Coding of Class I and II aminoacyl-tRNA synthetases

PubMed Central

Carter, Charles W.

2018-01-01

SUMMARY The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels—protozymes and Urzymes—associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric—middle base-pairing frequencies in sense/antisense alignments—that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins. PMID:28828732

Two Classes of New Optimal Asymmetric Quantum Codes

NASA Astrophysics Data System (ADS)

Chen, Xiaojing; Zhu, Shixin; Kai, Xiaoshan

2018-03-01

Let q be an even prime power and ω be a primitive element of F_{q2}. By analyzing the structure of cyclotomic cosets, we determine a sufficient condition for ω q- 1-constacyclic codes over F_{q2} to be Hermitian dual-containing codes. By the CSS construction, two classes of new optimal AQECCs are obtained according to the Singleton bound for AQECCs.

New class of photonic quantum error correction codes

NASA Astrophysics Data System (ADS)

Silveri, Matti; Michael, Marios; Brierley, R. T.; Salmilehto, Juha; Albert, Victor V.; Jiang, Liang; Girvin, S. M.

We present a new class of quantum error correction codes for applications in quantum memories, communication and scalable computation. These codes are constructed from a finite superposition of Fock states and can exactly correct errors that are polynomial up to a specified degree in creation and destruction operators. Equivalently, they can perform approximate quantum error correction to any given order in time step for the continuous-time dissipative evolution under these errors. The codes are related to two-mode photonic codes but offer the advantage of requiring only a single photon mode to correct loss (amplitude damping), as well as the ability to correct other errors, e.g. dephasing. Our codes are also similar in spirit to photonic ''cat codes'' but have several advantages including smaller mean occupation number and exact rather than approximate orthogonality of the code words. We analyze how the rate of uncorrectable errors scales with the code complexity and discuss the unitary control for the recovery process. These codes are realizable with current superconducting qubit technology and can increase the fidelity of photonic quantum communication and memories.

English-Thai Code-Switching of Teachers in ESP Classes

ERIC Educational Resources Information Center

Promnath, Korawan; Tayjasanant, Chamaipak

2016-01-01

The term code-switching (CS) that occurs in everyday situations, or naturalistic code-switching, has been a controversial strategy regarding whether it benefits or impedes language learning. The aim of this study was to investigate CS in conversations between teachers and students of ESP classes in order to explore the types and functions of CS…

PREFACE: 3rd International Congress on Ceramics (ICC3)

NASA Astrophysics Data System (ADS)

Niihara, Koichi; Ohji, Tatsuki; Sakka, Yoshio

2011-10-01

Early in 2005, the American Ceramic Society, the European Ceramic Society and the Ceramic Society of Japan announced a collaborative effort to provide leadership for the global ceramics community that would facilitate the use of ceramic and glass materials. That effort resulted in an agreement to organize a new biennial series of the International Congress on Ceramics, convened by the International Ceramic Federation (ICF). In order to share ideas and visions of the future for ceramic and glass materials, the 1st International Congress on Ceramics (ICC1) was held in Canada, 2006, under the organization of the American Ceramic Society, and the 2nd Congress (ICC2) was held in Italy, 2008, hosted by the European Ceramic Society. Organized by the Ceramic Society of Japan, the 3rd Congress (ICC3) was held in Osaka, Japan, 14-18 November 2010. Incorporating the 23rd Fall Meeting of the Ceramic Society of Japan and the 20th Iketani Conference, ICC3 was also co-organized by the Iketani Science and Technology Foundation, and was endorsed and supported by ICF, Asia-Oceania Ceramic Federation (AOCF) as well as many other organizations. Following the style of the previous two successful Congresses, the program was designed to advance ceramic and glass technologies to the next generation through discussion of the most recent advances and future perspectives, and to engage the worldwide ceramics community in a collective effort to expand the use of these materials in both conventional as well as new and exciting applications. ICC3 consisted of 22 voluntarily organized symposia in the most topical and essential themes of ceramic and glass materials, including Characterization, design and processing technologies Electro, magnetic and optical ceramics and devices Energy and environment related ceramics and systems Bio-ceramics and bio-technologies Ceramics for advanced industry and safety society Innovation in traditional ceramics It also contained the Plenary Session and the

Evidence of negative leaders which precede fast rise ICC pulses of upward

NASA Astrophysics Data System (ADS)

Yoshida, S.; Akita, M.; Morimoto, T.; Ushio, T.; Kawasaki, Z.; Wang, D.; Takagi, N.

2008-12-01

During winter thunderstorm season in Japan, a lightning observation campaign was conducted with using a VHF broadband digital interferometer (DITF), a capacitive antenna, and Rogowski coils to study the charge transfer mechanism associated with ICC pulses of upward lightning. All the detection systems recorded one upward negative lightning stroke hitting a lightning protection tower. The upward lightning consists of only the Initial Stage (IS) with one upward positive leader and six ICC pulses. The six ICC pulses are sub-classified clearly into two types according to current pulse shapes. The type 1 ICC pulses have a higher geometric mean (GM) current peak of 17 kA and a shorter GM 10-90% risetime of 8.9 μs, while the type 2 ICC pulses have a lower GM current peak of 0.34 kA and longer GM 10-90% risetime of 55 μs. The type 1 ICC pulses have the preceding negative leaders connecting to the channel of the continuing current, while the type 2 ICC pulses have no clear preceding negative leader. These negative leaders prior to the type 1 ICC pulses probably caused the current increases of the ICC pulses, which means that the negative leaders created the channels for the ICC pulses. The height of the space charge transferred by one of the type 1 ICC pulses was estimated about 700 m above sea level at most. This observation result is the first evidence to show explicitly the existence of the negative leaders prior to the fast rise ICC pulse. Furthermore, the result shows that space charge could exist at a low attitude such as 700 m above sea level. This fact is one of the reasons why upward lightning occurs even from rather low structures during winter thunderstorm season in Japan.

Adherence to ICCS nomenclature guidelines in subsequent literature: a bibliometric study.

PubMed

Dannaway, Jasan; Ng, Heryanto; Deshpande, Aniruddh V

2013-09-01

Since the publication of the 2006 International Children's Continence Society (ICCS) guidelines on terminologies for lower urinary tract dysfunction in children, little is known of their impact. In this study, we aim to quantify the adherence to the guidelines in the published literature, and to examine whether Medical Subject Headings (MeSH) in MEDLINE reflect the recommended "new" ICCS terminology. Seven pairs of pre-specified paired terms (obsolete and recommended by the ICCS) were searched, limited to paediatric literature published between 2002 and 2010. Their use in the literature was compared between the pre-guideline (2002-2005) and post-guideline (2007-2010) period and across geographical regions. MeSH in MEDLINE were examined for the use of ICCS preferred terminology. Publications in paediatric urinary incontinence have shown a 49% increase from 2002-2005 to 2007-2010 (55-82 per year). There was about a fourfold increase in the likelihood of usage of ICCS recommended terminologies post ICCS guideline publication (OR: 4.19, 95% CI: 3.04-5.78, P < 0.001). Approximately 25% of the studies published between 2007 and 2010 used obsolete terminologies. Analysis indicated satisfactory uptake for most terms, with the exception of "urotherapy." There was no significant geographical variation in uptake. More than half of the ICCS-recommended terms (4/7) did not appear in the current MeSH indexing tree and scope notes. Overall uptake of recommended terms following release of ICCS terminology guidelines was encouraging although it remains suboptimal for certain terms. Efforts need to be made to improve the current MEDLINE indexing so that MeSH terms reflect terminology recommended by the ICCS. Copyright © 2012 Wiley Periodicals, Inc.

PD-L1 and HLA Class I Antigen Expression and Clinical Course of the Disease in Intrahepatic Cholangiocarcinoma

PubMed Central

Sabbatino, Francesco; Villani, Vincenzo; Yearley, Jennifer H.; Deshpande, Vikram; Cai, Lei; Konstantinidis, Ioannis T.; Moon, Christina; Nota, Sjoerd; Wang, Yangyang; Al-Sukaini, Ahmad; Zhu, Andrew X.; Goyal, Lipika; Ting, David T.; Bardeesy, Nabeel; Hong, Theodore S.; Castillo, Carlos Fernandez-del; Tanabe, Kenneth K.; Lillemoe, Keith D.; Ferrone, Soldano; Ferrone, Cristina R.

2017-01-01

Purpose More effective therapy is needed for intrahepatic cholangiocarcinoma (ICC). The encouraging clinical results obtained with checkpoint molecule-specific monoclonal antibodies (mAb) have prompted us to investigate whether this type of immunotherapy may be applicable to ICC. The aims of this study were to determine whether (i) patients mount a T-cell immune response to their ICC, (ii) checkpoint molecules are expressed on both T cells and tumor cells, and (iii) tumor cells are susceptible to recognition by cognate T cells. Experimental Design Twenty-seven ICC tumors were analyzed for (i) lymphocyte infiltrate, (ii) HLA class I and HLA class II expression, and (iii) PD-1 and PD-L1 expression by T cells and ICC cells, respectively. The results of this analysis were correlated with the clinicopathologic characteristics of the patients investigated. Results Lymphocyte infiltrates were identified in all tumors. PD-L1 expression and HLA class I antigen expression by ICC cells was observed in 8 and 11, respectively, of the 27 tumors analyzed. HLA class I antigen expression correlated with CD8+ T-cell infiltrate. Furthermore, positive HLA class I antigen expression in combination with negative/rare PD-L1 expression was associated with favorable clinical course of the disease. Conclusions ICC patients are likely to mount a T-cell immune response against their own tumors. Defects in HLA class I antigen expression in combination with PD-L1 expression by ICC cells provide them with an immune escape mechanism. This mechanism justifies the implementation of immunotherapy with checkpoint molecule-specific mAbs in patients bearing ICC tumors without defects in HLA class I antigen expression. PMID:26373575

ICCE/ICCAI 2000 Keynote Papers.

ERIC Educational Resources Information Center

2000

This document contains the four keynote papers from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction). "Using Technologies To Model Student Problem Spaces" (David Jonassen) contrasts examples of semantic network, expert system, and systems modeling…

Making Homes Healthy: International Code Council Processes and Patterns.

PubMed

Coyle, Edward C; Isett, Kimberley R; Rondone, Joseph; Harris, Rebecca; Howell, M Claire Batten; Brandus, Katherine; Hughes, Gwendolyn; Kerfoot, Richard; Hicks, Diana

2016-01-01

Americans spend more than 90% of their time indoors, so it is important that homes are healthy environments. Yet many homes contribute to preventable illnesses via poor air quality, pests, safety hazards, and others. Efforts have been made to promote healthy housing through code changes, but results have been mixed. In support of such efforts, we analyzed International Code Council's (ICC) building code change process to uncover patterns of content and context that may contribute to successful adoptions of model codes. Discover patterns of facilitators and barriers to code amendments proposals. Mixed methods study of ICC records of past code change proposals. N = 2660. N/A. N/A. There were 4 possible outcomes for each code proposal studied: accepted as submitted, accepted as modified, accepted as modified by public comment, and denied. We found numerous correlates for final adoption of model codes proposed to the ICC. The number of proponents listed on a proposal was inversely correlated with success. Organizations that submitted more than 15 proposals had a higher chance of success than those that submitted fewer than 15. Proposals submitted by federal agencies correlated with a higher chance of success. Public comments in favor of a proposal correlated with an increased chance of success, while negative public comment had an even stronger negative correlation. To increase the chance of success, public health officials should submit their code changes through internal ICC committees or a federal agency, limit the number of cosponsors of the proposal, work with (or become) an active proposal submitter, and encourage public comment in favor of passage through their broader coalition.

ICCS 2009 User Guide for the International Database. Supplement 4: ICCS 2009 Sampling Stratification Information

ERIC Educational Resources Information Center

Brese, Falk; Jung, Michael; Mirazchiyski, Plamen; Schulz, Wolfram; Zuehlke, Olaf

2011-01-01

This supplement contains documentation on the explicit and implicit stratification variables included in the International Civic and Citizenship Education Study (ICCS) 2009 data files. The explicit strata are smaller sampling frames, created from the national sampling frames, from which national samples of schools were drawn. The implicit strata…

pH and temperature dual-sensitive liposome gel based on novel cleavable mPEG-Hz-CHEMS polymeric vaginal delivery system

PubMed Central

Chen, Daquan; Sun, Kaoxiang; Mu, Hongjie; Tang, Mingtan; Liang, Rongcai; Wang, Aiping; Zhou, Shasha; Sun, Haijun; Zhao, Feng; Yao, Jianwen; Liu, Wanhui

2012-01-01

Background In this study, a pH and temperature dual-sensitive liposome gel based on a novel cleavable hydrazone-based pH-sensitive methoxy polyethylene glycol 2000-hydrazone-cholesteryl hemisuccinate (mPEG-Hz-CHEMS) polymer was used for vaginal administration. Methods The pH-sensitive, cleavable mPEG-Hz-CHEMS was designed as a modified pH-sensitive liposome that would selectively degrade under locally acidic vaginal conditions. The novel pH-sensitive liposome was engineered to form a thermogel at body temperature and to degrade in an acidic environment. Results A dual-sensitive liposome gel with a high encapsulation efficiency of arctigenin was formed and improved the solubility of arctigenin characterized by Fourier transform infrared spectroscopy and differential scanning calorimetry. The dual-sensitive liposome gel with a sol-gel transition at body temperature was degraded in a pH-dependent manner, and was stable for a long period of time at neutral and basic pH, but cleavable under acidic conditions (pH 5.0). Arctigenin encapsulated in a dual-sensitive liposome gel was more stable and less toxic than arctigenin loaded into pH-sensitive liposomes. In vitro drug release results indicated that dual-sensitive liposome gels showed constant release of arctigenin over 3 days, but showed sustained release of arctigenin in buffers at pH 7.4 and pH 9.0. Conclusion This research has shed some light on a pH and temperature dual-sensitive liposome gel using a cleavable mPEG-Hz-CHEMS polymer for vaginal delivery. PMID:22679372

The First MS-Cleavable, Photo-Thiol-Reactive Cross-Linker for Protein Structural Studies

NASA Astrophysics Data System (ADS)

Iacobucci, Claudio; Piotrowski, Christine; Rehkamp, Anne; Ihling, Christian H.; Sinz, Andrea

2018-04-01

Cleavable cross-linkers are gaining increasing importance for chemical cross-linking/mass spectrometry (MS) as they permit a reliable and automated data analysis in structural studies of proteins and protein assemblies. Here, we introduce 1,3-diallylurea (DAU) as the first CID-MS/MS-cleavable, photo-thiol-reactive cross-linker. DAU is a commercially available, inexpensive reagent that efficiently undergoes an anti-Markovnikov hydrothiolation with cysteine residues in the presence of a radical initiator upon UV-A irradiation. Radical cysteine cross-linking proceeds via an orthogonal "click reaction" and yields stable alkyl sulfide products. DAU reacts at physiological pH and cross-linking reactions with peptides, and proteins can be performed at temperatures as low as 4 °C. The central urea bond is efficiently cleaved upon collisional activation during tandem MS experiments generating characteristic product ions. This improves the reliability of automated cross-link identification. Different radical initiators have been screened for the cross-linking reaction of DAU using the thiol-containing compounds cysteine and glutathione. Our concept has also been exemplified for the biologically relevant proteins bMunc13-2 and retinal guanylyl cyclase-activating protein-2. [Figure not available: see fulltext.

Synthesis and evaluations of an acid-cleavable, fluorescently labeled nucleotide as a reversible terminator for DNA sequencing.

PubMed

Tan, Lianjiang; Liu, Yazhi; Li, Xiaowei; Wu, Xin-Yan; Gong, Bing; Shen, Yu-Mei; Shao, Zhifeng

2016-02-11

An acid-cleavable linker based on a dimethylketal moiety was synthesized and used to connect a nucleotide with a fluorophore to produce a 3'-OH unblocked nucleotide analogue as an excellent reversible terminator for DNA sequencing by synthesis.

Highly ordered gold nanotubes using thiols at a cleavable block copolymer interface.

PubMed

Ryu, Ja-Hyoung; Park, Soojin; Kim, Bokyung; Klaikherd, Akamol; Russell, Thomas P; Thayumanavan, S

2009-07-29

We have prepared functionalized nanoporous thin films from a polystyrene-block-polyethylene oxide block copolymer, which was made cleavable due to the intervening disulfide bond. The cleavage reaction of the disulfide bond leaves behind free thiol groups inside the nanopores of polystyrene thin film. This nanoporous thin film can be used as a template for generating gold nanoring structures. This strategy can provide a facile method to form a highly ordered array of biopolymer or metal-polymer composite structures.

NIF ICCS network design and loading analysis

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

Tietbohl, G; Bryant, R

The National Ignition Facility (NIF) is housed within a large facility about the size of two football fields. The Integrated Computer Control System (ICCS) is distributed throughout this facility and requires the integration of about 40,000 control points and over 500 video sources. This integration is provided by approximately 700 control computers distributed throughout the NIF facility and a network that provides the communication infrastructure. A main control room houses a set of seven computer consoles providing operator access and control of the various distributed front-end processors (FEPs). There are also remote workstations distributed within the facility that allow providemore » operator console functions while personnel are testing and troubleshooting throughout the facility. The operator workstations communicate with the FEPs which implement the localized control and monitoring functions. There are different types of FEPs for the various subsystems being controlled. This report describes the design of the NIF ICCS network and how it meets the traffic loads that will are expected and the requirements of the Sub-System Design Requirements (SSDR's). This document supersedes the earlier reports entitled Analysis of the National Ignition Facility Network, dated November 6, 1996 and The National Ignition Facility Digital Video and Control Network, dated July 9, 1996. For an overview of the ICCS, refer to the document NIF Integrated Computer Controls System Description (NIF-3738).« less

Progress in digital color workflow understanding in the International Color Consortium (ICC) Workflow WG

NASA Astrophysics Data System (ADS)

McCarthy, Ann

2006-01-01

The ICC Workflow WG serves as the bridge between ICC color management technologies and use of those technologies in real world color production applications. ICC color management is applicable to and is used in a wide range of color systems, from highly specialized digital cinema color special effects to high volume publications printing to home photography. The ICC Workflow WG works to align ICC technologies so that the color management needs of these diverse use case systems are addressed in an open, platform independent manner. This report provides a high level summary of the ICC Workflow WG objectives and work to date, focusing on the ways in which workflow can impact image quality and color systems performance. The 'ICC Workflow Primitives' and 'ICC Workflow Patterns and Dimensions' workflow models are covered in some detail. Consider the questions, "How much of dissatisfaction with color management today is the result of 'the wrong color transformation at the wrong time' and 'I can't get to the right conversion at the right point in my work process'?" Put another way, consider how image quality through a workflow can be negatively affected when the coordination and control level of the color management system is not sufficient.

Increased brain uptake of targeted nanoparticles by adding an acid-cleavable linkage between transferrin and the nanoparticle core.

PubMed

Clark, Andrew J; Davis, Mark E

2015-10-06

Most therapeutic agents are excluded from entering the central nervous system by the blood-brain barrier (BBB). Receptor mediated transcytosis (RMT) is a common mechanism used by proteins, including transferrin (Tf), to traverse the BBB. Here, we prepared Tf-containing, 80-nm gold nanoparticles with an acid-cleavable linkage between the Tf and the nanoparticle core to facilitate nanoparticle RMT across the BBB. These nanoparticles are designed to bind to Tf receptors (TfRs) with high avidity on the blood side of the BBB, but separate from their multidentate Tf-TfR interactions upon acidification during the transcytosis process to allow release of the nanoparticle into the brain. These targeted nanoparticles show increased ability to cross an in vitro model of the BBB and, most important, enter the brain parenchyma of mice in greater amounts in vivo after systemic administration compared with similar high-avidity nanoparticles containing noncleavable Tf. In addition, we investigated this design with nanoparticles containing high-affinity antibodies (Abs) to TfR. With the Abs, the addition of the acid-cleavable linkage provided no improvement to in vivo brain uptake for Ab-containing nanoparticles, and overall brain uptake was decreased for all Ab-containing nanoparticles compared with Tf-containing ones. These results are consistent with recent reports of high-affinity anti-TfR Abs trafficking to the lysosome within BBB endothelium. In contrast, high-avidity, Tf-containing nanoparticles with the acid-cleavable linkage avoid major endothelium retention by shedding surface Tf during their transcytosis.

Purification of target proteins from intracellular inclusions mediated by intein cleavable polyhydroxyalkanoate synthase fusions.

PubMed

Du, Jinping; Rehm, Bernd H A

2017-11-02

Recombinant protein production and purification from Escherichia coli is often accompanied with expensive and complicated procedures, especially for therapeutic proteins. Here it was demonstrated that, by using an intein cleavable polyhydroxyalkanoate synthase fusion, recombinant proteins can be first produced and sequestered on a natural resin, the polyhydroxyalkanoate (PHA) inclusions, then separated from contaminating host proteins via simple PHA bead isolation steps, and finally purified by specific release into the soluble fraction induced by a pH reduction. By translationally fusing a target protein to PHA synthase using a self-cleaving intein as linker, intracellular production of PHA beads was achieved. Upon isolation of respective PHA beads the soluble pure target protein was released by a simple pH shift to 6. The utility of this approach was exemplified by producing six target proteins, including Aequorea victoria green fluorescent protein (GFP), Mycobacterium tuberculosis vaccine candidate Rv1626, the immunoglobulin G (IgG) binding ZZ domain of protein A derived from Staphylococcus aureus, human tumor necrosis factor alpha (TNFα), human granulocyte colony-stimulating factor (G-CSF), and human interferon alpha 2b (IFNα2b). Here a new method for production and purification of a tag-less protein was developed through intein cleavable polyhydroxyalkanoate synthase fusion. Pure target protein could be easily obtained without laborious downstream processing.

ICCE/ICCAI 2000 Full & Short Papers (Methodologies).

ERIC Educational Resources Information Center

2000

This document contains the full text of the following full and short papers on methodologies from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "A Methodology for Learning Pattern Analysis from Web Logs by Interpreting Web Page Contents" (Chih-Kai Chang and…

40 CFR 180.1294 - Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Trichoderma asperellum strain ICC 012... RESIDUES IN FOOD Exemptions From Tolerances § 180.1294 Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance. Trichoderma asperellum strain ICC 012 is exempted from the...

40 CFR 180.1294 - Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Trichoderma asperellum strain ICC 012... RESIDUES IN FOOD Exemptions From Tolerances § 180.1294 Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance. Trichoderma asperellum strain ICC 012 is exempted from the...

40 CFR 180.1294 - Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Trichoderma asperellum strain ICC 012... RESIDUES IN FOOD Exemptions From Tolerances § 180.1294 Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance. Trichoderma asperellum strain ICC 012 is exempted from the...

40 CFR 180.1294 - Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Trichoderma asperellum strain ICC 012... RESIDUES IN FOOD Exemptions From Tolerances § 180.1294 Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance. Trichoderma asperellum strain ICC 012 is exempted from the...

40 CFR 180.1294 - Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Trichoderma asperellum strain ICC 012... RESIDUES IN FOOD Exemptions From Tolerances § 180.1294 Trichoderma asperellum strain ICC 012; exemption from the requirement of a tolerance. Trichoderma asperellum strain ICC 012 is exempted from the...

Dogmas and controversies in compression therapy: report of an International Compression Club (ICC) meeting, Brussels, May 2011.

