010-01-01

    DNA-binding transcription factors (TFs) play a central role in transcription regulation, and computational approaches that help in elucidating complex mechanisms governing this basic biological process are of great use. In this perspective, we present the TFM-Explorer web server that is a toolbox to identify putative TF binding sites within a set of upstream regulatory sequences of genes sharing some regulatory mechanisms. TFM-Explorer finds local regions showing overrepresentation of binding sites. Accepted organisms are human, mouse, rat, chicken and drosophila. The server employs a number of features to help users to analyze their data: visualization of selected binding sites on genomic sequences, and selection of cis-regulatory modules. TFM-Explorer is available at http://bioinfo.lifl.fr/TFM. PMID:20522509

  7. Twine: display and analysis of cis-regulatory modules

    PubMed Central

    Pearson, Joseph C.; Crews, Stephen T.

    2013-01-01

    Summary: Many algorithms analyze enhancers for overrepresentation of known and novel motifs, with the goal of identifying binding sites for direct regulators of gene expression. Twine is a Java GUI with multiple graphical representations (‘Views’) of enhancer alignments that displays motifs, as IUPAC consensus sequences or position frequency matrices, in the context of phylogenetic conservation to facilitate cis-regulatory element discovery. Thresholds of phylogenetic conservation and motif stringency can be altered dynamically to facilitate detailed analysis of enhancer architecture. Views can be exported to vector graphics programs to generate high-quality figures for publication. Twine can be extended via Java plugins to manipulate alignments and analyze sequences. Availability: Twine is freely available as a compiled Java .jar package or Java source code at http://labs.bio.unc.edu/crews/twine/. Contact: steve_crews@unc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23658420

  8. Hearing on H.R. 6: Reform Proposals for Chapter 1. Hearing before the Subcommittee on Elementary, Secondary, and Vocational Education of the Committee on Education and Labor. House of Representatives, One Hundred Third Congress, First Session.

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. House Committee on Education and Labor.

    This report presents testimony and prepared statements from witnesses who addressed the reauthorization of the Elementary and Secondary Education Act and the reform of Chapter 1. The primary question addressed at these hearings concerns how Chapter 1 can be reformed to better integrate and serve the needs of limited English-proficient students.…

  9. Options for Staging Orbits in Cis-Lunar Space

    NASA Technical Reports Server (NTRS)

    Whitley, Ryan; Martinez, Roland

    2015-01-01

    NASA has been studying options to conduct missions beyond Low Earth Orbit, but within the Earth-Moon system, in preparation for deep space exploration including human missions to Mars. Referred to as the Proving Ground, this arena of exploration activities will enable the development of human spaceflight systems and operations to satisfy future exploration objectives beyond the cis-lunar environment. One option being considered includes the deployment of a habitable element or elements, which could be used as a central location for aggregation of supplies and resources for human missions in cis-lunar space and beyond. Characterizing candidate orbit locations for this asset and the impacts on system design and mission operations is important in the overall assessment of the options being considered. The orbits described in this paper were initially selected by taking advantage of previous studies conducted by NASA and the work of other authors. In this paper orbits are assessed for their relative attractiveness based on various factors. First, a set of constraints related to the capability of the combined Orion and SLS system to deliver humans and cargo to and from the orbit are evaluated. Second, the ability to support potential lunar surface activities is considered. Finally, deployed assets intended to spend multiple years in the Proving Ground would ideally require minimal station keeping costs to reduce the mass budget allocated to this function. Additional mission design drivers include potential for uninterrupted communication with deployed assets, thermal, communications, and other operational implications. The results of the characterization and evaluation of the selected orbits indicate a Near Rectilinear Orbit (NRO) is an attractive candidate as an aggregation point or staging location for operations. In this paper, the NRO is further described in terms which balance a number of key attributes that favor a variety of mission classes to meet multiple

  10. Options for Staging Orbits in Cis-Lunar Space

    NASA Technical Reports Server (NTRS)

    Martinez, Roland; Whitley, Ryan

    2016-01-01

    NASA has been studying options to conduct missions beyond Low Earth Orbit, but within the Earth-Moon system, in preparation for deep space exploration including human missions to Mars. Referred to as the Proving Ground, this arena of exploration activities will enable the development of human spaceflight systems and operations to satisfy future exploration objectives beyond the cis-lunar environment. One option being considered includes the deployment of a habitable element or elements, which could be used as a central location for aggregation of supplies and resources for human missions in cis-lunar space and beyond. Characterizing candidate orbit locations for this asset and the impacts on system design and mission operations is important in the overall assessment of the options being considered. The orbits described in this paper were initially selected by taking advantage of previous studies conducted by NASA and the work of other authors. In this paper orbits are assessed for their relative attractiveness based on various factors. A set of constraints related to the capability of the combined Orion and SLS system to deliver humans and cargo to and from the orbit are evaluated. Deployed assets intended to spend multiple years in the Proving Ground would ideally require minimal station keeping costs to reduce the mass budget allocated to this function. Additional mission design drivers include eclipse frequency, potential for uninterrupted communication with deployed assets, thermal, attitude control, communications, and other operational implications. Also the ability to support potential lunar surface activities and excursion missions beyond Earth-Moon space is considered. The results of the characterization and evaluation of the selected orbits indicate a Near Rectilinear Orbit (NRO) is an attractive candidate as an aggregation point or staging location for operations. In this paper, the NRO is further described in terms which balance a number of key

  11. Current Status and Future Development of Structuring and Modeling Intelligent Appearing Motion. Chapter 11

    NASA Technical Reports Server (NTRS)

    Alexander, Thomas; Ellis, Stephen R.

    2007-01-01

    The two topics covered by this symposium were intelligent appearing motion and Virtual Environments (VE). Both of these are broad research areas with enough content to fill large conferences. Their intersection has become important due to conceptual and technological advances enabling the introduction of intelligent appearing motion into Virtual Environments. This union brings new integration challenges and opportunities, some of which were examined at this symposium. This chapter was inspired by the contributions of several of the conference participants, but is not a complete review of all presentations. It will hopefully serve as a basis for formulating a new approach to the understanding of motion within VE

  12. Organocatalytic, Diastereo- and Enantioselective Synthesis of Nonsymmetric cis-Stilbene Diamines: A Platform for the Preparation of Single-Enantiomer cis-Imidazolines for Protein–Protein Inhibition

    PubMed Central

    2015-01-01

    The finding by scientists at Hoffmann-La Roche that cis-imidazolines could disrupt the protein–protein interaction between p53 and MDM2, thereby inducing apoptosis in cancer cells, raised considerable interest in this scaffold over the past decade. Initial routes to these small molecules (i.e., Nutlin-3) provided only the racemic form, with enantiomers being enriched by chromatographic separation using high-pressure liquid chromatography (HPLC) and a chiral stationary phase. Reported here is the first application of an enantioselective aza-Henry approach to nonsymmetric cis-stilbene diamines and cis-imidazolines. Two novel mono(amidine) organocatalysts (MAM) were discovered to provide high levels of enantioselection (>95% ee) across a broad range of substrate combinations. Furthermore, the versatility of the aza-Henry strategy for preparing nonsymmetric cis-imidazolines is illustrated by a comparison of the roles of aryl nitromethane and aryl aldimine in the key step, which revealed unique substrate electronic effects providing direction for aza-Henry substrate–catalyst matching. This method was used to prepare highly substituted cis-4,5-diaryl imidazolines that project unique aromatic rings, and these were evaluated for MDM2-p53 inhibition in a fluorescence polarization assay. The diversification of access to cis-stilbene diamine-derived imidazolines provided by this platform should streamline their further development as chemical tools for disrupting protein–protein interactions. PMID:25017623

  13. Mirror Lake: Past, present and future: Chapter 6

    USGS Publications Warehouse

    Likens, Gene E.; LaBaugh, James W.; Winter, Thomas C.; Likens, Gene E.

    2009-01-01

    This chapter discusses the hydrological and biogeochemical characteristics of Mirror Lake and the changes that resulted from air-land-water interactions and human activities. Since the formation of Mirror Lake, both the watershed and the lake have undergone many changes, such as vegetation development and basin filling. These changes are ongoing, and Mirror Lake is continuing along an aging pathway and ultimately, it will fill with sediment and no longer be a lake. The chapter also identifies major factors that affected the hydrology and biogeochemistry of Mirror Lake: acid rain, atmospheric deposition of lead and other heavy metals, increased human settlement around the lake, the construction of an interstate highway through the watershed of the Northeast Tributary, the construction of an access road through the West and Northeast watersheds to the lake, and climate change. The chapter also offers future recommendations for management and protection of Mirror Lake.

  14. Chapter A2. Selection of Equipment for Water Sampling

    USGS Publications Warehouse

    Wilde, Franceska D.; Radtke, Dean B.; Gibs, Jacob; Iwatsubo, Rick T.

    1998-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) describes protocols and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This chapter of the manual addresses the selection of equipment commonly used by USGS personnel to collect and process water-quality samples. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be posted on the World Wide Web on the USGS page 'National Field Manual for the Collection of Water-Quality Data.' The URL for this page is http://pubs.water.usgs.gov/twri9A/ (accessed March 20, 2003).

  15. Planning "and" Sprinting: Use of a Hybrid Project Management Methodology within a CIS Capstone Course

    ERIC Educational Resources Information Center

    Baird, Aaron; Riggins, Frederick J.

    2012-01-01

    An increasing number of information systems projects in industry are managed using hybrid project management methodologies, but this shift in project management methods is not fully represented in our CIS curriculums. CIS capstone courses often include an applied project that is managed with traditional project management methods (plan first,…

  16. The Influence of 13-cis Retinoic Acid on Human Meibomian Gland Epithelial Cells

    PubMed Central

    Ding, Juan; Kam, Wendy R.; Dieckow, Julia; Sullivan, David A.

    2013-01-01

    Purpose. Meibomian gland dysfunction (MGD) is a primary cause of dry eye disease. One of the risk factors for MGD is exposure to 13-cis retinoic acid (13-cis RA), a metabolite of vitamin A. However, the mechanism is not well understood. We hypothesize that 13-cis RA inhibits cell proliferation, promotes cell death, alters gene and protein expressions, and attenuates cell survival pathways in human meibomian gland epithelial cells. Methods. To test our hypotheses, immortalized human meibomian gland epithelial cells were cultured with or without 13-cis RA for varying doses and time. Cell proliferation, cell death, gene expression, and proteins involved in proliferation/survival and inflammation were evaluated. Results. We found that 13-cis RA inhibited cell proliferation, induced cell death, and significantly altered the expression of 6726 genes, including those involved in cell proliferation, cell death, differentiation, keratinization, and inflammation, in human meibomian gland epithelial cells. Further, 13-cis RA also reduced the phosphorylation of Akt and increased the generation of interleukin-1β and matrix metallopeptidase 9. Conclusions. Exposure to 13-cis RA inhibits cell proliferation, increases cell death, alters gene expression, changes signaling pathways, and promotes inflammatory mediator and protease expression in meibomian gland epithelial cells. These effects may be responsible, at least in part, for the 13-cis RA–related induction of MGD. PMID:23722388

  17. A CIS (Clinical Information System) Quality Evaluation Tool for Nursing Care Services

    ERIC Educational Resources Information Center

    Lee, Seon Ah

    2010-01-01

    The purpose of this study was to develop a tool to evaluate the quality of a clinical information system (CIS) conceived by nurses and conduct a pilot test with the developed tool as an initial assessment. CIS quality is required for successful implementation in information technology (IT) environments. The study started with the realization that…

  18. Cloning, Expression, and Characterization of cis-Polyprenyl Diphosphate Synthase from the Thermoacidophilic Archaeon Sulfolobus acidocaldarius

    PubMed Central

    Hemmi, Hisashi; Yamashita, Satoshi; Shimoyama, Takefumi; Nakayama, Toru; Nishino, Tokuzo

    2001-01-01

    cis-polyprenyl diphosphate synthases are involved in the biosynthesis of the glycosyl carrier lipid in most organisms. However, only little is known about this enzyme of archaea. In this report, we isolated the gene of cis-polyprenyl diphosphate synthase from a thermoacidophilic archaeon, Sulfolobus acidocaldarius, and characterized the recombinant enzyme. PMID:11114943

  19. Columbia River Coordinated Information System (CIS), 1992-1993 Annual Report.

    SciTech Connect

    Rowe, Mike; Roger, Phillip B.; O'Connor, Dick

    1993-11-01

    The purposes of this report are to: (1) describe the project to date; (2) to document the work and accomplishments of the (CIS) project for Fiscal Year 1993; and (3) to provide a glimpse of future project direction. The concept of a Coordinated Information System (CIS) as an approach to meeting the growing needs for regionally standardized anadromous fish information.

  20. Measurement and modeling of unsaturated hydraulic conductivity: Chapter 21

    USGS Publications Warehouse

    Perkins, Kim S.; Elango, Lakshmanan

    2011-01-01

    This chapter will discuss, by way of examples, various techniques used to measure and model hydraulic conductivity as a function of water content, K(). The parameters that describe the K() curve obtained by different methods are used directly in Richards’ equation-based numerical models, which have some degree of sensitivity to those parameters. This chapter will explore the complications of using laboratory measured or estimated properties for field scale investigations to shed light on how adequately the processes are represented. Additionally, some more recent concepts for representing unsaturated-zone flow processes will be discussed.

  1. CHAPTER 7. BERYLLIUM ANALYSIS BY NON-PLASMA BASED METHODS

    SciTech Connect

    Ekechukwu, A

    2009-04-20

    The most common method of analysis for beryllium is inductively coupled plasma atomic emission spectrometry (ICP-AES). This method, along with inductively coupled plasma mass spectrometry (ICP-MS), is discussed in Chapter 6. However, other methods exist and have been used for different applications. These methods include spectroscopic, chromatographic, colorimetric, and electrochemical. This chapter provides an overview of beryllium analysis methods other than plasma spectrometry (inductively coupled plasma atomic emission spectrometry or mass spectrometry). The basic methods, detection limits and interferences are described. Specific applications from the literature are also presented.

  2. The Western Aeronautical Test Range. Chapter 10 Tools

    NASA Technical Reports Server (NTRS)

    Knudtson, Kevin; Park, Alice; Downing, Robert; Sheldon, Jack; Harvey, Robert; Norcross, April

    2011-01-01

    The Western Aeronautical Test Range (WATR) staff at the NASA Dryden Flight Research Center is developing a translation software called Chapter 10 Tools in response to challenges posed by post-flight processing data files originating from various on-board digital recorders that follow the Range Commanders Council Inter-Range Instrumentation Group (IRIG) 106 Chapter 10 Digital Recording Standard but use differing interpretations of the Standard. The software will read the date files regardless of the vendor implementation of the source recorder, displaying data, identifying and correcting errors, and producing a data file that can be successfully processed post-flight

  3. Cis-9, trans-11 and trans-10, cis-12 CLA mixture does not change body composition, induces insulin resistance and increases serum HDL cholesterol level in rats.

    PubMed

    de Almeida, Mariana Macedo; de Souza, Yamara Oliveira; Dutra Luquetti, Sheila Cristina Potente; Sabarense, Céphora Maria; do Amaral Corrêa, José Otávio; da Conceição, Ellen Paula Santos; Lisboa, Patrícia Cristina; de Moura, Egberto Gaspar; Andrade Soares, Sara Malaguti; Moura Gualberto, Ana Cristina; Gameiro, Jacy; da Gama, Marco Antônio Sundfeld; Ferraz Lopes, Fernando César; González Garcia, Raúl Marcel

    2015-01-01

    Synthetic supplements of conjugated linoleic acid (CLA) containing 50:50 mixture of cis-9, trans-11 and trans-10, cis-12 CLA isomers have been commercialized in some places for reducing body fat. However the safety of this CLA mixture is controversial and in some countries the CLA usage as food supplement is not authorized. Changes in insulinemic control and serum lipids profile are potential negative effects related to consumption of CLA mixture. The present study aimed to evaluate the effects of a diet containing mixture of cis-9, trans-11 and trans-10, cis-12 CLA on prevention of obesity risk as well as on potential side effects such as insulin resistance and dyslipidemia in Wistar rats. Thirty male Wistar rats were randomly assigned to the following dietary treatments (n=10/group), for 60 days: Normolipidic Control (NC), diet containing 4.0% soybean oil (SO); High Fat-Control (HF-C), diet containing 24.0% SO; High Fat-synthetic CLA (HF-CLA), diet containing 1.5% of an isomeric CLA mixture (Luta-CLA 60) and 22.5% SO. Luta-CLA 60 (BASF) contained nearly 60% of CLA (cis-9, trans-11 and trans-10, cis-12 CLA at 50:50 ratio). The HF-CLA diet contained 0.3% of each CLA isomer. HF-CLA diet had no effect on dietary intake and body composition. HF-CLA-fed rats had lower levels of PPARγ protein in retroperitoneal adipose tissue, hyperinsulinemia compared to HF-C-fed rats, hyperglycemia compared to NC-fed rats while no differences in glycemia were observed between NC and HF-C groups, increased HOMA index and higher levels of serum HDL cholesterol. Thus, feeding rats with a high fat diet containing equal parts of cis-9, trans-11 and trans-10, cis-12 CLA isomers had no effect on body composition and induced insulin resistance. Despite HF-CLA-fed rats had increased serum HDL cholesterol levels, caution should be taken before synthetic supplements containing cis-9, trans-11 and trans-10, cis-12 CLA are recommended as a nutritional strategy for weight management.

  4. Cis-Golgi cisternal assembly and biosynthetic activation occur sequentially in plants and algae.

    PubMed

    Donohoe, Bryon S; Kang, Byung-Ho; Gerl, Mathias J; Gergely, Zachary R; McMichael, Colleen M; Bednarek, Sebastian Y; Staehelin, L Andrew

    2013-05-01

    The cisternal progression/maturation model of Golgi trafficking predicts that cis-Golgi cisternae are formed de novo on the cis-side of the Golgi. Here we describe structural and functional intermediates of the cis cisterna assembly process in high-pressure frozen algae (Scherffelia dubia, Chlamydomonas reinhardtii) and plants (Arabidopsis thaliana, Dionaea muscipula; Venus flytrap) as determined by electron microscopy, electron tomography and immuno-electron microscopy techniques. Our findings are as follows: (i) The cis-most (C1) Golgi cisternae are generated de novo from cisterna initiators produced by the fusion of 3-5 COPII vesicles in contact with a C2 cis cisterna. (ii) COPII vesicles fuel the growth of the initiators, which then merge into a coherent C1 cisterna. (iii) When a C1 cisterna nucleates its first cisterna initiator it becomes a C2 cisterna. (iv) C2-Cn cis cisternae grow through COPII vesicle fusion. (v) ER-resident proteins are recycled from cis cisternae to the ER via COPIa-type vesicles. (vi) In S. dubia the C2 cisternae are capable of mediating the self-assembly of scale protein complexes. (vii) In plants, ∼90% of native α-mannosidase I localizes to medial Golgi cisternae. (viii) Biochemical activation of cis cisternae appears to coincide with their conversion to medial cisternae via recycling of medial cisterna enzymes. We propose how the different cis cisterna assembly intermediates of plants and algae may actually be related to those present in the ERGIC and in the pre-cis Golgi cisterna layer in mammalian cells.

  5. Cis-Golgi cisternal assembly and biosynthetic activation occur sequentially in plants and algae

    PubMed Central

    Donohoe, Bryon S.; Kang, Byung-Ho; Gerl, Mathias J.; Gergely, Zachary R.; McMichael, Colleen M.; Bednarek, Sebastian Y.; Staehelin, L. Andrew

    2013-01-01

    The cisternal progression/maturation model of Golgi trafficking predicts that cis-Golgi cisternae are formed de novo on the cis-side of the Golgi. Here we describe structural and functional intermediates of the cis cisterna assembly process in high-pressure frozen algae (Scherffelia dubia, Chlamydomonas reinhardtii) and plants (Arabidopsis thaliana, Dionaea muscipula; Venus Flytrap) as determined by electron microscopy, electron tomography and immuno-electron microscopy techniques. Our findings are as follows: (1) The cis-most (C1) Golgi cisternae are generated de novo from cisterna initiators produced by the fusion of 3–5 COPII vesicles in contact with a C2 cis cisterna. (2) COPII vesicles fuel the growth of the initiators, which then merge into a coherent C1 cisterna. (3) When a C1 cisterna nucleates its first cisterna initiator it becomes a C2 cisterna. (4) C2-Cn cis cisternae grow through COPII vesicle fusion. (5) ER-resident proteins are recycled from cis cisternae to the ER via COPIa-type vesicles. (6) In S. dubia the C2 cisternae are capable of mediating the self-assembly of scale protein complexes. (7) In plants, ~90% of native α-mannosidase I localizes to medial Golgi cisternae. (8) Biochemical activation of cis cisternae appears to coincide with their conversion to medial cisternae via recycling of medial cisterna enzymes. We propose how the different cis cisterna assembly intermediates of plants and algae may actually be related to those present in the ERGIC and in the pre-cis Golgi cisterna layer in mammalian cells. PMID:23369235

  6. 9-cis β-Carotene Increased Cholesterol Efflux to HDL in Macrophages

    PubMed Central

    Bechor, Sapir; Zolberg Relevy, Noa; Harari, Ayelet; Almog, Tal; Kamari, Yehuda; Ben-Amotz, Ami; Harats, Dror; Shaish, Aviv

    2016-01-01

    Cholesterol efflux from macrophages is a key process in reverse cholesterol transport and, therefore, might inhibit atherogenesis. 9-cis-β-carotene (9-cis-βc) is a precursor for 9-cis-retinoic-acid (9-cis-RA), which regulates macrophage cholesterol efflux. Our objective was to assess whether 9-cis-βc increases macrophage cholesterol efflux and induces the expression of cholesterol transporters. Enrichment of a mouse diet with βc from the alga Dunaliella led to βc accumulation in peritoneal macrophages. 9-cis-βc increased the mRNA levels of CYP26B1, an enzyme that regulates RA cellular levels, indicating the formation of RA from βc in RAW264.7 macrophages. Furthermore, 9-cis-βc, as well as all-trans-βc, significantly increased cholesterol efflux to high-density lipoprotein (HDL) by 50% in RAW264.7 macrophages. Likewise, food fortification with 9-cis-βc augmented cholesterol efflux from macrophages ex vivo. 9-cis-βc increased both the mRNA and protein levels of ABCA1 and apolipoprotein E (APOE) and the mRNA level of ABCG1. Our study shows, for the first time, that 9-cis-βc from the diet accumulates in peritoneal macrophages and increases cholesterol efflux to HDL. These effects might be ascribed to transcriptional induction of ABCA1, ABCG1, and APOE. These results highlight the beneficial effect of βc in inhibition of atherosclerosis by improving cholesterol efflux from macrophages. PMID:27447665

  7. Application of CIS to high-efficiency PV module fabrication. Phase 3 final technical report

    SciTech Connect

    Basol, B M; Kapur, V K; Leidholm, C R; Halani, A; Roe, R; Norsworthy, G

    1998-08-01

    During this research period, researchers at International Solar Electric Technology (ISET) concentrated their efforts on three different areas of research. Within the National CIS R and D Team, ISET participated in the substrate/Mo interactions working group and investigated issues such as Na diffusion from the soda-lime glass substrate into the Mo layers and CIS films. Researchers determined that the Na content within the Mo layers was not a strong function of the nature of the Mo film. However, they found that diffusion through the Mo layers was a function of the Mo film characteristics as well as a very strong function of the CIS growth process itself. Researchers showed conclusively that the Na resided on the grain boundaries of CIS layers. Another team activity involved evaluation of CdS-free CIS solar cells. ZnO/CIS junctions prepared by the two-stage process showed light-soaking effects. Cells left under illumination improved in efficiency and were similar to the CdS/CIS junctions. After storage in the dark, however, efficiency deteriorated greatly for the ZnO/CIS device, most of the decline coming from the open-circuit voltage values. Much of the effort during this period was spent on developing a low-cost, non-vacuum CIS deposition technique. The method developed involves particulate deposition and formation of precursor layers followed by the conversion of these layers into CIS. Test modules of 40--60 cm{sup 2} were adapted to understand the issues involved in this novel technology. At the present time, the submodule efficiencies are 6--7%. Single-cell efficiencies are in the 10--13% range.