PubMed

Flour, Mieke; Clark, Michael; Partsch, Hugo; Mosti, Giovanni; Uhl, Jean-Francois; Chauveau, Michel; Cros, Francois; Gelade, Pierre; Bender, Dean; Andriessen, Anneke; Schuren, Jan; Cornu-Thenard, André; Arkans, Ed; Milic, Dragan; Benigni, Jean-Patrick; Damstra, Robert; Szolnoky, Gyozo; Schingale, Franz

2013-10-01

The International Compression Club (ICC) is a partnership between academics, clinicians and industry focused upon understanding the role of compression in the management of different clinical conditions. The ICC meet regularly and from these meetings have produced a series of eight consensus publications upon topics ranging from evidence-based compression to compression trials for arm lymphoedema. All of the current consensus documents can be accessed on the ICC website (http://www.icc-compressionclub.com/index.php). In May 2011, the ICC met in Brussels during the European Wound Management Association (EWMA) annual conference. With almost 50 members in attendance, the day-long ICC meeting challenged a series of dogmas and myths that exist when considering compression therapies. In preparation for a discussion on beliefs surrounding compression, a forum was established on the ICC website where presenters were able to display a summary of their thoughts upon each dogma to be discussed during the meeting. Members of the ICC could then provide comments on each topic thereby widening the discussion to the entire membership of the ICC rather than simply those who were attending the EWMA conference. This article presents an extended report of the issues that were discussed, with each dogma covered in a separate section. The ICC discussed 12 'dogmas' with areas 1 through 7 dedicated to materials and application techniques used to apply compression with the remaining topics (8 through 12) related to the indications for using compression. © 2012 The Authors. International Wound Journal © 2012 John Wiley & Sons Ltd and Medicalhelplines.com Inc.

40 CFR 180.1293 - Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Trichoderma gamsii strain ICC 080... RESIDUES IN FOOD Exemptions From Tolerances § 180.1293 Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance. Trichoderma gamsii strain ICC 080 is exempted from the requirement of...

40 CFR 180.1293 - Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Trichoderma gamsii strain ICC 080... RESIDUES IN FOOD Exemptions From Tolerances § 180.1293 Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance. Trichoderma gamsii strain ICC 080 is exempted from the requirement of...

40 CFR 180.1293 - Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Trichoderma gamsii strain ICC 080... RESIDUES IN FOOD Exemptions From Tolerances § 180.1293 Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance. Trichoderma gamsii strain ICC 080 is exempted from the requirement of...

40 CFR 180.1293 - Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Trichoderma gamsii strain ICC 080... RESIDUES IN FOOD Exemptions From Tolerances § 180.1293 Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance. Trichoderma gamsii strain ICC 080 is exempted from the requirement of...

40 CFR 180.1293 - Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Trichoderma gamsii strain ICC 080... RESIDUES IN FOOD Exemptions From Tolerances § 180.1293 Trichoderma gamsii strain ICC 080; exemption from the requirement of a tolerance. Trichoderma gamsii strain ICC 080 is exempted from the requirement of...

Evaluation of the accuracy of mono-energetic electron and beta-emitting isotope dose-point kernels using particle and heavy ion transport code system: PHITS.

PubMed

Shiiba, Takuro; Kuga, Naoya; Kuroiwa, Yasuyoshi; Sato, Tatsuhiko

2017-10-01

We assessed the accuracy of mono-energetic electron and beta-emitting isotope dose-point kernels (DPKs) calculated using the particle and heavy ion transport code system (PHITS) for patient-specific dosimetry in targeted radionuclide treatment (TRT) and compared our data with published data. All mono-energetic and beta-emitting isotope DPKs calculated using PHITS, both in water and compact bone, were in good agreement with those in literature using other MC codes. PHITS provided reliable mono-energetic electron and beta-emitting isotope scaled DPKs for patient-specific dosimetry. Copyright © 2017 Elsevier Ltd. All rights reserved.

SRMS maneuvers the ICC-VLD during STS-127 / Expedition 20 Joint Operations

NASA Image and Video Library

2009-07-19

S127-E-006934 (19 July 2009) --- Backdropped by a blue and white Earth, the remote manipulator system (RMS) arm of the Space Shuttle Endeavour, is about to hand off the Integrated Cargo Carrier (ICC) to the International Space Station (out of frame). The ICC is an unpressurized flat bed pallet and keel yoke assembly that was carried into space in the shuttle's payload bay.

ICCE/ICCAI 2000 Full & Short Papers (Collaborative Learning).

ERIC Educational Resources Information Center

2000

This document contains the full and short papers on collaborative learning from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction) covering the following topics: comparison of applying Internet to cooperative and traditional learning; a distributed backbone system for…

ICCE/ICCAI 2000 Full & Short Papers (Creative Learning).

ERIC Educational Resources Information Center

2000

This document contains the following full and short papers on creative learning from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "A Collaborative Learning Support System Based on Virtual Environment Server for Multiple Agents" (Takashi Ohno, Kenji…

ICCE/ICCAI 2000 Full & Short Papers (Student Modeling).

ERIC Educational Resources Information Center

2000

This document contains the following full and short papers on student modeling from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "A Computational Model for Learner's Motivation States in Individualized Tutoring System" (Behrouz H. Far and Anete H.…

Development of a Hypersensitive Periodate-Cleavable Amino Acid that is Methionine- and Disulfide-Compatible and its Application in MHC Exchange Reagents for T Cell Characterisation

PubMed Central

Amore, Alessia; Wals, Kim; Koekoek, Evelyn; Hoppes, Rieuwert; Toebes, Mireille; Schumacher, Ton N M; Rodenko, Boris; Ovaa, Huib

2013-01-01

Incorporation of cleavable linkers into peptides and proteins is of particular value in the study of biological processes. Here we describe the synthesis of a cleavable linker that is hypersensitive to oxidative cleavage as the result of the periodate reactivity of a vicinal amino alcohol moiety. Two strategies directed towards the synthesis of a building block suitable for solid-phase peptide synthesis were developed: a chemoenzymatic route, involving l-threonine aldolase, and an enantioselective chemical route; these led to α,γ-diamino-β-hydroxybutanoic acids in diastereoisomerically mixed and enantiopure forms, respectively. Incorporation of the 1,2-amino alcohol linker into the backbone of a peptide generated a conditional peptide that was rapidly cleaved at very low concentrations of sodium periodate. This cleavable peptide ligand was applied in the generation of MHC exchange reagents for the detection of antigen-specific T cells in peripheral blood cells. The extremely low concentration of periodate required to trigger MHC peptide exchange allowed the co-oxidation of methionine and disulfide residues to be avoided. Conditional MHC reagents hypersensitive to periodate can now be applied without limitations when UV irradiation is undesired or less practical. PMID:23280887

New Class of Quantum Error-Correcting Codes for a Bosonic Mode

NASA Astrophysics Data System (ADS)

Michael, Marios H.; Silveri, Matti; Brierley, R. T.; Albert, Victor V.; Salmilehto, Juha; Jiang, Liang; Girvin, S. M.

2016-07-01

We construct a new class of quantum error-correcting codes for a bosonic mode, which are advantageous for applications in quantum memories, communication, and scalable computation. These "binomial quantum codes" are formed from a finite superposition of Fock states weighted with binomial coefficients. The binomial codes can exactly correct errors that are polynomial up to a specific degree in bosonic creation and annihilation operators, including amplitude damping and displacement noise as well as boson addition and dephasing errors. For realistic continuous-time dissipative evolution, the codes can perform approximate quantum error correction to any given order in the time step between error detection measurements. We present an explicit approximate quantum error recovery operation based on projective measurements and unitary operations. The binomial codes are tailored for detecting boson loss and gain errors by means of measurements of the generalized number parity. We discuss optimization of the binomial codes and demonstrate that by relaxing the parity structure, codes with even lower unrecoverable error rates can be achieved. The binomial codes are related to existing two-mode bosonic codes, but offer the advantage of requiring only a single bosonic mode to correct amplitude damping as well as the ability to correct other errors. Our codes are similar in spirit to "cat codes" based on superpositions of the coherent states but offer several advantages such as smaller mean boson number, exact rather than approximate orthonormality of the code words, and an explicit unitary operation for repumping energy into the bosonic mode. The binomial quantum codes are realizable with current superconducting circuit technology, and they should prove useful in other quantum technologies, including bosonic quantum memories, photonic quantum communication, and optical-to-microwave up- and down-conversion.

ICCE/ICCAI 2000 Full & Short Papers (Lifelong Learning).

ERIC Educational Resources Information Center

2000

This document contains the following full and short papers on lifelong learning from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "A Study on the School Information Technology Pilot Scheme: Possibilities of Creative and Lifelong Learning" (Siu-Cheung Kong,…

ICCE/ICCAI 2000 Full & Short Papers (Educational Agent).

ERIC Educational Resources Information Center

2000

This document contains the full text of the following papers on educational agent from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "An Agent-Based Intelligent Tutoring System" (C.M. Bruff and M.A. Williams); (2) "Design of Systematic Concept…

Code of Ethical Conduct for Computer-Using Educators: An ICCE Policy Statement.

ERIC Educational Resources Information Center

Computing Teacher, 1987

1987-01-01

Prepared by the International Council for Computers in Education's Ethics and Equity Committee, this code of ethics for educators using computers covers nine main areas: curriculum issues, issues relating to computer access, privacy/confidentiality issues, teacher-related issues, student issues, the community, school organizational issues,…

Earth Processes: Reading the Isotopic Code

NASA Astrophysics Data System (ADS)

Basu, Asish; Hart, Stan

Publication of this monograph will coincide, to a precision of a few per mil, with the centenary of Henri Becquerel's discovery of "radiations actives" (C. R. Acad. Sci., Feb. 24, 1896). In 1896 the Earth was only 40 million years old according to Lord Kelvin. Eleven years later, Boltwood had pushed the Earth's age past 2000 million years, based on the first U/Pb chemical dating results. In exciting progression came discovery of isotopes by J. J. Thomson in 1912, invention of the mass spectrometer by Dempster (1918) and Aston (1919), the first measurement of the isotopic composition of Pb (Aston, 1927) and the final approach, using Pb-Pb isotopic dating, to the correct age of the Earth: close—2.9 Ga (Gerling, 1942), closer—3.0 Ga (Holmes, 1949) and closest—4.50 Ga (Patterson, Tilton and Inghram, 1953).

Online stable isotope analysis of dissolved organic carbon size classes using size exclusion chromatography coupled to an isotope ratio mass spectrometer.

PubMed

Malik, Ashish; Scheibe, Andrea; LokaBharathi, P A; Gleixner, Gerd

2012-09-18

Stable isotopic content of dissolved organic carbon (δ(13)C-DOC) provides valuable information on its origin and fate. In an attempt to get additional insights into DOC cycling, we developed a method for δ(13)C measurement of DOC size classes by coupling high-performance liquid chromatography (HPLC)-size exclusion chromatography (SEC) to online isotope ratio mass spectrometry (IRMS). This represents a significant methodological contribution to DOC research. The interface was evaluated using various organic compounds, thoroughly tested with soil-water from a C3-C4 vegetation change experiment, and also applied to riverine and marine DOC. δ(13)C analysis of standard compounds resulted in excellent analytical precision (≤0.3‰). Chromatography resolved soil DOC into 3 fractions: high molecular weight (HMW; 0.4-10 kDa), low molecular weight (LMW; 50-400 Da), and retained (R) fraction. Sample reproducibility for measurement of δ(13)C-DOC size classes was ±0.25‰ for HMW fraction, ± 0.54‰ for LMW fraction, and ±1.3‰ for R fraction. The greater variance in δ(13)C values of the latter fractions was due to their lower concentrations. The limit of quantification (SD ≤0.6‰) for each size fraction measured as a peak is 200 ng C (2 mg C/L). δ(13)C-DOC values obtained in SEC mode correlated significantly with those obtained without column in the μEA mode (p < 0.001, intercept 0.17‰), which rules out SEC-associated isotopic effects or DOC loss. In the vegetation change experiment, fractions revealed a clear trend in plant contribution to DOC; those in deeper soils and smaller size fractions had less plant material. It was also demonstrated that the technique can be successfully applied to marine and riverine DOC without further sample pretreatment.

Aqueous Processing for Printed Organic Electronics: Conjugated Polymers with Multistage Cleavable Side Chains

PubMed Central

2017-01-01

The ability to process conjugated polymers via aqueous solution is highly advantageous for reducing the costs and environmental hazards of large scale roll-to-roll processing of organic electronics. However, maintaining competitive electronic properties while achieving aqueous solubility is difficult for several reasons: (1) Materials with polar functional groups that provide aqueous solubility can be difficult to purify and characterize, (2) many traditional coupling and polymerization reactions cannot be performed in aqueous solution, and (3) ionic groups, though useful for obtaining aqueous solubility, can lead to a loss of solid-state order, as well as a screening of any applied bias. As an alternative, we report a multistage cleavable side chain method that combines desirable aqueous processing attributes without sacrificing semiconducting capabilities. Through the attachment of cleavable side chains, conjugated polymers have for the first time been synthesized, characterized, and purified in organic solvents, converted to a water-soluble form for aqueous processing, and brought through a final treatment to cleave the polymer side chains and leave behind the desired electronic material as a solvent-resistant film. Specifically, we demonstrate an organic soluble polythiophene that is converted to an aqueous soluble polyelectrolyte via hydrolysis. After blade coating from an aqueous solution, UV irradiation is used to cleave the polymer’s side chains, resulting in a solvent-resistant, electroactive polymer thin film. In application, this process results in aqueous printed materials with utility for solid-state charge transport in organic field effect transistors (OFETs), along with red to colorless electrochromism in ionic media for color changing displays, demonstrating its potential as a universal method for aqueous printing in organic electronics. PMID:28979937

Aqueous Processing for Printed Organic Electronics: Conjugated Polymers with Multistage Cleavable Side Chains.

PubMed

Schmatz, Brian; Yuan, Zhibo; Lang, Augustus W; Hernandez, Jeff L; Reichmanis, Elsa; Reynolds, John R

2017-09-27

The ability to process conjugated polymers via aqueous solution is highly advantageous for reducing the costs and environmental hazards of large scale roll-to-roll processing of organic electronics. However, maintaining competitive electronic properties while achieving aqueous solubility is difficult for several reasons: (1) Materials with polar functional groups that provide aqueous solubility can be difficult to purify and characterize, (2) many traditional coupling and polymerization reactions cannot be performed in aqueous solution, and (3) ionic groups, though useful for obtaining aqueous solubility, can lead to a loss of solid-state order, as well as a screening of any applied bias. As an alternative, we report a multistage cleavable side chain method that combines desirable aqueous processing attributes without sacrificing semiconducting capabilities. Through the attachment of cleavable side chains, conjugated polymers have for the first time been synthesized, characterized, and purified in organic solvents, converted to a water-soluble form for aqueous processing, and brought through a final treatment to cleave the polymer side chains and leave behind the desired electronic material as a solvent-resistant film. Specifically, we demonstrate an organic soluble polythiophene that is converted to an aqueous soluble polyelectrolyte via hydrolysis. After blade coating from an aqueous solution, UV irradiation is used to cleave the polymer's side chains, resulting in a solvent-resistant, electroactive polymer thin film. In application, this process results in aqueous printed materials with utility for solid-state charge transport in organic field effect transistors (OFETs), along with red to colorless electrochromism in ionic media for color changing displays, demonstrating its potential as a universal method for aqueous printing in organic electronics.

Figuring out the Statistics of the ICC World Cup 2011

ERIC Educational Resources Information Center

Shiwalkar, Jyoti P.; Deshpande, M. N.

2013-01-01

This paper deals with the analysis of cricket match results from the ICC World Cup 2011. We believe that such data provide good material for interesting classroom exercises. (Contains 7 tables and 1 figure.)

Isotope-coded ESI-enhancing derivatization reagents for differential analysis, quantification and profiling of metabolites in biological samples by LC/MS: A review.

PubMed

Higashi, Tatsuya; Ogawa, Shoujiro

2016-10-25

The analysis of the qualitative and quantitative changes of metabolites in body fluids and tissues yields valuable information for the diagnosis, pathological analysis and treatment of many diseases. Recently, liquid chromatography/electrospray ionization-(tandem) mass spectrometry [LC/ESI-MS(/MS)] has been widely used for these purposes due to the high separation capability of LC, broad coverage of ESI for various compounds and high specificity of MS(/MS). However, there are still two major problems to be solved regarding the biological sample analysis; lack of sensitivity and limited availability of stable isotope-labeled analogues (internal standards, ISs) for most metabolites. Stable isotope-coded derivatization (ICD) can be the answer for these problems. By the ICD, different isotope-coded moieties are introduced to the metabolites and one of the resulting derivatives can serve as the IS, which minimize the matrix effects. Furthermore, the derivatization can improve the ESI efficiency, fragmentation property in the MS/MS and chromatographic behavior of the metabolites, which lead to a high sensitivity and specificity in the various detection modes. Based on this background, this article reviews the recently-reported isotope-coded ESI-enhancing derivatization (ICEED) reagents, which are key components for the ICD-based LC/MS(/MS) studies, and their applications to the detection, identification, quantification and profiling of metabolites in human and animal samples. The LC/MS(/MS) using the ICEED reagents is the powerful method especially for the differential analysis (relative quantification) of metabolites in two comparative samples, simultaneous quantification of multiple metabolites whose stable isotope-labeled ISs are not available, and submetabolome profiling. Copyright © 2016 Elsevier B.V. All rights reserved.

ICCE/ICCAI 2000 Full & Short Papers (Intelligent Tutoring Systems).

ERIC Educational Resources Information Center

2000

This document contains the full and short papers on intelligent tutoring systems (ITS) from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction) covering the following topics: a framework for Internet-based distributed learning; a fuzzy-based assessment for the Perl tutoring…

ICCE/ICCAI 2000 Full & Short Papers (Interactive Learning Environments).

ERIC Educational Resources Information Center

2000

This document contains the full and short papers on interactive learning environments from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction) covering the following topics: a CAL system for appreciation of 3D shapes by surface development; a constructivist virtual physics…

ICCE/ICCAI 2000 Full & Short Papers (Web-Based Learning).

ERIC Educational Resources Information Center

2000

This document contains full and short papers on World Wide Web-based learning from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction). Topics covered include: design and development of CAL (Computer Assisted Learning) systems; design and development of WBI (Web-Based…

Gut inflammation and expression of ICC in a fetal lamb model of fetoscopic intervention for gastroschisis.

PubMed

Krebs, Thomas; Boettcher, Michael; Schäfer, Hansjörg; Eschenburg, Georg; Wenke, Katharina; Appl, Birgit; Roth, Beate; Andreas, Thomas; Schmitz, Carla; Fahje, Rebecca; Jacobsen, Birthe; Tiemann, Bastian; Reinshagen, Konrad; Hecher, Kurt; Bergholz, Robert

2014-08-01

The pathogenesis of intestinal dysmotility in gastroschisis is not completely understood. Peel formation and disorganization of interstitial Cajal cells (ICC) have been proposed in humans. The aim of this study was to evaluate the impact of prenatal coverage of gastroschisis on gut inflammation and expression of ICC in a fetal lamb model. Twenty-one German blackhead sheep with an abdominal wall defect that was created fetoscopically on day 77 of 145 days gestation were used in this study. Intrauterine surgery with the aim to cover the defect was performed 3 weeks later; two fetuses were covered completely, 5 partially and 11 remained uncovered. Three fetuses without gastroschisis were used as controls. All fetuses were retrieved by cesarean section at day 135. Samples of the small intestine were stained with hematoxylin and eosin for histologic analysis of peel formation and serosal and muscular thickness. For ICC detection, immunohistochemistry using anti-CD117 (c-Kit) antibody was used. In all samples with exposure to amniotic fluid, peel formation and significantly decreased ICC were found. Complete coverage reduced peel formation and disorganization of ICC compared to uncovered animals almost to the level of controls. Peel formation and ICC derangement were significantly reduced by prenatal coverage of gastroschisis. Moreover, this animal model mimics the histopathological bowel changes as seen in human gastroschisis and may, therefore, be used for further research on the pathophysiology and fetal therapy of this malformation.

Up to code: does your company's conduct meet world-class standards?

PubMed

Paine, Lynn; Deshpandé, Rohit; Margolis, Joshua D; Bettcher, Kim Eric

2005-12-01

Codes of conduct have long been a feature of corporate life. Today, they are arguably a legal necessity--at least for public companies with a presence in the United States. But the issue goes beyond U.S. legal and regulatory requirements. Sparked by corruption and excess of various types, dozens of industry, government, investor, and multisector groups worldwide have proposed codes and guidelines to govern corporate behavior. These initiatives reflect an increasingly global debate on the nature of corporate legitimacy. Given the legal, organizational, reputational, and strategic considerations, few companies will want to be without a code. But what should it say? Apart from a handful of essentials spelled out in Sarbanes-Oxley regulations and NYSE rules, authoritative guidance is sorely lacking. In search of some reference points for managers, the authors undertook a systematic analysis of a select group of codes. In this article, they present their findings in the form of a "codex," a reference source on code content. The Global Business Standards Codex contains a set of overarching principles as well as a set of conduct standards for putting those principles into practice. The GBS Codex is not intended to be adopted as is, but is meant to be used as a benchmark by those wishing to create their own world-class code. The provisions of the codex must be customized to a company's specific business and situation; individual companies' codes will include their own distinctive elements as well. What the codex provides is a starting point grounded in ethical fundamentals and aligned with an emerging global consensus on basic standards of corporate behavior.

A Catalytic Asymmetric Synthesis of Polysubstituted Piperidines Using a Rhodium (I) Catalyzed [2+2+2] Cycloaddition Employing a Cleavable Tether

PubMed Central

Martin, Timothy J.; Rovis, Tomislav

2013-01-01

An enantioselective rhodium (I) catalyzed [2+2+2] cycloaddition with a cleavable tether has been developed. The reaction proceeds with a variety of alkyne substrates in good yield and high enantioselectivity. Upon reduction of the vinylogous amide in high diastereoselectivity (>19:1) and cleavage of the tether, N-methylpiperidine products with functional group handles can be accessed. PMID:23606664

δ-Conotoxins synthesized using an acid-cleavable solubility tag approach reveal key structural determinants for NaV subtype selectivity.

PubMed

Peigneur, Steve; Paolini-Bertrand, Marianne; Gaertner, Hubert; Biass, Daniel; Violette, Aude; Stöcklin, Reto; Favreau, Philippe; Tytgat, Jan; Hartley, Oliver

2014-12-19

Conotoxins are venom peptides from cone snails with multiple disulfide bridges that provide a rigid structural scaffold. Typically acting on ion channels implicated in neurotransmission, conotoxins are of interest both as tools for pharmacological studies and as potential new medicines. δ-Conotoxins act by inhibiting inactivation of voltage-gated sodium channels (Nav). Their pharmacology has not been extensively studied because their highly hydrophobic character makes them difficult targets for chemical synthesis. Here we adopted an acid-cleavable solubility tag strategy that facilitated synthesis, purification, and directed disulfide bridge formation. Using this approach we readily produced three native δ-conotoxins from Conus consors plus two rationally designed hybrid peptides. We observed striking differences in Nav subtype selectivity across this group of compounds, which differ in primary structure at only three positions: 12, 23, and 25. Our results provide new insights into the structure-activity relationships underlying the Nav subtype selectivity of δ-conotoxins. Use of the acid-cleavable solubility tag strategy should facilitate synthesis of other hydrophobic peptides with complex disulfide bridge patterns. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

In situ fabrication of cleavable peptide arrays on polydimethylsiloxane and applications for kinase activity assays.

PubMed

Chen, Huang-Han; Hsiao, Yu-Chieh; Li, Jie-Ren; Chen, Shu-Hui

2015-03-20

Polydimethylsiloxane (PDMS) is widely used for microfabrication and bioanalysis; however, its surface functionalization is limited due to the lack of active functional groups and incompatibility with many solvents. We presented a novel approach for in situ fabrication of cleavable peptide arrays on polydimethylsiloxane (PDMS) viatert-butyloxycarbonyl (t-Boc)/trifluoroacetic acid (TFA) chemistry using gold nanoparticles (AuNPs) as the anchor and a disulfide/amine terminated hetero-polyethylene glycol as the cleavable linker. The method was fine tuned to use reagents compatible with the PDMS. Using 5-mer pentapeptide, Trp5, as a model, step-by-step covalent coupling during the reaction cycles was monitored by Attenuated total reflectance-Fourier transform infrared spectrometer (ATR-FTIR), X-ray photoelectron spectroscopy (XPS), or atomic force microscopy (AFM), and further confirmed by mass spectrometry (MS) detection of the cleaved peptides. Using such a method, heptapeptides of the PKA substrate, LRRASLG (Kemptide), and its point mutated analogs were fabricated in an array format for comparative studies of cAMP-dependent protein kinase (PKA) activity. Based on on-chip detection, Kemptide sequence exhibited the highest phosphorylation activity, which was detected to a 1.5-time lesser extent for the point mutated sequence (LRRGSLG) containing the recognition motif (RRXS), and was nearly undetectable for another point mutated sequence (LRLASLG) that lacked the recognition motif. These results indicate that the reported fabrication method is able to yield highly specific peptide sequences on PDMS, leading to a highly motif-sensitive enzyme activity assay. Copyright © 2015 Elsevier B.V. All rights reserved.