  8. 9-cis β-Carotene Increased Cholesterol Efflux to HDL in Macrophages.

    PubMed

    Bechor, Sapir; Zolberg Relevy, Noa; Harari, Ayelet; Almog, Tal; Kamari, Yehuda; Ben-Amotz, Ami; Harats, Dror; Shaish, Aviv

    2016-07-19

    Cholesterol efflux from macrophages is a key process in reverse cholesterol transport and, therefore, might inhibit atherogenesis. 9-cis-β-carotene (9-cis-βc) is a precursor for 9-cis-retinoic-acid (9-cis-RA), which regulates macrophage cholesterol efflux. Our objective was to assess whether 9-cis-βc increases macrophage cholesterol efflux and induces the expression of cholesterol transporters. Enrichment of a mouse diet with βc from the alga Dunaliella led to βc accumulation in peritoneal macrophages. 9-cis-βc increased the mRNA levels of CYP26B1, an enzyme that regulates RA cellular levels, indicating the formation of RA from βc in RAW264.7 macrophages. Furthermore, 9-cis-βc, as well as all-trans-βc, significantly increased cholesterol efflux to high-density lipoprotein (HDL) by 50% in RAW264.7 macrophages. Likewise, food fortification with 9-cis-βc augmented cholesterol efflux from macrophages ex vivo. 9-cis-βc increased both the mRNA and protein levels of ABCA1 and apolipoprotein E (APOE) and the mRNA level of ABCG1. Our study shows, for the first time, that 9-cis-βc from the diet accumulates in peritoneal macrophages and increases cholesterol efflux to HDL. These effects might be ascribed to transcriptional induction of ABCA1, ABCG1, and APOE. These results highlight the beneficial effect of βc in inhibition of atherosclerosis by improving cholesterol efflux from macrophages.

  9. Assembly and disassembly of the Golgi complex: two processes arranged in a cis-trans direction

    PubMed Central

    1992-01-01

    We have studied the disassembly and assembly of two morphologically and functionally distinct parts of the Golgi complex, the cis/middle and trans cisterna/trans network compartments. For this purpose we have followed the redistribution of three cis/middle- (GMPc-1, GMPc-2, MG 160) and two trans- (GMPt-1 and GMPt-2) Golgi membrane proteins during and after treatment of normal rat kidney (NRK) cells with brefeldin A (BFA). BFA induced complete disassembly of the cis/middle- and trans- Golgi complex and translocation of GMPc and GMPt to the ER. Cells treated for short times (3 min) with BFA showed extensive disorganization of both cis/middle- and trans-Golgi complexes. However, complete disorganization of the trans part required much longer incubations with the drug. Upon removal of BFA the Golgi complex was reassembled by a process consisting of three steps: (a) exist of cis/middle proteins from the ER and their accumulation into vesicular structures scattered throughout the cytoplasm; (b) gradual relocation and accumulation of the trans proteins in the vesicles containing the cis/middle proteins; and (c) assembly of the cisternae, and reconstruction of the Golgi complex within an area located in the vicinity of the centrosome from which the ER was excluded. Reconstruction of the cis/middle-Golgi complex occurred under temperature conditions inhibitory of the reorganization of the trans- Golgi complex, and was dependent on microtubules. Reconstruction of the trans-Golgi complex, disrupted with nocodazole after selective fusion of the cis/middle-Golgi complex with the ER, occurred after the release of cis/middle-Golgi proteins from the ER and the assembly of the cis/middle cisternae. PMID:1730750

  10. Stock Summary Reports for Columbia River Anadromous Salmonids, Volume 1; Oregon Subbasins Below Bonneville Dam, 1992 CIS Summary Report.

    SciTech Connect

    Olsen, Eric; Pierce, Paige; Hatch, Keith

    1993-05-01

    An essential component of the effort to rebuild the Columbia Basin's anadromous fish resources is that available information and experience be organized and shared among numerous organizations and individuals. Past experience and knowledge must form the basis for actions into the future. Much of this knowledge exists only in unpublished form in agency and individual files. Even that information which is published in the form of technical and contract reports receives only limited distribution and is often out of print and unavailable after a few years. Only a small fraction of the basin's collective knowledge is captured in permanent and readily available databases (such as the Northwest Environmental Database) or in recognized journals. State, tribal, and federal fishery managers have recognized these information management problems and have committed to a program, the Coordinated Information System Project, to capture and share more easily the core data and other information upon which management decisions are based. That project has completed scoping and identification of key information needs and development of a project plan. Work performed under the CIS project will be coordinated with and extend information contained in the Northwest Environmental Database. Construction of prototype systems will begin in Phase 3. This report is one in a series of seven describing the results of the Coordinated Information System scoping and needs identification phase. A brief description of each of these reports follows. This report (Roger 1992) summarizes and integrates the results of the next five reports and relates them to deliverables identified in the Phase II cooperative agreement. Broader issues of organization and operation which are not appropriate for the more focused reports are also discussed. This report should be viewed as an executive summary for the CIS project to date. If one wants a quick overview of the CIS project, this report and the project plan will

  11. 24 CFR 300.1 - Scope of chapter.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 2 2012-04-01 2012-04-01 false Scope of chapter. 300.1 Section 300.1 Housing and Urban Development Regulations Relating to Housing and Urban Development (Continued) GOVERNMENT NATIONAL MORTGAGE ASSOCIATION, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT GENERAL § 300.1...

  12. 24 CFR 300.1 - Scope of chapter.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 2 2011-04-01 2011-04-01 false Scope of chapter. 300.1 Section 300.1 Housing and Urban Development Regulations Relating to Housing and Urban Development (Continued) GOVERNMENT NATIONAL MORTGAGE ASSOCIATION, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT GENERAL § 300.1...

  13. Chapter 11. Quality evaluation of apple by computer vision

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Apple is one of the most consumed fruits in the world, and there is a critical need for enhanced computer vision technology for quality assessment of apples. This chapter gives a comprehensive review on recent advances in various computer vision techniques for detecting surface and internal defects ...

  14. From Literacy Activities to Entrepreneurship in Siete Pilas. Chapter 6.

    ERIC Educational Resources Information Center

    Chacon, Antonio; Polo, Angel

    This chapter describes a community development project in Siete Pilas (Spain), a village whose economy is based primarily on small family farms and unskilled labor. The project grew out of the Sierra Education Program, which in 1980 sent adult-education teachers to five villages in the Sierra de Ronda region. The goal was to stimulate a socially…

  15. Politics of Instructional Development in Higher Education. Chapter 9.

    ERIC Educational Resources Information Center

    Lawrason, Robin Edgar

    This chapter discusses the implementation and encouragement of instructional development on the university campus, with particular emphasis on the instability and political nature of the campus environment. Empirical data obtained from a survey of instructional development activities throughout the Delaware Valley of Pennsylvania and New Jersey…

  16. Elements of Mathematics, Book O: Intuitive Background. Chapter 5, Mappings.

    ERIC Educational Resources Information Center

    Exner, Robert; And Others

    The sixteen chapters of this book provide the core material for the Elements of Mathematics Program, a secondary sequence developed for highly motivated students with strong verbal abilities. The sequence is based on a functional-relational approach to mathematics teaching, and emphasizes teaching by analysis of real-life situations. This text is…

  17. APS Chapter 1 Evaluation Report 1984-1985.

    ERIC Educational Resources Information Center

    Kaemper, Jack; Morse, Kathy

    This report describes and evaluates the Albuquerque Public Schools (APS) 1984-85 Chapter 1 instructional program and its effect on student performance. The following information is reported or described: (1) conclusions and recommendations; (2) participating schools and cost summaries; (3) identification of eligible schools; (4) identification of…

  18. Chapter Two: Foundations for the Study of Practice

    ERIC Educational Resources Information Center

    Young, Richard F.

    2008-01-01

    In this chapter, the historical roots of contemporary Practice Theory are unearthed in the work of semioticians, philosophers, and anthropologists. Saussure's semiotic theory is contrasted with that of Peirce, and the importance of Peirce's work for understanding the context of signs is stressed. The philosophy of language in the writings of…

  19. Reading Recovery and ESEA Chapter 1: Issues and Possibilities.

    ERIC Educational Resources Information Center

    Zajano, Nancy C.

    The simultaneous implementation of Reading Recovery (an early intervention program designed to help children "at risk" of failure in their first year of reading instruction) and Chapter 1 programs in schools raises a number of issues as educators attempt to provide effective reading instruction within the policies and guidelines of both…

  20. Chapter 5: Long-term benefits analysis of EERE's programs

    SciTech Connect

    None, None

    2009-01-18

    This chapter provides an overview of the modeling approach used in MARKAL-GPRA06 to evaluate the benefits of EERE R&D programs and technologies. The program benefits reported in this section result from comparisons of each Program Case to the Baseline Case, as modeled in MARKAL-GPRA06.

  1. Economic and Societal Benefits of Soil Carbon Management (Chapter 1).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many papers and books on soil carbon management have addressed specific ecosystems such as agricultural lands, rangelands, forestlands, etc. This paper introduces a book within which each chapter begins by addressing a particular concern and potential options to manage it, along with their real and...

  2. Chapter 3: Crossing Boundaries--Foundation Degrees in England

    ERIC Educational Resources Information Center

    Longhurst, Derek

    2010-01-01

    This chapter traces the history, purposes, and distinctive features of the foundation degree, a short-cycle higher education qualification introduced in England in 2000-2001 and offered by both universities and further education colleges. The key characteristics of the foundation degree are discussed: employer involvement in curriculum development…

  3. Poverty in Rural America: Trends and Demographic Characteristics. Chapter 1.

    ERIC Educational Resources Information Center

    Hoppe, Robert

    This chapter examines recent trends in rural poverty and discusses some characteristics of the rural poor compared to the urban poor. Sources of poverty data for 1967-90 include the income supplement of the Census Bureau's annual Current Population Survey and personal income data compiled by the Bureau of Economic Analysis. "Rural" and…

  4. Chapter 13. Exploring Use of the Reserved Core

    SciTech Connect

    Holmen, John; Humphrey, Alan; Berzins, Martin

    2015-07-29

    In this chapter, we illustrate benefits of thinking in terms of thread management techniques when using a centralized scheduler model along with interoperability of MPI and PThread. This is facilitated through an exploration of thread placement strategies for an algorithm modeling radiative heat transfer with special attention to the 61st core. This algorithm plays a key role within the Uintah Computational Framework (UCF) and current efforts taking place at the University of Utah to model next-generation, large-scale clean coal boilers. In such simulations, this algorithm models the dominant form of heat transfer and consumes a large portion of compute time. Exemplified by a real-world example, this chapter presents our early efforts in porting a key portion of a scalability-centric codebase to the Intel Xeon Phi coprocessor. Specifically, this chapter presents results from our experiments profiling the native execution of a reverse Monte-Carlo ray tracing-based radiation model on a single coprocessor. These results demonstrate that our fastest run configurations utilized the 61st core and that performance was not profoundly impacted when explicitly oversubscribing the coprocessor operating system thread. Additionally, this chapter presents a portion of radiation model source code, a MIC-centric UCF cross-compilation example, and less conventional thread management technique for developers utilizing the PThreads threading model.

  5. An Evaluation of the Chapter 2 Inexpensive Book Distribution Program.

    ERIC Educational Resources Information Center

    Abbott, Catherine; And Others

    This report describes and evaluates the Chapter 2 Inexpensive Book Distribution Program (IBDP), a federal program designed to motivate children from age three to high school to read, and the Reading Is Fundamental (RIF) organization--the sole contractor of the IBDP. Following an executive summary, an introductory section presents basic…

  6. Endocrine and exocrine function of the bovine testis. Chapter 2

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter is devoted to the endocrine and exocrine function of the normal bovine male testes. The discussion begins with a historical review of the literature dating back to Aristotle’s (300 BC) initial description of the anatomy of the mammalian testes. The first microscopic examination of the t...

  7. Evaluation of the ECIA Chapter 1 Technical Assistance Centers (TACs).

    ERIC Educational Resources Information Center

    Reisner, Elizabeth; And Others

    This study evaluated the national network of Technical Assistance Centers (TACs), which provides technical assistance in evaluation and program improvement to state and local educational agencies responsible for implementing programs under Chapter 1 of the Education Consolidation and Improvement Act (ECIA). The U.S. Department of Education…

  8. RMP Guidance for Warehouses - Chapter 2: Applicability of Program Levels

    EPA Pesticide Factsheets

    Once you have determined that you have one or more processes subject to the Risk Management Plan rule (40 CFR part 68), this chapter helps you identify what actions you must take to comply. Processes fall under three different program levels.

  9. Chapter I Project Identification Program. Lafayette School Corporation.

    ERIC Educational Resources Information Center

    Lafayette School Corp., IN.

    The Kindergarten Intensified Development System (KIDS) Chapter I program of the Lafayette, Indiana, School Corporation is described in terms of the following: (1) district information; (2) state agency program information; (3) project information including staff degrees and experience, education needs, student selection, and participating schools;…

  10. Chapter 17 - Mistaken identity: Clarification of Rubus coreanus Miquel (bokbunja)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter was written to target the research communities currently studying (misidentified) native bokbunja (Rubus coreanus Miquel). Most Korean growers and researchers are cultivating or conducting work on R. occidentalis L. (American black raspberries), not R. coreanus. We summarized fruit, pla...

  11. 24 CFR 300.1 - Scope of chapter.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Scope of chapter. 300.1 Section 300.1 Housing and Urban Development Regulations Relating to Housing and Urban Development (Continued) GOVERNMENT NATIONAL MORTGAGE ASSOCIATION, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT GENERAL § 300.1...

  12. Chapter 8: The "Citizen" in Youth Civic Engagement

    ERIC Educational Resources Information Center

    Roholt, Ross VeLure; Hildreth, R. W.; Baizerman, Michael

    2007-01-01

    The concept of citizenship is a central, necessary, and defining feature of youth civic engagement. Any effort to educate young people for citizenship entails an implicit idea of what a "good citizen" is. There are a number of different and sometimes competing versions of what is a "good citizen." This chapter reviews "standard" accounts of…

  13. Chapter 5: Long-term benefits analysis of EERE's Programs

    SciTech Connect

    None, None

    2009-01-18

    This chapter provides an overview of the modeling approach used in MARKAL-GPRA05 to evaluate the benefits of EERE R&D programs and technologies. The program benefits reported in this section result from comparisons of each Program Case to the Baseline Case, as modeled in MARKAL-GPRA05.

  14. Ethical & Legal Issues in School Counseling. Chapter 3: Legal Issues.

    ERIC Educational Resources Information Center

    Remley, Theodore P., Jr.; And Others

    This document contains chapter 3 (7 articles) of a collection of 35 articles primarily from American Association for Counseling and Development (AACD) publications on the most important legal and ethical topics about which all school counselors need to be informed. "The Law and Ethical Practices in Elementary and Middle Schools" (Theodore P.…

  15. "Preescolar Na Casa": Teaching Parents To Teach Children. Chapter 3.

    ERIC Educational Resources Information Center

    Fernandez, Ermitas

    This chapter describes a school readiness program that has been implemented in rural Galicia (Spain) since 1977. Data reveal that 70 percent of Galicia's population lives in rural areas, the economy remains primarily agricultural, Galicians earn less than the national average and have the largest number of public assistance recipients, and there…

  16. Design Handbook for TREE. Chapter 12. Index, Symbols and Glossary

    DTIC Science & Technology

    1978-12-01

    CLASSIFICATION OF THIS PAGO ~eUn Date Enloted) UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE(ŕen Dar& Entered) TABLE OF CONTENTS Page INTRODUCTION 12-1...completed, this chapter will be revised. Additions and sug- gestions for the Index, Symbols, and Glossary that will be helpful to the user are solicited

  17. Next Chapter Book Club: What a Novel Idea

    ERIC Educational Resources Information Center

    Fish, Tom; Graff, Vicki

    2006-01-01

    In this article, the authors discuss a unique program of The Ohio State University's Nisonger Center--the Next Chapter Book Club (NCBC). The NCBC promotes literacy learning, community inclusion, and social connectedness for adolescents and adults with intellectual disabilities. Developed in 2002, the program has expanded from two clubs in…

  18. Effective Chapter 1 Practices in the Portland Public Schools.

    ERIC Educational Resources Information Center

    Kushmuk, James

    This report describes a research effort and some preliminary findings on effective school practices as they apply to the Portland (Oregon) Public Schools' Education Consolidation and Improvement Act (ECIA) Chapter 1 program, which is a supplementary basic skills instructional program for low-achieving students. Nearly 60 hours of unsystematic…

  19. My Career Chapter as a Tool for Reflective Practice

    ERIC Educational Resources Information Center

    McIlveen, Peter; Patton, Wendy

    2010-01-01

    The career assessment and counselling procedure "My Career Chapter" is presented as a tool for reflexive self-awareness within career counsellors. To demonstrate application of the procedure as a method of self-supervision, this paper presents a study in which the participant studies himself. Results indicate a reflexive consciousness for the…

  20. Influence of FFA Activities on Critical Thinking Skills in Texas Three-Star FFA Chapters

    ERIC Educational Resources Information Center

    Latham, Lindsey; Rayfield, John; Moore, Lori L.

    2015-01-01

    The purpose of this study was to determine the relationship of FFA activities on critical thinking skills of Texas FFA members in three-star FFA chapters. This descriptive study was conducted in eight purposively selected three-star FFA chapters throughout Texas. Three-star chapters are those chapters who have emerged as outstanding programs…

  1. Determination of 9-cis beta-carotene and zeta-carotene in biological samples.

    PubMed

    Qin, Jian; Yeum, Kyung-Jin; Johnson, Elizabeth J; Krinsky, Norman I; Russell, Robert M; Tang, Guangwen

    2008-09-01

    Concentrations of 9-cis beta-carotene (9-cis betaC) and zeta-carotene (zetaC) in biological samples may provide crucial information on the biological activities of these carotenoids. However, in high-performance liquid chromatography (HPLC) these carotenoids are often co-eluted. Therefore, there is an urgent need to develop a method for 9-cis betaC and zetaC quantitation. Both 9-cis betaC and zetaC have peak absorbance at 400 and 450 nm, respectively, whereas only 9-cis betaC has peak absorbance at 475 nm. We developed a HPLC method to quantitate 9-cis betaC and zetaC by using peak absorbance ratios. The 9-cis betaC/zetaC peak area was monitored at 475, 450 and 400 nm. The 9-cis betaC was quantified by using absorbance value at 475 nm; zetaC was then calculated from the 9-cis betaC/zetaC peak at 400 nm by subtracting 9-cis betaC contribution at 400 nm using the 400-nm/475-nm peak absorbance ratio of 9-cis betaC (0.39). This method was applied to determine 9-cis betaC and zetaC concentrations in serum and breast milk samples (n=12) from American lactating women and serum and breast adipose tissue samples (n=16) from Korean women with either benign or malignant breast tumors. 9-cis betaC concentrations in serum and breast milk of American women, and serum and adipose tissue of Korean women were 7.1+/-0.8 and 1.1+/-0.2 nM, and 15.6+/-1.1 nM and 0.2+/-0.1 nmol/g, respectively. zetaC concentrations in the above samples were 54.2+/-7.2 and 8.3+/-1.8 nM, and 49.0+/-3.9 nM and 0.3+/-0.1 nmol/g, respectively.

  2. Quality Child Care for All: A Guide to Integration.

    ERIC Educational Resources Information Center

    Panitch, Melanie

    This manual is intended to facilitate the integration of children with mental handicaps into child care centers in Canada and elsewhere. The first chapter looks at the background of integration in early childhood child care programs in Canada and identifies concerns of parents. The second chapter explores the practice of labelling children with…

  3. Vision for Micro Technology Space Missions. Chapter 2

    NASA Technical Reports Server (NTRS)

    Dennehy, Neil

    2005-01-01

    It is exciting to contemplate the various space mission applications that Micro Electro Mechanical Systems (MEMS) technology could enable in the next 10-20 years. The primary objective of this chapter is to both stimulate ideas for MEMS technology infusion on future NASA space missions and to spur adoption of the MEMS technology in the minds of mission designers. This chapter is also intended to inform non-space oriented MEMS technologists, researchers and decision makers about the rich potential application set that future NASA Science and Exploration missions will provide. The motivation for this chapter is therefore to lead the reader down a path to identify and it is exciting to contemplate the various space mission applications that Micro Electro Mechanical Systems (MEMS) technology could enable in the next 10-20 years. The primary objective of this chapter is to both stimulate ideas for MEMS technology infusion on future NASA space missions and to spur adoption of the MEMS technology in the minds of mission designers. This chapter is also intended to inform non-space oriented MEMS technologists, researchers and decision makers about the rich potential application set that future NASA Science and Exploration missions will provide. The motivation for this chapter is therefore to lead the reader down a path to identify and consider potential long-term, perhaps disruptive or revolutionary, impacts that MEMS technology may have for future civilian space applications. A general discussion of the potential for MEMS in space applications is followed by a brief showcasing of a few selected examples of recent MEMS technology developments for future space missions. Using these recent developments as a point of departure, a vision is then presented of several areas where MEMS technology might eventually be exploited in future Science and Exploration mission applications. Lastly, as a stimulus for future research and development, this chapter summarizes a set of barriers

  4. Detailed map of a cis-regulatory input function

    NASA Astrophysics Data System (ADS)

    Setty, Y.; Mayo, A. E.; Surette, M. G.; Alon, U.

    2003-06-01

    Most genes are regulated by multiple transcription factors that bind specific sites in DNA regulatory regions. These cis-regulatory regions perform a computation: the rate of transcription is a function of the active concentrations of each of the input transcription factors. Here, we used accurate gene expression measurements from living cell cultures, bearing GFP reporters, to map in detail the input function of the classic lacZYA operon of Escherichia coli, as a function of about a hundred combinations of its two inducers, cAMP and isopropyl -D-thiogalactoside (IPTG). We found an unexpectedly intricate function with four plateau levels and four thresholds. This result compares well with a mathematical model of the binding of the regulatory proteins cAMP receptor protein (CRP) and LacI to the lac regulatory region. The model is also used to demonstrate that with few mutations, the same region could encode much purer AND-like or even OR-like functions. This possibility means that the wild-type region is selected to perform an elaborate computation in setting the transcription rate. The present approach can be generally used to map the input functions of other genes.

  5. Assessing Computational Methods of Cis-Regulatory Module Prediction

    PubMed Central

    Su, Jing; Teichmann, Sarah A.; Down, Thomas A.

    2010-01-01

    Computational methods attempting to identify instances of cis-regulatory modules (CRMs) in the genome face a challenging problem of searching for potentially interacting transcription factor binding sites while knowledge of the specific interactions involved remains limited. Without a comprehensive comparison of their performance, the reliability and accuracy of these tools remains unclear. Faced with a large number of different tools that address this problem, we summarized and categorized them based on search strategy and input data requirements. Twelve representative methods were chosen and applied to predict CRMs from the Drosophila CRM database REDfly, and across the human ENCODE regions. Our results show that the optimal choice of method varies depending on species and composition of the sequences in question. When discriminating CRMs from non-coding regions, those methods considering evolutionary conservation have a stronger predictive power than methods designed to be run on a single genome. Different CRM representations and search strategies rely on different CRM properties, and different methods can complement one another. For example, some favour homotypical clusters of binding sites, while others perform best on short CRMs. Furthermore, most methods appear to be sensitive to the composition and structure of the genome to which they are applied. We analyze the principal features that distinguish the methods that performed well, identify weaknesses leading to poor performance, and provide a guide for users. We also propose key considerations for the development and evaluation of future CRM-prediction methods. PMID:21152003

  6. Using hexamers to predict cis-regulatory motifs in Drosophila

    PubMed Central

    Chan, Bob Y; Kibler, Dennis

    2005-01-01

    Background Cis-regulatory modules (CRMs) are short stretches of DNA that help regulate gene expression in higher eukaryotes. They have been found up to 1 megabase away from the genes they regulate and can be located upstream, downstream, and even within their target genes. Due to the difficulty of finding CRMs using biological and computational techniques, even well-studied regulatory systems may contain CRMs that have not yet been discovered. Results We present a simple, efficient method (HexDiff) based only on hexamer frequencies of known CRMs and non-CRM sequence to predict novel CRMs in regulatory systems. On a data set of 16 gap and pair-rule genes containing 52 known CRMs, predictions made by HexDiff had a higher correlation with the known CRMs than several existing CRM prediction algorithms: Ahab, Cluster Buster, MSCAN, MCAST, and LWF. After combining the results of the different algorithms, 10 putative CRMs were identified and are strong candidates for future study. The hexamers used by HexDiff to distinguish between CRMs and non-CRM sequence were also analyzed and were shown to be enriched in regulatory elements. Conclusion HexDiff provides an efficient and effective means for finding new CRMs based on known CRMs, rather than known binding sites. PMID:16253142

  7. Multigenome DNA sequence conservation identifies Hox cis-regulatory elements

    PubMed Central

    Kuntz, Steven G.; Schwarz, Erich M.; DeModena, John A.; De Buysscher, Tristan; Trout, Diane; Shizuya, Hiroaki; Sternberg, Paul W.; Wold, Barbara J.

    2008-01-01

    To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced ∼0.5% of the C. brenneri and C. sp. 3 PS1010 genomes, and compared five Caenorhabditis genomes (C. elegans, C. briggsae, C. brenneri, C. remanei, and C. sp. 3 PS1010) to find regulatory elements in 22.8 kb of noncoding sequence from the ceh-13/lin-39 Hox subcluster. We developed the MUSSA program to find ungapped DNA sequences with N-way transitive conservation, applied it to the ceh-13/lin-39 locus, and transgenically assayed 21 regions with both high and low degrees of conservation. This identified 10 functional regulatory elements whose activities matched known ceh-13/lin-39 expression, with 100% specificity and a 77% recovery rate. One element was so well conserved that a similar mouse Hox cluster sequence recapitulated the native nematode expression pattern when tested in worms. Our findings suggest that ungapped sequence comparisons can predict regulatory elements genome-wide. PMID:18981268

  8. A Cis-Regulatory Map of the Drosophila Genome

    PubMed Central

    Nègre, Nicolas; Brown, Christopher D.; Ma, Lijia; Bristow, Christopher Aaron; Miller, Steven W.; Wagner, Ulrich; Kheradpour, Pouya; Eaton, Matthew L.; Loriaux, Paul; Sealfon, Rachel; Li, Zirong; Ishii, Haruhiko; Spokony, Rebecca F.; Chen, Jia; Hwang, Lindsay; Cheng, Chao; Auburn, Richard P.; Davis, Melissa B.; Domanus, Marc; Shah, Parantu K.; Morrison, Carolyn A.; Zieba, Jennifer; Suchy, Sarah; Senderowicz, Lionel; Victorsen, Alec; Bild, Nicholas A.; Grundstad, A. Jason; Hanley, David; MacAlpine, David M.; Mannervik, Mattias; Venken, Koen; Bellen, Hugo; White, Robert; Russell, Steven; Grossman, Robert L.; Ren, Bing; Gerstein, Mark; Posakony, James W.; Kellis, Manolis; White, Kevin P.

    2011-01-01

    Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide 1,2 has successfully identified specific subtypes of regulatory elements 3. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb-Response Elements 4, chromatin states 5, transcription factor binding sites (TFBS) 6–9, PolII regulation 8, and insulator elements 10; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome based on more than 300 chromatin immuno-precipitation (ChIP) datasets for eight chromatin features, five histone deacetylases (HDACs) and thirty-eight site-specific transcription factors (TFs) at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and we validated a subset of predictions for promoters, enhancers, and insulators in vivo. We also identified nearly 2,000 genomic regions of dense TF binding associated with chromatin activity and accessibility. We discovered hundreds of new TF co-binding relationships and defined a TF network with over 800 potential regulatory relationships. PMID:21430782

  9. Cis-regulatory control of corticospinal system development and evolution

    PubMed Central

    Shim, Sungbo; Kwan, Kenneth Y.; Li, Mingfeng; Lefebvre, Veronique; Šestan, Nenad

    2012-01-01

    Summary The co-emergence of a six-layered cerebral neocortex and its corticospinal output system is one of the evolutionary hallmarks of mammals. However, the genetic programs that underlie their development and evolution remain poorly understood. Here we identify a conserved non-exonic element (E4) that acts as a cortex-specific enhancer for the nearby Fezf2, which is required for the specification of corticospinal neuron identity and connectivity. We find that SOX4 and SOX11 functionally compete with the repressor SOX5 in the trans-activation of E4. Cortex-specific double deletion of Sox4 and Sox11 leads to the loss of Fezf2 expression and failed specification of corticospinal neurons and, independent of Fezf2, a reeler-like inversion of layers. We show evidence supporting the emergence of functional SOX binding sites in E4 during tetrapod evolution and their subsequent stabilization in mammals and possibly amniotes. These findings reveal that SOX transcription factors converge onto a cis-acting element of Fezf2 and form critical components of a regulatory network controlling the identity and connectivity of corticospinal neurons. PMID:22678282

  10. Mechanism of cis-prenyltransferase reaction probed by substrate analogues

    SciTech Connect

    Lu, Yen-Pin; Liu, Hon-Ge; Teng, Kuo-Hsun; Liang, Po-Huang

    2010-10-01

    Research highlights: {yields} The extremely slow trans-OPPS reaction using 2-Fluoro-FPP supports the sequential mechanism with the carbocation intermediate. {yields} The similar UPPS reaction rate under single turnover supports the concerted mechanism, without the carbocation intermediate. {yields} The secondary kinetic isotope effect also supports associate transition state for UPPS reaction, without the carbocation intermediate. -- Abstract: Undecaprenyl pyrophosphate synthase (UPPS) is a cis-type prenyltransferases which catalyzes condensation reactions of farnesyl diphosphate (FPP) with eight isopentenyl pyrophosphate (IPP) units to generate C{sub 55} product. In this study, we used two analogues of FPP, 2-fluoro-FPP and [1,1-{sup 2}H{sub 2}]FPP, to probe the reaction mechanism of Escherichia coli UPPS. The reaction rate of 2-fluoro-FPP with IPP under single-turnover condition is similar to that of FPP, consistent with the mechanism without forming a farnesyl carbocation intermediate. Moreover, the deuterium secondary KIE of 0.985 {+-} 0.022 measured for UPPS reaction using [1,1-{sup 2}H{sub 2}]FPP supports the associative transition state. Unlike the sequential mechanism used by trans-prenyltransferases, our data demonstrate E. coli UPPS utilizes the concerted mechanism.

  11. Integrating the Curricula: A Collection.

    ERIC Educational Resources Information Center

    Fogarty, Robin, Ed.

    In response to the search for ways to create forms of schooling that are more holistic and natural, and more integrated and interwoven, this collection of articles pulls together elements of the multifaceted concept of curriculum integration. Divided into six sections, the chapters explore the reasons and rationale for moving toward more holistic…

  12. cis,cis-Muconic acid: separation and catalysis to bio-adipic acid for nylon-6,6 polymerization

    SciTech Connect

    Vardon, Derek R.; Rorrer, Nicholas A.; Salvachúa, Davinia; Settle, Amy E.; Johnson, Christopher W.; Menart, Martin J.; Cleveland, Nicholas S.; Ciesielski, Peter N.; Steirer, K. Xerxes; Dorgan, John R.; Beckham, Gregg T.

    2016-01-01

    cis,cis-Muconic acid is a polyunsaturated dicarboxylic acid that can be produced renewably via the biological conversion of sugars and lignin-derived aromatic compounds. Subsequently, muconic acid can be catalytically converted to adipic acid -- the most commercially significant dicarboxylic acid manufactured from petroleum. Nylon-6,6 is the major industrial application for adipic acid, consuming 85% of market demand; however, high purity adipic acid (99.8%) is required for polymer synthesis. As such, process technologies are needed to effectively separate and catalytically transform biologically derived muconic acid to adipic acid in high purity over stable catalytic materials. To that end, this study: (1) demonstrates bioreactor production of muconate at 34.5 g L-1 in an engineered strain of Pseudomonas putida KT2440, (2) examines the staged recovery of muconic acid from culture media, (3) screens platinum group metals (e.g., Pd, Pt, Rh, Ru) for activity and leaching stability on activated carbon (AC) and silica supports, (4) evaluates the time-on-stream performance of Rh/AC in a trickle bed reactor, and (5) demonstrates the polymerization of bio-adipic acid to nylon-6,6. Separation experiments confirmed AC effectively removed broth color compounds, but subsequent pH/temperature shift crystallization resulted in significant levels of Na, P, K, S and N in the crystallized product. Ethanol dissolution of muconic acid precipitated bulk salts, achieving a purity of 99.8%. Batch catalysis screening reactions determined that Rh and Pd were both highly active compared to Pt and Ru, but Pd leached significantly (1-9%) from both AC and silica supports. Testing of Rh/AC in a continuous trickle bed reactor for 100 h confirmed stable performance after 24 h, although organic adsorption resulted in reduced steady-state activity. Lastly, polymerization of bio-adipic acid with hexamethyldiamine produced nylon-6,6 with comparable properties to its petrochemical counterpart

  13. Organic Compounds in the C3H6O3 Family: Microwave Spectrum of cis-cis Dimethyl Carbonate

    NASA Astrophysics Data System (ADS)

    McGuire, B. A.; Widicus Weaver, S. L.; Lovas, F. J.; Plusquellic, D. F.; Blake, G. A.

    2011-05-01

    A number of recent spectroscopic and observational efforts have focused on simple sugars and sugar alcohols because of their importance in prebiotic astro- chemistry. The simplest sugar-related species, glycolaldehyde, has been detected in Sgr B2(N), as have its C2H4O2 structural isomers acetic acid and methyl formate. Additional studies of the C3-sugars with empirical formula C3H6O3, glyceraldehyde and dihydroxyacetone, resulted in no clear interstellar detection. Structural isomerism is extensive in interstellar clouds, and there is a high level of correlation between the relative energies of isomers and their relative abundances, with the lowest energy isomers detected in greatest abundance. The detected members of the C2H4O2 family, however, defy this trend, having relative abundances of (acetic acid):(glycolaldehyde):(methyl formate) of about 2:1:52, despite acetic acid being the lowest energy isomer. These puzzling abundance ratios and the lack of detection of the C3H6O3 sugars gives rise to the question: "Which is the most likely isomer in the C3H6O3 family to be detectable in inter- stellar clouds?" In an attempt to answer this question, we carried out geometry optimization calculations to determine the relative binding energies of the 13 members of the C3H6O3 family. Of the four lowest- energy isomers, only lactic acid [CH3CH(OH)COOH] and dimethyl carbonate [(CH3)2CO3] are commercially available, and lactic acid has been previously investigated spectroscopically. We have therefore conducted a laboratory study of dimethyl carbonate, measuring its rotational spectrum from 8.4 - 25.3 GHz using a Fourier-Transform microwave spectrometer, and from 227 - 350 GHz using a direct absorption spectrometer. We report on the theoretical calculations performed on the C3H6O3 family of isomers, the experimental studies of cis-cis dimethyl carbonate, and the implica- tions of these results for interstellar chemistry. The details of this work are also reported in Lovas et

  14. Low aqueous solubility of 11-cis-retinal limits the rate of pigment formation and dark adaptation in salamander rods.

    PubMed

    Frederiksen, Rikard; Boyer, Nicholas P; Nickle, Benjamin; Chakrabarti, Kalyan S; Koutalos, Yiannis; Crouch, Rosalie K; Oprian, Daniel; Cornwall, M Carter

    2012-06-01

    We report experiments designed to test the hypothesis that the aqueous solubility of 11-cis-retinoids plays a significant role in the rate of visual pigment regeneration. Therefore, we have compared the aqueous solubility and the partition coefficients in photoreceptor membranes of native 11-cis-retinal and an analogue retinoid, 11-cis 4-OH retinal, which has a significantly higher solubility in aqueous medium. We have then correlated these parameters with the rates of pigment regeneration and sensitivity recovery that are observed when bleached intact salamander rod photoreceptors are treated with physiological solutions containing these retinoids. We report the following results: (a) 11-cis 4-OH retinal is more soluble in aqueous buffer than 11-cis-retinal. (b) Both 11-cis-retinal and 11-cis 4-OH retinal have extremely high partition coefficients in photoreceptor membranes, though the partition coefficient of 11-cis-retinal is roughly 50-fold greater than that of 11-cis 4-OH retinal. (c) Intact bleached isolated rods treated with solutions containing equimolar amounts of 11-cis-retinal or 11-cis 4-OH retinal form functional visual pigments that promote full recovery of dark current, sensitivity, and response kinetics. However, rods treated with 11-cis 4-OH retinal regenerated on average fivefold faster than rods treated with 11-cis-retinal. (d) Pigment regeneration from recombinant and wild-type opsin in solution is slower when treated with 11-cis 4-OH retinal than with 11-cis-retinal. Based on these observations, we propose a model in which aqueous solubility of cis-retinoids within the photoreceptor cytosol can place a limit on the rate of visual pigment regeneration in vertebrate photoreceptors. We conclude that the cytosolic gap between the plasma membrane and the disk membranes presents a bottleneck for retinoid flux that results in slowed pigment regeneration and dark adaptation in rod photoreceptors.

  15. Asynchronous Replication, Mono-Allelic Expression, and Long Range Cis-Effects of ASAR6

    PubMed Central

    Smith, Leslie; Montagna, Christina; Thayer, Mathew J.

    2013-01-01

    Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program. The majority of genes on homologous chromosomes replicate synchronously. However, mono-allelically expressed genes such as imprinted genes, allelically excluded genes, and genes on female X chromosomes replicate asynchronously. We have identified a cis-acting locus on human chromosome 6 that controls this replication-timing program. This locus encodes a large intergenic non-coding RNA gene named Asynchronous replication and Autosomal RNA on chromosome 6, or ASAR6. Disruption of ASAR6 results in delayed replication, delayed mitotic chromosome condensation, and activation of the previously silent alleles of mono-allelic genes on chromosome 6. The ASAR6 gene resides within an ∼1.2 megabase domain of asynchronously replicating DNA that is coordinated with other random asynchronously replicating loci along chromosome 6. In contrast to other nearby mono-allelic genes, ASAR6 RNA is expressed from the later-replicating allele. ASAR6 RNA is synthesized by RNA Polymerase II, is not polyadenlyated, is restricted to the nucleus, and is subject to random mono-allelic expression. Disruption of ASAR6 leads to the formation of bridged chromosomes, micronuclei, and structural instability of chromosome 6. Finally, ectopic integration of cloned genomic DNA containing ASAR6 causes delayed replication of entire mouse chromosomes. PMID:23593023

  16. Bactericidal activity of the human skin fatty acid cis-6-hexadecanoic acid on Staphylococcus aureus.

    PubMed

    Cartron, Michaël L; England, Simon R; Chiriac, Alina Iulia; Josten, Michaele; Turner, Robert; Rauter, Yvonne; Hurd, Alexander; Sahl, Hans-Georg; Jones, Simon; Foster, Simon J

    2014-07-01

    Human skin fatty acids are a potent aspect of our innate defenses, giving surface protection against potentially invasive organisms. They provide an important parameter in determining the ecology of the skin microflora, and alterations can lead to increased colonization by pathogens such as Staphylococcus aureus. Harnessing skin fatty acids may also give a new avenue of exploration in the generation of control measures against drug-resistant organisms. Despite their importance, the mechanism(s) whereby skin fatty acids kill bacteria has remained largely elusive. Here, we describe an analysis of the bactericidal effects of the major human skin fatty acid cis-6-hexadecenoic acid (C6H) on the human commensal and pathogen S. aureus. Several C6H concentration-dependent mechanisms were found. At high concentrations, C6H swiftly kills cells associated with a general loss of membrane integrity. However, C6H still kills at lower concentrations, acting through disruption of the proton motive force, an increase in membrane fluidity, and its effects on electron transfer. The design of analogues with altered bactericidal effects has begun to determine the structural constraints on activity and paves the way for the rational design of new antistaphylococcal agents.

  17. Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses

    NASA Astrophysics Data System (ADS)

    Liu, Bingqiang; Zhou, Chuan; Li, Guojun; Zhang, Hanyuan; Zeng, Erliang; Liu, Qi; Ma, Qin

    2016-03-01

    Regulons are the basic units of the response system in a bacterial cell, and each consists of a set of transcriptionally co-regulated operons. Regulon elucidation is the basis for studying the bacterial global transcriptional regulation network. In this study, we designed a novel co-regulation score between a pair of operons based on accurate operon identification and cis regulatory motif analyses, which can capture their co-regulation relationship much better than other scores. Taking full advantage of this discovery, we developed a new computational framework and built a novel graph model for regulon prediction. This model integrates the motif comparison and clustering and makes the regulon prediction problem substantially more solvable and accurate. To evaluate our prediction, a regulon coverage score was designed based on the documented regulons and their overlap with our prediction; and a modified Fisher Exact test was implemented to measure how well our predictions match the co-expressed modules derived from E. coli microarray gene-expression datasets collected under 466 conditions. The results indicate that our program consistently performed better than others in terms of the prediction accuracy. This suggests that our algorithms substantially improve the state-of-the-art, leading to a computational capability to reliably predict regulons for any bacteria.

  18. Cis-trans isomerizations of beta-carotene and lycopene: a theoretical study.

    PubMed

    Guo, Wen-Hsin; Tu, Cheng-Yi; Hu, Ching-Han

    2008-09-25

    The all-trans to mono-cis isomerizations of polyenes and two C40H56 carotenes, beta-carotene and lycopene, at the ground singlet (S0) and triplet (T1) states are studied by means of quantum chemistry computations. At the S0 state of polyenes containing n acetylene units (Pn), we find that the energy barrier of the central C=C rotation decreases with n. In contrast, however, at the T 1 state, the rotational barrier increases with n. For the C40H56 carotenes, the rotational barriers of lycopene are lower than those of their beta-carotene counterparts. This difference renders the rotational rates of lycopene to be 1-2 orders of magnitude higher than those of beta-carotene at room temperature. For both these carotenes, the barrier is lowest for the rotation toward the 13-cis isomer. The relative abundances are in the following order: all-trans > 9-cis > 13-cis > 15-cis. Although the 5-cis isomer of lycopene has the lowest energy among the cis isomers, its formation from the all-trans form is restricted, owing to a very large rotational barrier. The possible physiological implications of this study are discussed.

  19. Thermal processing differentially affects lycopene and other carotenoids in cis-lycopene containing, tangerine tomatoes.

    PubMed

    Cooperstone, Jessica L; Francis, David M; Schwartz, Steven J

    2016-11-01

    Tangerine tomatoes, unlike red tomatoes, accumulate cis-lycopenes instead of the all-trans isomer. cis-Lycopene is the predominating isomeric form of lycopene found in blood and tissues. Our objective was to understand how thermal processing and lipid concentration affect carotenoid isomerisation and degradation in tangerine tomatoes. We conducted duplicated factorial designed experiments producing tangerine tomato juice and sauce, varying both processing time and lipid concentration. Carotenoids were extracted and analysed using high-performance liquid chromatography with photodiode array detection. Phytoene, phytofluene, ζ-carotene, neurosporene, tetra-cis-lycopene, all-trans-lycopene and other-cis-lycopenes were quantified. Tetra-cis-lycopene decreased with increasing heating time and reached 80% of the original level in sauce after processing times of 180min. All-trans-lycopene and other-cis-lycopenes increased with longer processing times. Total carotenoids and total lycopene decreased with increased heating times while phytoene and phytofluene were unchanged. These data suggest limiting thermal processing of tangerine tomato products if delivery of tetra-cis-lycopene is desirable.

  20. Initiative to Improve the Quality of Chapter 1 Projects. E.C.I.A. Chapter 1 Program.

    ERIC Educational Resources Information Center

    Bellingham Public Schools, WA.

    The Bellingham, Washington, Public Schools K-8 Chapter 1 Reading Program attempts to develop an enthusiastic and growing interest in reading, and to help each child work toward his or her potential through effective reading. The program is described in terms of the following: (1) district information; (2) program and project information; (3) goals…

  1. E.C.I.A. Chapter 1 KIDS Program: Initiative to Improve the Quality of Chapter 1 Projects.

    ERIC Educational Resources Information Center

    Bellingham Public Schools, WA.

    This report describes an Education Consolidation and Improvement Act-Chapter 1 program for at-risk kindergarten children in four Bellingham (Washington) elementary schools. Children in the program are included in regular kindergarten classes, which meet two full days each week and every other Friday. The children also attend the Kindergarten for…

  2. Secondary School Advanced Mathematics, Chapter 1, Organizing Geometric Knowledge, Chapter 2, Concepts and Skills in Algebra. Student's Text.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    This text is the first of five in the Secondary School Advanced Mathematics (SSAM) series which was designed to meet the needs of students who have completed the Secondary School Mathematics (SSM) program, and wish to continue their study of mathematics. The first chapter, devoted to organizing geometric knowledge, deals with the distinction…

  3. School Mathematics Study Group, Unit Number Two. Chapter 3 - Informal Algorithms and Flow Charts. Chapter 4 - Applications and Mathematics Models.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    This is the second unit of a 15-unit School Mathematics Study Group (SMSG) mathematics text for high school students. Topics presented in the first chapter (Informal Algorithms and Flow Charts) include: changing a flat tire; algorithms, flow charts, and computers; assignment and variables; input and output; using a variable as a counter; decisions…

  4. cis-trans-Isomerization of unsaturated fatty acids during /γ-irradiation of barley grains

    NASA Astrophysics Data System (ADS)

    Geißler, Christian; Brede, Ortwin; Reinhardt, Jürgen

    2003-06-01

    Gamma-irradiating barley grains with doses of 10-100 kGy, a dose dependent isomerization of the naturally occurring cis-unsaturated fatty acids such as oleic, cis-vaccenic, linoleic and also of linolenic acid was found. Whereas the effect was negligible up to 10 kGy, at 50 kGy the trans-fatty acid level became comparable to that of other natural products like butter fat which means that there is no essential nutrition danger. The cis-trans-isomerization found in barley grains is explained mainly by a thiyl radical driven process rather than direct isomerization.