Scalable and cleavable polysaccharide nanocarriers for the delivery of chemotherapy drugs.

PubMed

Wang, Hao; Dai, Tingting; Li, Shengli; Zhou, Shuyan; Yuan, Xiaojing; You, Jiayi; Wang, Chenglong; Mukwaya, Vincent; Zhou, Guangdong; Liu, Guojun; Wei, Xiaohui; Dou, Hongjing

2018-05-01

While polysaccharide-based nanocarriers have been recognized for their crucial roles in tumor theranostics, the industrial-scale production of nanotherapeutics still remains a significant challenge. Most current approaches adopt a postpolymerization self-assembly strategy that follows a separate synthetic step and thus suffers from subgram scale yields and a limited range of application. In this study, we demonstrate the kilogram-scale formation of polysaccharide-polyacrylate nanocarriers at concentrations of up to 5 wt% through a one-pot approach - starting from various acrylate monomers and polysaccharides - that combines aspects of hydrophobicity-induced self-assembly with the free radical graft copolymerization of acrylate monomers from polysaccharide backbones into a single process that is thus denoted as a graft copolymerization induced self-assembly. We also demonstrate that this novel approach is applicable to a broad range of polysaccharides and acrylates. Notably, by choosing a crosslinker that bears a disulfide group and two vinyl capping groups to structurally lock the nanocarriers, the products are rendered cleavable in the reducing environments encountered at tumor sites and thus provide ideal candidates for the construction of anticancer nanotherapeutic systems. In vitro and in vivo studies demonstrated that the use of this nanocarrier for the delivery of doxorubicin hydrochloride (DOX) significantly decreased the side effects of DOX and improved the bio-safety of the chemotherapy accordingly. While polysaccharide-based nanocarriers have been recognized for their crucial roles in tumor theranostics, the industrial-scale production of these nanotherapeutics still remains a significant challenge. Most current approaches adopt a post-polymerization self-assembly strategy which that follows a separate synthetic step, and thus suffers from sub-gram scale yields and a limited range of application. In this study, the hydrophobic effect was combined with

The weight hierarchies and chain condition of a class of codes from varieties over finite fields

NASA Technical Reports Server (NTRS)

Wu, Xinen; Feng, Gui-Liang; Rao, T. R. N.

1996-01-01

The generalized Hamming weights of linear codes were first introduced by Wei. These are fundamental parameters related to the minimal overlap structures of the subcodes and very useful in several fields. It was found that the chain condition of a linear code is convenient in studying the generalized Hamming weights of the product codes. In this paper we consider a class of codes defined over some varieties in projective spaces over finite fields, whose generalized Hamming weights can be determined by studying the orbits of subspaces of the projective spaces under the actions of classical groups over finite fields, i.e., the symplectic groups, the unitary groups and orthogonal groups. We give the weight hierarchies and generalized weight spectra of the codes from Hermitian varieties and prove that the codes satisfy the chain condition.

Intra-class correlation estimates for assessment of vitamin A intake in children.

PubMed

Agarwal, Girdhar G; Awasthi, Shally; Walter, Stephen D

2005-03-01

In many community-based surveys, multi-level sampling is inherent in the design. In the design of these studies, especially to calculate the appropriate sample size, investigators need good estimates of intra-class correlation coefficient (ICC), along with the cluster size, to adjust for variation inflation due to clustering at each level. The present study used data on the assessment of clinical vitamin A deficiency and intake of vitamin A-rich food in children in a district in India. For the survey, 16 households were sampled from 200 villages nested within eight randomly-selected blocks of the district. ICCs and components of variances were estimated from a three-level hierarchical random effects analysis of variance model. Estimates of ICCs and variance components were obtained at village and block levels. Between-cluster variation was evident at each level of clustering. In these estimates, ICCs were inversely related to cluster size, but the design effect could be substantial for large clusters. At the block level, most ICC estimates were below 0.07. At the village level, many ICC estimates ranged from 0.014 to 0.45. These estimates may provide useful information for the design of epidemiological studies in which the sampled (or allocated) units range in size from households to large administrative zones.

Protein quantification using a cleavable reporter peptide.

PubMed

Duriez, Elodie; Trevisiol, Stephane; Domon, Bruno

2015-02-06

Peptide and protein quantification based on isotope dilution and mass spectrometry analysis are widely employed for the measurement of biomarkers and in system biology applications. The accuracy and reliability of such quantitative assays depend on the quality of the stable-isotope labeled standards. Although the quantification using stable-isotope labeled peptides is precise, the accuracy of the results can be severely biased by the purity of the internal standards, their stability and formulation, and the determination of their concentration. Here we describe a rapid and cost-efficient method to recalibrate stable isotope labeled peptides in a single LC-MS analysis. The method is based on the equimolar release of a protein reference peptide (used as surrogate for the protein of interest) and a universal reporter peptide during the trypsinization of a concatenated polypeptide standard. The quality and accuracy of data generated with such concatenated polypeptide standards are highlighted by the quantification of two clinically important proteins in urine samples and compared with results obtained with conventional stable isotope labeled reference peptides. Furthermore, the application of the UCRP standards in complex samples is described.

ICCE/ICCAI 2000 Full & Short Papers (Artificial Intelligence in Education).

ERIC Educational Resources Information Center

2000

This document contains the full and short papers on artificial intelligence in education from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction) covering the following topics: a computational model for learners' motivation states in individualized tutoring system; a…

ICCE/ICCAI 2000 Full & Short Papers (Virtual Lab/Classroom/School).

ERIC Educational Resources Information Center

2000

This document contains the following full and short papers on virtual laboratories, classrooms, and schools from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "A Collaborative Learning Support System Based on Virtual Environment Server for Multiple…

L-type calcium channels refine the neural population code of sound level.

PubMed

Grimsley, Calum Alex; Green, David Brian; Sivaramakrishnan, Shobhana

2016-12-01

The coding of sound level by ensembles of neurons improves the accuracy with which listeners identify how loud a sound is. In the auditory system, the rate at which neurons fire in response to changes in sound level is shaped by local networks. Voltage-gated conductances alter local output by regulating neuronal firing, but their role in modulating responses to sound level is unclear. We tested the effects of L-type calcium channels (Ca L : Ca V 1.1-1.4) on sound-level coding in the central nucleus of the inferior colliculus (ICC) in the auditory midbrain. We characterized the contribution of Ca L to the total calcium current in brain slices and then examined its effects on rate-level functions (RLFs) in vivo using single-unit recordings in awake mice. Ca L is a high-threshold current and comprises ∼50% of the total calcium current in ICC neurons. In vivo, Ca L activates at sound levels that evoke high firing rates. In RLFs that increase monotonically with sound level, Ca L boosts spike rates at high sound levels and increases the maximum firing rate achieved. In different populations of RLFs that change nonmonotonically with sound level, Ca L either suppresses or enhances firing at sound levels that evoke maximum firing. Ca L multiplies the gain of monotonic RLFs with dynamic range and divides the gain of nonmonotonic RLFs with the width of the RLF. These results suggest that a single broad class of calcium channels activates enhancing and suppressing local circuits to regulate the sensitivity of neuronal populations to sound level. Copyright © 2016 the American Physiological Society.

L-type calcium channels refine the neural population code of sound level

PubMed Central

Grimsley, Calum Alex; Green, David Brian

2016-01-01

The coding of sound level by ensembles of neurons improves the accuracy with which listeners identify how loud a sound is. In the auditory system, the rate at which neurons fire in response to changes in sound level is shaped by local networks. Voltage-gated conductances alter local output by regulating neuronal firing, but their role in modulating responses to sound level is unclear. We tested the effects of L-type calcium channels (CaL: CaV1.1–1.4) on sound-level coding in the central nucleus of the inferior colliculus (ICC) in the auditory midbrain. We characterized the contribution of CaL to the total calcium current in brain slices and then examined its effects on rate-level functions (RLFs) in vivo using single-unit recordings in awake mice. CaL is a high-threshold current and comprises ∼50% of the total calcium current in ICC neurons. In vivo, CaL activates at sound levels that evoke high firing rates. In RLFs that increase monotonically with sound level, CaL boosts spike rates at high sound levels and increases the maximum firing rate achieved. In different populations of RLFs that change nonmonotonically with sound level, CaL either suppresses or enhances firing at sound levels that evoke maximum firing. CaL multiplies the gain of monotonic RLFs with dynamic range and divides the gain of nonmonotonic RLFs with the width of the RLF. These results suggest that a single broad class of calcium channels activates enhancing and suppressing local circuits to regulate the sensitivity of neuronal populations to sound level. PMID:27605536

PFLOTRAN: Reactive Flow & Transport Code for Use on Laptops to Leadership-Class Supercomputers

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

Hammond, Glenn E.; Lichtner, Peter C.; Lu, Chuan

PFLOTRAN, a next-generation reactive flow and transport code for modeling subsurface processes, has been designed from the ground up to run efficiently on machines ranging from leadership-class supercomputers to laptops. Based on an object-oriented design, the code is easily extensible to incorporate additional processes. It can interface seamlessly with Fortran 9X, C and C++ codes. Domain decomposition parallelism is employed, with the PETSc parallel framework used to manage parallel solvers, data structures and communication. Features of the code include a modular input file, implementation of high-performance I/O using parallel HDF5, ability to perform multiple realization simulations with multiple processors permore » realization in a seamless manner, and multiple modes for multiphase flow and multicomponent geochemical transport. Chemical reactions currently implemented in the code include homogeneous aqueous complexing reactions and heterogeneous mineral precipitation/dissolution, ion exchange, surface complexation and a multirate kinetic sorption model. PFLOTRAN has demonstrated petascale performance using 2{sup 17} processor cores with over 2 billion degrees of freedom. Accomplishments achieved to date include applications to the Hanford 300 Area and modeling CO{sub 2} sequestration in deep geologic formations.« less

ICCS 2009 Asian Report: Civic Knowledge and Attitudes among Lower-Secondary Students in Five Asian Countries

ERIC Educational Resources Information Center

Fraillon, Julian; Schulz, Wolfram; Ainley, John

2012-01-01

This report presents findings from the Asian regional module of the International Civic and Citizenship Education Study (ICCS), sponsored by the International Association for the Evaluation of Educational Achievement (IEA). ICCS studied the ways in which young people in lower-secondary schools are prepared to undertake their roles as citizens.…

ICCE/ICCAI 2000 Full & Short Papers (Knowledge Construction and Navigation).

ERIC Educational Resources Information Center

2000

This document contains the following full and short papers on knowledge construction and navigation from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "An XML-Based Tool for Building and Using Conceptual Maps in Education and Training Environments"…

ICCE/ICCAI 2000 Full & Short Papers (Computer-Assisted Language Learning).

ERIC Educational Resources Information Center

2000

This document contains the following full and short papers on computer-assisted language learning (CALL) from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "A Computer-Assisted English Abstract Words Learning Environment on the Web" (Wenli Tsou and…

Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

PubMed Central

Wang, Jigang; Zhang, Chong-Jing; Zhang, Jianbin; He, Yingke; Lee, Yew Mun; Chen, Songbi; Lim, Teck Kwang; Ng, Shukie; Shen, Han-Ming; Lin, Qingsong

2015-01-01

Target-identification and understanding of mechanism-of-action (MOA) are challenging for development of small-molecule probes and their application in biology and drug discovery. For example, although aspirin has been widely used for more than 100 years, its molecular targets have not been fully characterized. To cope with this challenge, we developed a novel technique called quantitative acid-cleavable activity-based protein profiling (QA-ABPP) with combination of the following two parts: (i) activity-based protein profiling (ABPP) and iTRAQ™ quantitative proteomics for identification of target proteins and (ii) acid-cleavable linker-based ABPP for identification of peptides with specific binding sites. It is known that reaction of aspirin with its target proteins leads to acetylation. We thus applied the above technique using aspirin-based probes in human cancer HCT116 cells. We identified 1110 target proteins and 2775 peptides with exact acetylation sites. By correlating these two sets of data, 523 proteins were identified as targets of aspirin. We used various biological assays to validate the effects of aspirin on inhibition of protein synthesis and induction of autophagy which were elicited from the pathway analysis of Aspirin target profile. This technique is widely applicable for target identification in the field of drug discovery and biology, especially for the covalent drugs. PMID:25600173

Changes in membrane cholesterol affect caveolin-1 localization and ICC-pacing in mouse jejunum.

PubMed

Daniel, E E; Bodie, Gregory; Mannarino, Marco; Boddy, Geoffrey; Cho, Woo-Jung

2004-07-01

Pacing of mouse is dependent on the spontaneous activity of interstitial cells of Cajal in the myenteric plexus (ICC-MP). These ICC, as well as intestinal smooth muscle, contain small membrane invaginations called caveolae. Caveolae are signaling centers formed by insertions of caveolin proteins in the inner aspect of the plasma membrane. Caveolins bind signaling proteins and thereby negatively modulate their signaling. We disrupted caveolae by treating intestinal segments with methyl beta-clodextrin (CD) to remove cholesterol or with water-soluble cholesterol (WSC) to load cholesterol. Both of these treatments reduced pacing frequencies, and these effects were reversed by the other agent. These treatments also inhibited paced contractions, but complete reversal was not observed. To evaluate the specificity of the effects of CD and WSC, additional studies were made of their effects on responses to carbamoyl choline and to stimulation of cholinergic nerves. Neither of these treatments affected these sets of responses compared with their respective time controls. Immunochemical and ultrastructural studies showed that caveolin 1 was present in smooth muscle membranes and ICC-MP. CD depleted both caveolin 1 and caveolae, whereas WSC increased the amount of caveolin 1 immunoreactivity and altered its distribution but failed to increase the number of caveolae. The effects of each agent were reversed in major part by the other. We conclude that signaling through caveolae may play a role in pacing by ICC but does not affect responses to acetylcholine from nerves or when added exogenously.

Multiple component codes based generalized LDPC codes for high-speed optical transport.

PubMed

Djordjevic, Ivan B; Wang, Ting

2014-07-14

A class of generalized low-density parity-check (GLDPC) codes suitable for optical communications is proposed, which consists of multiple local codes. It is shown that Hamming, BCH, and Reed-Muller codes can be used as local codes, and that the maximum a posteriori probability (MAP) decoding of these local codes by Ashikhmin-Lytsin algorithm is feasible in terms of complexity and performance. We demonstrate that record coding gains can be obtained from properly designed GLDPC codes, derived from multiple component codes. We then show that several recently proposed classes of LDPC codes such as convolutional and spatially-coupled codes can be described using the concept of GLDPC coding, which indicates that the GLDPC coding can be used as a unified platform for advanced FEC enabling ultra-high speed optical transport. The proposed class of GLDPC codes is also suitable for code-rate adaption, to adjust the error correction strength depending on the optical channel conditions.

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification.

PubMed

Cenik, Can; Chua, Hon Nian; Singh, Guramrit; Akef, Abdalla; Snyder, Michael P; Palazzo, Alexander F; Moore, Melissa J; Roth, Frederick P

2017-03-01

Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5 ' proximal- i ntron- m inus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N 1 -methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N 1 -methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC. © 2017 Cenik et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

ICCS 2009 European Report: Civic Knowledge, Attitudes, and Engagement among Lower-Secondary Students in 24 European Countries

ERIC Educational Resources Information Center

Kerr, David; Sturman, Linda; Schulz, Wolfram; Burge, Bethan

2010-01-01

The International Civic and Citizenship Education Study (ICCS) studied the ways in which countries prepare their young people to undertake their roles as citizens. ICCS was based on the premise that preparing students for citizenship involves helping them develop relevant knowledge and understanding and form positive attitudes toward being a…

Metal isotope coded profiling of organic ligands by mass spectrometry in aquatic environments

NASA Astrophysics Data System (ADS)

Wichard, Thomas; Deicke, Michael; Frieder Mohr, Jan; Klein, Martin

2017-04-01

Metal isotope coded profiling (MICP) introduces a universal discovery platform for metal chelating natural products that act as metallophores, ion buffers or sequestering agents. The detection of cation and oxoanion complexing ligands is facilitated by the identification of unique isotopic signatures created by the application of isotopically pure metals. We present a targeted analysis of low-molecular-weight organic ligands based on fast UHPLC-ESI-MS measurements. Replacement of, for example, natural iron or molybdenum with isotopically pure 54Fe/58Fe (ratio 1:1) or 95Mo/98Mo (ratio 1:1) causes easily detectable unique isotopic signatures in the mass spectra of potential metal-complexing ligands. This can be achieved under laboratory conditions not only in growth media, but also by spiking directly aqueous samples or solid-phase extracts. Importantly, as the relative affinity of the metallophores for e.g., Mo or Fe is dependent on the pH, all experiments needs to be conducted under pH-controlled conditions. The improved ionization efficiency of some metal complexes helps to enhance the signal-to-noise ratio compared to the free ligand at the same chromatographic conditions. The methodology does not necessarily depend on HR-ESI-MS measurements (e.g., Q-Exactive Orbitrap) and can be applied to any mass spectrometer. With MICP, two birds can be killed with one stone: (i) the identification of metallophores (e.g., siderophores, molybdophores) for metal uptake by any organism and (ii) organic ligands which solely work as metal buffer in dissolved organic matter (DOM). We currently address following two main research lines: First, DOM has often been used as a proxy for bio-productivity in terms of a carbon source; however, the specific impact of DOM as a "metal buffer" for biological processes is still under-investigated. Upon the administration of individual isotopes or isotopic pairs, for example, 54Fe/58Fe, 63Cu/65Cu, 66Zn/68Zn, or 95Mo/98Mo and subsequent

ICCE/ICCAI 2000 Full & Short Papers (Virtual Reality in Education).

ERIC Educational Resources Information Center

2000

This document contains the full text of the following full and short papers on virtual reality in education from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "A CAL System for Appreciation of 3D Shapes by Surface Development (C3D-SD)" (Stephen C. F. Chan, Andy…

STS-105 ICC is moved to the payload canister for transport to pad 39A

NASA Technical Reports Server (NTRS)

2001-01-01

KENNEDY SPACE CENTER, Fla. -- The Integrated Cargo Carrier is lowered into the payload canister in front of the Multi-Purpose Logistics Module Leonardo. The ICC holds several payloads for mission STS-105, the Early Ammonia Servicer and two experiment containers. The canister will transport the MPLM and ICC transport to Launch Pad 39A where they will be placed in the payload bay of Space Shuttle Discovery. Launch of STS-105 is scheduled for 5:38 p.m. EDT Aug. 9

ICCE/ICCAI 2000 Full & Short Papers (Multimedia and Hypermedia in Education).

ERIC Educational Resources Information Center

2000

This document contains the full and short papers on multimedia and hypermedia in education from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction) covering the following topics: learner-centered navigation path planning in world Wide Web-based learning; the relation…

Tooth size discrepancies in Class II division 1 and Class III malocclusion requiring surgical-orthodontic or orthodontic treatment.

PubMed

McSwiney, Timothy P; Millett, Declan T; McIntyre, Grant T; Barry, Mark K; Cronin, Michael S

2014-06-01

To compare mean anterior (AR) and mean overall (OR) tooth size ratios, prevalence of clinically significant tooth size discrepancies (TSDs) and correlation between AR and OR in subjects with Class II division 1 and Class III malocclusion treated by surgical-orthodontic or orthodontic means. Retrospective, cross-sectional. State-funded and private clinics. From pre-treatment cohorts of 770 surgical and 610 non-surgical subjects, Class II division 1 and Class III malocclusion groups were identified with 60 surgical and 60 non-surgical subjects, comprising 30 males and 30 females, in each. AR and OR were calculated by landmarking digital models. Differences in AR and OR and their relationship were analysed using two-way analysis of variance (ANOVA) and a correlation coefficient, respectively. The proportions of the surgical and non-surgical groups with a TSD were assessed using logistic regression. Intra-examiner reproducibility involved re-landmarking 30 randomly selected image sets and differences in ARs and ORs were compared using a paired t-test. Random error was assessed using the intraclass correlation coefficient (ICC). Analyses were performed using SAS (SAS Institute Inc., Cary, NC, USA) at the 5% level of significance. There were no statistically significant differences associated with the measurement of either the mean AR (P = 0·913) or the mean OR (P = 0·874). ICC values were very high (AR = 0·95; OR = 0·90). Differences existed between both Class II and Class III surgical (AR: P<0·001; OR: P<0·001) and non-surgical groups (AR: P = 0·012; OR: P = 0·003). The AR and OR relationship was strong (correlation coefficient = 0·72). The highest percentage of clinically significant TSDs was seen in the AR of both Class II and Class III surgical groups (23·3%). In the cohort examined: AR and OR differed significantly for malocclusion groups. The prevalence of clinically significant TSDs did not differ significantly between

ICCE/ICCAI 2000 Full & Short Papers (Evaluation of Learning and Systems).

ERIC Educational Resources Information Center

2000

This document contains the full and short papers on evaluation of learning and systems from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction) covering the following topics: a new method for efficient study of Kanji using mnemonics and software; a study on the relation…

STS-105 ICC is moved to the payload canister for transport to pad 39A

NASA Technical Reports Server (NTRS)

2001-01-01

KENNEDY SPACE CENTER, Fla. -- A crane is attached to the Integrated Cargo Carrier in the Space Station Processing Facility in order to move it to the payload canister. The ICC holds several payloads for mission STS-105, the Early Ammonia Servicer and two experiment containers. The ICC will join the Multi-Purpose Logistics Module Leonardo in the payload canister for transport to Launch Pad 39A where they will be placed in the payload bay of Space Shuttle Discovery. Launch of STS-105 is scheduled for 5:38 p.m. EDT Aug. 9

STS-105 ICC is moved to the payload canister for transport to pad 39A

NASA Technical Reports Server (NTRS)

2001-01-01

KENNEDY SPACE CENTER, Fla. -- An overhead crane in the Space Station Processing Facility lifts the Integrated Cargo Carrier from its workstand to move it to the payload canister. The ICC holds several payloads for mission STS-105, the Early Ammonia Servicer and two experiment containers. The ICC will join the Multi-Purpose Logistics Module Leonardo in the payload canister for transport to Launch Pad 39A where they will be placed in the payload bay of Space Shuttle Discovery. Launch of STS-105 is scheduled for 5:38 p.m. EDT Aug. 9

STS-105 ICC is moved to the payload canister for transport to pad 39A

NASA Technical Reports Server (NTRS)

2001-01-01

KENNEDY SPACE CENTER, Fla. -- An overhead crane in the Space Station Processing Facility moves the Integrated Cargo Carrier toward the payload canister (right). The ICC holds several payloads for mission STS-105, the Early Ammonia Servicer and two experiment containers. The ICC will join the Multi-Purpose Logistics Module Leonardo already in the payload canister for transport to Launch Pad 39A where they will be placed in the payload bay of Space Shuttle Discovery. Launch of STS-105 is scheduled for 5:38 p.m. EDT Aug. 9

Calculation of electron and isotopes dose point kernels with fluka Monte Carlo code for dosimetry in nuclear medicine therapy

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

Botta, F; Di Dia, A; Pedroli, G

The calculation of patient-specific dose distribution can be achieved by Monte Carlo simulations or by analytical methods. In this study, fluka Monte Carlo code has been considered for use in nuclear medicine dosimetry. Up to now, fluka has mainly been dedicated to other fields, namely high energy physics, radiation protection, and hadrontherapy. When first employing a Monte Carlo code for nuclear medicine dosimetry, its results concerning electron transport at energies typical of nuclear medicine applications need to be verified. This is commonly achieved by means of calculation of a representative parameter and comparison with reference data. Dose point kernel (DPK),more » quantifying the energy deposition all around a point isotropic source, is often the one.Methods: fluka DPKs have been calculated in both water and compact bone for monoenergetic electrons (10–3 MeV) and for beta emitting isotopes commonly used for therapy (89Sr, 90Y, 131I, 153Sm, 177Lu, 186Re, and 188Re). Point isotropic sources have been simulated at the center of a water (bone) sphere, and deposed energy has been tallied in concentric shells. fluka outcomes have been compared to penelope v.2008 results, calculated in this study as well. Moreover, in case of monoenergetic electrons in water, comparison with the data from the literature (etran, geant4, mcnpx) has been done. Maximum percentage differences within 0.8·RCSDA and 0.9·RCSDA for monoenergetic electrons (RCSDA being the continuous slowing down approximation range) and within 0.8·X90 and 0.9·X90 for isotopes (X90 being the radius of the sphere in which 90% of the emitted energy is absorbed) have been computed, together with the average percentage difference within 0.9·RCSDA and 0.9·X90 for electrons and isotopes, respectively.Results: Concerning monoenergetic electrons, within 0.8·RCSDA (where 90%–97% of the particle energy is deposed), fluka and penelope agree mostly within 7%, except for 10 and 20 keV electrons (12% in

Clickable prodrugs bearing potent and hydrolytically cleavable nicotinamide phosphoribosyltransferase inhibitors.