  5. Diastereoselective syntheses of substituted cis-hydrindanones featuring sequential inter- and intramolecular Michael reactions.

    PubMed

    Liu, Junjia; Marsini, Maurice A; Bedell, T Aaron; Reider, Paul J; Sorensen, Erik J

    2016-06-30

    The hydrindane (bicyclo[4.3.0]nonane) structural motif (1) and related cis-1-hydrindanone skeleton (2) are common substructures in many natural products. Herein, we describe efficient access to substituted cis-1-hydrindanones enabled by a sequence of Michael reactions. A copper-catalyzed intermolecular Michael addition of a cyclic silyl ketene acetal to a β-substituted-α-alkoxycarbonyl-cyclopentenone enables construction of a quaternary center and is followed, after incorporation of an additional Michael acceptor, by a second, intramolecular addition of a nucleophilic β-ketoester. This strategy affords stereoselective access to substituted bicyclic cis-hydrindanone ring systems containing up to three contiguous stereocenters.

  6. Designing CIS to improve decisions in depression disease management: a discourse analysis of front line practice.

    PubMed

    Mirel, Barbara; Ackerman, Mark S; Kerber, Kevin; Klinkman, Michael

    2006-01-01

    Clinical care management promises to help diminish the major health problem of depression. To realize this promise, front line clinicians must know which care management interventions are best for which patients and act accordingly. Unfortunately, the detailed intervention data required for such differentiated assessments are missing in most clinical information systems (CIS). To determine frontline clinicians' needs for these data and to identify the data that CIS should keep, we conducted an 18 month ethnographic study and discourse analysis of telehealth depression care management. Results show care managers need data-based evidence to choose best options, and discourse analysis suggests some personalized interventions that CIS should and can feasibly capture for evidence.

  7. Atmospheric chemistry of cis-CF3CHdbnd CHCl (HCFO-1233zd(Z)): Kinetics of the gas-phase reactions with Cl atoms, OH radicals, and O3

    NASA Astrophysics Data System (ADS)

    Andersen, Lene Løffler; Østerstrøm, Freja From; Sulbaek Andersen, Mads P.; Nielsen, Ole John; Wallington, Timothy J.

    2015-10-01

    FTIR smog chamber techniques were used to measure the rate coefficients k(Cl + cis-CF3CHdbnd CHCl) = (6.26 ± 0.84) × 10-11, k(OH + cis-CF3CHdbnd CHCl) = (8.45 ± 1.52) × 10-13, and k(O3 + cis-CF3CHdbnd CHCl) = (1.53 ± 0.12) × 10-21 cm3 molecule-1 s-1. The atmospheric lifetime of cis-CF3CHdbnd CHCl is determined by reaction with OH radicals and is estimated to be 14 days. The infrared spectrum of cis-CF3CHdbnd CHCl was recorded and the integrated absorption over the range 600-2000 cm-1 was measured to be (1.48 ± 0.07) × 10-16 cm molecule-1. Accounting for non-uniform horizontal and vertical mixing leads to a GWP100 value of essentially zero. Correction to account for unwanted Cl atom chemistry in our previous relative rate study of the kinetics of the reaction of OH with trans-CF3CHdbnd CHCl gives k(OH + trans-CF3CHdbnd CHCl) = (3.61 ± 0.37) × 10-13 cm3 molecule-1 s-1.

  8. A Mutational Analysis of the Active Site Loop Residues in cis-3-Chloroacrylic Acid Dehalogenase

    PubMed Central

    Schroeder, Gottfried K.; Huddleston, Jamison P.; Johnson, William H.; Whitman, Christian P.

    2013-01-01

    cis -3-Chloroacrylic acid dehalogenase (cis-CaaD) from Pseudomonas pavonaceae 170 and a homologue from Corynebacterium glutamicum designated Cg10062 share 34% sequence identity (54% similarity). The former catalyzes a key step in a bacterial catabolic pathway for the nematocide 1,3-dichloropropene, whereas the latter has no known biological activity. Although Cg10062 has the six active site residues (Pro-1, His-28, Arg-70, Arg-73, Tyr-103, Glu-114) that are critical for cis-CaaD activity, it shows only a low level cis-CaaD activity and lacks the specificity of cis-CaaD: Cg10062 processes both isomers of 3-chloroacrylate with a preference for the cis-isomer. Although the basis for these differences is unknown, a comparison of the crystal structures of the enzymes covalently modified by an adduct resulting from their incubation with the same inhibitor offers a possible explanation. A 6-residue active site loop in cis-CaaD shows a strikingly different conformation from that observed in Cg10062: the loop closes down on the active site of cis-CaaD, but not on that of Cg10062. In order to examine what this loop might contribute to cis-CaaD catalysis and specificity, the residues were changed individually to those found in Cg10062. Subsequent kinetic and mechanistic analysis suggests that the T34A mutant of cis-CaaD is more Cg10062-like. The mutant enzyme shows a 4-fold increase in Km (using cis-3-bromoacrylate), but not to the degree observed for Cg10062 (687-fold). The mutation also causes a 4-fold decrease in the burst rate (compared to the wild type cis-CaaD), whereas Cg10062 shows no burst rate. More telling is the reaction of the T34A mutant of cis-CaaD with the alternate substrate, 2,3-butadienoate. In the presence of NaBH4 and the allene, cis-CaaD is completely inactivated after one turnover due to the covalent modification of Pro-1. The same experiment with Cg10062 does not result in the covalent modification of Pro-1. The different outcomes are attributed to

  9. CIS-lunar space infrastructure lunar technologies: Executive summary

    NASA Technical Reports Server (NTRS)

    Faller, W.; Hoehn, A.; Johnson, S.; Moos, P.; Wiltberger, N.

    1989-01-01

    Technologies necessary for the creation of a cis-Lunar infrastructure, namely: (1) automation and robotics; (2) life support systems; (3) fluid management; (4) propulsion; and (5) rotating technologies, are explored. The technological focal point is on the development of automated and robotic systems for the implementation of a Lunar Oasis produced by Automation and Robotics (LOAR). Under direction from the NASA Office of Exploration, automation and robotics were extensively utilized as an initiating stage in the return to the Moon. A pair of autonomous rovers, modular in design and built from interchangeable and specialized components, is proposed. Utilizing a buddy system, these rovers will be able to support each other and to enhance their individual capabilities. One rover primarily explores and maps while the second rover tests the feasibility of various materials-processing techniques. The automated missions emphasize availability and potential uses of Lunar resources, and the deployment and operations of the LOAR program. An experimental bio-volume is put into place as the precursor to a Lunar environmentally controlled life support system. The bio-volume will determine the reproduction, growth and production characteristics of various life forms housed on the Lunar surface. Physicochemical regenerative technologies and stored resources will be used to buffer biological disturbances of the bio-volume environment. The in situ Lunar resources will be both tested and used within this bio-volume. Second phase development on the Lunar surface calls for manned operations. Repairs and re-configuration of the initial framework will ensue. An autonomously-initiated manned Lunar oasis can become an essential component of the United States space program.

  10. Small RNAs Originated from Pseudogenes: cis- or trans-Acting?

    PubMed Central

    Guo, Xingyi; Zhang, Zhaolei; Gerstein, Mark B.; Zheng, Deyou

    2009-01-01

    Pseudogenes are significant components of eukaryotic genomes, and some have acquired novel regulatory roles. To date, no study has characterized rice pseudogenes systematically or addressed their impact on the structure and function of the rice genome. In this genome-wide study, we have identified 11,956 non-transposon-related rice pseudogenes, most of which are from gene duplications. About 12% of the rice protein-coding genes, half of which are in singleton families, have a pseudogene paralog. Interestingly, we found that 145 of these pseudogenes potentially gave rise to antisense small RNAs after examining ∼1.5 million small RNAs from developing rice grains. The majority (>50%) of these antisense RNAs are 24-nucleotides long, a feature often seen in plant repeat-associated small interfering RNAs (siRNAs) produced by RNA-dependent RNA polymerase (RDR2) and Dicer-like protein 3 (DCL3), suggesting that some pseudogene-derived siRNAs may be implicated in repressing pseudogene transcription (i.e., cis-acting). Multiple lines of evidence, however, indicate that small RNAs from rice pseudogenes might also function as natural antisense siRNAs either by interacting with the complementary sense RNAs from functional parental genes (38 cases) or by forming double-strand RNAs with transcripts of adjacent paralogous pseudogenes (2 cases) (i.e., trans-acting). Further examinations of five additional small RNA libraries revealed that pseudogene-derived antisense siRNAs could be produced in specific rice developmental stages or physiological growth conditions, suggesting their potentially important roles in normal rice development. In summary, our results show that pseudogenes derived from protein-coding genes are prevalent in the rice genome, and a subset of them are strong candidates for producing small RNAs with novel regulatory roles. Our findings suggest that pseudogenes of exapted functions may be a phenomenon ubiquitous in eukaryotic organisms. PMID:19649160

  11. Geometry matters: inverse cytotoxic relationship for cis/trans-Ru(ii) polypyridyl complexes from cis/trans-[PtCl2(NH3)2].

    PubMed

    Wachter, Erin; Zamora, Ana; Heidary, David K; Ruiz, José; Glazer, Edith C

    2016-08-09

    Two thermally activated ruthenium(ii) polypyridyl complexes, cis-Ru(bpy)2Cl2 and trans-Ru(qpy)Cl2 were investigated to determine the impact of the geometric arrangement of the exchangable ligands on the potential of the compounds to act as chemotherapeutics. In contrast to the geometry requirements for cisplatin, trans-Ru(qpy)Cl2 was 7.1-9.5× more cytotoxic than cis-Ru(bpy)2Cl2. This discovery could open up a new area of metal-based chemotherapeutic research.

  12. Planning and setting objectives in field studies: Chapter 2

    USGS Publications Warehouse

    Fisher, Robert N.; Dodd, C. Kenneth

    2016-01-01

    This chapter enumerates the steps required in designing and planning field studies on the ecology and conservation of reptiles, as these involve a high level of uncertainty and risk. To this end, the chapter differentiates between goals (descriptions of what one intends to accomplish) and objectives (the measurable steps required to achieve the established goals). Thus, meeting a specific goal may require many objectives. It may not be possible to define some of them until certain experiments have been conducted; often evaluations of sampling protocols are needed to increase certainty in the biological results. And if sampling locations are fixed and sampling events are repeated over time, then both study-specific covariates and sampling-specific covariates should exist. Additionally, other critical design considerations for field study include obtaining permits, as well as researching ethics and biosecurity issues.

  13. Characterization of eastern US spruce-fir soils. Book chapter

    SciTech Connect

    Fernandez, I.J.

    1992-01-01

    The spruce-fir forest of the eastern United States encompasses a diverse range of edaphic conditions due to differences in surficial geology, mineralogy, elevation, and climate. This chapter describes the characteristics of soils supporting eastern spruce-fir ecosystems, including soil properties that are important in understanding forest function and the consequences of atmospheric deposition to forested ecosystems. Chapter 1 describes the silvical characteristics of the spruce-fir forest. The Spruce-Fir Research Cooperative included six intensive study sites; five were high-elevation research sites located from western North Carolina to New Hampshire, with one low-elevation site in Maine. Information gained from research at these sites, and other relevant research from these regions, provides the basis for this description of eastern U. S. spruce-fir soils.

  14. Development of a Launch Vehicle Manufacturing Process. Chapter 4

    NASA Technical Reports Server (NTRS)

    Vickers, John; Munafo, Paul M. (Technical Monitor)

    2002-01-01

    One of the goals of this chapter is to provide sufficient information so that you can develop a manufacturing process for a potential launch vehicle. With the variety of manufacturing options available, you might ask how this can possibly be done in the span of a single chapter. Actually, it will be quite simple because a basic manufacturing process is nothing more than a set of logical steps that are iterated until they produce a desired product. Although these statements seem simple and logical, don't let this simplicity fool you. Manufacturing problems with launch vehicles and their subassemblies have been the primary cause of project failures because the vehicle concept delivered to the manufacturing floor could not be built as designed.

  15. Hydrologic processes and the water budget: Chapter 2

    USGS Publications Warehouse

    Rosenberry, Donald O.; Winter, Thomas C.; Winter, Thomas C.; Likens, Gene E.

    2009-01-01

    This chapter focuses on the hydrological setting of Mirror Lake and its water budget. It first describes the glacial deposits and bedrock topography in the Mirror Lake area. It then provides an overview of the hydrologic processes associated with Mirror Lake and examines the field and analytical methods used to determine its water budget. It presents results from the hydrologic studies, which are based on monthly and annual water budgets for the calendar years 1981 through 2000.

  16. HARAMEKHALA – TANTRA (THE FIRST CHAPTER ON MEDICINE)

    PubMed Central

    Sharma, P.V.

    1986-01-01

    This translation of Haramekhala – tantra of the author is based on Banaras Hindu University manuscript which seems to be a novel one. The manuscript runs into 133 stanzas in all in the form of dialogue between lord Siva and goddess Parvati. This is only the first chapter (of the great work) dealing with medicine. From stanza 109 onwards some magic spells are described and as such those have not been included in this translation. PMID:22557515

  17. Habitat characteristics of North American tortoises: chapter 9

    USGS Publications Warehouse

    Nussear, Kenneth E.; Tuberville, Tracey D.

    2014-01-01

    North American tortoises are distributed in semi-arid and temperate deserts and coastal regions of the southern United States and Mexico. The five species currently recognized each have specific habitat requirements, which they fulfill through their selection of, and interaction with unique habitat constituents. In this chapter we discuss the physiographic and geological associations, perennial and annual vegetation components, shelter sites, and climatic conditions associated with the species’ habitats, as well as the potential threats to their habitat.

  18. Introduction: Aims and Requirements of Future Aerospace Vehicles. Chapter 1

    NASA Technical Reports Server (NTRS)

    Rodriguez, Pedro I.; Smeltzer, Stanley S., III; McConnaughey, Paul (Technical Monitor)

    2001-01-01

    The goals and system-level requirements for the next generation aerospace vehicles emphasize safety, reliability, low-cost, and robustness rather than performance. Technologies, including new materials, design and analysis approaches, manufacturing and testing methods, operations and maintenance, and multidisciplinary systems-level vehicle development are key to increasing the safety and reducing the cost of aerospace launch systems. This chapter identifies the goals and needs of the next generation or advanced aerospace vehicle systems.

  19. Chapter 16Tracing Nitrogen Sources and Cycling in Catchments

    USGS Publications Warehouse

    Kendall, Carol

    1998-01-01

    This chapter focuses on the uses of isotopes to understand water chemistry.I Isotopic compositions generally cannot be interpreted successfully in the absence of other chemical and hydrologic data. The chapter focusses on uses of isotopes in tracing sources and cycling of nitrogen in the water-component of forested catchment, and on dissolved nitrate in shallow waters, nutrient uptake studies in agricultural areas, large-scale tracer experiments, groundwater contamination studies, food-web investigations, and uses of compound-specific stable isotope techniques. Shallow waters moving along a flowpath through a relatively uniform material and reacting with minerals probably do not achieve equilibrium but gradually approach some steady-state composition. The chapter also discusses the use of isotopic techniques to assess impacts of changes in land-management practices and land use on water quality. The analysis of individual molecular components for isotopic composition has much potential as a method for tracing the source, biogeochemistry, and degradation of organic liquids and gases because different materials have characteristic isotope spectrums or biomarkers.

  20. Inducible defenses in food webs: Chapter 3.4

    USGS Publications Warehouse

    Vos, Matthijs; Kooi, Bob W.; DeAngelis, Donald L.; Mooij, Wolf M.; de Ruiter, Peter; Wolters, Volkmar; Moore, John C.; Melville-Smith, Kimberly

    2005-01-01

    This chapter reviews the predicted effects of induced defenses on trophic structure and two aspects of stability, “local” stability and persistence, as well as presenting novel results on a third, resilience. Food webs are structures of populations in a given location organized according to their predator–prey interactions. Interaction strengths and, therefore, prey defenses are generally recognized as important ecological factors affecting food webs. Despite this, surprisingly, little light has been shed on the food web-level consequences of inducible defenses. Inducible defenses occur in many taxa in both terrestrial and aquatic food webs. They include refuge use, reduced activity, adaptive life history changes, the production of toxins, synomones and extrafloral nectar, and the formation of colonies, helmets, thorns, or spines. In the chapter, theoretical results for the effects of inducible defenses on trophic structure and the three aspects of stability are reviewed. This is done, in part, using bifurcation analysis—a type of analysis that is applied to nonlinear dynamic systems described by a set of ordinary differential or difference equations. The work presented in the chapter suggests that heterogeneity, as caused by induced defenses in prey species, has major effects on the functioning of food webs. Inducible defenses occur in many species in both aquatic and terrestrial systems, and theoretical work indicates they have major effects on important food web properties such as trophic structure, local stability, persistence, and resilience.

  1. The ecological situation and C.I.S. scientists' work on the SPS problem

    NASA Astrophysics Data System (ADS)

    Prisniakov, V.

    A brief historical perspective of the former USSR and current Confederation of Independent States (CIS) research and development activities relating to the Solar Power Satellite (SPS) concept is presented. Particular emphasis is on the ecological aspects of the SPS concept.

  2. Microwave Spectrum and Molecular Structure of the ARGON-CIS-1,2-DICHLOROETHYLENE Complex

    NASA Astrophysics Data System (ADS)

    Marshall, Mark D.; Leung, Helen O.; Nelson, Craig J.; Yoon, Leonard H.

    2016-06-01

    The non-planar molecular structure of the complex formed between the argon atom and cis-1,2-dichloroethylene is determined via analysis of its microwave spectrum. Spectra of the 35Cl and 37Cl isotopologues are observed in natural abundance and the nuclear quadrupole splitting due to the two chlorine nuclei is fully resolved. In addition, the complete quadrupole coupling tensor for the cis-1,2-dichloroethylene molecule, including the single non-zero off-diagonal element, has been determined. Unlike the argon-cis-1,2-difluoroethylene and the argon-vinyl chloride complexes, tunneling between the two equivalent non-planar configurations of argon-cis-1,2-dichloroethylene is not observed.

  3. cis-3-Chloroacrylic Acid: A New Cotton Defoliant and Crop Desiccant.

    PubMed

    Herrett, R A; Kurtz, A N

    1963-09-20

    cis-3-Chloroacrylic acid is a potent cotton defoliant and a crop desiccant. Relationships between structure and activity indicate a relatively high degree of specificity, since minor modifications in structure result in loss of activity.

  4. Isolation of cis-3-Amino-l-Proline from Cultured Mycelia of Morchella esculenta Fr.

    PubMed

    Moriguchi, M; Sada, S; Hatanaka, S

    1979-11-01

    cis-3-Amino-l-proline, identified once as a nonprotein amino acid from the fruiting bodies of Morchella esculenta Fr., was isolated also from the growth medium and cultured mycelia of the same fungus.

  5. Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

    PubMed Central

    Ivan, Andra; Halfon, Marc S; Sinha, Saurabh

    2008-01-01

    We consider the problem of predicting cis-regulatory modules without knowledge of motifs. We formulate this problem in a pragmatic setting, and create over 30 new data sets, using Drosophila modules, to use as a 'benchmark'. We propose two new methods for the problem, and evaluate these, as well as two existing methods, on our benchmark. We find that the challenge of predicting cis-regulatory modules ab initio, without any input of relevant motifs, is a realizable goal. PMID:18226245

  6. Précis of The brain and emotion.

    PubMed

    Rolls, E T

    2000-04-01

    The topics treated in The brain and emotion include the definition, nature, and functions of emotion (Ch. 3); the neural bases of emotion (Ch. 4); reward, punishment, and emotion in brain design (Ch. 10); a theory of consciousness and its application to understanding emotion and pleasure (Ch. 9); and neural networks and emotion-related learning (Appendix). The approach is that emotions can be considered as states elicited by reinforcers (rewards and punishers). This approach helps with understanding the functions of emotion, with classifying different emotions, and in understanding what information-processing systems in the brain are involved in emotion, and how they are involved. The hypothesis is developed that brains are designed around reward- and punishment-evaluation systems, because this is the way that genes can build a complex system that will produce appropriate but flexible behavior to increase fitness (Ch. 10). By specifying goals rather than particular behavioral patterns of responses, genes leave much more open the possible behavioral strategies that might be required to increase fitness. The importance of reward and punishment systems in brain design also provides a basis for understanding the brain mechanisms of motivation, as described in Chapters 2 for appetite and feeding, 5 for brain-stimulation reward, 6 for addiction, 7 for thirst, and 8 for sexual behavior.

  7. Photochemical trans-/cis-isomerization and quantitation of zearalenone in edible oils.

    PubMed

    Köppen, Robert; Riedel, Juliane; Proske, Matthias; Drzymala, Sarah; Rasenko, Tatjana; Durmaz, Vedat; Weber, Marcus; Koch, Matthias

    2012-11-28

    The emphasis of the present work was to investigate the photochemical conversion of trans- to cis-zearalenone in edible oils under real-life conditions. For quantitation purposes a cis-zearalenone standard was synthesized and characterized for its identity and purity (≥95%) by (1)H NMR, X-ray crystallography, HPLC fluorescence and mass spectrometric detection. In a sample survey of 12 edible oils (9 corn oils, 3 hempseed oils) from local supermarkets all corn oils contained trans-zearalenone (median 194 μg/kg), but no cis-zearalenone was detected. For alteration studies trans-zearalenone contaminated corn oils were exposed to sunlight over 4 and 30 weeks, revealing an obvious shift toward cis-zearalenone up to a cis/trans ratio of 9:1 by storage in colorless glass bottles. Irradiation experiments of trans-zearalenone in different organic solvents confirmed the preferred formation of cis-zearalenone possibly caused by entropic effects rather than by enthalpic entities as investigated by quantum chemical and classical force field simulations.

  8. Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry.

    PubMed

    Zheng, Xueyun; Renslow, Ryan S; Makola, Mpho M; Webb, Ian K; Deng, Liulin; Thomas, Dennis G; Govind, Niranjan; Ibrahim, Yehia M; Kabanda, Mwadham M; Dubery, Ian A; Heyman, Heino M; Smith, Richard D; Madala, Ntakadzeni E; Baker, Erin S

    2017-04-06

    Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/trans isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.

  9. The Clinical Interview Schedule-Revised (CIS-R)-Malay Version, Clinical Validation.

    PubMed

    Subramaniam, Kavitha; Krishnaswamy, Saroja; Jemain, Abdul Aziz; Hamid, Abdul; Patel, Vikram

    2006-01-01

    Use of instruments or questionnaires in different cultural settings without proper validation can result in inaccurate results. Issues like reliability, validity, feasibility and acceptability should be considered in the use of an instrument. The study aims to determine the usefulness of the CIS-R Malay version in detecting common mental health problems specifically to establish the validity. The CIS-R instrument (PROQSY* format) was translated through the back translation process into Malay. Inter rater reliability was established for raters who were medical students. Cases and controls for the study were psychiatric in patients, out patient and relatives or friends accompanying the patients to the clinic or visiting the inpatients. The Malay version of CIS-R was administered to all cases and controls. All cases and controls involved in the study were rated by psychiatrists for psychiatric morbidity using the SCID as a guideline. Specificity and sensitivity of the CIS-R to the assessment by the psychiatrist were determined. The Malay version of CIS-R showed 100% sensitivity and 96.15% specificity at a cut off score of 9. The CIS-R can be a useful instrument for clinical and research use in the Malaysian population for diagnosing common mental disorders like depression and anxiety.

  10. Sensory integration functions of children with cochlear implants.

    PubMed

    Koester, AnjaLi Carrasco; Mailloux, Zoe; Coleman, Gina Geppert; Mori, Annie Baltazar; Paul, Steven M; Blanche, Erna; Muhs, Jill A; Lim, Deborah; Cermak, Sharon A

    2014-01-01

    OBJECTIVE. We investigated sensory integration (SI) function in children with cochlear implants (CIs). METHOD. We analyzed deidentified records from 49 children ages 7 mo to 83 mo with CIs. Records included Sensory Integration and Praxis Tests (SIPT), Sensory Processing Measure (SPM), Sensory Profile (SP), Developmental Profile 3 (DP-3), and Peabody Developmental Motor Scales (PDMS), with scores depending on participants' ages. We compared scores with normative population mean scores and with previously identified patterns of SI dysfunction. RESULTS. One-sample t tests revealed significant differences between children with CIs and the normative population on the majority of the SIPT items associated with the vestibular and proprioceptive bilateral integration and sequencing (VPBIS) pattern. Available scores for children with CIs on the SPM, SP, DP-3, and PDMS indicated generally typical ratings. CONCLUSION. SIPT scores in a sample of children with CIs reflected the VPBIS pattern of SI dysfunction, demonstrating the need for further examination of SI functions in children with CIs during occupational therapy assessment and intervention planning.

  11. Synthesis of trans- and cis-4'-hydroxylomustine and development of validated analytical method for lomustine and trans- and cis-4'-hydroxylomustine in canine plasma.

    PubMed

    Dirikolu, L; Chakkath, T; Fan, T; Mente, Nolan R

    2009-01-01

    In veterinary medicine, lomustine has been successfull used primarily for the treatment of resistant lymphoma and also for the treatment of mast cell tumors, intracranial meningioma, epitheliotropic lymphoma, and histiocytic sarcoma in dogs either alone or in combination with other chemotherapeutic agents. Even though lomustine is commonly used in dogs primarily for the treatment of resistant lymphoma, there is no pharmacokinetics information available regarding this compound in dogs. In the present study, we developed and validated a simple high-performance liquid chromatography (HPLC) method with a one-step liquid-liquid extraction procedure to detect and quantify lomustine and its two monohydroxylated metabolites (trans- and cis-4'-hydroxylomustine) in canine plasma for future pharmacokinetic studies. The HPLC-diode-array detection method reported here readily detects lomustine, cis-4'-hydroxylomustine, and trans-4'-hydroxylomustine in canine plasma with a limit of detection of lomustine, cis-4'-hydroxylomustine, and trans-4'-hydroxylomustine in plasma of about 10 ng/120 microL, 5 ng/120 microL, and 5 ng/120 microL, respectively. The mean extraction efficiency values for lomustine, cis-4'-hydroxylomustine, and trans-4'-hydroxylomustine were 73%, 90%, and 89%, respectively, from canine plasma samples on HPLC. The present study also provides stability information about lomustine and its two monohydroxylated metabolites in canine plasma and methanol solution stored at various conditions.

  12. Rotational Analysis of Bands in the High-Resolution Infrared Spectra of cis,cis- and trans,trans-1,4-difluorobutadiene-2-d1

    SciTech Connect

    Craig, Norman C.; Easterday, Clay C.; Nemchick, Deacon J.; Williamson, Drew; Sams, Robert L.

    2012-02-01

    Pure samples of cis,cis- and trans,trans-1,4-difluorobutadiene-2-d1 have been synthesized, and high-resolution (0.0015 cm-1) infrared spectra have been recorded for these nonpolar molecules in the gas phase. For the cis,cis isomer, the rotational structure in two C-type bands at 775 and 666 cm-1 and one A-type band at 866 cm-1 has been analyzed to yield a combined set of 2020 ground state combination differences (GSCDs). Ground state rotational constants fit to these GSCDs are A0 = 0.4195790(4), B0 = 0.0536508(8), and C0 = 0.0475802(9) cm-1. For the trans,trans isomer, three Ctype bands at 856, 839, and 709 cm-1 have been investigated to give a combined set of 1624 GSCDs. Resulting ground state rotational constants for this isomer are A0 = 0.9390117(8), B0 = 0.0389225(4), and C0 = 0.0373778(3) cm-1. Small inertial defects confirm the planarity of both isomers in the ground state. Upper state rotational constants have been determined for most of the transitions. The ground state rotational constants for the two isotopologues will contribute to the data set needed for determining semiexperimental equilibrium structures for the nonpolar isomers of 1,4- difluorobutadiene.

  13. Integration of human papillomavirus type 16 in cervical cancer cells

    PubMed Central

    Kanopiene, Daiva; Stumbryte, Ausra; Bausyte, Raminta; Kirvelaitis, Edgaras; Simanaviciene, Vaida; Zvirbliene, Aurelija

    2015-01-01

    Cervical cancer remains an important cause of women morbidity and mortality. The progression of cervical pathology correlates with the HPV integration into the host genome. However, the data on the viral integration status in cervical dysplasias are controversial. The aim of the current study was to evaluate the status of HPV integration in two types of cervical pathology – invasive and non invasive cervical cancer (e.g. carcinoma in situ). 156 women were included in the study: 66 women were diagnosed with invasive cervical cancer (CC) and 90 with non invasive cervical cancer (carcinoma in situ, CIS). 74.2% [95% PI: 63.64÷84.76] of specimens collected from women with diagnosed CC and 85.6% [95% PI: 85.53÷92.85] of CIS specimens were positive for HPV. The most prevalent HPV genotype in both groups was HPV16. To evaluate HPV integration, three selected HPV16 E2 gene fragments were analyzed by PCR. In the majority of CC and CIS specimens the amplification of all three HPV16 E2 gene fragments was observed. The episomal HPV16 form was detected in the majority of CC and CIS specimens. The deletion of all three HPV16 E2 gene fragments was detected in 9.4% of CC specimens and 2.2% of CIS specimens. Finally, integration status could not be used as diagnostical additional test to distinguish between invasive and non invasive cervical cancer. PMID:28352670

  14. Chapter Leadership Profiles among Citizen Activists in the Drunk Driving Movement.

    ERIC Educational Resources Information Center

    Ungerleider, Steven; Bloch, Steven

    1987-01-01

    Study of Mothers Against Drunk Drivers (MADD) analyzed the chapter emphasis, levels of satisfaction and relationship to national office on several measures. Surveying 212 chapters, MADD leadership provided profile of independent, autonomous activists in the drunk driving countermeasure movement. (Author)

  15. Necessity and Utility of a Virtual Laboratory in AVT-113. Chapter 2

    NASA Technical Reports Server (NTRS)

    Lamar, John E.; Luckring, James M.

    2009-01-01

    The Virtual Laboratory (VL) was to be an integral part of the database service that NASA provided to the international community, and for a brief period the VL was fully operational in the CAWAPI facet of the AVT-113 task group. This chapter details how one can construct a VL and also some of the lessons learned along the way that required changes to be made. The VL was to support both the CAWAPI and VFE-2 facets but due to the lack of funding and sufficient Information Technology (IT) support people with the right skills, the VFE-2 facet only reached the advanced planning stage with little software in place. However, both efforts point out the value of a VL in a task group like AVT-113 and illustrate that there needs to be a budgeted item for the IT effort to bring the VL to full operational status in each application.

  16. Streamflow and fluvial sediment transport in Pool C, restored section of the Kissimmee River: Chapter 2

    USGS Publications Warehouse

    Mossa, Joann; Gellis, Allen C.; Hupp, Cliff R.; Pearman, J. Leroy; Garfield, Ursula; Schenk, Edward R.; Rasmussen, Jim; Habermehl, Philip J.; Mossa, Joann; Valdes, Jose

    2009-01-01

    The Kissimmee River Restoration Project was authorized by Congress in 1992 to restore more than 64 km2 (square kilometers) of river/floodplain ecosystem including 69 km of meandering river channel and 10,900 hectares (ha) of wetlands. Although biologic monitoring is an integral and active part of the Kissimmee River restoration, by 2007 geomorphic monitoring that included sediment transport was lacking. In 2007, the U.S. Geological Survey (USGS) entered into a cooperative agreement with the South Florida Water Management District (SFWMD) to determine sediment transport characteristics of the restored section of the Kissimmee River in Pool C. Sediment transport characteristics that are monitored include suspended-sediment concentrations and loads, bedload, and bed material. In addition, the organic content of suspended sediment and bedload was determined. This chapter describes methods and results of the sediment transport monitoring from July 2007 through September 2008 in the Kissimmee River in Pool C.

  17. Fundamentals of Physics, Part 3 (Chapters 22-33)

    NASA Astrophysics Data System (ADS)

    Halliday, David; Resnick, Robert; Walker, Jearl

    2004-03-01

    Chapter 21. Electric Charge. Why do video monitors in surgical rooms increase the risk of bacterial contamination? 21-1 What Is Physics? 21-2 Electric Charge. 21-3 Conductors and Insulators. 21-4 Coulomb's Law. 21-5 Charge Is Quantized. 21-6 Charge Is Conserved. Review & Summary. Questions. Problems. Chapter 22. Electric Fields. What causes sprites, those brief .ashes of light high above lightning storms? 22-1 What Is Physics? 22-2 The Electric Field. 22-3 Electric Field Lines. 22-4 The Electric Field Due to a Point Charge. 22-5 The Electric Field Due to an Electric Dipole. 22-6 The Electric Field Due to a Line of Charge. 22-7 The Electric Field Due to a Charged Disk. 22-8 A Point Charge in an Electric Field. 22-9 A Dipole in an Electric Field. Review & Summary. Questions. Problems. Chapter 23. Gauss' Law. How can lightning harm you even if it do es not strike you? 23-1 What Is Physics? 23-2 Flux. 23-3 Flux of an Electric Field. 23-4 Gauss' Law. 23-5 Gauss' Law and Coulomb's Law. 23-6 A Charged Isolated Conductor. 23-7 Applying Gauss' Law: Cylindrical Symmetry. 23-8 Applying Gauss' Law: Planar Symmetry. 23-9 Applying Gauss' Law: Spherical Symmetry. Review & Summary. Questions. Problems. Chapter 24. Electric Potential. What danger does a sweater pose to a computer? 24-1 What Is Physics? 24-2 Electric Potential Energy. 24-3 Electric Potential. 24-4 Equipotential Surfaces. 24-5 Calculating the Potential from the Field. 24-6 Potential Due to a Point Charge. 24-7 Potential Due to a Group of Point Charges. 24-8 Potential Due to an Electric Dipole. 24-9 Potential Due to a Continuous Charge Distribution. 24-10 Calculating the Field from the Potential. 24-11 Electric Potential Energy of a System of Point Charges. 24-12 Potential of a Charged Isolated Conductor. Review & Summary. Questions. Problems. Chapter 25. Capacitance. How did a fire start in a stretcher being withdrawn from an oxygen chamber? 25-1 What Is Physics? 25-2 Capacitance. 25-3 Calculating the Capacitance. 25

  18. Chapter 2: Simulations of the Structure of Cellulose

    SciTech Connect

    Matthews, J. F.; Himmel, M. E.; Brady, J. W.

    2010-01-01

    Cellulose is the homopolymer of (1 {yields} 4)-{beta}-D-glucose. The chemical composition of this polymer is simple, but understanding the conformation and packing of cellulose molecules is challenging. This chapter describes the structure of cellulose from the perspective of molecular mechanics simulations, including conformational analysis of cellobiose and simulations of hydrated cellulose I{beta} with CSFF and GLYCAM06, two sets of force field parameters developed specifically for carbohydrates. Many important features observed in these simulations are sensitive to differences in force field parameters, giving rise to dramatically different structures. The structures and properties of non-naturally occurring cellulose allomorphs (II, III, and IV) are also discussed.

  19. Skull lichens: a curious chapter in the history of phytotherapy.

    PubMed

    Modenesi, P

    2009-04-01

    Lichens growing on skulls were known in late medieval times as usnea or moss of a dead man's skull and were recommended as highly beneficial in various diseases. They were, in addition, the main ingredient of Unguentum armariun, a liniment used in a curious medical practice: the magnetic cure of wounds. We can place this chapter of the history of phytotherapy within the wider cultural context of the period, which saw the definition of nature become increasingly more fluid and open to a variety of novel interpretations.

  20. Aerothermodynamics of Blunt Body Entry Vehicles. Chapter 3

    NASA Technical Reports Server (NTRS)

    Hollis, Brian R.; Borrelli, Salvatore

    2011-01-01

    In this chapter, the aerothermodynamic phenomena of blunt body entry vehicles are discussed. Four topics will be considered that present challenges to current computational modeling techniques for blunt body environments: turbulent flow, non-equilibrium flow, rarefied flow, and radiation transport. Examples of comparisons between computational tools to ground and flight-test data will be presented in order to illustrate the challenges existing in the numerical modeling of each of these phenomena and to provide test cases for evaluation of Computational Fluid Dynamics (CFD) code predictions.

  1. Fundamentals of Physics, Part 2 (Chapters 12-20)

    NASA Astrophysics Data System (ADS)

    Halliday, David; Resnick, Robert; Walker, Jearl

    2003-12-01

    Chapter 12 Equilibrium and Elasticity. What injury can occur to a rock climber hanging by a crimp hold? 12-1 What Is Physics? 12-2 Equilibrium. 12-3 The Requirements of Equilibrium. 12-4 The Center of Gravity. 12-5 Some Examples of Static Equilibrium. 12-6 Indeterminate Structures. 12-7 Elasticity. Review & Summary Questions Problems. Chapter 13 Gravitation. What lies at the center of our Milky Way galaxy? 13-1 What Is Physics? 13-2 Newton's Law of Gravitation. 13-3 Gravitation and the Principle of Superposition. 13-4 Gravitation Near Earth's Surface. 13-5 Gravitation Inside Earth. 13-6 Gravitational Potential Energy. 13-7 Planets and Satellites: Kepler's Laws. 13-8 Satellites: Orbits and Energy. 13-9 Einstein and Gravitation. Review & Summary Questions Problems. Chapter 14 Fluids. What causes ground effect in race car driving? 14-1 What Is Physics? 14-2 What Is a Fluid? 14-3 Density and Pressure. 14-4 Fluids at Rest. 14-5 Measuring Pressure. 14-6 Pascal's Principle. 14-7 Archimedes' Principle. 14-8 Ideal Fluids in Motion. 14-9 The Equation of Continuity. 14-10 Bernoulli's Equation. Review & SummaryQuestionsProblems. Chapter 15 Oscillations. What is the "secret" of a skilled diver's high catapult in springboard diving? 15-1 What Is Physics? 15-2 Simple Harmonic Motion. 15-3 The Force Law for Simple Harmonic Motion. 15-4 Energy in Simple Harmonic Motion. 15-5 An Angular Simple Harmonic Oscillator. 15-6 Pendulums. 15-7 Simple Harmonic Motion and Uniform Circular Motion. 15-8 Damped Simple Harmonic Motion. 15-9 Forced Oscillations and Resonance. Review & Summary Questions Problems. Chapter 16 Waves--I. How can a submarine wreck be located by distant seismic stations? 16-1 What Is Physics? 16-2 Types of Waves. 16-3 Transverse and Longitudinal Waves. 16-4 Wavelength and Frequency. 16-5 The Speed of a Traveling Wave. 16-6 Wave Speed on a Stretched String. 16-7 Energy and Power of a Wave Traveling Along a String. 16-8 The Wave Equation. 16-9 The Principle of Superposition

  2. MIL-STD-1553 multiplex applications handbook. Addendum: Chapter 11

    NASA Astrophysics Data System (ADS)

    1983-03-01

    This document contains data words and message formats to be used for MIL-STD-1553 data bust applications. This document is intended as a guide for military & private sector designers to identify standard data words and messages for use in future avionics systems and subsystems. This report is to be Chapter 11 in the existing MIL-STD-1553 Multiplex Applications handbook which the Defense Materials Standards and Specifications Office (DMSSO) plans for publications as a Military Handbook on MIL-STD-1553.

  3. Transiently-Evoked Otoacoustic Emissions (teoaes) in Monitoring Adult Cis-Platin Patients.

    NASA Astrophysics Data System (ADS)

    Ribera, John Everett

    1995-01-01

    There is evidence to suggest that otoacoustic emissions (OAEs) reflect the integrity of cochlear outer hair cell (OHC) function. Cis-platin (CDDP) is a potent ototoxic chemotherapeutic agent that tends to destroy or disable OHCs. Therefore, this study was designed to answer the following questions: (1) Can TEOAEs be used in monitoring for ototoxicity in adult VA oncology patients receiving CDDP treatment? (2) If so, how sensitive are TEOAEs in detecting significant changes when compared to Audiometry in a VA population? and (3) Which of several TEOAE measures is the most sensitive to changes in hearing due to CDDP ototoxicity in a VA population?. In Experiment I, VA Medical Center patients were recruited (control group) and tested using a conventional audiometer and the ILO88 Otoacoustic Analyzer on three separate days. Data from this experiment were used to develop change criteria in each of four TEOAE measures (Reproducibility, Compare, 1 kHz Band Analysis, and OAE Response) for Experiment II. Experiment II was of similar design with the exception that the subjects (experimental group) were patients enrolled from the oncology ward and were administered CDDP after the first and second test sessions. Data from both groups and all test measures revealed (1) that there was no ear effect in any of the test conditions, (2) there was a group (drug) effect, and (3) there was a frequency effect at 2 kHz. Audiometry detected changes in 56% of the experimental subjects, while the number of changes varied among the TEOAE measures studied. Compare agreed with Audiometry more often and performed better than any other TEOAE measure in detecting change. Based on these findings, incorporation of Compare into an audiometric test battery to monitor for ototoxicity in the VA population is feasible. There is evidence to suggest that as measurement techniques are refined TEOAE analysis will become a valid test for monitoring of adult CDDP patients.

  4. Molecular mechanism of 9-cis-retinoic acid inhibition of adipogenesis in 3T3-L1 cells

    SciTech Connect

    Sagara, Chiaki; Takahashi, Katsuhiko; Kagechika, Hiroyuki; Takahashi, Noriko

    2013-03-29

    Highlights: ► We examined the effects of 9-cis-RA on adipogenesis in mouse preadipocyte 3T3-L1. ► 9-cis-RA inhibited lipid accumulation in adipogenetically-induced 3T3-L1 cells. ► A RXR pan-antagonist suppressed the inhibitory effects of 9-cis-RA on adipogenesis. ► This antagonist had no effects on RXRα and PPARγ levels in 9-cis-RA-treated cells. ► 9-cis-RA-induced decrease in both RXRα and PPARγ was independent of RXR activation. -- Abstract: Retinoic acid (RA) signaling is mediated by specific nuclear hormone receptors. Here we examined the effects of 9-cis-RA on adipogenesis in mouse preadipocyte 3T3-L1 cells. 9-cis-RA inhibits the lipid accumulation of adipogenetically induced 3T3-L1 cells. The complex of retinoid X receptor α (RXRα) with peroxisome proliferator-activated receptor γ (PPARγ) is a major transcription factor in the process of adipogenesis, and the levels of these molecules were decreased by 9-cis-RA treatment. A RXR pan-antagonist suppressed 9-cis-RA’s inhibitory effects on adipogenesis, but not on the intracellular levels of both RXRα and PPARγ. These results suggest that 9-cis-RA could inhibit adipogenesis by activating RXR, and decrease both RXR and PPARγs levels in a RXR activation-independent manner.

  5. Preparation and characterization of cis-{Lambda}-[Ru(bpy){sub 2}(py)(O)]{sup 2+}

    SciTech Connect

    Hua, Xiao; Lappin, A.G.

    1995-02-15

    High-oxidation-state oxo complexes of ruthenium with polypyridine ligands such as cis-[Ru(bpy){sub 2}(py)O]{sup 2+} (bpy = 2,2{prime}-bipyridine, py = pyridine) are efficient stoichiometric and catalytic oxidants in a variety of organic and inorganic oxidation reactions. Recently, it was also reported that cis-[Ru(bpy){sub 2}(py)O]{sup 2+} is an efficient DNA cleavage agent. The results of mechanistic studies involving cis-[Ru(bpy){sub 2}(py)(O)]{sup 2+} suggest that oxidation of PPh{sub 3} to Ph{sub 3}PO or (CH{sub 3}){sub 2}S to (CH{sub 3}){sub 2}SO occurs by O atom transfer in oxidation of alcohols to aldehydes may occur by hydride transfer and oxidation of hydroquinones occurs by proton-coupled electron transfer. The complex cis-[Ru(bpy){sub 2}(py)(O)]{sup 2+} and its reduced form, cis-[Ru(bpy){sub 2}(py)(H{sub 2}O)]{sup 2+}, are chiral at the metal center. Stereoselective oxygen atom transfer from the chiral oxidant to an organic substrate is a possibility. Most well-studied asymmetric oxidation reactions of this sort are dependent on the selectivity of chiral ligands. Stereoselective oxidation directly involving the chiral metal center has not been studied extensively although the topic has been addressed. In this paper, the preparation and characterization of optically active cis-[Ru(bpy){sub 2}(py)(O)]{sup 2+} from optically active cis-[Ru(bpy){sub 2}(py)(H{sub 2}O)]{sup 2+} and the asymmetric oxidation of methyl p-tolyl sulfide by this chiral oxidant to chiral sulfoxide are reported.

  6. On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions

    NASA Astrophysics Data System (ADS)

    Tarpine, Ryan; Istrail, Sorin

    The regulatory genome is about the “system level organization of the core genomic regulatory apparatus, and how this is the locus of causality underlying the twin phenomena of animal development and animal evolution” (E.H. Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Academic Press, 2006). Information processing in the regulatory genome is done through regulatory states, defined as sets of transcription factors (sequence-specific DNA binding proteins which determine gene expression) that are expressed and active at the same time. The core information processing machinery consists of modular DNA sequence elements, called cis-modules, that interact with transcription factors. The cis-modules “read” the information contained in the regulatory state of the cell through transcription factor binding, “process” it, and directly or indirectly communicate with the basal transcription apparatus to determine gene expression. This endowment of each gene with the information-receiving capacity through their cis-regulatory modules is essential for the response to every possible regulatory state to which it might be exposed during all phases of the life cycle and in all cell types. We present here a set of challenges addressed by our CYRENE research project aimed at studying the cis-regulatory code of the regulatory genome. The CYRENE Project is devoted to (1) the construction of a database, the cis-Lexicon, containing comprehensive information across species about experimentally validated cis-regulatory modules; and (2) the software development of a next-generation genome browser, the cis-Browser, specialized for the regulatory genome. The presentation is anchored on three main computational challenges: the Gene Naming Problem, the Consensus Sequence Bottleneck Problem, and the Logic Function Inference Problem.

  7. Chapter 2 Formula, 1989-90: Major Points. Publication No. 89.32.

    ERIC Educational Resources Information Center

    Baenen, Nancy R.