PubMed

Sadrerafi, Keivan; Mason, Emilia O; Lee, Mark W

2018-01-01

Our previous study indicated that carborane containing small-molecule 1-(hydroxymethyl)-7-(4'-( trans -3″-(3'″-pyridyl)acrylamido)butyl)-1,7-dicarbadodecaborane (hm-MC4-PPEA), was a potent inhibitor of nicotinamide phosphoribosyltransferase (Nampt). Nampt has been shown to be upregulated in most cancers and is a promising target for the treatment of many different types of cancers, including breast cancers. To increase the selectivity of hm-MC4-PPEA toward cancer cells, three prodrugs were synthesized with different hydrolyzable linkers: ester, carbonate, and carbamate. Using click chemistry a fluorophore was attached to these prodrugs to act as a model for our conjugation strategy and to serve as an aid for prodrug stability studies. The stabilities of these drug conjugates were tested in phosphate-buffered saline (PBS) at normothermia (37°C) using three different pH levels, 5.5, 7.5, and 9.5, as well as in horse serum at physiological pH. The stability of each was monitored using reversed-phase HPLC equipped with both diode array and fluorescence detection. The inhibitory activity of hm-MC4-PPEA was also measured using a commercially available colorimetric assay. The biological activities of the drug conjugates as well as those of the free drug (hm-MC4-PPEA), were evaluated using the MTT assay against the human breast cancer cell lines T47D and MCF7, as well as the noncancerous, transformed, Nampt-dependent human breast epithelium cell line 184A1. hm-MC4-PPEA showed to be a potent inhibitor of recombinant Nampt activity, exhibiting an IC50 concentration of 6.8 nM. The prodrugs showed great stability towards hydrolytic degradation under neutral, mildly acidic and mildly basic conditions. The carbamate prodrug also showed to be stable in rat serum. However, the carbonate and the ester prodrug release at various rates in serum presumably owing to the presence of several different classes of esterase. The biological activities of the drug conjugates correlate

Implementation of ASME Code, Section XI, Code Case N-770, on Alternative Examination Requirements for Class 1 Butt Welds Fabricated with Alloy 82/182

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

Sullivan, Edmund J.; Anderson, Michael T.

In May 2010, the NRC issued a proposed notice of rulemaking that includes a provision to add a new section to its rules to require licensees to implement ASME Code Case N-770, ‘‘Alternative Examination Requirements and Acceptance Standards for Class 1 PWR Piping and Vessel Nozzle Butt Welds Fabricated with UNS N06082 or UNS W86182 Weld Filler Material With or Without the Application of Listed Mitigation Activities, Section XI, Division 1,’’ with 15 conditions. Code Case N-770 contains baseline and inservice inspection (ISI) requirements for unmitigated butt welds fabricated with Alloy 82/182 material and preservice and ISI requirements for mitigatedmore » butt welds. The NRC stated that application of ASME Code Case N-770 is necessary because the inspections currently required by the ASME Code, Section XI, were not written to address stress corrosion cracking Alloy 82/182 butt welds, and the safety consequences of inadequate inspections can be significant. The NRC expects to issue the final rule incorporating this code case into its regulations in the spring 2011 time frame. This paper discusses the new examination requirements, the conditions that NRC is imposing , and the major concerns with implementation of the new Code Case.« less

Protograph LDPC Codes Over Burst Erasure Channels

NASA Technical Reports Server (NTRS)

Divsalar, Dariush; Dolinar, Sam; Jones, Christopher

2006-01-01

In this paper we design high rate protograph based LDPC codes suitable for binary erasure channels. To simplify the encoder and decoder implementation for high data rate transmission, the structure of codes are based on protographs and circulants. These LDPC codes can improve data link and network layer protocols in support of communication networks. Two classes of codes were designed. One class is designed for large block sizes with an iterative decoding threshold that approaches capacity of binary erasure channels. The other class is designed for short block sizes based on maximizing minimum stopping set size. For high code rates and short blocks the second class outperforms the first class.

Improvements in the MGA Code Provide Flexibility and Better Error Analysis

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

Ruhter, W D; Kerr, J

2005-05-26

The Multi-Group Analysis (MGA) code is widely used to determine nondestructively the relative isotopic abundances of plutonium by gamma-ray spectrometry. MGA users have expressed concern about the lack of flexibility and transparency in the code. Users often have to ask the code developers for modifications to the code to accommodate new measurement situations, such as additional peaks being present in the plutonium spectrum or expected peaks being absent. We are testing several new improvements to a prototype, general gamma-ray isotopic analysis tool with the intent of either revising or replacing the MGA code. These improvements will give the user themore » ability to modify, add, or delete the gamma- and x-ray energies and branching intensities used by the code in determining a more precise gain and in the determination of the relative detection efficiency. We have also fully integrated the determination of the relative isotopic abundances with the determination of the relative detection efficiency to provide a more accurate determination of the errors in the relative isotopic abundances. We provide details in this paper on these improvements and a comparison of results obtained with current versions of the MGA code.« less

Calculation of electron and isotopes dose point kernels with fluka Monte Carlo code for dosimetry in nuclear medicine therapy

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

Botta, F.; Mairani, A.; Battistoni, G.

Purpose: The calculation of patient-specific dose distribution can be achieved by Monte Carlo simulations or by analytical methods. In this study, fluka Monte Carlo code has been considered for use in nuclear medicine dosimetry. Up to now, fluka has mainly been dedicated to other fields, namely high energy physics, radiation protection, and hadrontherapy. When first employing a Monte Carlo code for nuclear medicine dosimetry, its results concerning electron transport at energies typical of nuclear medicine applications need to be verified. This is commonly achieved by means of calculation of a representative parameter and comparison with reference data. Dose point kernelmore » (DPK), quantifying the energy deposition all around a point isotropic source, is often the one. Methods: fluka DPKs have been calculated in both water and compact bone for monoenergetic electrons (10{sup -3} MeV) and for beta emitting isotopes commonly used for therapy ({sup 89}Sr, {sup 90}Y, {sup 131}I, {sup 153}Sm, {sup 177}Lu, {sup 186}Re, and {sup 188}Re). Point isotropic sources have been simulated at the center of a water (bone) sphere, and deposed energy has been tallied in concentric shells. fluka outcomes have been compared to penelope v.2008 results, calculated in this study as well. Moreover, in case of monoenergetic electrons in water, comparison with the data from the literature (etran, geant4, mcnpx) has been done. Maximum percentage differences within 0.8{center_dot}R{sub CSDA} and 0.9{center_dot}R{sub CSDA} for monoenergetic electrons (R{sub CSDA} being the continuous slowing down approximation range) and within 0.8{center_dot}X{sub 90} and 0.9{center_dot}X{sub 90} for isotopes (X{sub 90} being the radius of the sphere in which 90% of the emitted energy is absorbed) have been computed, together with the average percentage difference within 0.9{center_dot}R{sub CSDA} and 0.9{center_dot}X{sub 90} for electrons and isotopes, respectively. Results: Concerning monoenergetic

A Cleavable N-Terminal Signal Peptide Promotes Widespread Olfactory Receptor Surface Expression in HEK293T Cells

PubMed Central

Shepard, Blythe D.; Natarajan, Niranjana; Protzko, Ryan J.; Acres, Omar W.; Pluznick, Jennifer L.

2013-01-01

Olfactory receptors (ORs) are G protein-coupled receptors that detect odorants in the olfactory epithelium, and comprise the largest gene family in the genome. Identification of OR ligands typically requires OR surface expression in heterologous cells; however, ORs rarely traffic to the cell surface when exogenously expressed. Therefore, most ORs are orphan receptors with no known ligands. To date, studies have utilized non-cleavable rhodopsin (Rho) tags and/or chaperones (i.e. Receptor Transporting Protein, RTP1S, Ric8b and Gαolf) to improve surface expression. However, even with these tools, many ORs still fail to reach the cell surface. We used a test set of fifteen ORs to examine the effect of a cleavable leucine-rich signal peptide sequence (Lucy tag) on OR surface expression in HEK293T cells. We report here that the addition of the Lucy tag to the N-terminus increases the number of ORs reaching the cell surface to 7 of the 15 ORs (as compared to 3/15 without Rho or Lucy tags). Moreover, when ORs tagged with both Lucy and Rho were co-expressed with previously reported chaperones (RTP1S, Ric8b and Gαolf), we observed surface expression for all 15 receptors examined. In fact, two-thirds of Lucy-tagged ORs are able to reach the cell surface synergistically with chaperones even when the Rho tag is removed (10/15 ORs), allowing for the potential assessment of OR function with only an 8-amino acid Flag tag on the mature protein. As expected for a signal peptide, the Lucy tag was cleaved from the mature protein and did not alter OR-ligand binding and signaling. Our studies demonstrate that widespread surface expression of ORs can be achieved in HEK293T cells, providing promise for future large-scale deorphanization studies. PMID:23840901

Effects of Electroacupuncture on Interstitial Cells of Cajal (ICC) Ultrastructure and Connexin 43 Protein Expression in the Gastrointestinal Tract of Functional Dyspepsia (FD) Rats

PubMed Central

Zhang, Guoshan; Xie, Shen; Hu, Wei; Liu, Yuer; Liu, Mailan; Liu, Mi; Chang, Xiaorong

2016-01-01

Background Gastrointestinal motility disorder is the main clinical manifestation in functional dyspepsia (FD) patients. Electroacupuncture is effective in improving gastrointestinal motility disorder in FD; however, the underlying mechanism remains unclear. It has been demonstrated that interstitial cells of Cajal (ICC) are pacemaker cells in the gastrointestinal tract, and the pacemaker potential is transmitted to nearby cells through gap junctions between ICC or ICC and the smooth muscle. Therefore, this study aimed to assess the effects of electroacupuncture on ICC ultrastructure and expression of the gap junction protein connexin 43 (Cx43) in FD rats. Material/Methods The animals were randomized into 3 groups: control, model, and electroacupuncture. Electroacupuncture was applied at Zusanli (ST36) in the electroacupuncture group daily for 10 days, while no electroacupuncture was applied to model group animals. Results Ultrastructure of ICC recovered normally in gastric antrum and small intestine specimens was improved, with Cx43 expression levels in these tissues significantly increased in the electroacupuncture group compared with the model group. Conclusions These findings indicated that electroacupuncture is effective in alleviating ICC damage and reduces Cx43 levels in FD rats, and suggest that ICC and Cx43 are involved in electroacupuncture treatment in rats with FD to improve gastrointestinal motility disorders. PMID:27297942

Effects of Electroacupuncture on Interstitial Cells of Cajal (ICC) Ultrastructure and Connexin 43 Protein Expression in the Gastrointestinal Tract of Functional Dyspepsia (FD) Rats.

PubMed

Zhang, Guoshan; Xie, Shen; Hu, Wei; Liu, Yuer; Liu, Mailan; Liu, Mi; Chang, Xiaorong

2016-06-14

BACKGROUND Gastrointestinal motility disorder is the main clinical manifestation in functional dyspepsia (FD) patients. Electroacupuncture is effective in improving gastrointestinal motility disorder in FD; however, the underlying mechanism remains unclear. It has been demonstrated that interstitial cells of Cajal (ICC) are pacemaker cells in the gastrointestinal tract, and the pacemaker potential is transmitted to nearby cells through gap junctions between ICC or ICC and the smooth muscle. Therefore, this study aimed to assess the effects of electroacupuncture on ICC ultrastructure and expression of the gap junction protein connexin 43 (Cx43) in FD rats. MATERIAL AND METHODS The animals were randomized into 3 groups: control, model, and electroacupuncture. Electroacupuncture was applied at Zusanli (ST36) in the electroacupuncture group daily for 10 days, while no electroacupuncture was applied to model group animals. RESULTS Ultrastructure of ICC recovered normally in gastric antrum and small intestine specimens was improved, with Cx43 expression levels in these tissues significantly increased in the electroacupuncture group compared with the model group. CONCLUSIONS These findings indicated that electroacupuncture is effective in alleviating ICC damage and reduces Cx43 levels in FD rats, and suggest that ICC and Cx43 are involved in electroacupuncture treatment in rats with FD to improve gastrointestinal motility disorders.

Implementation of Rule 8 of the International Code of Nomenclature of Prokaryotes for the renaming of classes. Request for an Opinion.

PubMed

Oren, Aharon; Parte, Aidan; Garrity, George M

2016-10-01

The new version of Rule 8 of the International Code of Nomenclature of Prokaryotes as approved in Istanbul in 2008 has the clear advantage of establishing a uniform way to name classes of prokaryotes, similar to the way other higher taxa are named. However, retroactive implementation of the modified Rule is problematic as it destabilizes the nomenclature and requires the replacement of a large number of names of classes that have been validly published, which would be in violation of Principle 1 of the Code. Therefore, we call upon the International Committee on Systematics of Prokaryotes and its Judicial Commission to reconsider the retroactivity of Rule 8.

A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS)

NASA Astrophysics Data System (ADS)

Iacobucci, Claudio; Hage, Christoph; Schäfer, Mathias; Sinz, Andrea

2017-10-01

The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies. [Figure not available: see fulltext.

High-coverage quantitative proteomics using amine-specific isotopic labeling.

PubMed

Melanson, Jeremy E; Avery, Steven L; Pinto, Devanand M

2006-08-01

Peptide dimethylation with isotopically coded formaldehydes was evaluated as a potential alternative to techniques such as the iTRAQ method for comparative proteomics. The isotopic labeling strategy and custom-designed protein quantitation software were tested using protein standards and then applied to measure proteins levels associated with Alzheimer's disease (AD). The method provided high accuracy (10% error), precision (14% RSD) and coverage (70%) when applied to the analysis of a standard solution of BSA by LC-MS/MS. The technique was then applied to measure protein abundance levels in brain tissue afflicted with AD relative to normal brain tissue. 2-D LC-MS analysis identified 548 unique proteins (p<0.05). Of these, 349 were quantified with two or more peptides that met the statistical criteria used in this study. Several classes of proteins exhibited significant changes in abundance. For example, elevated levels of antioxidant proteins and decreased levels of mitochondrial electron transport proteins were observed. The results demonstrate the utility of the labeling method for high-throughput quantitative analysis.

Isotopic composition of atmospheric moisture from pan water evaporation measurements.

PubMed

Devi, Pooja; Jain, Ashok Kumar; Rao, M Someshwer; Kumar, Bhishm

2015-01-01

A continuous and reliable time series data of the stable isotopic composition of atmospheric moisture is an important requirement for the wider applicability of isotope mass balance methods in atmospheric and water balance studies. This requires routine sampling of atmospheric moisture by an appropriate technique and analysis of moisture for its isotopic composition. We have, therefore, used a much simpler method based on an isotope mass balance approach to derive the isotopic composition of atmospheric moisture using a class-A drying evaporation pan. We have carried out the study by collecting water samples from a class-A drying evaporation pan and also by collecting atmospheric moisture using the cryogenic trap method at the National Institute of Hydrology, Roorkee, India, during a pre-monsoon period. We compared the isotopic composition of atmospheric moisture obtained by using the class-A drying evaporation pan method with the cryogenic trap method. The results obtained from the evaporation pan water compare well with the cryogenic based method. Thus, the study establishes a cost-effective means of maintaining time series data of the isotopic composition of atmospheric moisture at meteorological observatories. The conclusions drawn in the present study are based on experiments conducted at Roorkee, India, and may be examined at other regions for its general applicability.

Accumulate repeat accumulate codes

NASA Technical Reports Server (NTRS)

Abbasfar, A.; Divsalar, D.; Yao, K.

2004-01-01

In this paper we propose an innovative channel coding scheme called Accumulate Repeat Accumulate codes. This class of codes can be viewed as trubo-like codes, namely a double serial concatenation of a rate-1 accumulator as an outer code, a regular or irregular repetition as a middle code, and a punctured accumulator as an inner code.

A Model Code of Ethics for the Use of Computers in Education.

ERIC Educational Resources Information Center

Shere, Daniel T.; Cannings, Terence R.

Two Delphi studies were conducted by the Ethics and Equity Committee of the International Council for Computers in Education (ICCE) to obtain the opinions of experts on areas that should be covered by ethical guides for the use of computers in education and for software development, and to develop a model code of ethics for each of these areas.…

ICT: isotope correction toolbox.

PubMed

Jungreuthmayer, Christian; Neubauer, Stefan; Mairinger, Teresa; Zanghellini, Jürgen; Hann, Stephan

2016-01-01

Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Class of near-perfect coded apertures

NASA Technical Reports Server (NTRS)

Cannon, T. M.; Fenimore, E. E.

1977-01-01

Coded aperture imaging of gamma ray sources has long promised an improvement in the sensitivity of various detector systems. The promise has remained largely unfulfilled, however, for either one of two reasons. First, the encoding/decoding method produces artifacts, which even in the absence of quantum noise, restrict the quality of the reconstructed image. This is true of most correlation-type methods. Second, if the decoding procedure is of the deconvolution variety, small terms in the transfer function of the aperture can lead to excessive noise in the reconstructed image. It is proposed to circumvent both of these problems by use of a uniformly redundant array (URA) as the coded aperture in conjunction with a special correlation decoding method.

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

PubMed Central

Laurent, Georges St.; Vyatkin, Yuri; Antonets, Denis; Ri, Maxim; Qi, Yao; Saik, Olga; Shtokalo, Dmitry; de Hoon, Michiel J.L.; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Arner, Erik; Forrest, Alistair R.R.; Nicolas, Estelle; McCaffrey, Timothy A.; Carninci, Piero; Hayashizaki, Yoshihide; Wahlestedt, Claes; Kapranov, Philipp

2016-01-01

Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlincRNAs genes likely function in cis to activate nearby genes. This effect while most pronounced in closely spaced vlincRNA–gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlincRNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs. PMID:27001520

Isotopic Dependence of GCR Fluence behind Shielding

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Wilson, John W.; Saganti, Premkumar; Kim, Myung-Hee Y.; Cleghorn, Timothy; Zeitlin, Cary; Tripathi, Ram K.

2006-01-01

In this paper we consider the effects of the isotopic composition of the primary galactic cosmic rays (GCR), nuclear fragmentation cross-sections, and isotopic-grid on the solution to transport models used for shielding studies. Satellite measurements are used to describe the isotopic composition of the GCR. For the nuclear interaction data-base and transport solution, we use the quantum multiple-scattering theory of nuclear fragmentation (QMSFRG) and high-charge and energy (HZETRN) transport code, respectively. The QMSFRG model is shown to accurately describe existing fragmentation data including proper description of the odd-even effects as function of the iso-spin dependence on the projectile nucleus. The principle finding of this study is that large errors (+/-100%) will occur in the mass-fluence spectra when comparing transport models that use a complete isotopic-grid (approx.170 ions) to ones that use a reduced isotopic-grid, for example the 59 ion-grid used in the HZETRN code in the past, however less significant errors (<+/-20%) occur in the elemental-fluence spectra. Because a complete isotopic-grid is readily handled on small computer workstations and is needed for several applications studying GCR propagation and scattering, it is recommended that they be used for future GCR studies.

Effect of Isotope Mass in Simulations of JET H-mode Discharges

NASA Astrophysics Data System (ADS)

Snyder, S. E.; Onjun, T.; Kritz, A. H.; Bateman, G.; Parail, V.

2004-11-01

In JET type-I ELMy H-mode discharges, it is found that the height of the pressure pedestal increases and the frequency of the ELMs decreases with increasing isotope mass. These experimentally observed trends are obtained in these simulations only if the pedestal width increases with isotope mass. Simulations are carried out using the JETTO integrated modeling code with a dynamic model for the H-mode pedestal and the ELMs.(T. Onjun et al, Phys. Plasmas 11 (2004) 1469 and 3006.) The HELENA and MISHKA stability codes are applied to calibrate the stability criteria used to trigger ELM crashes in the JETTO code and to explore possible access to second stability in the pedestal. In the simulations, transport in the pedestal is given by the ion thermal neoclassical diffusivity, which increases with isotope mass. Consequently, as the isotope mass is increased, the pressure gradient and the bootstrap current in the pedestal rebuild more slowly after each ELM crash. Several models are explored in which the pedestal width increases with isotope mass.

Water Isotopes in the GISS GCM: History, Applications and Potential

NASA Astrophysics Data System (ADS)

Schmidt, G. A.; LeGrande, A. N.; Field, R. D.; Nusbaumer, J. M.

2017-12-01

Water isotopes have been incorporated in the GISS GCMs since the pioneering work of Jean Jouzel in the 1980s. Since 2005, this functionality has been maintained within the master branch of the development code and has been usable (and used) in all subsequent versions. This has allowed a wide variety of applications, across multiple time-scales and interests, to be tackled coherently. Water isotope tracers have been used to debug the atmospheric model code, tune parameterisations of moist processes, assess the isotopic fingerprints of multiple climate drivers, produce forward models for remotely sensed isotope products, and validate paleo-climate interpretations from the last millennium to the Eocene. We will present an overview of recent results involving isotope tracers, including improvements in models for the isotopic fractionation processes themselves, and demonstrate the potential for using these tracers and models more systematically in paleo-climate reconstructions and investigations of the modern hydrological cycle.

Some partial-unit-memory convolutional codes

NASA Technical Reports Server (NTRS)

Abdel-Ghaffar, K.; Mceliece, R. J.; Solomon, G.

1991-01-01

The results of a study on a class of error correcting codes called partial unit memory (PUM) codes are presented. This class of codes, though not entirely new, has until now remained relatively unexplored. The possibility of using the well developed theory of block codes to construct a large family of promising PUM codes is shown. The performance of several specific PUM codes are compared with that of the Voyager standard (2, 1, 6) convolutional code. It was found that these codes can outperform the Voyager code with little or no increase in decoder complexity. This suggests that there may very well be PUM codes that can be used for deep space telemetry that offer both increased performance and decreased implementational complexity over current coding systems.

Site-directed decapsulation of bolaamphiphilic vesicles with enzymatic cleavable surface groups.

PubMed

Popov, Mary; Grinberg, Sarina; Linder, Charles; Waner, Tal; Levi-Hevroni, Bosmat; Deckelbaum, Richard J; Heldman, Eliahu

2012-06-10

Stable nano-sized vesicles with a monolayer encapsulating membrane were prepared from novel bolaamphiphiles with choline ester head groups. The head groups were covalently bound to the alkyl chain of the bolaamphiphiles either via the nitrogen atom of the choline moiety, or via the choline ester's methyl group. Both types of bolaamphiphiles competed with acetylthiocholine for binding to acetylcholine esterase (AChE), yet, only the choline ester head groups bound to the alkyl chain via the nitrogen atom of the choline moiety were hydrolyzed by the enzyme. Likewise, only vesicles composed of bolaamphiphiles with head groups that were hydrolyzed by AChE released their encapsulated material upon exposure to the enzyme. Injection of carboxyfluorescein (CF)-loaded vesicles with cleavable choline ester head groups into mice resulted in the accumulation of CF in tissues that express high AChE activity, including the brain. By comparison, when vesicles with choline ester head groups that are not hydrolyzed by AChE were injected into mice, there was no accumulation of CF in tissues that highly express the enzyme. These results imply that bolaamphiphilic vesicles with surface groups that are substrates to enzymes which are highly expressed in target organs may potentially be used as a drug delivery system with controlled site-directed drug release. Copyright © 2011 Elsevier B.V. All rights reserved.