    Programs implemented in 1989-90 by the Austin (Texas) Independent School District (AISD) using Chapter 2 Formula federal funds are described. Chapter 2 Formula provides federal funds to the states through the Elementary and Secondary Education Act of 1965 as amended in 1988. Chapter 2 funds can support programs that meet the educational needs of…

  8. Chapter 12: the anatomical foundations of clinical neurology.

    PubMed

    Bentivoglio, Marina; Mazzarello, Paolo

    2010-01-01

    The chapter provides an itinerary of knowledge on nervous system anatomy as one of the pillars of clinical neurology. The journey starts from the Renaissance explosion on the approach to the human body, its functions and its diseases, dealing with the seminal contributions of Leonardo da Vinci and Vesalius. The itinerary proceeds through the contributions of the 17th century, especially by Thomas Willis and the pioneering investigations of Marcello Malpighi and Antony van Leeuwenhoek, and onto the 18th century. The itinerary thus leads to the progress from gross anatomy to the microscopic investigation of the nervous system in the 19th century: the reticular theories, the revolution of the neural doctrine and their protagonists (Camillo Golgi and Santiago Ramón y Cajal), which initiated the modern era of the neurosciences. The chapter also includes sections on the contributions of developmental neuroanatomy to neurology, on the history of tract tracing, and on the cytoarchitecture of the cerebral cortex. The never-ending story of the anatomical foundations of clinical neurology continues to evolve at the dawn of the 21st century, including knowledge that guides deep brain stimulation, and novel approaches to the anatomy of the living brain based on rapidly developing neuroimaging technology.

  9. Synthesis of 7-azabicyclo[2.2.1]heptane and 2-oxa-4-azabicyclo[3.3.1]non-3-ene derivatives by base-promoted heterocyclization of alkyl N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)carbamates and N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamides.

    PubMed

    Gómez-Sanchez, Elena; Soriano, Elena; Marco-Contelles, José

    2007-11-09

    We have studied the base-promoted heterocyclization of alkyl N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)carbamates and N-(cis(trans)-3,trans(cis)-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamides, investigating the effect of the nitrogen protecting group and the relative configuration of the leaving group at C3 and C4 on the outcome of this reaction. We have observed that the sodium hydride-promoted heterocyclization of alkyl N-(cis-3,trans-4-dibromocyclohex-1-yl)carbamates (10, 12, 14, 16, 18) is a convenient method for the synthesis of 7-azabicyclo[2.2.1]heptane derivatives. For instance, the reaction of tert-butyl N-(cis-3,trans-4-dibromocyclohex-1-yl)carbamate (10) with sodium hydride in DMF at room temperature provides 2-bromo-7-[(tert-butoxy)carbonyl]-7-azabicyclo[2.2.1]heptane (2) (52% yield), whose t-BuOK-promoted hydrogen bromide elimination affords 7-[(tert-butoxy)carbonyl]-7-azabicyclo[2.2.1]hept-2-ene (31) in 78% yield, an intermediate in the total synthesis of epibatidine (1). However, the NaH/DMF-mediated heterocyclization of alkyl N-(trans-3,cis-4-dibromocyclohex-1-yl)carbamates (11, 13) is a more structure dependent reaction, where the nucleophilic attack of the oxygen atom of the protecting group controls the outcome of the reaction, giving rise to benzooxazolone and 2-oxa-4-azabicyclo[3.3.1]non-3-ene derivatives, respectively, from low to moderate yields, in complex reaction mixtures. Conversely, the NaH/DMF heterocyclizations of N-(cis-3,trans-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamide (40) or N-(trans-3,cis-4-dibromocyclohex-1-yl)-2,2,2-trifluoroacetamide (42) are very clean reactions giving 7-azabicyclo[2.2.1]heptane or 2-oxa-4-azabicyclo[3.3.1]non-3-ene derivatives, respectively, in good yields. Finally, a mechanistic investigation, based on DFT calculations, has been carried out to rationalize the formation of the different adducts.

  10. Experiences gained by establishing the IAMG Student Chapter Freiberg

    NASA Astrophysics Data System (ADS)

    Ernst, Sebastian M.; Liesenberg, Veraldo; Shahzad, Faisal

    2013-04-01

    The International Association for Mathematical Geosciences (IAMG) Student Chapter Freiberg was founded in 2007 at the Technische Universität Bergakademie Freiberg (TUBAF) in Germany by national and international graduate and undergraduate students of various geoscientific as well as natural science disciplines. The major aim of the IAMG is to promote international cooperation in the application and use of Mathematics in Geosciences research and technology. The IAMG encourages all types of students and young scientists to found and maintain student chapters, which can even receive limited financial support by the IAMG. Following this encouragement, generations of students at TUBAF have build up and established a prosperous range of activities. These might be an example and an invitation for other young scientists and institutions worldwide to run similar activities. We, some of the current and former students behind the student chapter, have organised talks, membership drives, student seminars, guest lectures, several short courses and even international workshops. Some notable short courses were held by invited IAMG distinguished lecturers. The topics included "Statistical analysis in the Earth Sciences using R - a language and environment for statistical computing and graphics", "Geomathematical Natural Resource Modeling" and "Introduction to Geostatistics for Environmental Applications and Natural Resources Evaluation: Basic Concepts and Examples". Furthermore, we conducted short courses by ourselves. Here, the topics included basic introductions into MATLAB, object oriented programming concepts for geoscientists using MATLAB and an introduction to the Keyhole Markup Language (KML). Most of those short courses lasted several days and provided an excellent and unprecedented teaching experience for us. We were given credit by attending students for filling gaps in our university's curriculum by providing in-depth and hands-on tutorials on topics, which were merely

  11. Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis[W

    PubMed Central

    Cubillos, Francisco A.; Stegle, Oliver; Grondin, Cécile; Canut, Matthieu; Tisné, Sébastien; Gy, Isabelle

    2014-01-01

    cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments. PMID:25428981

  12. Stress-Mediated cis-Element Transcription Factor Interactions Interconnecting Primary and Specialized Metabolism in planta

    PubMed Central

    Sheshadri, S. A.; Nishanth, M. J.; Simon, Bindu

    2016-01-01

    Plant specialized metabolites are being used worldwide as therapeutic agents against several diseases. Since the precursors for specialized metabolites come through primary metabolism, extensive investigations have been carried out to understand the detailed connection between primary and specialized metabolism at various levels. Stress regulates the expression of primary and specialized metabolism genes at the transcriptional level via transcription factors binding to specific cis-elements. The presence of varied cis-element signatures upstream to different stress-responsive genes and their transcription factor binding patterns provide a prospective molecular link among diverse metabolic pathways. The pattern of occurrence of these cis-elements (overrepresentation/common) decipher the mechanism of stress-responsive upregulation of downstream genes, simultaneously forming a molecular bridge between primary and specialized metabolisms. Though many studies have been conducted on the transcriptional regulation of stress-mediated primary or specialized metabolism genes, but not much data is available with regard to cis-element signatures and transcription factors that simultaneously modulate both pathway genes. Hence, our major focus would be to present a comprehensive analysis of the stress-mediated interconnection between primary and specialized metabolism genes via the interaction between different transcription factors and their corresponding cis-elements. In future, this study could be further utilized for the overexpression of the specific transcription factors that upregulate both primary and specialized metabolism, thereby simultaneously improving the yield and therapeutic content of plants. PMID:27933071

  13. cis p-tau: early driver of brain injury and tauopathy blocked by antibody

    PubMed Central

    Mannix, Rebekah; Qiu, Jianhua; Moncaster, Juliet; Chen, Chun-Hau; Yao, Yandan; Lin, Yu-Min; Driver, Jane A; Sun, Yan; Wei, Shuo; Luo, Man-Li; Albayram, Onder; Huang, Pengyu; Rotenberg, Alexander; Ryo, Akihide; Goldstein, Lee E; Pascual-Leone, Alvaro; McKee, Ann C.; Meehan, William; Zhou, Xiao Zhen; Lu, Kun Ping

    2015-01-01

    Traumatic brain injury (TBI), characterized by acute neurological dysfunction, is one of the best known environmental risk factors for chronic traumatic encephalopathy (CTE) and Alzheimer's disease (AD), whose defining pathologic features include tauopathy made of phosphorylated tau (p-tau). However, tauopathy has not been detected in early stages after TBI and how TBI leads to tauopathy is unknown. Here we find robust cis p-tau pathology after sport- and military-related TBI in humans and mice. Acutely after TBI in mice and stress in vitro, neurons prominently produce cis p-tau, which disrupts axonal microtubule network and mitochondrial transport, spreads to other neurons, and leads to apoptosis. This process, termed “cistauosis”, appears long before other tauopathy. Treating TBI mice with cis antibody blocks cistauosis, prevents tauopathy development and spread, and restores many TBI-related structural and functional sequelae. Thus, cis p-tau is a major early driver after TBI and leads to tauopathy in CTE and AD, and cis antibody may be further developed to detect and treat TBI, and prevent progressive neurodegeneration after injury. PMID:26176913

  14. Gene expression caused by alkylating agents and cis-diamminedichloroplatinum(II) in Escherichia coli.

    PubMed

    Fram, R J; Crockett, J; Volkert, M R

    1988-09-01

    Previous work has demonstrated heterogeneous effects of methylating agents on induction of DNA damage inducible genes in Escherichia coli. These studies employed E. coli mutants that have fusions of the lac operon to genes induced by treatment with sublethal levels of alkylating agents. These mutants were selected from random insertions of the Mu-dl (Apr lac) phage by screening for induction of beta-galactosidase activity in the presence of methylmethanesulfonate or N-methyl-N'-nitro-N-nitrosoguanidine. The current report extends these findings by analyzing gene expression caused by mechlorethamine, chloroethylnitrosoureas and cis-diamminedichloroplatinum(II) (cis-DDP). The results demonstrate heterogeneous effects by these agents on gene expression. While 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea induces alkA, other nitrosoureas, mechlorethamine, and cis-DDP do not cause expression of this gene. Further, while all nitrosoureas caused expression of aidC, mechlorethamine and cis-DDP did not. Lastly, cis-DDP caused marked expression of a sulA fusion mutant while not inducing any of the other E. coli fusion mutants.

  15. [Analysis of cis-9, trans-11-conjugated linoleic acid in milk fat by capillary gas chromatography].

    PubMed

    Wang, Xiaojing; Shen, Xiangzhen; Han, Hangru; Zhao, Ruqian; Chen, Jie

    2006-11-01

    Conjugated linoleic acid (CLA) is a term representing a mixture of positional and geometric isomers of octadecadienoic acid with a conjugated double bond system. Conjugated linoleic acid has attracted a great deal of interest among nutritionists because it is a natural fat component that appears to have a number of health improvement properties. The cis-9, trans-11-CLA is the major CLA isomer found in dairy products accounting for 75% to 90% of the total CLA in milk fat. A capillary gas chromatographic method equipped with a flame ionization detector for the analysis of the cis-9, trans-11-CLA in milk fat was developed. The cis-9, trans-11-CLA was extracted with hexane-isopropanol, methylated with methanol-sodium methylate and cis-9, trans-11-CLA was separated and quantified using gas chromatography. Retention time of the peaks was used for qualitative analysis, while external standard method was used for quantitative analysis. The recovery of the cis-9, trans-11-CLA was 100.26%. The relative standard deviation was 1.9% (n = 6). This method presented is advantageous for high precision, high sensitivity analysis with smaller sample size and simpler pretreatment. It would be of significance for analyzing the contents of other fatty acids in the milk and milk products.

  16. Antibody against early driver of neurodegeneration cis P-tau blocks brain injury and tauopathy.

    PubMed

    Kondo, Asami; Shahpasand, Koorosh; Mannix, Rebekah; Qiu, Jianhua; Moncaster, Juliet; Chen, Chun-Hau; Yao, Yandan; Lin, Yu-Min; Driver, Jane A; Sun, Yan; Wei, Shuo; Luo, Man-Li; Albayram, Onder; Huang, Pengyu; Rotenberg, Alexander; Ryo, Akihide; Goldstein, Lee E; Pascual-Leone, Alvaro; McKee, Ann C; Meehan, William; Zhou, Xiao Zhen; Lu, Kun Ping

    2015-07-23

    Traumatic brain injury (TBI), characterized by acute neurological dysfunction, is one of the best known environmental risk factors for chronic traumatic encephalopathy and Alzheimer's disease, the defining pathologic features of which include tauopathy made of phosphorylated tau protein (P-tau). However, tauopathy has not been detected in the early stages after TBI, and how TBI leads to tauopathy is unknown. Here we find robust cis P-tau pathology after TBI in humans and mice. After TBI in mice and stress in vitro, neurons acutely produce cis P-tau, which disrupts axonal microtubule networks and mitochondrial transport, spreads to other neurons, and leads to apoptosis. This process, which we term 'cistauosis', appears long before other tauopathy. Treating TBI mice with cis antibody blocks cistauosis, prevents tauopathy development and spread, and restores many TBI-related structural and functional sequelae. Thus, cis P-tau is a major early driver of disease after TBI and leads to tauopathy in chronic traumatic encephalopathy and Alzheimer's disease. The cis antibody may be further developed to detect and treat TBI, and prevent progressive neurodegeneration after injury.

  17. Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.

    PubMed

    Cubillos, Francisco A; Stegle, Oliver; Grondin, Cécile; Canut, Matthieu; Tisné, Sébastien; Gy, Isabelle; Loudet, Olivier

    2014-11-01

    cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.

  18. The search for cis-regulatory driver mutations in cancer genomes.

    PubMed

    Poulos, Rebecca C; Sloane, Mathew A; Hesson, Luke B; Wong, Jason W H

    2015-10-20

    With the advent of high-throughput and relatively inexpensive whole-genome sequencing technology, the focus of cancer research has begun to shift toward analyses of somatic mutations in non-coding cis-regulatory elements of the cancer genome. Cis-regulatory elements play an important role in gene regulation, with mutations in these elements potentially resulting in changes to the expression of linked genes. The recent discoveries of recurrent TERT promoter mutations in melanoma, and recurrent mutations that create a super-enhancer regulating TAL1 expression in T-cell acute lymphoblastic leukaemia (T-ALL), have sparked significant interest in the search for other somatic cis-regulatory mutations driving cancer development. In this review, we look more closely at the TERT promoter and TAL1 enhancer alterations and use these examples to ask whether other cis-regulatory mutations may play a role in cancer susceptibility. In doing so, we make observations from the data emerging from recent research in this field, and describe the experimental and analytical approaches which could be adopted in the hope of better uncovering the true functional significance of somatic cis-regulatory mutations in cancer.

  19. Revisiting the 'cis-effect' in 1,2-difluoro derivatives of ethylene and diazene using ab initio multireference methods

    NASA Astrophysics Data System (ADS)

    Banerjee, Debi; Ghosh, Anirban; Chattopadhyay, Sudip; Ghosh, Pradipta; Chaudhuri, Rajat K.

    2014-12-01

    The relative stabilities of cis- and trans- isomers of 1,2-difluoroethylene and 1,2-difluorodiazene have been studied via the state-specific multireference coupled cluster (SS-MRCC) method and its perturbative counterpart through the computation of the optimised structures and corresponding energies. Despite the existence of several cis-destabilising mechanisms, present calculations reveal the energetic preference of the cis- isomer (the cis-effect) for the systems considered here. Differences in structural parameters and vibrational frequencies among cis- and trans- isomers have been discussed. Very good agreement of our estimates has been found with the benchmark theoretical and experimental results. The SS-MRCC methods produce a smooth and consistent behaviour across the entire torsional surface for the cis-trans isomerisation indicating that the method has sufficient flexibility to model large changes in electronic structure that accompany chemical changes.

  20. Combining anti-cancer drugs with artificial sweeteners: synthesis and anti-cancer activity of saccharinate (sac) and thiosaccharinate (tsac) complexes cis-[Pt(sac)2(NH3)2] and cis-[Pt(tsac)2(NH3)2].

    PubMed

    Al-Jibori, Subhi A; Al-Jibori, Ghassan H; Al-Hayaly, Lamaan J; Wagner, Christoph; Schmidt, Harry; Timur, Suna; Baris Barlas, F; Subasi, Elif; Ghosh, Shishir; Hogarth, Graeme

    2014-12-01

    The new platinum(II) complexes cis-[Pt(sac)2(NH3)2] (sac=saccharinate) and cis-[Pt(tsac)2(NH3)2] (tsac=thiosaccharinate) have been prepared, the X-ray crystal structure of cis-[Pt(sac)2(NH3)2] x H2O reveals that both saccharinate anions are N-bound in a cis-arrangement being inequivalent in both the solid-state and in solution at room temperature. Preliminary anti-cancer activity has been assessed against A549 human alveolar type-II like cell lines with the thiosaccharinate complex showing good activity.

  1. No Excess of Cis-Regulatory Variation Associated with Intraspecific Selection in Wild Pearl Millet (Cenchrus americanus)

    PubMed Central

    Rhoné, Bénédicte; Mariac, Cédric; Couderc, Marie; Berthouly-Salazar, Cécile; Ousseini, Issaka Salia

    2017-01-01

    Several studies suggest that cis-regulatory mutations are the favorite target of evolutionary changes, one reason being that cis-regulatory mutations might have fewer deleterious pleiotropic effects than protein-coding mutations. A review of the process also suggests that this bias towards adaptive cis-regulatory variation might be less pronounced at the intraspecific level compared with the interspecific level. In this study, we assessed the contribution of cis-regulatory variation to adaptation at the intraspecific level using populations of wild pearl millet (Cenchrus americanus ssp. monodii) sampled along an environmental gradient in Niger. From RNA sequencing of hybrids to assess allele-specific expression, we identified genes with cis-regulatory divergence between two parental accessions collected in contrasted environmental conditions. This revealed that ∼15% of transcribed genes showed cis-regulatory variation. Intersecting the gene set exhibiting cis-regulatory variation with the gene set identified as targets of selection revealed no excess of cis-acting mutations among the selected genes. We additionally found no excess of cis-regulatory variation among genes associated with adaptive traits. As our approach relied on methods identifying mainly genes submitted to strong selection pressure or with high phenotypic effect, the contribution of cis-regulatory changes to soft selection or polygenic adaptive traits remains to be tested. However our results favor the hypothesis that enrichment of adaptive cis-regulatory divergence builds up over time. For short evolutionary time-scales, cis-acting mutations are not predominantly involved in adaptive evolution associated with strong selective signal. PMID:28137746

  2. Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

    PubMed Central

    2013-01-01

    Background Brassica rapa includes several important leaf vegetable crops whose production is often damaged by high temperature. Cis-natural antisense transcripts (cis-NATs) and cis-NATs-derived small interfering RNAs (nat-siRNAs) play important roles in plant development and stress responses. However, genome-wide cis-NATs in B. rapa are not known. The NATs and nat-siRNAs that respond to heat stress have never been well studied in B. rapa. Here, we took advantage of RNA-seq and small RNA (sRNA) deep sequencing technology to identify cis-NATs and heat responsive nat-siRNAs in B. rapa. Results Analyses of four RNA sequencing datasets revealed 1031 cis-NATs B. rapa ssp. chinensis cv Wut and B. rapa ssp. pekinensis cv. Bre. Based on sequence homology between Arabidopsis thaliana and B. rapa, 303 conserved cis-NATs in B. rapa were found to correspond to 280 cis-NATs in Arabidopsis; the remaining 728 novel cis-NATs were identified as Brassica-specific ones. Using six sRNA libraries, 4846 nat-siRNAs derived from 150 cis-NATs were detected. Differential expression analysis revealed that nat-siRNAs derived from 12 cis-NATs were responsive to heat stress, and most of them showed strand bias. Real-time PCR indicated that most of the transcripts generating heat-responsive nat-siRNAs were upregulated under heat stress, while the transcripts from the opposite strands of the same loci were downregulated. Conclusions Our results provide the first subsets of genome-wide cis-NATs and heat-responsive nat-siRNAs in B. rapa; these sRNAs are potentially useful for the genetic improvement of heat tolerance in B. rapa and other crops. PMID:24320882

  3. Trajectory Design Tools for Libration and Cis-Lunar Environments

    NASA Technical Reports Server (NTRS)

    Folta, David C.; Webster, Cassandra M.; Bosanac, Natasha; Cox, Andrew; Guzzetti, Davide; Howell, Kathleen C.

    2016-01-01

    Innovative trajectory design tools are required to support challenging multi-body regimes with complex dynamics, uncertain perturbations, and the integration of propulsion influences. Two distinctive tools, Adaptive Trajectory Design and the General Mission Analysis Tool have been developed and certified to provide the astrodynamics community with the ability to design multi-body trajectories. In this paper we discuss the multi-body design process and the capabilities of both tools. Demonstrable applications to confirmed missions, the Lunar IceCube Cubesat lunar mission and the Wide-Field Infrared Survey Telescope (WFIRST) Sun-Earth L2 mission, are presented.

  4. Unlocking Learning: Chapter 1 in Correctional Facilities. Effective Practices Study Findings: National Study of the Chapter 1 Neglected or Delinquent Program.

    ERIC Educational Resources Information Center

    Rowe, Brenda J. D.; Pfannenstiel, Judy C.

    Part of a 3-year study of the Chapter 1 Neglected or Delinquent (Chapter 1 N or D) Program providing compensatory education services to youths in state-operated juvenile and adult correctional facilities, this report presents case studies of nine facilities that have developed particularly effective programs. The study used teacher questionnaires,…

  5. Siemens solar CIS photovoltaic module and system performance at the National Renewable Energy Laboratory

    SciTech Connect

    Strand, T.; Kroposki, B.; Hansen, R.; Willett, D.

    1996-05-01

    This paper evaluates the individual module and array performance of Siemens Solar Industries copper indium diselenide (CIS) polycrystalline thin-film technology. This is accomplished by studying module and array performance over time. Preliminary temperature coefficients for maximum power, maximum-power voltage, maximum-power current, open-circuit voltage, short-circuit current, and fill factor are determined at both the module and array level. These coefficients are used to correct module/array performance to 25{degrees}C to evaluate stability. The authors show that CIS exhibits a strong inverse correlation between array power and back-of-module temperature. This is due mainly to the narrow bandgap of the CIS material, which results in a strong inverse correlation between voltage and temperature. They also show that the temperature-corrected module and array performance has been relatively stable over the evaluation interval ({approx}2 years).

  6. A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis

    SciTech Connect

    Keys, David N.; Lee, Byung-in; Di Gregorio, Anna; Harafuji, Naoe; Detter, Chris; Wang, Mei; Kahsai, Orsalem; Ahn, Sylvia; Arellano, Andre; Zhang, Quin; Trong, Stephan; Doyle, Sharon A.; Satoh, Noriyuki; Satou, Yutaka; Saiga, Hidetoshi; Christian, Allen; Rokhsar, Dan; Hawkins, Trevor L.; Levine, Mike; Richardson, Paul

    2005-01-05

    A screen for the systematic identification of cis-regulatory elements within large (>100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.

  7. The plant-unique cis-element that mediates signaling from multiple endoplasmic reticulum stress sensors.

    PubMed

    Hayashi, Shimpei; Takaiwa, Fumio

    2013-06-01

    The accumulation of unfolded proteins in the ER lumen induces intracellular signaling mediated by the ER stress sensor protein IRE1. Our recent study identified a new common cis-element of ER stress-responsive genes (such as rice BiP paralogs and WRKY45) that were regulated via an IRE1-dependent pathway. ER stress-responsive cis-elements had been expected to be conserved between plants and mammals. However, contrary to expectations, sequences of the plant cis-element, pUPRE-II, were not identical to those of its mammalian counterpart. Additionally, pUPRE-II also interacted with another ER stress sensor protein and mediated multiple signaling pathways. Here, we provide a summary of the results that suggest the complicated mechanism underlying the regulation of ER stress-responsive gene expression in plants.

  8. Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

    PubMed Central

    Sharov, Alexei A.; Ko, Minoru S.H.