Trace-shortened Reed-Solomon codes

NASA Technical Reports Server (NTRS)

Mceliece, R. J.; Solomon, G.

1994-01-01

Reed-Solomon (RS) codes have been part of standard NASA telecommunications systems for many years. RS codes are character-oriented error-correcting codes, and their principal use in space applications has been as outer codes in concatenated coding systems. However, for a given character size, say m bits, RS codes are limited to a length of, at most, 2(exp m). It is known in theory that longer character-oriented codes would be superior to RS codes in concatenation applications, but until recently no practical class of 'long' character-oriented codes had been discovered. In 1992, however, Solomon discovered an extensive class of such codes, which are now called trace-shortened Reed-Solomon (TSRS) codes. In this article, we will continue the study of TSRS codes. Our main result is a formula for the dimension of any TSRS code, as a function of its error-correcting power. Using this formula, we will give several examples of TSRS codes, some of which look very promising as candidate outer codes in high-performance coded telecommunications systems.

Synchronization Control for a Class of Discrete-Time Dynamical Networks With Packet Dropouts: A Coding-Decoding-Based Approach.

PubMed

Wang, Licheng; Wang, Zidong; Han, Qing-Long; Wei, Guoliang

2017-09-06

The synchronization control problem is investigated for a class of discrete-time dynamical networks with packet dropouts via a coding-decoding-based approach. The data is transmitted through digital communication channels and only the sequence of finite coded signals is sent to the controller. A series of mutually independent Bernoulli distributed random variables is utilized to model the packet dropout phenomenon occurring in the transmissions of coded signals. The purpose of the addressed synchronization control problem is to design a suitable coding-decoding procedure for each node, based on which an efficient decoder-based control protocol is developed to guarantee that the closed-loop network achieves the desired synchronization performance. By applying a modified uniform quantization approach and the Kronecker product technique, criteria for ensuring the detectability of the dynamical network are established by means of the size of the coding alphabet, the coding period and the probability information of packet dropouts. Subsequently, by resorting to the input-to-state stability theory, the desired controller parameter is obtained in terms of the solutions to a certain set of inequality constraints which can be solved effectively via available software packages. Finally, two simulation examples are provided to demonstrate the effectiveness of the obtained results.

Nanoporous Films with Sub-10 nm in Pore Size from Acid-Cleavable Block Copolymers.

PubMed

Li, Yayuan; Xu, Yawei; Cao, Shubo; Zhao, Yongbin; Qu, Ting; Iyoda, Tomokazu; Chen, Aihua

2017-03-01

Nanoporous thin films with pore size of sub-10 nm are fabricated using an acid-cleavable block copolymer (BCP), a benzoic imine junction between poly(ethylene oxide) (PEO) and poly(methacrylate) (PMAAz) bearing an azobenzene side chain (denoted as PEO-bei-PMAAz) as the precursor. After a thermal annealing, the block copolymers are self-assembled to form highly ordered PEO cylinders within a PMAAz matrix normal to the film, even in the case of low BCP molecular weight due to the existing of the liquid crystalline (LC) azobenzene rigid segment. Thus, PMAAz thin films with pore size of ≈7 nm and density of ≈10 12 cm -2 are obtained after removal of the PEO minor phase by breaking the benzoic imine junction under mild acidic conditions. This work enriches the nanoporous polymer films from BCP precursors and introduces the LC property as a functionality which can further enhance the mechanical properties of the films and broaden their applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

PubMed

St Laurent, Georges; Vyatkin, Yuri; Antonets, Denis; Ri, Maxim; Qi, Yao; Saik, Olga; Shtokalo, Dmitry; de Hoon, Michiel J L; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Arner, Erik; Forrest, Alistair R R; Nicolas, Estelle; McCaffrey, Timothy A; Carninci, Piero; Hayashizaki, Yoshihide; Wahlestedt, Claes; Kapranov, Philipp

2016-04-20

Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlinc RNAs genes likely function in cisto activate nearby genes. This effect while most pronounced in closely spaced vlinc RNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlinc RNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

14th EuCheMS International Conference on Chemistry and the Environment ICCE 2013: IEC-WTC, Barcelona, Spain, 25-28 June 2013.

PubMed

Luis, Santiago V; Jover, Eric

2014-10-01

The 14th European Association of Chemical and Molecular Sciences (EuCheMS) International Conference on Chemistry and the Environment (ICCE 2013) took place on 25-28 June 2013 at the IEC and the WTC in Barcelona, Spain. The ICCE is a well-established biannual conference organized by the Division of Chemistry and the EuCheMS.

Assets as a Socioeconomic Status Index: Categorical Principal Components Analysis vs. Latent Class Analysis.

PubMed

Sartipi, Majid; Nedjat, Saharnaz; Mansournia, Mohammad Ali; Baigi, Vali; Fotouhi, Akbar

2016-11-01

Some variables like Socioeconomic Status (SES) cannot be directly measured, instead, so-called 'latent variables' are measured indirectly through calculating tangible items. There are different methods for measuring latent variables such as data reduction methods e.g. Principal Components Analysis (PCA) and Latent Class Analysis (LCA). The purpose of our study was to measure assets index- as a representative of SES- through two methods of Non-Linear PCA (NLPCA) and LCA, and to compare them for choosing the most appropriate model. This was a cross sectional study in which 1995 respondents filled the questionnaires about their assets in Tehran. The data were analyzed by SPSS 19 (CATPCA command) and SAS 9.2 (PROC LCA command) to estimate their socioeconomic status. The results were compared based on the Intra-class Correlation Coefficient (ICC). The 6 derived classes from LCA based on BIC, were highly consistent with the 6 classes from CATPCA (Categorical PCA) (ICC = 0.87, 95%CI: 0.86 - 0.88). There is no gold standard to measure SES. Therefore, it is not possible to definitely say that a specific method is better than another one. LCA is a complicated method that presents detailed information about latent variables and required one assumption (local independency), while NLPCA is a simple method, which requires more assumptions. Generally, NLPCA seems to be an acceptable method of analysis because of its simplicity and high agreement with LCA.

Fundamental differences between optimization code test problems in engineering applications

NASA Technical Reports Server (NTRS)

Eason, E. D.

1984-01-01

The purpose here is to suggest that there is at least one fundamental difference between the problems used for testing optimization codes and the problems that engineers often need to solve; in particular, the level of precision that can be practically achieved in the numerical evaluation of the objective function, derivatives, and constraints. This difference affects the performance of optimization codes, as illustrated by two examples. Two classes of optimization problem were defined. Class One functions and constraints can be evaluated to a high precision that depends primarily on the word length of the computer. Class Two functions and/or constraints can only be evaluated to a moderate or a low level of precision for economic or modeling reasons, regardless of the computer word length. Optimization codes have not been adequately tested on Class Two problems. There are very few Class Two test problems in the literature, while there are literally hundreds of Class One test problems. The relative performance of two codes may be markedly different for Class One and Class Two problems. Less sophisticated direct search type codes may be less likely to be confused or to waste many function evaluations on Class Two problems. The analysis accuracy and minimization performance are related in a complex way that probably varies from code to code. On a problem where the analysis precision was varied over a range, the simple Hooke and Jeeves code was more efficient at low precision while the Powell code was more efficient at high precision.

Stable isotope reactive transport modeling in water-rock interactions during CO2 injection

NASA Astrophysics Data System (ADS)

Hidalgo, Juan J.; Lagneau, Vincent; Agrinier, Pierre

2010-05-01

Stable isotopes can be of great usefulness in the characterization and monitoring of CO2 sequestration sites. Stable isotopes can be used to track the migration of the CO2 plume and identify leakage sources. Moreover, they provide unique information about the chemical reactions that take place on the CO2-water-rock system. However, there is a lack of appropriate tools that help modelers to incorporate stable isotope information into the flow and transport models used in CO2 sequestration problems. In this work, we present a numerical tool for modeling the transport of stable isotopes in groundwater reactive systems. The code is an extension of the groundwater single-phase flow and reactive transport code HYTEC [2]. HYTEC's transport module was modified to include element isotopes as separate species. This way, it is able to track isotope composition of the system by computing the mixing between the background water and the injected solution accounting for the dependency of diffusion on the isotope mass. The chemical module and database have been expanded to included isotopic exchange with minerals and the isotope fractionation associated with chemical reactions and mineral dissolution or precipitation. The performance of the code is illustrated through a series of column synthetic models. The code is also used to model the aqueous phase CO2 injection test carried out at the Lamont-Doherty Earth Observatory site (Palisades, New York, USA) [1]. References [1] N. Assayag, J. Matter, M. Ader, D. Goldberg, and P. Agrinier. Water-rock interactions during a CO2 injection field-test: Implications on host rock dissolution and alteration effects. Chemical Geology, 265(1-2):227-235, July 2009. [2] Jan van der Lee, Laurent De Windt, Vincent Lagneau, and Patrick Goblet. Module-oriented modeling of reactive transport with HYTEC. Computers & Geosciences, 29(3):265-275, April 2003.

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

New quantum codes constructed from quaternary BCH codes

NASA Astrophysics Data System (ADS)

Xu, Gen; Li, Ruihu; Guo, Luobin; Ma, Yuena

2016-10-01

In this paper, we firstly study construction of new quantum error-correcting codes (QECCs) from three classes of quaternary imprimitive BCH codes. As a result, the improved maximal designed distance of these narrow-sense imprimitive Hermitian dual-containing quaternary BCH codes are determined to be much larger than the result given according to Aly et al. (IEEE Trans Inf Theory 53:1183-1188, 2007) for each different code length. Thus, families of new QECCs are newly obtained, and the constructed QECCs have larger distance than those in the previous literature. Secondly, we apply a combinatorial construction to the imprimitive BCH codes with their corresponding primitive counterpart and construct many new linear quantum codes with good parameters, some of which have parameters exceeding the finite Gilbert-Varshamov bound for linear quantum codes.

Metabolically Generated Stable Isotope-Labeled Deoxynucleoside Code for Tracing DNA N6-Methyladenine in Human Cells.

PubMed

Liu, Baodong; Liu, Xiaoling; Lai, Weiyi; Wang, Hailin

2017-06-06

DNA N 6 -methyl-2'-deoxyadenosine (6mdA) is an epigenetic modification in both eukaryotes and bacteria. Here we exploited stable isotope-labeled deoxynucleoside [ 15 N 5 ]-2'-deoxyadenosine ([ 15 N 5 ]-dA) as an initiation tracer and for the first time developed a metabolically differential tracing code for monitoring DNA 6mdA in human cells. We demonstrate that the initiation tracer [ 15 N 5 ]-dA undergoes a specific and efficient adenine deamination reaction leading to the loss the exocyclic amine 15 N, and further utilizes the purine salvage pathway to generate mainly both [ 15 N 4 ]-dA and [ 15 N 4 ]-2'-deoxyguanosine ([ 15 N 4 ]-dG) in mammalian genomes. However, [ 15 N 5 ]-dA is largely retained in the genomes of mycoplasmas, which are often found in cultured cells and experimental animals. Consequently, the methylation of dA generates 6mdA with a consistent coding pattern, with a predominance of [ 15 N 4 ]-6mdA. Therefore, mammalian DNA 6mdA can be potentially discriminated from that generated by infecting mycoplasmas. Collectively, we show a promising approach for identification of authentic DNA 6mdA in human cells and determine if the human cells are contaminated with mycoplasmas.

Accumulate repeat accumulate codes

NASA Technical Reports Server (NTRS)

Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

2004-01-01

In this paper we propose an innovative channel coding scheme called 'Accumulate Repeat Accumulate codes' (ARA). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes, thus belief propagation can be used for iterative decoding of ARA codes on a graph. The structure of encoder for this class can be viewed as precoded Repeat Accumulate (RA) code or as precoded Irregular Repeat Accumulate (IRA) code, where simply an accumulator is chosen as a precoder. Thus ARA codes have simple, and very fast encoder structure when they representing LDPC codes. Based on density evolution for LDPC codes through some examples for ARA codes, we show that for maximum variable node degree 5 a minimum bit SNR as low as 0.08 dB from channel capacity for rate 1/2 can be achieved as the block size goes to infinity. Thus based on fixed low maximum variable node degree, its threshold outperforms not only the RA and IRA codes but also the best known LDPC codes with the dame maximum node degree. Furthermore by puncturing the accumulators any desired high rate codes close to code rate 1 can be obtained with thresholds that stay close to the channel capacity thresholds uniformly. Iterative decoding simulation results are provided. The ARA codes also have projected graph or protograph representation that allows for high speed decoder implementation.

Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection.

PubMed

Fleming, Damarius S; Miller, Laura C

2018-04-01

It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs have emerged as having an important role in the immune system in humans. The study uses transcriptomic read counts to profile the type and quantity of both well and lesser characterized sncRNAs, such as microRNAs and small nucleolar RNAs to identify and quantify the classes of sncRNA expressed in whole blood between healthy and highly pathogenic PRRSV-infected pigs. Our results returned evidence on nine classes of sncRNA, four of which were consistently statistically significantly different based on Fisher's Exact Test, that can be detected and possibly interrogated for their effect on host dysregulation during PRRSV infections. Published by Elsevier Inc.

Development and evaluation of a suite of isotope reference gases for methane in air

NASA Astrophysics Data System (ADS)

Sperlich, Peter; Uitslag, Nelly A. M.; Richter, Jürgen M.; Rothe, Michael; Geilmann, Heike; van der Veen, Carina; Röckmann, Thomas; Blunier, Thomas; Brand, Willi A.

2016-08-01

Measurements from multiple laboratories have to be related to unifying and traceable reference material in order to be comparable. However, such fundamental reference materials are not available for isotope ratios in atmospheric methane, which led to misinterpretations of combined data sets in the past. We developed a method to produce a suite of synthetic CH4-in-air standard gases that can be used to unify methane isotope ratio measurements of laboratories in the atmospheric monitoring community. Therefore, we calibrated a suite of pure methane gases of different methanogenic origin against international referencing materials that define the class="text">VSMOW (Vienna Standard Mean Ocean Water) and VPDB (Vienna Pee Dee Belemnite) isotope scales. The isotope ratios of our pure methane gases range between -320 and +40 ‰ for class="text">δ2H-CH4 and between -70 and -40 ‰ for class="text">δ13C-CH4, enveloping the isotope ratios of tropospheric methane (about -85 and -47 ‰ for class="text">δ2H-CH4 and class="text">δ13C-CH4 respectively). Estimated uncertainties, including the full traceability chain, are < 1.5 ‰ and < 0.2 ‰ for δ2H and δ13C calibrations respectively. Aliquots of the calibrated pure methane gases have been diluted with methane-free air to atmospheric methane levels and filled into 5 L glass flasks. The synthetic CH4-in-air standards comprise atmospheric oxygen/nitrogen ratios as well as argon, krypton and nitrous oxide mole fractions to prevent gas-specific measurement artefacts. The resulting synthetic CH4-in-air standards are referred to as class="text">JRAS-M16 (Jena Reference Air Set - Methane 2016) and will be available to the atmospheric monitoring community. class="text">JRAS-M16 may be used as unifying isotope scale anchor for isotope ratio measurements in atmospheric methane, so that data sets can be merged into a consistent

Umchs5, a gene coding for a class IV chitin synthase in Ustilago maydis.

PubMed

Xoconostle-Cázares, B; Specht, C A; Robbins, P W; Liu, Y; León, C; Ruiz-Herrera, J

1997-12-01

A fragment corresponding to a conserved region of a fifth gene coding for chitin synthase in the plant pathogenic fungus Ustilago maydis was amplified by means of the polymerase chain reaction (PCR). The amplified fragment was utilized as a probe for the identification of the whole gene in a genomic library of the fungus. The predicted gene product of Umchs5 has highest similarity with class IV chitin synthases encoded by the CHS3 genes from Saccharomyces cerevisiae and Candida albicans, chs-4 from Neurospora crassa, and chsE from Aspergillus nidulans. Umchs5 null mutants were constructed by substitution of most of the coding sequence with the hygromycin B resistance cassette. Mutants displayed significant reduction in growth rate, chitin content, and chitin synthase activity, specially in the mycelial form. Virulence to corn plantules was also reduced in the mutants. PCR was also used to obtain a fragment of a sixth chitin synthase, Umchs6. It is suggested that multigenic control of chitin synthesis in U. maydis operates as a protection mechanism for fungal viability in which the loss of one activity is partially compensated by the remaining enzymes. Copyright 1997 Academic Press.

Statistical Evaluation of the Rodin–Ohno Hypothesis: Sense/Antisense Coding of Ancestral Class I and II Aminoacyl-tRNA Synthetases

PubMed Central

Chandrasekaran, Srinivas Niranj; Yardimci, Galip Gürkan; Erdogan, Ozgün; Roach, Jeffrey; Carter, Charles W.

2013-01-01

We tested the idea that ancestral class I and II aminoacyl-tRNA synthetases arose on opposite strands of the same gene. We assembled excerpted 94-residue Urgenes for class I tryptophanyl-tRNA synthetase (TrpRS) and class II Histidyl-tRNA synthetase (HisRS) from a diverse group of species, by identifying and catenating three blocks coding for secondary structures that position the most highly conserved, active-site residues. The codon middle-base pairing frequency was 0.35 ± 0.0002 in all-by-all sense/antisense alignments for 211 TrpRS and 207 HisRS sequences, compared with frequencies between 0.22 ± 0.0009 and 0.27 ± 0.0005 for eight different representations of the null hypothesis. Clustering algorithms demonstrate further that profiles of middle-base pairing in the synthetase antisense alignments are correlated along the sequences from one species-pair to another, whereas this is not the case for similar operations on sets representing the null hypothesis. Most probable reconstructed sequences for ancestral nodes of maximum likelihood trees show that middle-base pairing frequency increases to approximately 0.42 ± 0.002 as bacterial trees approach their roots; ancestral nodes from trees including archaeal sequences show a less pronounced increase. Thus, contemporary and reconstructed sequences all validate important bioinformatic predictions based on descent from opposite strands of the same ancestral gene. They further provide novel evidence for the hypothesis that bacteria lie closer than archaea to the origin of translation. Moreover, the inverse polarity of genetic coding, together with a priori α-helix propensities suggest that in-frame coding on opposite strands leads to similar secondary structures with opposite polarity, as observed in TrpRS and HisRS crystal structures. PMID:23576570

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.

PubMed

Seligmann, Hervé; Warthi, Ganesh

2017-01-01

A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').

Digital Isotope Coding to Trace the Growth Process of Individual Single-Walled Carbon Nanotubes.

PubMed

Otsuka, Keigo; Yamamoto, Shun; Inoue, Taiki; Koyano, Bunsho; Ukai, Hiroyuki; Yoshikawa, Ryo; Xiang, Rong; Chiashi, Shohei; Maruyama, Shigeo

2018-04-24

Single-walled carbon nanotubes (SWCNTs) are attracting increasing attention as an ideal material for high-performance electronics through the preparation of arrays of purely semiconducting SWCNTs. Despite significant progress in the controlled synthesis of SWCNTs, their growth mechanism remains unclear due to difficulties in analyzing the time-resolved growth of individual SWCNTs under practical growth conditions. Here we present a method for tracing the diverse growth profiles of individual SWCNTs by embedding digitally coded isotope labels. Raman mapping showed that, after various incubation times, SWCNTs elongated monotonically until their abrupt termination. Ex situ analysis offered an opportunity to capture rare chirality changes along the SWCNTs, which resulted in sudden acceleration/deceleration of the growth rate. Dependence on growth parameters, such as temperature and carbon concentration, was also traced along individual SWCNTs, which could provide clues to chirality control. Systematic growth studies with a variety of catalysts and conditions, which combine the presented method with other characterization techniques, will lead to further understanding and control of chirality, length, and density of SWCNTs.

Energy-Constrained Recharge, Assimilation, and Fractional Crystallization (EC-RAχFC): A Visual Basic computer code for calculating trace element and isotope variations of open-system magmatic systems

NASA Astrophysics Data System (ADS)

Bohrson, Wendy A.; Spera, Frank J.

2007-11-01

Volcanic and plutonic rocks provide abundant evidence for complex processes that occur in magma storage and transport systems. The fingerprint of these processes, which include fractional crystallization, assimilation, and magma recharge, is captured in petrologic and geochemical characteristics of suites of cogenetic rocks. Quantitatively evaluating the relative contributions of each process requires integration of mass, species, and energy constraints, applied in a self-consistent way. The energy-constrained model Energy-Constrained Recharge, Assimilation, and Fractional Crystallization (EC-RaχFC) tracks the trace element and isotopic evolution of a magmatic system (melt + solids) undergoing simultaneous fractional crystallization, recharge, and assimilation. Mass, thermal, and compositional (trace element and isotope) output is provided for melt in the magma body, cumulates, enclaves, and anatectic (i.e., country rock) melt. Theory of the EC computational method has been presented by Spera and Bohrson (2001, 2002, 2004), and applications to natural systems have been elucidated by Bohrson and Spera (2001, 2003) and Fowler et al. (2004). The purpose of this contribution is to make the final version of the EC-RAχFC computer code available and to provide instructions for code implementation, description of input and output parameters, and estimates of typical values for some input parameters. A brief discussion highlights measures by which the user may evaluate the quality of the output and also provides some guidelines for implementing nonlinear productivity functions. The EC-RAχFC computer code is written in Visual Basic, the programming language of Excel. The code therefore launches in Excel and is compatible with both PC and MAC platforms. The code is available on the authors' Web sites http://magma.geol.ucsb.edu/and http://www.geology.cwu.edu/ecrafc) as well as in the auxiliary material.

Coordinated design of coding and modulation systems

NASA Technical Reports Server (NTRS)

Massey, J. L.

1976-01-01

Work on partial unit memory codes continued; it was shown that for a given virtual state complexity, the maximum free distance over the class of all convolutional codes is achieved within the class of unit memory codes. The effect of phase-lock loop (PLL) tracking error on coding system performance was studied by using the channel cut-off rate as the measure of quality of a modulation system. Optimum modulation signal sets for a non-white Gaussian channel considered an heuristic selection rule based on a water-filling argument. The use of error correcting codes to perform data compression by the technique of syndrome source coding was researched and a weight-and-error-locations scheme was developed that is closely related to LDSC coding.

Reactive transport modeling of stable carbon isotope fractionation in a multi-phase multi-component system during carbon sequestration

DOE PAGES

Zhang, Shuo; DePaolo, Donald J.; Zheng, Liange; ...

2014-12-31

Carbon stable isotopes can be used in characterization and monitoring of CO 2 sequestration sites to track the migration of the CO 2 plume and identify leakage sources, and to evaluate the chemical reactions that take place in the CO 2-water-rock system. However, there are few tools available to incorporate stable isotope information into flow and transport codes used for CO 2 sequestration problems. We present a numerical tool for modeling the transport of stable carbon isotopes in multiphase reactive systems relevant to geologic carbon sequestration. The code is an extension of the reactive transport code TOUGHREACT. The transport modulemore » of TOUGHREACT was modified to include separate isotopic species of CO 2 gas and dissolved inorganic carbon (CO 2, CO 3 2-, HCO 3 -,…). Any process of transport or reaction influencing a given carbon species also influences its isotopic ratio. Isotopic fractionation is thus fully integrated within the dynamic system. The chemical module and database have been expanded to include isotopic exchange and fractionation between the carbon species in both gas and aqueous phases. The performance of the code is verified by modeling ideal systems and comparing with theoretical results. Efforts are also made to fit field data from the Pembina CO 2 injection project in Canada. We show that the exchange of carbon isotopes between dissolved and gaseous carbon species combined with fluid flow and transport, produce isotopic effects that are significantly different from simple two-component mixing. These effects are important for understanding the isotopic variations observed in field demonstrations.« less

Deciphering Systemic Wound Responses of the Pumpkin Extrafascicular Phloem by Metabolomics and Stable Isotope-Coded Protein Labeling1[C][W

PubMed Central

Gaupels, Frank; Sarioglu, Hakan; Beckmann, Manfred; Hause, Bettina; Spannagl, Manuel; Draper, John; Lindermayr, Christian; Durner, Jörg

2012-01-01

In cucurbits, phloem latex exudes from cut sieve tubes of the extrafascicular phloem (EFP), serving in defense against herbivores. We analyzed inducible defense mechanisms in the EFP of pumpkin (Cucurbita maxima) after leaf damage. As an early systemic response, wounding elicited transient accumulation of jasmonates and a decrease in exudation probably due to partial sieve tube occlusion by callose. The energy status of the EFP was enhanced as indicated by increased levels of ATP, phosphate, and intermediates of the citric acid cycle. Gas chromatography coupled to mass spectrometry also revealed that sucrose transport, gluconeogenesis/glycolysis, and amino acid metabolism were up-regulated after wounding. Combining ProteoMiner technology for the enrichment of low-abundance proteins with stable isotope-coded protein labeling, we identified 51 wound-regulated phloem proteins. Two Sucrose-Nonfermenting1-related protein kinases and a 32-kD 14-3-3 protein are candidate central regulators of stress metabolism in the EFP. Other proteins, such as the Silverleaf Whitefly-Induced Protein1, Mitogen Activated Protein Kinase6, and Heat Shock Protein81, have known defensive functions. Isotope-coded protein labeling and western-blot analyses indicated that Cyclophilin18 is a reliable marker for stress responses of the EFP. As a hint toward the induction of redox signaling, we have observed delayed oxidation-triggered polymerization of the major Phloem Protein1 (PP1) and PP2, which correlated with a decline in carbonylation of PP2. In sum, wounding triggered transient sieve tube occlusion, enhanced energy metabolism, and accumulation of defense-related proteins in the pumpkin EFP. The systemic wound response was mediated by jasmonate and redox signaling. PMID:23085839

Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II

PubMed Central

Norman, Paul J.; Norberg, Steven J.; Guethlein, Lisbeth A.; Nemat-Gorgani, Neda; Royce, Thomas; Wroblewski, Emily E.; Dunn, Tamsen; Mann, Tobias; Alicata, Claudia; Hollenbach, Jill A.; Chang, Weihua; Shults Won, Melissa; Gunderson, Kevin L.; Abi-Rached, Laurent; Ronaghi, Mostafa; Parham, Peter

2017-01-01

The most polymorphic part of the human genome, the MHC, encodes over 160 proteins of diverse function. Half of them, including the HLA class I and II genes, are directly involved in immune responses. Consequently, the MHC region strongly associates with numerous diseases and clinical therapies. Notoriously, the MHC region has been intractable to high-throughput analysis at complete sequence resolution, and current reference haplotypes are inadequate for large-scale studies. To address these challenges, we developed a method that specifically captures and sequences the 4.8-Mbp MHC region from genomic DNA. For 95 MHC homozygous cell lines we assembled, de novo, a set of high-fidelity contigs and a sequence scaffold, representing a mean 98% of the target region. Included are six alternative MHC reference sequences of the human genome that we completed and refined. Characterization of the sequence and structural diversity of the MHC region shows the approach accurately determines the sequences of the highly polymorphic HLA class I and HLA class II genes and the complex structural diversity of complement factor C4A/C4B. It has also uncovered extensive and unexpected diversity in other MHC genes; an example is MUC22, which encodes a lung mucin and exhibits more coding sequence alleles than any HLA class I or II gene studied here. More than 60% of the coding sequence alleles analyzed were previously uncharacterized. We have created a substantial database of robust reference MHC haplotype sequences that will enable future population scale studies of this complicated and clinically important region of the human genome. PMID:28360230

Mechanical code comparator

DOEpatents

Peter, Frank J.; Dalton, Larry J.; Plummer, David W.

2002-01-01

A new class of mechanical code comparators is described which have broad potential for application in safety, surety, and security applications. These devices can be implemented as micro-scale electromechanical systems that isolate a secure or otherwise controlled device until an access code is entered. This access code is converted into a series of mechanical inputs to the mechanical code comparator, which compares the access code to a pre-input combination, entered previously into the mechanical code comparator by an operator at the system security control point. These devices provide extremely high levels of robust security. Being totally mechanical in operation, an access control system properly based on such devices cannot be circumvented by software attack alone.

Accumulate Repeat Accumulate Coded Modulation

NASA Technical Reports Server (NTRS)

Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

2004-01-01

In this paper we propose an innovative coded modulation scheme called 'Accumulate Repeat Accumulate Coded Modulation' (ARA coded modulation). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes that are combined with high level modulation. Thus at the decoder belief propagation can be used for iterative decoding of ARA coded modulation on a graph, provided a demapper transforms the received in-phase and quadrature samples to reliability of the bits.

Analysis of reaction cross-section production in neutron induced fission reactions on uranium isotope using computer code COMPLET.

PubMed

Asres, Yihunie Hibstie; Mathuthu, Manny; Birhane, Marelgn Derso

2018-04-22

This study provides current evidence about cross-section production processes in the theoretical and experimental results of neutron induced reaction of uranium isotope on projectile energy range of 1-100 MeV in order to improve the reliability of nuclear stimulation. In such fission reactions of 235 U within nuclear reactors, much amount of energy would be released as a product that able to satisfy the needs of energy to the world wide without polluting processes as compared to other sources. The main objective of this work is to transform a related knowledge in the neutron-induced fission reactions on 235 U through describing, analyzing and interpreting the theoretical results of the cross sections obtained from computer code COMPLET by comparing with the experimental data obtained from EXFOR. The cross section value of 235 U(n,2n) 234 U, 235 U(n,3n) 233 U, 235 U(n,γ) 236 U, 235 U(n,f) are obtained using computer code COMPLET and the corresponding experimental values were browsed by EXFOR, IAEA. The theoretical results are compared with the experimental data taken from EXFOR Data Bank. Computer code COMPLET has been used for the analysis with the same set of input parameters and the graphs were plotted by the help of spreadsheet & Origin-8 software. The quantification of uncertainties stemming from both experimental data and computer code calculation plays a significant role in the final evaluated results. The calculated results for total cross sections were compared with the experimental data taken from EXFOR in the literature, and good agreement was found between the experimental and theoretical data. This comparison of the calculated data was analyzed and interpreted with tabulation and graphical descriptions, and the results were briefly discussed within the text of this research work. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

The NordICC Study: Rationale and design of a randomized trial on colonoscopy screening for colorectal cancer

PubMed Central

F.Kaminski, Michal; Bretthauer, Michael; Zauber, Ann G.; Kuipers, Ernst J.; Adami, Hans-Olov; van Ballegooijen, Marjolein; Regula, Jaroslaw; van Leerdam, Monique; Stefansson, Tryggvi; Påhlman, Lars; Dekker, Evelien; Hernán, Miguel A.; Garborg, Kjetil; Hoff, Geir

2017-01-01

Background While colonoscopy screening is widely used in several European countries and the United States, no randomised trials exist to quantify its benefits. The Nordic-European Initiative on Colorectal Cancer (NordICC) is a multinational, randomized controlled trial aiming at investigating the effect of colonoscopy screening on CRC incidence and mortality. This paper describes the rationale and design of the NordICC trial. Material and methods Men and women age 55 to 64 years are drawn from the population registries in the participating countries and randomly assigned to either once-only colonoscopy screening with removal of all detected lesions, or no screening (standard of care in the trial regions). All individuals are followed for 15 years after inclusion using dedicated national registries. Results The primary endpoints of the trial are cumulative CRC-specific death and CRC incidence during 15 years of follow up. We hypothesize a 50% CRC mortality-reducing efficacy of the colonoscopy intervention and predict 50% compliance, yielding a 25% mortality reduction among those invited to screening. For 90% power and a two-sided alpha level of 0.05, using a 2:1 randomisation, 45,600 individuals will be randomised to control, and 22,800 individuals to the colonoscopy group. Interim analyses of the effect of colonoscopy on CRC incidence and mortality will be performed at 10 years follow-up. Conclusions The aim of the NordICC trial is to quantify the effectiveness of population-based colonoscopy screening. This will allow development of evidence-based guidelines for CRC screening in the general population. PMID:22723185

Pacific Northwest (PNW) Hydrologic Landscape (HL) polygons and HL code

EPA Pesticide Factsheets

A five-letter hydrologic landscape code representing five indices of hydrologic form that are related to hydrologic function: climate, seasonality, aquifer permeability, terrain, and soil permeability. Each hydrologic assessment unit is classified by one of the 81 different five-letter codes representing these indices. Polygon features in this dataset were created by aggregating (dissolving boundaries between) adjacent, similarly-coded hydrologic assessment units. Climate Classes: V-Very wet, W-Wet, M-Moist, D-Dry, S-Semiarid, A-Arid. Seasonality Sub-Classes: w-Fall or winter, s-Spring. Aquifer Permeability Classes: H-High, L-Low. Terrain Classes: M-Mountain, T-Transitional, F-Flat. Soil Permeability Classes: H-High, L-Low.

Identification of cellular MMP substrates using quantitative proteomics: isotope-coded affinity tags (ICAT) and isobaric tags for relative and absolute quantification (iTRAQ).

PubMed

Butler, Georgina S; Dean, Richard A; Morrison, Charlotte J; Overall, Christopher M

2010-01-01

Identification of protease substrates is essential to understand the functional consequences of normal proteolytic processing and dysregulated proteolysis in disease. Quantitative proteomics and mass spectrometry can be used to identify protease substrates in the cellular context. Here we describe the use of two protein labeling techniques, Isotope-Coded Affinity Tags (ICAT and Isobaric Tags for Relative and Absolute Quantification (iTRAQ), which we have used successfully to identify novel matrix metalloproteinase (MMP) substrates in cell culture systems (1-4). ICAT and iTRAQ can label proteins and protease cleavage products of secreted proteins, protein domains shed from the cell membrane or pericellular matrix of protease-transfected cells that have accumulated in conditioned medium, or cell surface proteins in membrane preparations; isotopically distinct labels are used for control cells. Tryptic digestion and tandem mass spectrometry of the generated fragments enable sequencing of differentially labeled but otherwise identical pooled peptides. The isotopic tag, which is unique for each label, identifies the peptides originating from each sample, for instance, protease-transfected or control cells, and comparison of the peak areas enables relative quantification of the peptide in each sample. Thus proteins present in altered amounts between protease-expressing and null cells are implicated as protease substrates and can be further validated as such.

An improved and validated RNA HLA class I SBT approach for obtaining full length coding sequences.

PubMed

Gerritsen, K E H; Olieslagers, T I; Groeneweg, M; Voorter, C E M; Tilanus, M G J

2014-11-01

The functional relevance of human leukocyte antigen (HLA) class I allele polymorphism beyond exons 2 and 3 is difficult to address because more than 70% of the HLA class I alleles are defined by exons 2 and 3 sequences only. For routine application on clinical samples we improved and validated the HLA sequence-based typing (SBT) approach based on RNA templates, using either a single locus-specific or two overlapping group-specific polymerase chain reaction (PCR) amplifications, with three forward and three reverse sequencing reactions for full length sequencing. Locus-specific HLA typing with RNA SBT of a reference panel, representing the major antigen groups, showed identical results compared to DNA SBT typing. Alleles encountered with unknown exons in the IMGT/HLA database and three samples, two with Null and one with a Low expressed allele, have been addressed by the group-specific RNA SBT approach to obtain full length coding sequences. This RNA SBT approach has proven its value in our routine full length definition of alleles. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Meteorites and their parent bodies: Evidence from oxygen isotopes

NASA Technical Reports Server (NTRS)

Clayton, R. N.

1978-01-01

Isotopic abundance variations among meteorites are used to establish genetic associations between meteorite classes. Oxygen isotope distributions between group II E irons with H-group ordinary chondrites and enstatic meteorites indicate that the parent bodies were formed out of pre-solar material that was not fully mixed at the time condensation occurred within the solar nebula.

Efficient production of native lunasin with correct N-terminal processing by using the pH-induced self-cleavable Ssp DnaB mini-intein system in Escherichia coli.

PubMed

Setrerrahmane, Sarra; Zhang, Yi; Dai, Guangzhi; Lv, Jing; Tan, Shuhua

2014-09-01

To develop an efficient and cost-effective approach for the production of small preventive peptide lunasin with correct natural N terminus, a synthetic gene was designed by OPTIMIZER & Gene Designer and cloned into pTWIN1 vector at SapI and PstI sites. Thus, lunasin was N-terminally fused to the pH-induced self-cleavable Ssp DnaB mini-intein linked to a chitin binding domain (CBD) with no extra residues. The resultant fusion protein was highly expressed by lactose induction in Escherichia coli BL21 (DE3) in a 7-l bioreactor and bound to a chitin affinity column. After washing the impurities, the Ssp DnaB intein mediated on-column self-cleavage was easily triggered by shifting pH and temperature to allow the native lunasin released. The final purified lunasin yielded up to 75 mg/l medium. Tricine/SDS-PAGE and matrix-assisted laser desorption time-of-flight (MALDI-TOF)/mass spectrometry (MS) verified the structural authenticity of the product, implying the correct cleavage at the junction between Ssp DnaB intein and lunasin. MTT assay confirmed its potent proliferation inhibitory activity to human cancer cells HCT-116 and MDA-MB-231; however, no cytotoxicity to normal human lens epithelial cell SRA01/04 and hepatoma HepG2. Taken together, we provide a novel strategy to produce recombinant native lunasin with correct N-terminal processing by using the pH-induced self-cleavable Ssp DnaB mini-intein.

Dual Targeting of Intracellular Pathogenic Bacteria with a Cleavable Conjugate of Kanamycin and an Antibacterial Cell-Penetrating Peptide.

PubMed

Brezden, Anna; Mohamed, Mohamed F; Nepal, Manish; Harwood, John S; Kuriakose, Jerrin; Seleem, Mohamed N; Chmielewski, Jean

2016-08-31

Bacterial infection caused by intracellular pathogens, such as Mycobacterium, Salmonella, and Brucella, is a burgeoning global health epidemic that necessitates urgent action. However, the therapeutic value of a number of antibiotics, including aminoglycosides, against intracellular pathogenic bacteria is compromised due to their inability to traverse eukaryotic membranes. For this significant problem to be addressed, a cleavable conjugate of the antibiotic kanamycin and a nonmembrane lytic, broad-spectrum antimicrobial peptide with efficient mammalian cell penetration, P14LRR, was prepared. This approach allows kanamycin to enter mammalian cells as a conjugate linked via a tether that breaks down in the reducing environment within cells. Potent antimicrobial activity of the P14KanS conjugate was demonstrated in vitro, and this reducible conjugate effectively cleared intracellular pathogenic bacteria within macrophages more potently than that of a conjugate lacking the disulfide moiety. Notably, successful clearance of Mycobacterium tuberculosis within macrophages was observed with the dual antibiotic conjugate, and Salmonella levels were significantly reduced in an in vivo Caenorhabditis elegans model.

29 CFR 782.8 - Special classes of carriers.

Code of Federal Regulations, 2011 CFR

2011-07-01

... subject to its jurisdiction. (New Pittsburgh Coal Co. v. Hocking Valley Ry. Co., 24 I.C.C. 244; Corona Coal Co. v. Secretary of War, 69 I.C.C. 389; Bunker Coal from Alabama to Gulf Ports, 227 I.C.C. 485.) The intrastate delivery of chandleries, including cordage, canvas, repair parts, wire rope, etc., to...

29 CFR 782.8 - Special classes of carriers.

Code of Federal Regulations, 2010 CFR

2010-07-01

... subject to its jurisdiction. (New Pittsburgh Coal Co. v. Hocking Valley Ry. Co., 24 I.C.C. 244; Corona Coal Co. v. Secretary of War, 69 I.C.C. 389; Bunker Coal from Alabama to Gulf Ports, 227 I.C.C. 485.) The intrastate delivery of chandleries, including cordage, canvas, repair parts, wire rope, etc., to...

Interframe vector wavelet coding technique

NASA Astrophysics Data System (ADS)

Wus, John P.; Li, Weiping

1997-01-01

Wavelet coding is often used to divide an image into multi- resolution wavelet coefficients which are quantized and coded. By 'vectorizing' scalar wavelet coding and combining this with vector quantization (VQ), vector wavelet coding (VWC) can be implemented. Using a finite number of states, finite-state vector quantization (FSVQ) takes advantage of the similarity between frames by incorporating memory into the video coding system. Lattice VQ eliminates the potential mismatch that could occur using pre-trained VQ codebooks. It also eliminates the need for codebook storage in the VQ process, thereby creating a more robust coding system. Therefore, by using the VWC coding method in conjunction with the FSVQ system and lattice VQ, the formulation of a high quality very low bit rate coding systems is proposed. A coding system using a simple FSVQ system where the current state is determined by the previous channel symbol only is developed. To achieve a higher degree of compression, a tree-like FSVQ system is implemented. The groupings are done in this tree-like structure from the lower subbands to the higher subbands in order to exploit the nature of subband analysis in terms of the parent-child relationship. Class A and Class B video sequences from the MPEG-IV testing evaluations are used in the evaluation of this coding method.

Bayesian Integration of Isotope Ratio for Geographic Sourcing of Castor Beans

PubMed Central

Webb-Robertson, Bobbie-Jo; Kreuzer, Helen; Hart, Garret; Ehleringer, James; West, Jason; Gill, Gary; Duckworth, Douglas

2012-01-01

Recent years have seen an increase in the forensic interest associated with the poison ricin, which is extracted from the seeds of the Ricinus communis plant. Both light element (C, N, O, and H) and strontium (Sr) isotope ratios have previously been used to associate organic material with geographic regions of origin. We present a Bayesian integration methodology that can more accurately predict the region of origin for a castor bean than individual models developed independently for light element stable isotopes or Sr isotope ratios. Our results demonstrate a clear improvement in the ability to correctly classify regions based on the integrated model with a class accuracy of 60.9 ± 2.1% versus 55.9 ± 2.1% and 40.2 ± 1.8% for the light element and strontium (Sr) isotope ratios, respectively. In addition, we show graphically the strengths and weaknesses of each dataset in respect to class prediction and how the integration of these datasets strengthens the overall model. PMID:22919270

A Comparative Study of "The International Educational Technology Conference" (IETC) and "The International Conference on Computers in Education" (ICCE): The Program, Essay Distribution, the Themes, and Research Methods

ERIC Educational Resources Information Center

Chen, Gwo-Dong; Chen, Chun-Hsiang; Wang, Chin-Yeh; Li, Liang-Yi

2012-01-01

The article aims to compare international conferences, "The International Educational Technology Conference" (IETC, 2011) and "The International Conference on Computers in Education" (ICCE, 2010), from various dimensions. The comparison is expected to conclude a better approach for every IETC and ICCE to be held. (Contains 4…

Validity and reliability assessment of a peer evaluation method in team-based learning classes.

PubMed

Yoon, Hyun Bae; Park, Wan Beom; Myung, Sun-Jung; Moon, Sang Hui; Park, Jun-Bean

2018-03-01

Team-based learning (TBL) is increasingly employed in medical education because of its potential to promote active group learning. In TBL, learners are usually asked to assess the contributions of peers within their group to ensure accountability. The purpose of this study is to assess the validity and reliability of a peer evaluation instrument that was used in TBL classes in a single medical school. A total of 141 students were divided into 18 groups in 11 TBL classes. The students were asked to evaluate their peers in the group based on evaluation criteria that were provided to them. We analyzed the comments that were written for the highest and lowest achievers to assess the validity of the peer evaluation instrument. The reliability of the instrument was assessed by examining the agreement among peer ratings within each group of students via intraclass correlation coefficient (ICC) analysis. Most of the students provided reasonable and understandable comments for the high and low achievers within their group, and most of those comments were compatible with the evaluation criteria. The average ICC of each group ranged from 0.390 to 0.863, and the overall average was 0.659. There was no significant difference in inter-rater reliability according to the number of members in the group or the timing of the evaluation within the course. The peer evaluation instrument that was used in the TBL classes was valid and reliable. Providing evaluation criteria and rules seemed to improve the validity and reliability of the instrument.

A photo-cleavable biotin affinity tag for the facile release of a photo-crosslinked carbohydrate-binding protein.

PubMed

Chang, Tsung-Che; Adak, Avijit K; Lin, Ting-Wei; Li, Pei-Jhen; Chen, Yi-Ju; Lai, Chain-Hui; Liang, Chien-Fu; Chen, Yu-Ju; Lin, Chun-Cheng

2016-03-15

The use of photo-crosslinking glycoprobes represents a powerful strategy for the covalent capture of labile protein complexes and allows detailed characterization of carbohydrate-mediated interactions. The selective release of target proteins from solid support is a key step in functional proteomics. We envisaged that light activation can be exploited for releasing labeled protein in a dual photo-affinity probe-based strategy. To investigate this possibility, we designed a trifunctional, galactose-based, multivalent glycoprobe for affinity labeling of carbohydrate-binding proteins. The resulting covalent protein-probe adduct is attached to a photo-cleavable biotin affinity tag; the biotin moiety enables specific presentation of the conjugate on streptavidin-coated beads, and the photolabile linker allows the release of the labeled proteins. This dual probe promotes both the labeling and the facile cleavage of the target protein complexes from the solid surfaces and the remainder of the cell lysate in a completely unaltered form, thus eliminating many of the common pitfalls associated with traditional affinity-based purification methods. Copyright © 2016 Elsevier Ltd. All rights reserved.

Automated determination of the stable carbon isotopic composition (δ13C) of total dissolved inorganic carbon (DIC) and total nonpurgeable dissolved organic carbon (DOC) in aqueous samples: RSIL lab codes 1851 and 1852

USGS Publications Warehouse

Révész, Kinga M.; Doctor, Daniel H.

2014-01-01

The purposes of the Reston Stable Isotope Laboratory (RSIL) lab codes 1851 and 1852 are to determine the total carbon mass and the ratio of the stable isotopes of carbon (δ13C) for total dissolved inorganic carbon (DIC, lab code 1851) and total nonpurgeable dissolved organic carbon (DOC, lab code 1852) in aqueous samples. The analysis procedure is automated according to a method that utilizes a total carbon analyzer as a peripheral sample preparation device for analysis of carbon dioxide (CO2) gas by a continuous-flow isotope ratio mass spectrometer (CF-IRMS). The carbon analyzer produces CO2 and determines the carbon mass in parts per million (ppm) of DIC and DOC in each sample separately, and the CF-IRMS determines the carbon isotope ratio of the produced CO2. This configuration provides a fully automated analysis of total carbon mass and δ13C with no operator intervention, additional sample preparation, or other manual analysis. To determine the DIC, the carbon analyzer transfers a specified sample volume to a heated (70 °C) reaction vessel with a preprogrammed volume of 10% phosphoric acid (H3PO4), which allows the carbonate and bicarbonate species in the sample to dissociate to CO2. The CO2 from the reacted sample is subsequently purged with a flow of helium gas that sweeps the CO2 through an infrared CO2 detector and quantifies the CO2. The CO2 is then carried through a high-temperature (650 °C) scrubber reactor, a series of water traps, and ultimately to the inlet of the mass spectrometer. For the analysis of total dissolved organic carbon, the carbon analyzer performs a second step on the sample in the heated reaction vessel during which a preprogrammed volume of sodium persulfate (Na2S2O8) is added, and the hydroxyl radicals oxidize the organics to CO2. Samples containing 2 ppm to 30,000 ppm of carbon are analyzed. The precision of the carbon isotope analysis is within 0.3 per mill for DIC, and within 0.5 per mill for DOC.