    2009-01-01

    We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences. PMID:19740934

  9. Purification and properties of cis-toluene dihydrodiol dehydrogenase from Pseudomonas putida.

    PubMed Central

    Rogers, J E; Gibson, D T

    1977-01-01

    The purification of (+)-cis-1(S),2(R)-dihydroxy-3-methylcyclohexa-3,5-diene dehydrogenase from cells of Pseudomonas putida grown with toluene as the sole source of carbon and energy is reported. The molecular weight of the enzyme is 104,000 at pH 9.7. The enzyme is composed of four apparently identical subunits with molecular weights of 27,000. The enzyme is specific for nicotinamide adenine dinucleotide and oxidizes a number of cis-dihydrodiols. Both enantiomers of a racemic mixture of cis-1,2-dihydroxyl-1,2-dihydronaphthalene dihydrodiol are oxidized by the enzyme. No enzymatic activity is observed with trans-1,2-dihydroxyl-1,2-dihydronaphthalene dihydrodiol. PMID:16865

  10. Antioxidant and antiatherogenic activity of cis-Hinokiresinol from Trapa pseudoincisa.

    PubMed

    Song, Myoung-Chong; Yang, Hye-Joung; Bang, Myun-Ho; Kim, Dae-Keun; Jeong, Tae-Sook; Kim, Jong-Pyung; Baek, Nam-In

    2007-11-01

    cis-Hinokiresinol, also known as (+)-nyasol, was isolated for the first time from an aquatic herbaceous plant, Trapa pseudoincisa NAKAI, via silica gel and octadecyl silica gel column chromatographies. The chemical structure was determined via analyses of the spectroscopic data, including NMR, MS and IR. cis-Hinokiresinol was also found to exhibit antioxidant and antiatherogenic activities. The ICso values for the scavenging activities of cis-hinokiresinol on ABTS cation and superoxide anion radicals were 45.6 and 40.5 microM, respectively. The IC50 values for the inhibitory effects on Lp-PLA2, hACAT1, hACAT2 and LDL-oxidation were 284.7, 280.6, 398.9 and 5.6 microM, respectively.

  11. Detection of trans–cis flips and peptide-plane flips in protein structures

    SciTech Connect

    Touw, Wouter G.; Joosten, Robbie P.; Vriend, Gert

    2015-07-28

    A method is presented to detect peptide bonds that need either a trans–cis flip or a peptide-plane flip. A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans–cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans–cis flips and many thousands of hitherto unknown peptide-plane flips. A few examples are highlighted for which a correction of the peptide-plane geometry leads to a correction of the understanding of the structure–function relation. All data, including 1088 manually validated cases, are freely available and the method is available from a web server, a web-service interface and through WHAT-CHECK.

  12. The Integration of Immigrant Families in the United States.

    ERIC Educational Resources Information Center

    Fix, Michael; Zimmermann, Wendy; Passel, Jeffrey S.

    This paper examines the assimilation of immigrant families in the United States. Chapter 1, "Introduction," reviews basic issues. Chapter 2, "Why Discuss the Integration of Immigrant Families?" examines such issues as continuing mismatches between immigration and immigrant policies, population dispersal, the shifting political…

  13. Environmental Medicine: Integrating a Missing Element into Medical Education.

    ERIC Educational Resources Information Center

    Pope, Andrew M., Ed.; Rall, David P., Ed.

    This volume articulates a general program of implementation strategies and provides practical advice for integrating environmental medicine content into medical education. Chapter 1 is an introduction to the issues and the organization of the volume. Chapter 2 lays the foundation for a curriculum centered on six competency-based learning…

  14. Developing Integrated Programs: A Transdisciplinary Approach for Early Intervention.

    ERIC Educational Resources Information Center

    Coling, Marcia Cain

    This book presents an amalgam of early intervention ideas from the fields of education, occupational therapy, and physical therapy for children with developmental delays. An introductory chapter describes the approach's three theoretical bases: neurodevelopmental treatment (NDT), sensory integration, and Piagetian theory. Chapter 1 considers…

  15. Children's Moral Emotions and Moral Cognition: Towards an Integrative Perspective

    ERIC Educational Resources Information Center

    Malti, Tina; Latzko, Brigitte

    2010-01-01

    This chapter presents a brief introduction to the developmental and educational literature linking children's moral emotions to cognitive moral development. A central premise of the chapter is that an integrative developmental perspective on moral emotions and moral cognition provides an important conceptual framework for understanding children's…

  16. Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes.

    PubMed

    Chen, Xiaowei Sylvia; Brown, Chris M

    2012-10-01

    Messenger ribonucleic acids (RNAs) contain a large number of cis-regulatory RNA elements that function in many types of post-transcriptional regulation. These cis-regulatory elements are often characterized by conserved structures and/or sequences. Although some classes are well known, given the wide range of RNA-interacting proteins in eukaryotes, it is likely that many new classes of cis-regulatory elements are yet to be discovered. An approach to this is to use computational methods that have the advantage of analysing genomic data, particularly comparative data on a large scale. In this study, a set of structural discovery algorithms was applied followed by support vector machine (SVM) classification. We trained a new classification model (CisRNA-SVM) on a set of known structured cis-regulatory elements from 3'-untranslated regions (UTRs) and successfully distinguished these and groups of cis-regulatory elements not been strained on from control genomic and shuffled sequences. The new method outperformed previous methods in classification of cis-regulatory RNA elements. This model was then used to predict new elements from cross-species conserved regions of human 3'-UTRs. Clustering of these elements identified new classes of potential cis-regulatory elements. The model, training and testing sets and novel human predictions are available at: http://mRNA.otago.ac.nz/CisRNA-SVM.

  17. Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast.

    PubMed

    Schaefke, Bernhard; Emerson, J J; Wang, Tzi-Yuan; Lu, Mei-Yeh Jade; Hsieh, Li-Ching; Li, Wen-Hsiung

    2013-09-01

    Gene expression evolution can be caused by changes in cis- or trans-regulatory elements or both. As cis and trans regulation operate through different molecular mechanisms, cis and trans mutations may show different inheritance patterns and may be subjected to different selective constraints. To investigate these issues, we obtained and analyzed gene expression data from two Saccharomyces cerevisiae strains and their hybrid, using high-throughput sequencing. Our data indicate that compared with other types of genes, those with antagonistic cis-trans interactions are more likely to exhibit over- or underdominant inheritance of expression level. Moreover, in accordance with previous studies, genes with trans variants tend to have a dominant inheritance pattern, whereas cis variants are enriched for additive inheritance. In addition, cis regulatory differences contribute more to expression differences between species than within species, whereas trans regulatory differences show a stronger association between divergence and polymorphism. Our data indicate that in the trans component of gene expression differences genes subjected to weaker selective constraints tend to have an excess of polymorphism over divergence compared with those subjected to stronger selective constraints. In contrast, in the cis component, this difference between genes under stronger and weaker selective constraint is mostly absent. To explain these observations, we propose that purifying selection more strongly shapes trans changes than cis changes and that positive selection may have significantly contributed to cis regulatory divergence.

  18. Stereoisomers of carotenoids: spectroscopic properties of locked and unlocked cis-isomers of spheroidene.

    PubMed

    Pendon, Zeus D; Sullivan, James O; van der Hoef, Ineke; Lugtenburg, Johan; Cua, Agnes; Bocian, David F; Birge, Robert R; Frank, Harry A

    2005-11-01

    A systematic optical spectroscopic and computational investigation of a series of locked-cis-isomers of spheroidene has been carried out with the goal being to better understand the relationships between stereochemistry, photochemistry, photophysics and biological function of geometric isomers of carotenoids. The spectroscopic properties of 15,15'-locked-cis-spheroidene, 13,14-locked-cis-spheroidene, 11, 12-locked-cis-spheroidene in solution are compared with those observed for unlocked spheroidene. The locked-cis bonds are incapable of undergoing cis-to-trans isomerization and therefore provide an effective means of exploring the relationship between specific stereoisomers and molecular spectroscopy. Samples of the molecules were purified using a high performance liquid chromatography (HPLC) apparatus equipped with a diode array detector, which records the absorption spectra immediately as the molecules emerge from the column and prior to any isomerization that might occur. For several stable isomers, resonance Raman (rR) spectroscopy was carried out to assign their configurations. Quantum computations of absorption spectra were performed using ZINDO/S and also MNDO-PSDCI methods employing nearly full single and double configuration interaction within the pi-electron manifold. Also, for a few test cases, ground state minimizations were done using density functional methods (B3LYP/6-31G(d)). The MNDO-PSDCI methods coupled with the density functional ground state minimization provide an accurate assignment of the positions of the 2(1)Ag - , 1(1)Bu +, and 1(1)Ag + excited states and also address the nature of the forbidden 1(1)Bu - state, whose location is uncertain for polyenes and carotenoids. We demonstrate that the configurational description of the 1(1)Bu - state is sufficiently unique to preclude assignment of its energy based on the characterization of surrounding excited singlet states. The experimental and computational data also offer important insights

  19. The Hawaiian Volcano Observatory: a natural laboratory for studying basaltic volcanism: Chapter 1 in Characteristics of Hawaiian volcanoes

    USGS Publications Warehouse

    Tilling, Robert I.; Kauahikaua, James P.; Brantley, Steven R.; Neal, Christina A.; Poland, Michael P.; Takahashi, T. Jane; Landowski, Claire M.

    2014-01-01

    This chapter summarizes HVO’s history and some of the scientific achievements made possible by this permanent observatory over the past century as it grew from a small wooden structure with only a small staff and few instruments to a modern, well-staffed, world-class facility with state-of-the-art monitoring networks that constantly track volcanic and earthquake activity. The many successes of HVO, from improving basic knowledge about basaltic volcanism to providing hands-on experience and training for hundreds of scientists and students and serving as the testing ground for new instruments and technologies, stem directly from the acquisition, integration, and analysis of multiple datasets that span many decades of observations of frequent eruptive activity. HVO’s history of the compilation, interpretation, and communication of long-term volcano monitoring and eruption data (for instance, seismic, geodetic, and petrologic-geochemical data and detailed eruption chronologies) is perhaps unparalleled in the world community of volcano observatories. The discussion and conclusions drawn in this chapter, which emphasize developments since the 75th anniversary of HVO in 1987, are general and retrospective and are intended to provide context for the more detailed, topically focused chapters of this volume.

  20. The Virtues of Organizational Integrity

    ERIC Educational Resources Information Center

    Young, Robert B.

    2011-01-01

    In this chapter, the author begins by describing the organizational virtues that are associated with structural and ethical integrity. Virtues are the focus instead of behaviors, traits, or values, because virtues contain all these components: the stable characteristics of traits, the behaviors that are evidence of traits, and the values that…

  1. Quasi-one dimensional (Q1D) nanostructures: Synthesis, integration and device application

    NASA Astrophysics Data System (ADS)

    Chien, Chung-Jen

    Quasi-one-dimensional (Q1D) nanostructures such as nanotubes and nanowires have been widely regarded as the potential building blocks for nanoscale electronic, optoelectronic and sensing devices. In this work, the content can be divided into three categories: Nano-material synthesis and characterizations, alignment and integration, physical properties and application. The dissertation consists of seven chapters as following. Chapter 1 will give an introduction to low dimensional nano-materials. Chapter 2 explains the mechanism how Q1D nanostructure grows. Chapter 3 describes the methods how we horizontally and vertically align the Q1D nanostructure. Chapter 4 and 5 are the electrical and optical device characterization respectively. Chapter 6 demonstrates the integration of Q1D nanostructures and the device application. The last chapter will discuss the future work and conclusion of the thesis.

  2. Introduction to physical properties and elasticity models: Chapter 20

    USGS Publications Warehouse

    Dvorkin, Jack; Helgerud, Michael B.; Waite, William F.; Kirby, Stephen H.; Nur, Amos

    2003-01-01

    Estimating the in situ methane hydrate volume from seismic surveys requires knowledge of the rock physics relations between wave speeds and elastic moduli in hydrate/sediment mixtures. The elastic moduli of hydrate/sediment mixtures depend on the elastic properties of the individual sedimentary particles and the manner in which they are arranged. In this chapter, we present some rock physics data currently available from literature. The unreferenced values in Table I were not measured directly, but were derived from other values in Tables I and II using standard relationships between elastic properties for homogeneous, isotropic material. These derivations allow us to extend the list of physical property estimates, but at the expense of introducing uncertainties due to combining property values measured under different physical conditions. This is most apparent in the case of structure II (sII) hydrate for which very few physical properties have been measured under identical conditions.

  3. The NASA Glen Research Center's Hypersonic Tunnel Facility. Chapter 16

    NASA Technical Reports Server (NTRS)

    Woike, Mark R.; Willis, Brian P.

    2001-01-01

    The NASA Glenn Research Center's Hypersonic Tunnel Facility (HTF) is a blow-down, freejet wind tunnel that provides true enthalpy flight conditions for Mach numbers of 5, 6, and 7. The Hypersonic Tunnel Facility is unique due to its large scale and use of non-vitiated (clean air) flow. A 3MW graphite core storage heater is used to heat the test medium of gaseous nitrogen to the high stagnation temperatures required to produce true enthalpy conditions. Gaseous oxygen is mixed into the heated test flow to generate the true air simulation. The freejet test section is 1.07m (42 in.) in diameter and 4.3m (14 ft) in length. The facility is well suited for the testing of large scale airbreathing propulsion systems. In this chapter, a brief history and detailed description of the facility are presented along with a discussion of the facility's application towards hypersonic airbreathing propulsion testing.

  4. NASA's MERBoard: An Interactive Collaborative Workspace Platform. Chapter 4

    NASA Technical Reports Server (NTRS)

    Trimble, Jay; Wales, Roxana; Gossweiler, Rich

    2003-01-01

    This chapter describes the ongoing process by which a multidisciplinary group at NASA's Ames Research Center is designing and implementing a large interactive work surface called the MERBoard Collaborative Workspace. A MERBoard system involves several distributed, large, touch-enabled, plasma display systems with custom MERBoard software. A centralized server and database back the system. We are continually tuning MERBoard to support over two hundred scientists and engineers during the surface operations of the Mars Exploration Rover Missions. These scientists and engineers come from various disciplines and are working both in small and large groups over a span of space and time. We describe the multidisciplinary, human-centered process by which this h4ERBoard system is being designed, the usage patterns and social interactions that we have observed, and issues we are currently facing.

  5. Chapter 9: The rock coast of the USA

    USGS Publications Warehouse

    Hapke, Cheryl J.; Adams, Peter N.; Allan, Jonathan; Ashton, Andrew; Griggs, Gary B.; Hampton, Monty A.; Kelly, Joseph; Young, Adam P.

    2014-01-01

    The coastline of the USA is vast and comprises a variety of landform types including barrier islands, mainland beaches, soft bluffed coastlines and hard rocky coasts. The majority of the bluffed and rocky coasts are found in the northeastern part of the country (New England) and along the Pacific coast. Rocky and bluffed landform types are commonly interspersed along the coastline and occur as a result of relative lowering of sea level from tectonic or isostatic forcing, which can occur on timescales ranging from instantaneous to millenia. Recent research on sea cliffs in the contiguous USA has focused on a broad range of topics from documenting erosion rates to identifying processes and controls on morphology to prediction modelling. This chapter provides a detailed synthesis of recent and seminal research on rocky coast geomorphology along open-ocean coasts of the continental United States (USA).

  6. Structural equation modeling: building and evaluating causal models: Chapter 8

    USGS Publications Warehouse

    Grace, James B.; Scheiner, Samuel M.; Schoolmaster, Donald R.

    2015-01-01

    Scientists frequently wish to study hypotheses about causal relationships, rather than just statistical associations. This chapter addresses the question of how scientists might approach this ambitious task. Here we describe structural equation modeling (SEM), a general modeling framework for the study of causal hypotheses. Our goals are to (a) concisely describe the methodology, (b) illustrate its utility for investigating ecological systems, and (c) provide guidance for its application. Throughout our presentation, we rely on a study of the effects of human activities on wetland ecosystems to make our description of methodology more tangible. We begin by presenting the fundamental principles of SEM, including both its distinguishing characteristics and the requirements for modeling hypotheses about causal networks. We then illustrate SEM procedures and offer guidelines for conducting SEM analyses. Our focus in this presentation is on basic modeling objectives and core techniques. Pointers to additional modeling options are also given.

  7. The role of infectious disease in marine communities: chapter 5

    USGS Publications Warehouse

    Lafferty, Kevin D.; Harvell, C. Drew

    2014-01-01

    Marine ecologists recognize that infectious diseases play and important role in ocean ecosystems. This role may have increased in some host taxa over time (Ward and Lafferty 2004). We begin this chapter by introducing infectious agents and their relationships with their hosts in marine systems. We then put infectious disease agents with their hosts in marine systems. We then put infectious disease agents in the perspective of marine biodiversity and discuss the various factors that affect parasites. Specifically, we introduce some basin epidemiological concepts, including the effects of stress and free-living diversity on parasites. Following this, we give brief consideration to communities of parasites within their hosts, particularly as these can lead to general insights into community ecology. We also give examples of how infectious diseases affect host populations, scaling up to marine communities. Finally, we present examples of marine infectious disease that impair conservation and fisheries.

  8. Dynamic Potential Barrier Effects in Hydrogen Tunneling in Trans-cis Isomerizations

    DTIC Science & Technology

    1993-05-07

    for the cis. As the molecular transla- Schrodinger equation for a molecule to be separated lion and rotation are sepaiated out, the static poten- into...tunneling in multi-dimensional eluding cis and trans conformers of HSiOH. systems semiclassically . However, it is often neces- HSi’ 8OH. HSiOD, and HSi"OD...two equations , liat can he written generally as 1 (r, r. r. (, , V, where rt, 01, and (p, describe the first H-atom. and r., fl, and p2 the second

  9. Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

    PubMed Central

    Ablikim, Utuq; Bomme, Cédric; Xiong, Hui; Savelyev, Evgeny; Obaid, Razib; Kaderiya, Balram; Augustin, Sven; Schnorr, Kirsten; Dumitriu, Ileana; Osipov, Timur; Bilodeau, René; Kilcoyne, David; Kumarappan, Vinod; Rudenko, Artem; Berrah, Nora; Rolles, Daniel

    2016-01-01

    An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C2H2Br2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. The experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model. PMID:27910943

  10. Undecaprenyl diphosphate synthase, a cis-prenyltransferase synthesizing lipid carrier for bacterial cell wall biosynthesis.

    PubMed

    Teng, Kuo-Hsun; Liang, Po-Huang

    2012-11-01

    A group of prenyltransferases produce linear lipids by catalyzing consecutive condensation reactions of farnesyl diphosphate (FPP) with specific numbers of isopentenyl diphosphate (IPP), a common building block of isoprenoid compounds. Depending on the stereochemistry of the double bonds formed during IPP condensation, these prenyltransferases are categorized as cis- and trans-types. Undecaprenyl diphosphate synthase (UPPS) that catalyzes chain elongation of FPP by consecutive condensation reactions with eight IPP, to form C₅₅ lipid carrier for bacterial cell wall biosynthesis, serves as a model for understanding cis-prenyltransferases. In this review, the current knowledge in UPPS kinetics, mechanisms, structures, and inhibitors is summarized.

  11. Separation of cis and trans Isomers of Polyproline by FAIMS Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Creese, Andrew J.; Cooper, Helen J.

    2016-12-01

    High field asymmetric waveform ion mobility spectrometry (FAIMS) is well-established as a tool for separating peptide isomers (sequence inversions and post-translationally modified localization variants). Here, we demonstrate the FAIMS is able to differentiate cis and trans isomers of polyproline. Polyproline assumes an all- cis conformation—the PPI helix—in 1-propanol, and an all- trans conformation—the PPII helix—in aqueous solutions. Differentiation of these conformers may be achieved both through use of a cylindrical FAIMS device and a miniaturized ultrahigh field planar FAIMS device.

  12. Large area low cost processing for CIS photovoltaics. Final technical report

    SciTech Connect

    B. Basol; G. Norsworthy; C. Leidholm; A. Halani; R. Roe; V. Kapur

    1999-07-22

    An ink coating method was developed for CIS absorber deposition. The technique involves four processing steps: (1) preparation of a Cu-In alloy powder, (2) preparation of an ink using this powder, (3) deposition of the ink on a substrate in the form of a precursor layer, and (4) selenization to convert the Cu-In precursor into a fused CIS film. Absorbers grown by this low-cost, large-area method were used in the fabrication of 10.5% efficient solar cells.

  13. Phytotoxic cis-clerodane diterpenoids from the Chinese liverwort Scapania stephanii.

    PubMed

    Li, Rui-Juan; Sun, Yi; Sun, Bin; Wang, Xiao-Ning; Liu, Shan-Shan; Zhou, Jin-Chuan; Ye, Jian-Ping; Zhao, Yu; Liu, Lei; Lee, Kuo-Hsiung; Lou, Hong-Xiang

    2014-09-01

    Five cis-clerodane diterpenoids, stephanialides A-E, along with seven known cis-clerodanes, scaparvins A-C, parvitexins B and C, 3-chloro-4-hydroxy-parvitexin A, and scapanialide B, were isolated from the Chinese liverwort Scapania stephanii. Their structures were established unequivocally on the basis of spectroscopic data. The absolute configuration of stephanialide A was determined by analysis of CD data using the octant rule. Phytotoxic activity evaluation showed that this type of diterpenoids can significantly inhibit root elongation of the seeds of Arabidopsis thaliana, Lepidium sativum and Brassica pekinensis.

  14. Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

    NASA Astrophysics Data System (ADS)

    Ablikim, Utuq; Bomme, Cédric; Xiong, Hui; Savelyev, Evgeny; Obaid, Razib; Kaderiya, Balram; Augustin, Sven; Schnorr, Kirsten; Dumitriu, Ileana; Osipov, Timur; Bilodeau, René; Kilcoyne, David; Kumarappan, Vinod; Rudenko, Artem; Berrah, Nora; Rolles, Daniel

    2016-12-01

    An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C2H2Br2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. The experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model.

  15. cis-Regulatory Mutations Are a Genetic Cause of Human Limb Malformations

    PubMed Central

    VanderMeer, Julia E.; Ahituv, Nadav

    2011-01-01

    The underlying mutations that cause human limb malformations are often difficult to determine, particularly for limb malformations that occur as isolated traits. Evidence from a variety of studies shows that cis-regulatory mutations, specifically in enhancers, can lead to some of these isolated limb malformations. Here, we provide a review of human limb malformations that have been shown to be caused by enhancer mutations and propose that cis-regulatory mutations will continue to be identified as the cause of additional human malformations as our understanding of regulatory sequences improves. PMID:21509892

  16. The Role of Cis-Lunar Space in Future Global Space Exploration

    NASA Technical Reports Server (NTRS)

    Bobskill, Marianne R.; Lupisella, Mark L.