Implementation of Energy Code Controls Requirements in New Commercial Buildings

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

Rosenberg, Michael I.; Hart, Philip R.; Hatten, Mike

Most state energy codes in the United States are based on one of two national model codes; ANSI/ASHRAE/IES 90.1 (Standard 90.1) or the International Code Council (ICC) International Energy Conservation Code (IECC). Since 2004, covering the last four cycles of Standard 90.1 updates, about 30% of all new requirements have been related to building controls. These requirements can be difficult to implement and verification is beyond the expertise of most building code officials, yet the assumption in studies that measure the savings from energy codes is that they are implemented and working correctly. The objective of the current research ismore » to evaluate the degree to which high impact controls requirements included in commercial energy codes are properly designed, commissioned and implemented in new buildings. This study also evaluates the degree to which these control requirements are realizing their savings potential. This was done using a three-step process. The first step involved interviewing commissioning agents to get a better understanding of their activities as they relate to energy code required controls measures. The second involved field audits of a sample of commercial buildings to determine whether the code required control measures are being designed, commissioned and correctly implemented and functioning in new buildings. The third step includes compilation and analysis of the information gather during the first two steps. Information gathered during these activities could be valuable to code developers, energy planners, designers, building owners, and building officials.« less

Steroid isotopic standards for gas chromatography-combustion isotope ratio mass spectrometry (GCC-IRMS).

PubMed

Zhang, Ying; Tobias, Herbert J; Brenna, J Thomas

2009-03-01

Carbon isotope ratio (CIR) analysis of urinary steroids using gas chromatography-combustion isotope ratio mass spectrometry (GCC-IRMS) is a recognized test to detect illicit doping with synthetic testosterone. There are currently no universally used steroid isotopic standards (SIS). We adapted a protocol to prepare isotopically uniform steroids for use as a calibrant in GCC-IRMS that can be analyzed under the same conditions as used for steroids extracted from urine. Two separate SIS containing a mixture of steroids were created and coded CU/USADA 33-1 and CU/USADA 34-1, containing acetates and native steroids, respectively. CU/USADA 33-1 contains 5alpha-androstan-3beta-ol acetate (5alpha-A-AC), 5alpha-androstan-3alpha-ol-17-one acetate (androsterone acetate, A-AC), 5beta-androstan-3alpha-ol-11, 17-dione acetate (11-ketoetiocholanolone acetate, 11k-AC) and 5alpha-cholestane (Cne). CU/USADA 34-1 contains 5beta-androstan-3alpha-ol-17-one (etiocholanolone, E), 5alpha-androstan-3alpha-ol-17-one (androsterone, A), and 5beta-pregnane-3alpha, 20alpha-diol (5betaP). Each mixture was prepared and dispensed into a set of about 100 ampoules using a protocol carefully designed to minimize isotopic fractionation and contamination. A natural gas reference material, NIST RM 8559, traceable to the international standard Vienna PeeDee Belemnite (VPDB) was used to calibrate the SIS. Absolute delta(13)C(VPDB) and Deltadelta(13)C(VPDB) values from randomly selected ampoules from both SIS indicate uniformity of steroid isotopic composition within measurement reproducibility, SD(delta(13)C)<0.2 per thousand. This procedure for creation of isotopic steroid mixtures results in consistent standards with isotope ratios traceable to the relevant international reference material.

Mmp-9 responsive PEG cleavable nanovesicles for efficient delivery of chemotherapeutics to pancreatic cancer.

PubMed

Kulkarni, Prajakta S; Haldar, Manas K; Nahire, Rahul R; Katti, Preeya; Ambre, Avinash H; Muhonen, Wallace W; Shabb, John B; Padi, Sathish K R; Singh, Raushan K; Borowicz, Pawel P; Shrivastava, D K; Katti, Kalpana S; Reindl, Katie; Guo, Bin; Mallik, Sanku

2014-07-07

Significant differences in biochemical parameters between normal and tumor tissues offer an opportunity to chemically design drug carriers which respond to these changes and deliver the drugs at the desired site. For example, overexpression of the matrix metalloproteinase-9 (MMP-9) enzyme in the extracellular matrix of tumor tissues can act as a trigger to chemically modulate the drug delivery from the carriers. In this study, we have synthesized an MMP-9-cleavable, collagen mimetic lipopeptide which forms nanosized vesicles with the POPC, POPE-SS-PEG, and cholesteryl-hemisuccinate lipids. The lipopeptide retains the triple-helical conformation when incorporated into these nanovesicles. The PEG groups shield the substrate lipopeptides from hydrolysis by MMP-9. However, in the presence of elevated glutathione levels, the PEG groups are reductively removed, exposing the lipopeptides to MMP-9. The resultant peptide-bond cleavage disturbs the vesicles' lipid bilayer, leading to the release of encapsulated contents. These PEGylated nanovesicles are capable of encapsulating the anticancer drug gemcitabine with 50% efficiency. They were stable in physiological conditions and in human serum. Effective drug release was demonstrated using the pancreatic ductal carcinoma cells (PANC-1 and MIAPaCa-2) in two-dimensional and three-dimensional "tumor-like" spheroid cultures. A reduction in tumor growth was observed after intravenous administration of the gemcitabine-encapsulated nanovesicles in the xenograft model of athymic, female nude mice.

MMP-9 Responsive PEG Cleavable Nanovesicles for Efficient Delivery of Chemotherapeutics to Pancreatic Cancer

PubMed Central

2015-01-01

Significant differences in biochemical parameters between normal and tumor tissues offer an opportunity to chemically design drug carriers which respond to these changes and deliver the drugs at the desired site. For example, overexpression of the matrix metalloproteinase-9 (MMP-9) enzyme in the extracellular matrix of tumor tissues can act as a trigger to chemically modulate the drug delivery from the carriers. In this study, we have synthesized an MMP-9-cleavable, collagen mimetic lipopeptide which forms nanosized vesicles with the POPC, POPE-SS-PEG, and cholesteryl-hemisuccinate lipids. The lipopeptide retains the triple-helical conformation when incorporated into these nanovesicles. The PEG groups shield the substrate lipopeptides from hydrolysis by MMP-9. However, in the presence of elevated glutathione levels, the PEG groups are reductively removed, exposing the lipopeptides to MMP-9. The resultant peptide-bond cleavage disturbs the vesicles’ lipid bilayer, leading to the release of encapsulated contents. These PEGylated nanovesicles are capable of encapsulating the anticancer drug gemcitabine with 50% efficiency. They were stable in physiological conditions and in human serum. Effective drug release was demonstrated using the pancreatic ductal carcinoma cells (PANC-1 and MIAPaCa-2) in two-dimensional and three-dimensional “tumor-like” spheroid cultures. A reduction in tumor growth was observed after intravenous administration of the gemcitabine-encapsulated nanovesicles in the xenograft model of athymic, female nude mice. PMID:24827725

A single CT for attenuation correction of both rest and stress SPECT myocardial perfusion imaging: a retrospective feasibility study

PubMed Central

Ahlman, Mark A; Nietert, Paul J; Wahlquist, Amy E; Serguson, Jill M; Berry, Max W; Suranyi, Pal; Liu, Songtao; Spicer, Kenneth M

2014-01-01

Purpose: In the effort to reduce radiation exposure to patients undergoing myocardial perfusion imaging (MPI) with SPECT/CT, we evaluate the feasibility of a single CT for attenuation correction (AC) of single-day rest (R)/stress (S) perfusion. Methods: Processing of 20 single isotope and 20 dual isotope MPI with perfusion defects were retrospectively repeated in three steps: (1) the standard method using a concurrent R-CT for AC of R-SPECT and S-CT for S-SPECT; (2) the standard method repeated; and (3) with the R-CT used for AC of S-SPECT, and the S-CT used for AC of R-SPECT. Intra-Class Correlation Coefficients (ICC) and Choen’s kappa were used to measure intra-operator variability in sum scoring. Results: The highest level of intra-operator reliability was seen with the reproduction of the sum rest score (SRS) and sum stress score (SSS) (ICC > 95%). ICCs were > 85% for SRS and SSS when alternate CTs were used for AC, but when sum difference scores were calculated, ICC values were much lower (~22% to 27%), which may imply that neither CT substitution resulted in a reproducible difference score. Similar results were seen when evaluating dichotomous outcomes (sum scores difference of ≥ 4) when comparing different processing techniques (kappas ~0.32 to 0.43). Conclusions: When a single CT is used for AC of both rest and stress SPECT, there is disproportionately high variability in sum scoring that is independent of user error. This information can be used to direct further investigation in radiation reduction for common imaging exams in nuclear medicine. PMID:24482701

Variation in the isotopic composition of striped weakfish Cynoscion guatucupa of the Southwest Atlantic Ocean in response to dietary shifts.

PubMed

Viola, M N Paso; Riccialdelli, L; Jaureguizar, A; Panarello, H O; Cappozzo, H L

2018-05-01

The aim of this study was to analyze the isotopic composition in muscle of striped weakfish Cynoscion guatucupa from Southwest Atlantic Ocean in order to evaluate a possible variation in δ13C and δ15N in response to dietary shifts that occur as animals grow. We also explored for isotopic evidence of differences between sample locations. The results showed an agreement between isotope analysis and previous conventional studies. Differences in the isotope composition between sampling location were not observed. A positive relation exists between isotope values and total body length of the animals. The Cluster analysis defined three groups of size classes, validated by the MDS. Differences in the relative consumption of prey species in each size class were also observed performing isotope mixing models (SIAR). Variation in δ15N among size classes would be associated with the consumption of a different type of prey as animals grow. Small striped weakfish feed on small crustaceans and progressively increase their consumption of fish (anchovy, Engraulis anchoita), increasing by this way their isotope values. On the other hand, differences in δ13C values seemed to be related to age-class specific spatial distribution patterns. Therefore, large and small striped weakfish remain specialized but feeding on different prey at different trophic levels. These results contribute to the study of the diet of striped weakfish, improve the isotopic ecology models and highlight on the importance of accounting for variation in the isotopic composition in response to dietary shifts with the size of one of the most important fishery resources in the region.

ICCS 2009 Latin American Report: Civic Knowledge and Attitudes among Lower-Secondary Students in Six Latin American Countries

ERIC Educational Resources Information Center

Schulz, Wolfram; Ainley, John; Friedman, Tim; Lietz, Petra

2011-01-01

The International Civic and Citizenship Education Study (ICCS) focused on the ways in which young people are prepared to undertake their roles as citizens. Preparing students for citizenship involves developing relevant knowledge and understanding as well as encouraging the formation of positive attitudes toward being a citizen. Descriptions of…

Quantitation of viable Coxiella burnetii in milk using an integrated cell culture-polymerase chain reaction (ICC-PCR) assay.

PubMed

Stewart, Diana; Shieh, Y-Carol; Tortorello, Mary; Kukreja, Ankush; Shazer, Arlette; Schlesser, Joseph

2015-11-01

The obligate intracellular pathogen Coxiella burnetii has long been considered the most heat resistant pathogen in raw milk, making it the reference pathogen for determining pasteurisation conditions for milk products. New milk formulations and novel non-thermal processes require validation of effectiveness which requires a more practical method for analysis than using the currently used animal model for assessing Coxiella survival. Also, there is an interest in better characterising thermal inactivation of Coxiella in various milk formulations. To avoid the use of the guinea pig model for evaluating Coxiella survival, an Integrated Cell Culture-PCR (ICC-PCR) method was developed for determining Coxiella viability in milk. Vero cell cultures were directly infected from Coxiella-contaminated milk in duplicate 24-well plates. Viability of the Coxiella in milk was shown by a ≥ 0.5 log genome equivalent (ge)/ml increase in the quantity of IS111a gene from the baseline post-infection (day 0) level after 9-11 d propagation. Coxiella in skim, 2%, and whole milk, and half and half successfully infected Vero cells and increased in number by at least 2 logs using a 48-h infection period followed by 9-d propagation time. As few as 125 Coxiella ge/ml in whole milk was shown to infect and propagate at least 2 logs in the optimised ICC-PCR assay, though variable confirmation of propagation was shown for as low as 25 Coxiella ge/ml. Applicability of the ICC-PCR method was further proven in an MPN format to quantitate the number of viable Coxiella remaining in whole milk after 60 °C thermal treatment at 0, 20, 40, 60 and 90 min.

Malocclusion Class II division 1 skeletal and dental relationships measured by cone-beam computed tomography.

PubMed

Xu, Yiling; Oh, Heesoo; Lagravère, Manuel O

2017-09-01

The purpose of this study was to locate traditionally-used landmarks in two-dimensional (2D) images and newly-suggested ones in three-dimensional (3D) images (cone-beam computer tomographies [CBCTs]) and determine possible relationships between them to categorize patients with Class II-1 malocclusion. CBCTs from 30 patients diagnosed with Class II-1 malocclusion were obtained from the University of Alberta Graduate Orthodontic Program database. The reconstructed images were downloaded and visualized using the software platform AVIZO ® . Forty-two landmarks were chosen and the coordinates were then obtained and analyzed using linear and angular measurements. Ten images were analyzed three times to determine the reliability and measurement error of each landmark using Intra-Class Correlation coefficient (ICC). Descriptive statistics were done using the SPSS statistical package to determine any relationships. ICC values were excellent for all landmarks in all axes, with the highest measurement error of 2mm in the y-axis for the Gonion Left landmark. Linear and angular measurements were calculated using the coordinates of each landmark. Descriptive statistics showed that the linear and angular measurements used in the 2D images did not correlate well with the 3D images. The lowest standard deviation obtained was 0.6709 for S-GoR/N-Me, with a mean of 0.8016. The highest standard deviation was 20.20704 for ANS-InfraL, with a mean of 41.006. The traditional landmarks used for 2D malocclusion analysis show good reliability when transferred to 3D images. However, they did not reveal specific skeletal or dental patterns when trying to analyze 3D images for malocclusion. Thus, another technique should be considered when classifying 3D CBCT images for Class II-1malocclusion. Copyright © 2017 CEO. Published by Elsevier Masson SAS. All rights reserved.

Bayesian Integration of Isotope Ratio for Geographic Sourcing of Castor Beans

DOE PAGES

Webb-Robertson, Bobbie-Jo; Kreuzer, Helen; Hart, Garret; ...

2012-01-01

Recenmore » t years have seen an increase in the forensic interest associated with the poison ricin, which is extracted from the seeds of the Ricinus communis plant. Both light element (C, N, O, and H) and strontium (Sr) isotope ratios have previously been used to associate organic material with geographic regions of origin. We present a Bayesian integration methodology that can more accurately predict the region of origin for a castor bean than individual models developed independently for light element stable isotopes or Sr isotope ratios. Our results demonstrate a clear improvement in the ability to correctly classify regions based on the integrated model with a class accuracy of 60.9 ± 2.1 % versus 55.9 ± 2.1 % and 40.2 ± 1.8 % for the light element and strontium (Sr) isotope ratios, respectively. In addition, we show graphically the strengths and weaknesses of each dataset in respect to class prediction and how the integration of these datasets strengthens the overall model.« less

Bayesian Integration of Isotope Ratios for Geographic Sourcing of Castor Beans

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

Webb-Robertson, Bobbie-Jo M.; Kreuzer, Helen W.; Hart, Garret L.

Recent years have seen an increase in the forensic interest associated with the poison ricin, which is extracted from the seeds of the Ricinus communis plant. Both light element (C, N, O, and H) and strontium (Sr) isotope ratios have previously been used to associate organic material with geographic regions of origin. We present a Bayesian integration methodology that can more accurately predict the region of origin for a castor bean than individual models developed independently for light element stable isotopes or Sr isotope ratios. Our results demonstrate a clear improvement in the ability to correctly classify regions based onmore » the integrated model with a class accuracy of 6 0 . 9 {+-} 2 . 1 % versus 5 5 . 9 {+-} 2 . 1 % and 4 0 . 2 {+-} 1 . 8 % for the light element and strontium (Sr) isotope ratios, respectively. In addition, we show graphically the strengths and weaknesses of each dataset in respect to class prediction and how the integration of these datasets strengthens the overall model.« less

Bayesian Integration of Isotope Ratio for Geographic Sourcing of Castor Beans

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

Webb-Robertson, Bobbie-Jo; Kreuzer, Helen; Hart, Garret

Recenmore » t years have seen an increase in the forensic interest associated with the poison ricin, which is extracted from the seeds of the Ricinus communis plant. Both light element (C, N, O, and H) and strontium (Sr) isotope ratios have previously been used to associate organic material with geographic regions of origin. We present a Bayesian integration methodology that can more accurately predict the region of origin for a castor bean than individual models developed independently for light element stable isotopes or Sr isotope ratios. Our results demonstrate a clear improvement in the ability to correctly classify regions based on the integrated model with a class accuracy of 60.9 ± 2.1 % versus 55.9 ± 2.1 % and 40.2 ± 1.8 % for the light element and strontium (Sr) isotope ratios, respectively. In addition, we show graphically the strengths and weaknesses of each dataset in respect to class prediction and how the integration of these datasets strengthens the overall model.« less

Isotope and multiband effects in layered superconductors.

PubMed

Bussmann-Holder, Annette; Keller, Hugo

2012-06-13

In this review we consider three classes of superconductors, namely cuprate superconductors, MgB(2) and the new Fe based superconductors. All of these three systems are layered materials and multiband compounds. Their pairing mechanisms are under discussion with the exception of MgB(2), which is widely accepted to be a 'conventional' electron-phonon interaction mediated superconductor, but extending the Bardeen-Cooper-Schrieffer (BCS) theory to account for multiband effects. Cuprates and Fe based superconductors have higher superconducting transition temperatures and more complex structures. Superconductivity is doping dependent in these material classes unlike in MgB(2) which, as a pure compound, has the highest values of T(c) and a rapid suppression of superconductivity with doping takes place. In all three material classes isotope effects have been observed, including exotic ones in the cuprates, and controversial ones in the Fe based materials. Before the area of high-temperature superconductivity, isotope effects on T(c) were the signature for phonon mediated superconductivity-even when deviations from the BCS value to smaller values were observed. Since the discovery of high T(c) materials this is no longer evident since competing mechanisms might exist and other mediating pairing interactions are discussed which are of purely electronic origin. In this work we will compare the three different material classes and especially discuss the experimentally observed isotope effects of all three systems and present a rather general analysis of them. Furthermore, we will concentrate on multiband signatures which are not generally accepted in cuprates even though they are manifest in various experiments, the evidence for those in MgB(2), and indications for them in the Fe based compounds. Mostly we will consider experimental data, but when possible also discuss theoretical models which are suited to explain the data.

Glycan reductive isotope labeling for quantitative glycomics.

PubMed

Xia, Baoyun; Feasley, Christa L; Sachdev, Goverdhan P; Smith, David F; Cummings, Richard D

2009-04-15

Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed glycan reductive isotope labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [(12)C(6)]aniline and [(13)C(6)]aniline. These dual-labeled aniline-tagged glycans can be recovered by reverse-phase chromatography and can be quantified based on ultraviolet (UV) absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins, using this method. This technique allows linear relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of glycomics.

Benchmarking of Heavy Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in designing and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

The general theory of convolutional codes

NASA Technical Reports Server (NTRS)

Mceliece, R. J.; Stanley, R. P.

1993-01-01

This article presents a self-contained introduction to the algebraic theory of convolutional codes. This introduction is partly a tutorial, but at the same time contains a number of new results which will prove useful for designers of advanced telecommunication systems. Among the new concepts introduced here are the Hilbert series for a convolutional code and the class of compact codes.

A Fast linking approach for CMYK to CMYK conversion preserving black separation in ICC color management system

NASA Astrophysics Data System (ADS)

Zeng, Huanzhao

2003-12-01

In the linking step of the standard ICC color management workflow for CMYK to CMYK conversion, a CMM takes an AToBn tag (n = 0, 1, or 2) from a source ICC profile to convert a color from the source color space to PCS (profile connection space), and then takes a BToAn tag from the destination ICC profile to convert the color from PCS to the destination color space. This approach may give satisfactory result perceptually or colorimetrically. However, it does not preserve the K channel for CMYK to CMYK conversion, which is often required in graphic art"s market. The problem is that the structure of a BtoAn tag is designed to convert colors from PCS to a device color space ignoring the K values from the source color space. Different approaches have been developed to control K in CMYK to CMYK printing, yet none of them well fits into the "Profile - PCS - Profile" model in the ICC color management system. A traditional approach is to transform the source CMYK to the destination CMYK by 1-D TRC curves and GCR/UCR tables. This method is so simple that it cannot accurately transform colors perceptually or colorimetrically. Another method is to build a 4-D CMYK to CMYK closed-loop lookup table (LUT) (or a deviceLink ICC profile) for the color transformation. However, this approach does not fit into opened color management workflows for it ties the source and the destination color spaces in the color characterization step. A specialized CMM may preserve K for a limit number of colors by mapping those CMYK colors to some carefully chosen PCS colors in both the AToBi tag and the BToAi tag. A more complete solution is to move to smart linking in which gamut mapping is performed in the real-time linking at a CMM. This method seems to solve all problems existed in the CMYK to CMYK conversion. However, it introduces new problems: 1) gamut mapping at real-time linking is often unacceptable slow; 2) gamut mapping may not be optimized or may be unreliable; 3) manual adjustment for

Learning Discriminative Binary Codes for Large-scale Cross-modal Retrieval.

PubMed

Xu, Xing; Shen, Fumin; Yang, Yang; Shen, Heng Tao; Li, Xuelong

2017-05-01

Hashing based methods have attracted considerable attention for efficient cross-modal retrieval on large-scale multimedia data. The core problem of cross-modal hashing is how to learn compact binary codes that construct the underlying correlations between heterogeneous features from different modalities. A majority of recent approaches aim at learning hash functions to preserve the pairwise similarities defined by given class labels. However, these methods fail to explicitly explore the discriminative property of class labels during hash function learning. In addition, they usually discard the discrete constraints imposed on the to-be-learned binary codes, and compromise to solve a relaxed problem with quantization to obtain the approximate binary solution. Therefore, the binary codes generated by these methods are suboptimal and less discriminative to different classes. To overcome these drawbacks, we propose a novel cross-modal hashing method, termed discrete cross-modal hashing (DCH), which directly learns discriminative binary codes while retaining the discrete constraints. Specifically, DCH learns modality-specific hash functions for generating unified binary codes, and these binary codes are viewed as representative features for discriminative classification with class labels. An effective discrete optimization algorithm is developed for DCH to jointly learn the modality-specific hash function and the unified binary codes. Extensive experiments on three benchmark data sets highlight the superiority of DCH under various cross-modal scenarios and show its state-of-the-art performance.

Generalized Bezout's Theorem and its applications in coding theory

NASA Technical Reports Server (NTRS)

Berg, Gene A.; Feng, Gui-Liang; Rao, T. R. N.

1996-01-01

This paper presents a generalized Bezout theorem which can be used to determine a tighter lower bound of the number of distinct points of intersection of two or more curves for a large class of plane curves. A new approach to determine a lower bound on the minimum distance (and also the generalized Hamming weights) for algebraic-geometric codes defined from a class of plane curves is introduced, based on the generalized Bezout theorem. Examples of more efficient linear codes are constructed using the generalized Bezout theorem and the new approach. For d = 4, the linear codes constructed by the new construction are better than or equal to the known linear codes. For d greater than 5, these new codes are better than the known codes. The Klein code over GF(2(sup 3)) is also constructed.

A Micelle Self-Assembled from Doxorubicin-Arabinoxylan Conjugates with pH-Cleavable Bond for Synergistic Antitumor Therapy

NASA Astrophysics Data System (ADS)

Wang, Jie; Li, Yanli; Dong, Xia; Wang, Ying; Chong, Xiaodan; Yu, Tai; Zhang, Fulei; Chen, Di; Zhang, Li; Gao, Jie; Yang, Cheng; Han, Jun; Li, Wei

2017-01-01

Nanomedicine offers new hope to overcome the low solubility and high side toxicity to normal tissue appeared in traditional chemotherapy. The biocompatibility and intracellular drug accumulation is still a big challenge for the nano-based formulations. Herein, a medical-used biocompatible arabinoxylan (AX) is used to develop to delivery chemodrug doxorubicin (DOX). The solubility of DOX is obviously enhanced via the hydrogen bond formed with AX which results in an amphiphilic AX-DOX. A micelle with pH-cleavable bond is thus self-assembled from such AX-DOX with DOX core and AX shell. The inner DOX can be easily released out at low intracellular pH, which obviously enhanced its in vitro cytotoxicity against breast cancer cells (MCF-7). Interestingly, an unexpected apoptosis is evoked except for the proliferation inhibition. Moreover, the therapeutic effects are further synergistically promoted by the enhanced permeability and retention (EPR) and intracellular pH-triggered drug release. Consequently, the in vivo intratumor accumulation of DOX, the tumor inhibition was significantly promoted after intravenous administration to the Balb/c nude mice bearing MCF-7 tumors. These in vitro/vivo results indicated that the AX-DOX micellular formulation holds high potential in cancer therapy.