    2012-01-01

    Cis-lunar space offers affordable near-term opportunities to help pave the way for future global human exploration of deep space, acting as a bridge between present missions and future deep space missions. While missions in cis-lunar space have value unto themselves, they can also play an important role in enabling and reducing risk for future human missions to the Moon, Near-Earth Asteroids (NEAs), Mars, and other deep space destinations. The Cis-Lunar Destination Team of NASA's Human Spaceflight Architecture Team (HAT) has been analyzing cis-lunar destination activities and developing notional missions (or "destination Design Reference Missions" [DRMs]) for cis-lunar locations to inform roadmap and architecture development, transportation and destination elements definition, operations, and strategic knowledge gaps. The cis-lunar domain is defined as that area of deep space under the gravitational influence of the earth-moon system. This includes a set of earth-centered orbital locations in low earth orbit (LEO), geosynchronous earth orbit (GEO), highly elliptical and high earth orbits (HEO), earth-moon libration or "Lagrange" points (E-ML1 through E-ML5, and in particular, E-ML1 and E-ML2), and low lunar orbit (LLO). To help explore this large possibility space, we developed a set of high level cis-lunar mission concepts in the form of a large mission tree, defined primarily by mission duration, pre-deployment, type of mission, and location. The mission tree has provided an overall analytical context and has helped in developing more detailed design reference missions that are then intended to inform capabilities, operations, and architectures. With the mission tree as context, we will describe two destination DRMs to LEO and GEO, based on present human space exploration architectural considerations, as well as our recent work on defining mission activities that could be conducted with an EML1 or EML2 facility, the latter of which will be an emphasis of this

  17. Précis on The Cognitive-Emotional Brain.

    PubMed

    Pessoa, Luiz

    2015-01-01

    In The Cognitive-Emotional Brain (Pessoa 2013), I describe the many ways that emotion and cognition interact and are integrated in the brain. The book summarizes five areas of research that support this integrative view and makes four arguments to organize each area. (1) Based on rodent and human data, I propose that the amygdala's functions go beyond emotion as traditionally conceived. Furthermore, the processing of emotion-laden information is capacity limited, thus not independent of attention and awareness. (2) Cognitive-emotional interactions in the human prefrontal cortex (PFC) assume diverse forms and are not limited to mutual suppression. Particularly, the lateral PFC is a focal point for cognitive-emotional interactions. (3) Interactions between motivation and cognition can be seen across a range of perceptual and cognitive tasks. Motivation shapes behavior in specific ways--for example, by reducing response conflict or via selective effects on working memory. Traditional accounts, by contrast, typically describe motivation as a global activation independent of particular control demands. (4) Perception and cognition are directly influenced by information with affective or motivational content in powerful ways. A dual competition model outlines a framework for such interactions at the perceptual and executive levels. A specific neural architecture is proposed that embeds emotional and motivational signals into perception and cognition through multiple channels. (5) A network perspective should supplant the strategy of understanding the brain in terms of individual regions. More broadly, in a network view of brain architecture, "emotion" and "cognition" may be used as labels of certain behaviors, but will not map cleanly into compartmentalized pieces of the brain.

  18. Tactical Integrated Air Defense System

    DTIC Science & Technology

    1978-06-09

    and integrated. The discussion in %,hapter II sunmmarlies the effective. ness of their integration experiences. 4 Any evaluation of current air...require- ments. Therefore, to serve as a baseline for evaluating the present IAD capabilities of the United States, Chapter III contains an analysis...of the present Soviet tactical air threat. Given the historical background and operational requirements for IAD, an evaluation of the present United

  19. Genome-wide discovery of cis-elements in promoter sequences using gene expression.

    PubMed

    Troukhan, Maxim; Tatarinova, Tatiana; Bouck, John; Flavell, Richard B; Alexandrov, Nickolai N

    2009-04-01

    The availability of complete or nearly complete genome sequences, a large number of 5' expressed sequence tags, and significant public expression data allow for a more accurate identification of cis-elements regulating gene expression. We have implemented a global approach that takes advantage of available expression data, genomic sequences, and transcript information to predict cis-elements associated with specific expression patterns. The key components of our approach are: (1) precise identification of transcription start sites, (2) specific locations of cis-elements relative to the transcription start site, and (3) assessment of statistical significance for all sequence motifs. By applying our method to promoters of Arabidopsis thaliana and Mus musculus, we have identified motifs that affect gene expression under specific environmental conditions or in certain tissues. We also found that the presence of the TATA box is associated with increased variability of gene expression. Strong correlation between our results and experimentally determined motifs shows that the method is capable of predicting new functionally important cis-elements in promoter sequences.

  20. The cis-AB blood group phenotype: fundamental lessons in glycobiology.

    PubMed

    Yazer, Mark H; Olsson, Martin L; Palcic, Monica M

    2006-07-01

    The cis-AB phenotype can raise questions about an apparently paradoxical inheritance of the ABO blood group, such as the birth of an O child from an AB mother. These subtype ABO alleles confer the ability to create both A and B antigens with a single enzyme. A variety of different cis-AB enzymes have been reported and many feature an interchange of amino acids between the normal A enzyme sequence and its B counterpart, rendering the mutant enzyme capable of creating both antigens. The resulting red blood cells do not usually express A or B antigen at the same level that would be expected on common group A(1) or B red blood cells, and the results of investigations into the kinetics of the cis-AB enzyme more clearly predict the extent of antigen expression. By correctly identifying the cis-AB phenotype, the blood bank can be of assistance to a clinician faced with a patient with what appears to be a genetically impossible ABO blood group.

  1. CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data.

    PubMed

    O'Connor, Timothy; Bodén, Mikael; Bailey, Timothy L

    2016-10-24

    Identifying the genomic regions and regulatory factors that control the transcription of genes is an important, unsolved problem. The current method of choice predicts transcription factor (TF) binding sites using chromatin immunoprecipitation followed by sequencing (ChIP-seq), and then links the binding sites to putative target genes solely on the basis of the genomic distance between them. Evidence from chromatin conformation capture experiments shows that this approach is inadequate due to long-distance regulation via chromatin looping. We present CisMapper, which predicts the regulatory targets of a TF using the correlation between a histone mark at the TF's bound sites and the expression of each gene across a panel of tissues. Using both chromatin conformation capture and differential expression data, we show that CisMapper is more accurate at predicting the target genes of a TF than the distance-based approaches currently used, and is particularly advantageous for predicting the long-range regulatory interactions typical of tissue-specific gene expression. CisMapper also predicts which TF binding sites regulate a given gene more accurately than using genomic distance. Unlike distance-based methods, CisMapper can predict which transcription start site of a gene is regulated by a particular binding site of the TF.

  2. High-valent iron-mediated cis-hydroxyacetoxylation of olefins.

    PubMed

    Mas-Balleste, Ruben; Fujita, Megumi; Que, Lawrence

    2008-04-14

    Evidence is obtained for the unprecedented cis-1,2-hydroxy-acetoxylation of olefins as minor products of the epoxidation of olefins by H2O2 that is catalyzed by nonheme iron complexes in the presence of acetic acid, providing further support for the previously proposed [(TPA)FeV(O)(OAc)]2+ oxidant.

  3. Screening of advanced potato breeding clones for resistance to cold-induced-sweetening (CIS)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The advantages of processing potatoes from low temperature storage are well known. It had previously been reported that clones with A-II isozymes of UDP-glucose pyrophosphorylase (UGPase) and low vacuolar acid invertase (VAcInv) activity demonstrate increased resistance to CIS. This study reports o...

  4. Effect of pore velocity on biodegradation of cis-dichloroethene (DCE) in column experiments.

    PubMed

    Mendoza-Sanchez, Itza; Autenrieth, Robin L; McDonald, Thomas J; Cunningham, Jeffrey A

    2010-06-01

    Column experiments were conducted to evaluate the effect of pore velocity on the extent of biodegradation of cis-dichloroethene (cis-DCE) during transport in porous media. Columns were filled with homogeneous glass beads and inoculated with a culture capable of complete dechlorination of tetrachloroethene to ethene. A constant concentration of cis-DCE was maintained in the columns' influent. Three different pore velocities were tested in duplicate, subjecting each column to a constant velocity. At high flow velocity, degradation of cis-DCE to ethene was nearly complete within the residence time of the columns. However, at medium and low flow velocities, incomplete dechlorination was observed. After 7 weeks, DNA was harvested from the columns to determine differences in the microbial populations. Results suggest that Dehalococcoides sp. were present in higher quantities in the high-velocity columns, consistent with the observed dechlorination. These results suggest that, at contaminated groundwater sites, heterogeneity of groundwater velocity may be one factor that contributes to heterogeneous distribution of biological activity.

  5. REMPI and MATI spectroscopic study of selected cis and trans 3-chlorostyrene rotamers

    NASA Astrophysics Data System (ADS)

    Dong, Changwu; Zhang, Lijuan; Liu, Sheng; Hu, Lili; Cheng, Min; Du, Yikui; Zhu, Qihe; Zhang, Cunhao

    2013-10-01

    The ab initio and DFT calculations predict two stable rotamers, cis and trans, for 3-chlorostyrene in each of the S0, S1 and D0 states. In the two-color resonant two-photon ionization (2C-R2PI) spectra, the band origins of S1 ← S0 electronic transition of cis and trans 3-chlorostyrene appears respectively at 33 766 ± 3 and 34 061 ± 3 cm-1. The mass-analyzed threshold ionization (MATI) spectra give the adiabatic ionization energies of 69 701 ± 4 cm-1 and 69 571 ± 4 cm-1 for cis and trans rotamers. Within the experimental detection limit, the measured transition energies are the same for both the 35Cl and 37Cl isotopomers. The observed active modes of rotamers in the S1 and D0 states involve mainly the in-plane ring deformation and substituent-sensitive bending vibration. It is derived from the 2C-R2PI and MATI spectroscopic data that the cis rotamer is more stable than the trans rotamer by 218 ± 30, 513 ± 30 and 88 ± 30 cm-1 for the S0, S1 and D0 states, respectively.

  6. Single-step electrodeposition of CIS thin films with the complexing agent triethanolamine

    NASA Astrophysics Data System (ADS)

    Chiu, Yu-Shuen; Hsieh, Mu-Tao; Chang, Chih-Min; Chen, Chun-Shuo; Whang, Thou-Jen

    2014-04-01

    Some difficulties have long been encountered by single-step electrodeposition such as the optimization of electrolyte composition, deposition potentials, deposition time, and pH values. The approach of introducing ternary components into single-step electrodeposition is rather challenging especially due to the different values of the equilibrium potential for each constituent. Complexing agents play an important role in single-step electrodeposition of CuInSe2 (CIS), since the equilibrium potential of every constituent can be brought closer to each other when complexing agents are employed. In this work, single-step electrodeposition of CIS was enhanced by adding triethanolamine (TEA) into deposition bath, the CIS thin films were improved consequently in the form of polycrystalline cauliflower structures through the examination of SEM images and XRD patterns. The optimum composition of the solution for single-step electrodeposition of CIS is found to be 5 mM CuCl2, 22 mM InCl3, and 22 mM SeO2 at pH 1.5 with 0.1 M TEA. The structures, compositions, and morphologies of as-deposited and of annealed films were investigated.

  7. The Differences Between Cis- and Trans-Gene Inactivation Caused by Heterochromatin in Drosophila.

    PubMed

    Abramov, Yuriy A; Shatskikh, Aleksei S; Maksimenko, Oksana G; Bonaccorsi, Silvia; Gvozdev, Vladimir A; Lavrov, Sergey A

    2016-01-01

    Position-effect variegation (PEV) is the epigenetic disruption of gene expression near the de novo-formed euchromatin-heterochromatin border. Heterochromatic cis-inactivation may be accompanied by the trans-inactivation of genes on a normal homologous chromosome in trans-heterozygous combination with a PEV-inducing rearrangement. We characterize a new genetic system, inversion In(2)A4, demonstrating cis-acting PEV as well as trans-inactivation of the reporter transgenes on the homologous nonrearranged chromosome. The cis-effect of heterochromatin in the inversion results not only in repression but also in activation of genes, and it varies at different developmental stages. While cis-actions affect only a few juxtaposed genes, trans-inactivation is observed in a 500-kb region and demonstrates а nonuniform pattern of repression with intermingled regions where no transgene repression occurs. There is no repression around the histone gene cluster and in some other euchromatic sites. trans-Inactivation is accompanied by dragging of euchromatic regions into the heterochromatic compartment, but the histone gene cluster, located in the middle of the trans-inactivated region, was shown to be evicted from the heterochromatin. We demonstrate that trans-inactivation is followed by de novo HP1a accumulation in the affected transgene; trans-inactivation is specifically favored by the chromatin remodeler SAYP and prevented by Argonaute AGO2.

  8. The Differences Between Cis- and Trans-Gene Inactivation Caused by Heterochromatin in Drosophila

    PubMed Central

    Abramov, Yuriy A.; Shatskikh, Aleksei S.; Maksimenko, Oksana G.; Bonaccorsi, Silvia; Gvozdev, Vladimir A.; Lavrov, Sergey A.

    2016-01-01

    Position-effect variegation (PEV) is the epigenetic disruption of gene expression near the de novo–formed euchromatin-heterochromatin border. Heterochromatic cis-inactivation may be accompanied by the trans-inactivation of genes on a normal homologous chromosome in trans-heterozygous combination with a PEV-inducing rearrangement. We characterize a new genetic system, inversion In(2)A4, demonstrating cis-acting PEV as well as trans-inactivation of the reporter transgenes on the homologous nonrearranged chromosome. The cis-effect of heterochromatin in the inversion results not only in repression but also in activation of genes, and it varies at different developmental stages. While cis-actions affect only a few juxtaposed genes, trans-inactivation is observed in a 500-kb region and demonstrates а nonuniform pattern of repression with intermingled regions where no transgene repression occurs. There is no repression around the histone gene cluster and in some other euchromatic sites. trans-Inactivation is accompanied by dragging of euchromatic regions into the heterochromatic compartment, but the histone gene cluster, located in the middle of the trans-inactivated region, was shown to be evicted from the heterochromatin. We demonstrate that trans-inactivation is followed by de novo HP1a accumulation in the affected transgene; trans-inactivation is specifically favored by the chromatin remodeler SAYP and prevented by Argonaute AGO2. PMID:26500261

  9. Enantioselective access to 2,7-cis-disubstituted oxepanes: formal synthesis of (+)-isolaurepan.

    PubMed

    Carreño, M Carmen; Des Mazery, Renaud; Urbano, Antonio; Colobert, Françoise; Solladié, Guy

    2004-01-22

    [reaction: see text] The asymmetric synthesis of 2,7-cis-disubstituted oxepanes bearing a sulfoxide is achieved from commercially available precursors in only five steps. The key step is the highly diastereoselective Et3SiH/TMSOTf-promoted reductive cyclization of enantiopure hydroxysulfinyl aryl or alkyl ketones.

  10. Cis- and trans-platinum and palladium complexes: a comparative study review as antitumour agents.

    PubMed

    al-Allaf, T A; Rashan, L J

    2001-01-01

    A large body of novel platinum and palladium complexes, in both the cis- and trans-forms, with various donor ligands, e.g. beta-carboline alkaloids, pyrazoles, DMSO, ferrocenylphosphines,...... have been tested for their antitumour activity against number of fluid suspension (P388, L1210, K562, and Raji) and solid tumour (KB, T47D, SW948, HeLa, A549, L929, Hep-2, RD,...) cell lines. Remarkable cytotoxic effects against these cell lines were observed by some of these complexes. The preliminary results indicated that most of the trans-palladium complexes showed a better activity than the cis-platinum isomers and superior activity than that of the cis-palladium isomers. More importantly they showed activities equal to (or superior than) those of cisplatin, carboplatin and oxaliplatin (the anti-cancer drugs) in vitro. Although these results are preliminary, however, encouraging since they are in a disagreement with the previous studies that cis-isomers are more active than trans-ones; the complexes which have not received the required attention from the vast number of researchers in this field.

  11. Biodegradation of cis-1,2-Dichloroethene in Simulated Underground Thermal Energy Storage Systems.

    PubMed

    Ni, Zhuobiao; van Gaans, Pauline; Smit, Martijn; Rijnaarts, Huub; Grotenhuis, Tim

    2015-11-17

    Underground thermal energy storage (UTES) use has showed a sharp rise in numbers in the last decades, with aquifer thermal energy storage (ATES) and borehole thermal energy storage (BTES) most widely used. In many urban areas with contaminated aquifers, there exists a desire for sustainable heating and cooling with UTES and a need for remediation. We investigated the potential synergy between UTES and bioremediation with batch experiments to simulate the effects of changing temperature and liquid exchange that occur in ATES systems, and of only temperature change occurring in BTES systems on cis-DCE reductive dechlorination. Compared to the natural situation (NS) at a constant temperature of 10 °C, both UTES systems with 25/5 °C for warm and cold well performed significantly better in cis-DCE (cis-1,2-dichloroethene) removal. The overall removal efficiency under mimicked ATES and BTES conditions were respectively 13 and 8.6 times higher than in NS. Inoculation with Dehalococcoides revealed that their initial presence is a determining factor for the dechlorination process. Temperature was the dominating factor when Dehalococcoides abundance was sufficient. Stimulated biodegradation was shown to be most effective in the mimicked ATES warm well because of the combined effect of suitable temperature, sustaining biomass growth, and regular cis-DCE supply.

  12. Purification and some properties of a novel heat-stable cis-toluene dihydrodiol dehydrogenase.

    PubMed Central

    Simpson, H D; Green, J; Dalton, H

    1987-01-01

    cis-Toluene dihydrodiol dehydrogenase was purified 200-fold from cells of a thermotolerant Bacillus species grown with toluene as the sole source of carbon and energy. The purified enzyme preparation was remarkably heat-stable and exhibited a half-life of 100 min at 80 degrees C, the temperature optimum. The activation energy of the reaction was 36 kJ.mol-1. Isoelectric focusing indicated that the pI of the native enzyme was 6.4 and that of the denatured enzyme 6.5. Although the pH optimum was 9.8, the enzyme was most stable at pH 8. The Mr of the enzyme was approx. 172,000 as determined by gel filtration and 166,000 by polyacrylamide-gel electrophoresis. The enzyme was composed of six apparently identical subunits with Mr values of 29,500. Kinetic analysis revealed that the Km for cis-toluene dihydrodiol was 92 microM and for NAD+ was 80 microM. The apparent Km values for cis-benzene dihydrodiol and cis-naphthalene dihydrodiol were 330 microM and 51 microM respectively. The enzyme was inhibited by mercurials but was unaffected by metal-ion chelators. Steady-state kinetics and product-inhibition patterns suggested that the enzyme mechanism was ordered Bi Bi. PMID:3446178

  13. Insect kinin analogs with cis-peptide bond motif 4-aminopyroglutamate: Optimal stereochemistry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The insect kinins are present in a wide variety of insects and function as potent diuretic peptides, though they are subject to rapid degradation by internal peptidases. Insect kinin analogs incorporating stereochemical variants of (2S,4S)-4-aminopyroglutamate (APy), a cis-peptide bond motif, demon...

  14. Probing the interactions between boronic acids and cis-diol-containing biomolecules by affinity capillary electrophoresis.

    PubMed

    Lü, Chenchen; Li, Hengye; Wang, Heye; Liu, Zhen

    2013-02-19

    The affinity of boronic acids to cis-diol-containing biomolecules has found wide applications in many fields, such as sensing, separation, drug delivery, and functional materials. A sound understanding of the binding interactions will greatly facilitate exquisite applications of this chemistry. Although a few analytical tools have been available for the characterization of the interactions, these techniques are associated with some apparent drawbacks, so they are only applicable to a limited range of boronic acids and cis-diol-containing biomolecules. Therefore, a widely applicable method is still greatly needed. In this work, an affinity capillary electrophoresis (ACE) method was established and validated to probe the interactions between boronic acids and cis-diol-containing biomolecules. The method was proven to be applicable to almost all types of cis-diol-containing biomolecules and boronic acids. Based on this method, a quantitative, comparative study on the interactions between 14 boronic acids that have important potentials for application with 5 typical monosaccharides of biological importance was carried out. The findings provided new insights into boronate affinity interactions, particularly the relationship between the binding strength with the molecular structures of the binding species. Besides, effects of pH and temperature on the binding strength were also investigated. This method exhibited several significant advantages, including (1) possibility of simultaneous study of multiple interactions, (2) low requirement on the purity of the binding species, (3) wide applicability, and (4) high accuracy and precision.

  15. Local structure in the disordered solid solution of cis- and trans-perinones.

    PubMed

    Teteruk, Jaroslav L; Glinnemann, Jürgen; Heyse, Winfried; Johansson, Kristoffer E; van de Streek, Jacco; Schmidt, Martin U

    2016-06-01

    The cis- and trans-isomers of the polycyclic aromatic compound perinone, C26H12N4O2, form a solid solution (Vat Red 14). This solid solution is isotypic to the crystal structures of cis-perinone (Pigment Red 194) and trans-perinone (Pigment Orange 34) and exhibits a combined positional and orientational disorder: In the crystal, each molecular position is occupied by either a cis- or trans-perinone molecule, both of which have two possible molecular orientations. The structure of cis-perinone exhibits a twofold orientational disorder, whereas the structure of trans-perinone is ordered. The crystal structure of the solid solution was determined by single-crystal X-ray analysis. Extensive lattice-energy minimizations with force-field and DFT-D methods were carried out on combinatorially complete sets of ordered models. For the disordered systems, local structures were calculated, including preferred local arrangements, ordering lengths, and probabilities for the arrangement of neighbouring molecules. The superposition of the atomic positions of all energetically favourable calculated models corresponds well with the experimentally determined crystal structures, explaining not only the atomic positions, but also the site occupancies and anisotropic displacement parameters.

  16. Role of Human DNA Polymerase kappa in Extension Opposite from a cis-syn Thymine Dimer

    SciTech Connect

    R Vasquez-Del Carpio; T Silverstein; S Lone; R Johnson; L Prakash; S Prakash; A Aggarwal

    2011-12-31

    Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase {Kappa} (Pol{Kappa}), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Pol{Kappa} in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Pol{Kappa} in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.

  17. Characteristic structural features of indolicidin: effects of the cis-trans isomerism on its conformation.

    PubMed

    Leitgeb, Balázs

    2014-01-01

    Indolicidin is an antimicrobial peptide showing a broad spectrum of antibacterial and antifungal activities, and according to the cis-trans isomerism of three Xaa-Pro peptide bonds, eight different stereoisomers could be distinguished for this peptide. As the cis-trans isomerism about the Xaa-Pro peptide bonds was not considered in previous studies, the structural features of distinct stereoisomeric forms were not characterized in detail, so far. In this theoretical study, the influences of cis-trans isomerism on the conformation of indolicidin were investigated, as well as the typical structural properties of each stereoisomer were determined, focusing on the secondary structures and intramolecular interactions. Based on the results derived from the molecular dynamics simulations, it could be concluded that the eight different stereoisomeric forms of indolicidin adopted characteristic conformational features. Nevertheless, the appearance of various turn structures and intramolecular interactions proved to be dependent on the cis or trans nature of Xaa-Pro peptide bonds, indicating the relevant role of Pro amino acids in determining the three-dimensional structure of this peptide.

  18. IRIS Toxicological Review of cis- & trans-1,2-Dichloroethylene (Interagency Science Consultation Draft)

    EPA Science Inventory

    On September 24, 2009, the Toxicological Review of cis- and trans-1,2-dichloroethylene and the charge to external peer reviewers were released for external peer review and public comment. The Toxicological Review and charge were reviewed internally by EPA and by other federal ag...

  19. IRIS Toxicological Review of cis- & trans-1,2-Dichloroethylene (Interagency Science Discussion Draft)

    EPA Science Inventory

    EPA is releasing the draft report, Toxicological Review of cis-1,2-Dichloroethylene and trans-1,2-Dichloroethylene, that was distributed to Federal agencies and White House Offices for comment during the Science Discussion step of the Rotationally Resolved Spectroscopy of the nu(8) Band of cis-Methyl Nitrite

    SciTech Connect

    Goss, Lisa M.; Mortensen, Clay D.; Blake, Thomas A.

    2004-06-01

    The 770-880 cm-1 region of the methyl nitrite spectrum has been recorded at a resolution of 0.0015 cm-1 in a static cell. Consistent with published determinations of the barrier to internal rotation of the methyl group, bands belonging to the trans isomer are very congested while those belonging to the cis isomer are more tractable.