Organic chemistry of Murchison meteorite: Carbon isotopic fractionation

NASA Technical Reports Server (NTRS)

Yuen, G. U.; Blair, N. E.; Desmarais, D. J.; Cronin, J. R.; Chang, S.

1986-01-01

The carbon isotopic composition of individual organic compounds of meteoritic origin remains unknown, as most reported carbon isotopic ratios are for bulk carbon or solvent extractable fractions. The researchers managed to determine the carbon isotopic ratios for individual hydrocarbons and monocarboxylic acids isolated from a Murchison sample by a freeze-thaw-ultrasonication technique. The abundances of monocarboxylic acids and saturated hydrocarbons decreased with increasing carbon number and the acids are more abundant than the hydrocarbon with the same carbon number. For both classes of compounds, the C-13 to C-12 ratios decreased with increasing carbon number in a roughly parallel manner, and each carboxylic acid exhibits a higher isotopic number than the hydrocarbon containing the same number of carbon atoms. These trends are consistent with a kinetically controlled synthesis of higher homologues for lower ones.

Constructions for finite-state codes

NASA Technical Reports Server (NTRS)

Pollara, F.; Mceliece, R. J.; Abdel-Ghaffar, K.

1987-01-01

A class of codes called finite-state (FS) codes is defined and investigated. These codes, which generalize both block and convolutional codes, are defined by their encoders, which are finite-state machines with parallel inputs and outputs. A family of upper bounds on the free distance of a given FS code is derived from known upper bounds on the minimum distance of block codes. A general construction for FS codes is then given, based on the idea of partitioning a given linear block into cosets of one of its subcodes, and it is shown that in many cases the FS codes constructed in this way have a d sub free which is as large as possible. These codes are found without the need for lengthy computer searches, and have potential applications for future deep-space coding systems. The issue of catastropic error propagation (CEP) for FS codes is also investigated.

Polymeric micellar nanoplatforms for Fenton reaction as a new class of antibacterial agents.

PubMed

Park, Seong-Cheol; Kim, Nam-Hong; Yang, Wonseok; Nah, Jae-Woon; Jang, Mi-Kyeong; Lee, Dongwon

2016-01-10

Reactive oxygen species (ROS) produced by host phagocytes exert antibacterial action against a variety of pathogens and ROS-induced oxidative stress is the governing mechanism for the antibacterial activity of major bactericidal antibiotics. In particular, hydroxyl radical is a strong and nonselective oxidant which can damage biomolecules such as DNA, proteins and lipids. Ferrous ion is known to convert mild oxidant hydrogen peroxide (H2O2) into highly reactive and toxic hydroxyl radicals, referred to as Fenton reaction. Herein, we report a new class of antibacterial agents based on Fenton reaction-performing nanostructures, composed of H2O2-generating polymer (PCAE) and iron-containing ferrocene. Amphiphilic PCAE was designed to incorporate H2O2-generating cinnamaldehyde through acid-cleavable linkages and self-assemble to form thermodynamically stable micelles which could encapsulate ferrocene in their hydrophobic core. All the experiments in vitro display that ferrocene-loaded PCAE micelles produce hydroxyl radicals to kill Escherichia coli and Pseudomonas aeruginosa through membrane damages. Intraperitoneally injected ferrocene-loaded PCAE micelles significantly reduced the lung damages and therefore increased the survival rate of mice infected with drug resistant P. aeruginosa. Given their potent antibacterial activity, ferrocene-loaded PCAE micelles hold great potential as a new class of ROS-manipulating antibacterial agents. Copyright © 2015 Elsevier B.V. All rights reserved.

Isotopic Measurements of Organic Sulfonates From The Murchison Meteorite

NASA Technical Reports Server (NTRS)

Cooper, G. W.; Chang, S.; DeVincenzi, Donald L. (Technical Monitor)

1995-01-01

Organic sulfonates and phosphonates have been extracted from the Murchison meteorite for stable isotope measurements. Preliminary stable isotope measurements of individual alkyl sulfonates, R-SO3H (R=C(sub n)H(sub 2n+l)), are shown. These compounds were found in aqueous extracts of Murchison. Both groups show trends similar to other homologous series of organic compounds indigenous to Murchison. Molecular abundances decrease with increasing carbon number, and all possible isomers at each carbon number (through C-4) are present. Carbon isotope measurements of the sulfonates show a decrease in the C-13/C-12 ratio with increasing carbon number. The overall objectives of this project are to obtain dime element carbon, hydrogen, and sulfur - intramolecular isotopic analyses of individual sulfonates, and isotopic measurement of carbon and hydrogen of the phosphonates as a group. The Murchison meteorite is the best characterized carbonaceous chondrite with respect to organic chemistry. The finding of organic sulfonates and phosphonates in Murchison is of interest because they are the first well-characterized series of sulfur and phosphorus containing organic compounds found in meteorites. Also, meteorites, comets, and interplanetary dust particles may have been involved in chemical evolution on the early Earth. Because of the critical role of organic phosphorus and sulfur in all living systems, it is particularly interesting to see examples of abiotic syntheses of these classes of compounds. The study of the isotopic composition of the sulfonates and phosphonates can yield insight into their possible interstellar origin as well as their mechanisms of synthesis in the early solar system. Previous isotopic analyses of other classes of organic compounds indigenous to meteorites, e.g., amino acids, carboxylic acids, and hydrocarbons indicate the possibility that interstellar molecules were incorporated into meteorite parent bodies. In these compounds the ratios of heavy to

Injury Severity Score coding: Data analyst v. emerging m-health technology.

PubMed

Spence, R T; Zargaran, E; Hameed, M; Fong, D; Shangguan, E; Martinez, R; Navsaria, P; Nicol, A

2016-09-08

The cost of Abbreviated Injury Scale (AIS) coding has limited its utility in areas of the world with the highest incidence of trauma. We hypothesised that emerging mobile health (m-health) technology could offer a cost-effective alternative to the current gold-standard AIS mechanism in a high-volume trauma centre in South Africa. A prospectively collected sample of consecutive patients admitted following a traumatic injury that required an operation during a 1-month period was selected for the study. AISs and Injury Severity Scores (ISSs) were generated by clinician-entered data using an m-health application (ISS eTHR) as well as by a team of AIS coders at Vancouver General Hospital, Canada (ISS VGH). Rater agreements for ISSs were analysed using Bland-Altman plots with 95% limits of agreement (LoA) and kappa statistics of the ISSs grouped into ordinal categories. Reliability was analysed using a two-way mixed-model intraclass correlation coefficient (ICC). Calibration and discrimination of univariate logistic regression models built to predict in-hospital complications using ISSs coded by the two methods were also compared. Fifty-seven patients were managed operatively during the study period. The mean age of the cohort was 27.2 years (range 14 - 62), and 96.3% were male. The mechanism of injury was penetrating in 93.4% of cases, of which 52.8% were gunshot injuries. The LoA fell within -8.6 - 9.4. The mean ISS difference was 0.4 (95% CI -0.8 - 1.6). The kappa statistic was 0.53. The ICC of the individual ISS was 0.88 (95% CI 0.81 - 0.93) and the categorical ISS was 0.81 (95% CI 0.68 - 0.87). Model performance to predict in-hospital complications using either the ISS eTHR or the ISS VGH was equivalent. ISSs calculated by the eTHR and gold-standard coding were comparable. Emerging m-health technology provides a cost-effective alternative for injury severity scoring.

Bulk hydrogen stable isotope composition of seaweeds: Clear separation between Ulvophyceae and other classes.

PubMed

Carvalho, Matheus C; Carneiro, Pedro Bastos de Macedo; Dellatorre, Fernando Gaspar; Gibilisco, Pablo Ezequiel; Sachs, Julian; Eyre, Bradley D

2017-10-01

Little is known about the bulk hydrogen stable isotope composition (δ 2 H) of seaweeds. This study investigated the bulk δ 2 H in several different seaweed species collected from three different beaches in Brazil, Australia, and Argentina. Here, we show that Ulvophyceae (a group of green algae) had lower δ 2 H values (between -94‰ and -130‰) than red algae (Florideophyceae), brown algae (Phaeophyceae), and species from the class Bryopsidophyceae (another group of green algae). Overall the latter three groups of seaweeds had δ 2 H values between -50‰ and -90‰. These findings were similar at the three different geographic locations. Observed differences in δ 2 H values were probably related to differences in hydrogen (H) metabolism among algal groups, also observed in the δ 2 H values of their lipids. The marked difference between the δ 2 H values of Ulvophyecae and those of the other groups could be useful to trace the food source of food webs in coastal rocky shores, to assess the impacts of green tides on coastal ecosystems, and to help clarify aspects of their phylogeny. However, reference materials for seaweed δ 2 H are required before the full potential of using the δ 2 H of seaweeds for ecological studies can be exploited. © 2017 Phycological Society of America.

u-Constacyclic codes over F_p+u{F}_p and their applications of constructing new non-binary quantum codes

NASA Astrophysics Data System (ADS)

Gao, Jian; Wang, Yongkang

2018-01-01

Structural properties of u-constacyclic codes over the ring F_p+u{F}_p are given, where p is an odd prime and u^2=1. Under a special Gray map from F_p+u{F}_p to F_p^2, some new non-binary quantum codes are obtained by this class of constacyclic codes.

Characterization of Non-coding DNA Satellites Associated with Sweepoviruses (Genus Begomovirus, Geminiviridae) – Definition of a Distinct Class of Begomovirus-Associated Satellites

PubMed Central

Lozano, Gloria; Trenado, Helena P.; Fiallo-Olivé, Elvira; Chirinos, Dorys; Geraud-Pouey, Francis; Briddon, Rob W.; Navas-Castillo, Jesús

2016-01-01

Begomoviruses (family Geminiviridae) are whitefly-transmitted, plant-infecting single-stranded DNA viruses that cause crop losses throughout the warmer parts of the World. Sweepoviruses are a phylogenetically distinct group of begomoviruses that infect plants of the family Convolvulaceae, including sweet potato (Ipomoea batatas). Two classes of subviral molecules are often associated with begomoviruses, particularly in the Old World; the betasatellites and the alphasatellites. An analysis of sweet potato and Ipomoea indica samples from Spain and Merremia dissecta samples from Venezuela identified small non-coding subviral molecules in association with several distinct sweepoviruses. The sequences of 18 clones were obtained and found to be structurally similar to tomato leaf curl virus-satellite (ToLCV-sat, the first DNA satellite identified in association with a begomovirus), with a region with significant sequence identity to the conserved region of betasatellites, an A-rich sequence, a predicted stem–loop structure containing the nonanucleotide TAATATTAC, and a second predicted stem–loop. These sweepovirus-associated satellites join an increasing number of ToLCV-sat-like non-coding satellites identified recently. Although sharing some features with betasatellites, evidence is provided to suggest that the ToLCV-sat-like satellites are distinct from betasatellites and should be considered a separate class of satellites, for which the collective name deltasatellites is proposed. PMID:26925037

hi-class: Horndeski in the Cosmic Linear Anisotropy Solving System

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

Zumalacárregui, Miguel; Bellini, Emilio; Sawicki, Ignacy

We present the public version of hi-class (www.hiclass-code.net), an extension of the Boltzmann code CLASS to a broad ensemble of modifications to general relativity. In particular, hi-class can calculate predictions for models based on Horndeski's theory, which is the most general scalar-tensor theory described by second-order equations of motion and encompasses any perfect-fluid dark energy, quintessence, Brans-Dicke, f ( R ) and covariant Galileon models. hi-class has been thoroughly tested and can be readily used to understand the impact of alternative theories of gravity on linear structure formation as well as for cosmological parameter extraction.

Chromium isotopic anomalies in the Allende meteorite

NASA Technical Reports Server (NTRS)

Papanastassiou, D. A.

1986-01-01

Abundances of the chromium isotopes in terrestrial and bulk meteorite samples are identical to 0.01 percent. However, Ca-Al-rich inclusions from the Allende meteorite show endemic isotopic anomalies in chromium which require at least three nucleosynthetic components. Large anomalies at Cr-54 in a special class of inclusions are correlated with large anomalies at Ca-48 and Ti-50 and provide strong support for a component reflecting neutron-rich nucleosynthesis at nuclear statistical equilibrium. This correlation suggests that materials from very near the core of an exploding massive star may be injected into the interstellar medium.

GLYCAN REDUCTIVE ISOTOPE LABELING (GRIL) FOR QUANTITATIVE GLYCOMICS

PubMed Central

Xia, Baoyun; Feasley, Christa L.; Sachdev, Goverdhan P.; Smith, David F.; Cummings, Richard D.

2009-01-01

Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed Glycan Reductive Isotope Labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [12C6]-aniline and [13C6]-aniline. These dual-labeled aniline-tagged glycans can be recovered by reversed-phase chromatography and quantified based on UV-absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins using this method. This technique allows for linear, relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of Glycomics. PMID:19454239

Treatment of isomers in nucleosynthesis codes

NASA Astrophysics Data System (ADS)

Reifarth, René; Fiebiger, Stefan; Göbel, Kathrin; Heftrich, Tanja; Kausch, Tanja; Köppchen, Christoph; Kurtulgil, Deniz; Langer, Christoph; Thomas, Benedikt; Weigand, Mario

2018-03-01

The decay properties of long-lived excited states (isomers) can have a significant impact on the destruction channels of isotopes under stellar conditions. In sufficiently hot environments, the population of isomers can be altered via thermal excitation or de-excitation. If the corresponding lifetimes are of the same order of magnitude as the typical time scales of the environment, the isomers have to be treated explicitly. We present a general approach to the treatment of isomers in stellar nucleosynthesis codes and discuss a few illustrative examples. The corresponding code is available online at http://exp-astro.de/isomers/.

Plasmids encoding therapeutic agents

DOEpatents

Keener, William K [Idaho Falls, ID

2007-08-07

Plasmids encoding anti-HIV and anti-anthrax therapeutic agents are disclosed. Plasmid pWKK-500 encodes a fusion protein containing DP178 as a targeting moiety, the ricin A chain, an HIV protease cleavable linker, and a truncated ricin B chain. N-terminal extensions of the fusion protein include the maltose binding protein and a Factor Xa protease site. C-terminal extensions include a hydrophobic linker, an L domain motif peptide, a KDEL ER retention signal, another Factor Xa protease site, an out-of-frame buforin II coding sequence, the lacZ.alpha. peptide, and a polyhistidine tag. More than twenty derivatives of plasmid pWKK-500 are described. Plasmids pWKK-700 and pWKK-800 are similar to pWKK-500 wherein the DP178-encoding sequence is substituted by RANTES- and SDF-1-encoding sequences, respectively. Plasmid pWKK-900 is similar to pWKK-500 wherein the HIV protease cleavable linker is substituted by a lethal factor (LF) peptide-cleavable linker.

Thermal Neutron Capture onto the Stable Tungsten Isotopes

NASA Astrophysics Data System (ADS)

Hurst, A. M.; Firestone, R. B.; Sleaford, B. W.; Summers, N. C.; Revay, Zs.; Szentmiklósi, L.; Belgya, T.; Basunia, M. S.; Capote, R.; Choi, H.; Dashdorj, D.; Escher, J.; Krticka, M.; Nichols, A.

2012-02-01

Thermal neutron-capture measurements of the stable tungsten isotopes have been carried out using the guided thermal-neutron beam at the Budapest Reactor. Prompt singles spectra were collected and analyzed using the HYPERMET γ-ray analysis software package for the compound tungsten systems 183W, 184W, and 187W, prepared from isotopically-enriched samples of 182W, 183W, and 186W, respectively. These new data provide both confirmation and new insights into the decay schemes and structure of the tungsten isotopes reported in the Evaluated Gamma-ray Activation File based upon previous elemental analysis. The experimental data have also been compared to Monte Carlo simulations of γ-ray emission following the thermal neutron-capture process using the statistical-decay code DICEBOX. Together, the experimental cross sections and modeledfeeding contribution from the quasi continuum, have been used to determine the total radiative thermal neutron-capture cross sections for the tungsten isotopes and provide improved decay-scheme information for the structural- and neutron-data libraries.

Error-correction coding for digital communications

NASA Astrophysics Data System (ADS)

Clark, G. C., Jr.; Cain, J. B.

This book is written for the design engineer who must build the coding and decoding equipment and for the communication system engineer who must incorporate this equipment into a system. It is also suitable as a senior-level or first-year graduate text for an introductory one-semester course in coding theory. Fundamental concepts of coding are discussed along with group codes, taking into account basic principles, practical constraints, performance computations, coding bounds, generalized parity check codes, polynomial codes, and important classes of group codes. Other topics explored are related to simple nonalgebraic decoding techniques for group codes, soft decision decoding of block codes, algebraic techniques for multiple error correction, the convolutional code structure and Viterbi decoding, syndrome decoding techniques, and sequential decoding techniques. System applications are also considered, giving attention to concatenated codes, coding for the white Gaussian noise channel, interleaver structures for coded systems, and coding for burst noise channels.

Introduction to Chemistry and Applications in Nature of Mass Independent Isotope Effects Special Feature

PubMed Central

Thiemens, Mark H.

2013-01-01

Stable isotope ratio variations are regulated by physical and chemical laws. These rules depend on a relation with mass differences between isotopes. New classes of isotope variation effects that deviate from mass dependent laws, termed mass independent isotope effects, were discovered in 1983 and have a wide range of applications in basic chemistry and nature. In this special edition, new applications of these effects to physical chemistry, solar system origin models, terrestrial atmospheric and biogenic evolution, polar paleo climatology, snowball earth geology, and present day atmospheric sciences are presented. PMID:24167299

Introduction to chemistry and applications in nature of mass independent isotope effects special feature.

PubMed

Thiemens, Mark H

2013-10-29

Stable isotope ratio variations are regulated by physical and chemical laws. These rules depend on a relation with mass differences between isotopes. New classes of isotope variation effects that deviate from mass dependent laws, termed mass independent isotope effects, were discovered in 1983 and have a wide range of applications in basic chemistry and nature. In this special edition, new applications of these effects to physical chemistry, solar system origin models, terrestrial atmospheric and biogenic evolution, polar paleo climatology, snowball earth geology, and present day atmospheric sciences are presented.

Bruyères-le-Châtel Neutron Evaluations of Actinides with the TALYS Code: The Fission Channel

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

Romain, P., E-mail: pascal.romain@cea.fr; Morillon, B.; Duarte, H.

For several years, various neutron evaluations of plutonium and uranium isotopes have been performed at Bruyères-le-Châtel (BRC), from 1 keV up to 30 MeV. Since only nuclear reaction models have been used to produce these evaluations, our approach was named the “Full Model” approach. Total, shape elastic and direct inelastic cross sections were obtained from the coupled channels model using a dispersive optical potential developed for actinides, with a large enough coupling scheme including the lowest octupolar band. All other cross sections were calculated using the Hauser-Feshbach theory (TALYS code) with a pre-equilibrium component above 8–10 MeV. In this paper,more » we focus our attention on the fission channel. More precisely, we will present the BRC contribution to fission modeling and the philosophy adopted in our “Full Model” approach. Performing evaluations with the “Full Model” approach implies the optimization of a large number of model parameters. With increasing neutron incident energy, many residual nuclei produced by nucleon emission also lead to fission. All available experimental data assigned to various fission mechanisms of the same nucleus were used to determine fission barrier parameters. For uranium isotopes, triple-humped fission barriers were required in order to reproduce accurately variations of the experimental fission cross sections. Our BRC fission modeling has shown that the effects of the class II or class III states located in the wells of the fission barrier sometimes provide an anti-resonant transmission rather than a resonant one. Consistent evaluations were produced for a large series of U and Pu isotopes. Resulting files were tested against integral data.« less

The analysis of convolutional codes via the extended Smith algorithm

NASA Technical Reports Server (NTRS)

Mceliece, R. J.; Onyszchuk, I.

1993-01-01

Convolutional codes have been the central part of most error-control systems in deep-space communication for many years. Almost all such applications, however, have used the restricted class of (n,1), also known as 'rate 1/n,' convolutional codes. The more general class of (n,k) convolutional codes contains many potentially useful codes, but their algebraic theory is difficult and has proved to be a stumbling block in the evolution of convolutional coding systems. In this article, the situation is improved by describing a set of practical algorithms for computing certain basic things about a convolutional code (among them the degree, the Forney indices, a minimal generator matrix, and a parity-check matrix), which are usually needed before a system using the code can be built. The approach is based on the classic Forney theory for convolutional codes, together with the extended Smith algorithm for polynomial matrices, which is introduced in this article.

Physics of the Isotopic Dependence of Galactic Cosmic Ray Fluence Behind Shielding

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Saganti, Premkumar B.; Hu, Xiao-Dong; Kim, Myung-Hee Y.; Cleghorn, Timothy F.; Wilson, John W.; Tripathi, Ram K.; Zeitlin, Cary J.

2003-01-01

For over 25 years, NASA has supported the development of space radiation transport models for shielding applications. The NASA space radiation transport model now predicts dose and dose equivalent in Earth and Mars orbit to an accuracy of plus or minus 20%. However, because larger errors may occur in particle fluence predictions, there is interest in further assessments and improvements in NASA's space radiation transport model. In this paper, we consider the effects of the isotopic composition of the primary galactic cosmic rays (GCR) and the isotopic dependence of nuclear fragmentation cross-sections on the solution to transport models used for shielding studies. Satellite measurements are used to describe the isotopic composition of the GCR. Using NASA's quantum multiple-scattering theory of nuclear fragmentation (QMSFRG) and high-charge and energy (HZETRN) transport code, we study the effect of the isotopic dependence of the primary GCR composition and secondary nuclei on shielding calculations. The QMSFRG is shown to accurately describe the iso-spin dependence of nuclear fragmentation. The principal finding of this study is that large errors (plus or minus 100%) will occur in the mass-fluence spectra when comparing transport models that use a complete isotope grid (approximately 170 ions) to ones that use a reduced isotope grid, for example the 59 ion-grid used in the HZETRN code in the past, however less significant errors (less than 20%) occur in the elemental-fluence spectra. Because a complete isotope grid is readily handled on small computer workstations and is needed for several applications studying GCR propagation and scattering, it is recommended that they be used for future GCR studies.

School and class-level variations and patterns of physical activity: a multilevel analysis of Danish high school students.

PubMed

Steenholt, Carina Bjørnskov; Pisinger, Veronica Sofie Clara; Danquah, Ida Høgstedt; Tolstrup, Janne Schurmann

2018-02-14

There is limited knowledge of physical activity (PA) patterns among high school students. High schools plays an important role as context for the students, but it is uncertain to what extent schools influence student participation in PA during leisure time. The purpose of this study is to describe patterns of PA and assess variations between schools and classes in PA, in a large cohort of Danish high school students. Self-reported cross-sectional data came from The Danish National Youth Study, comprising a total of 70,674 students attending 119 different schools and 3213 classes. Multilevel logistic regressions were applied to evaluate the association between socio-demographic variables and patterns of PA, and to assess the impact of schools and classes on PA measures. Students whose parents have achieved a lower level of education, older students and girls of perceived ethnic minority generally participated less in several forms of PA during leisure time. Substantial variations between schools were observed in terms of participation in PA at school during leisure time and in terms of use of active transportation to and from school. The school-level accounted for 9% (intra-class correlation coefficient (ICC) = 0.09 (95% CI: 0.06-0.11)) and 8% (ICC = 0.08 (95% CI: 0.07-0.11)) of the variation for participation in PA during leisure time and active transportation. Overall, students whose parents achieved a lower level of education, older students and girls of perceived ethnic minority represent vulnerable groups in relation to participation in several forms of PA during leisure time. The ICCs indicate that schools, in particular, have the potential to influence participation in PA at school during leisure time and active transportation to and from school. Thus, high schools should encourage and facilitate activities aimed at engaging students in PA during leisure time as well as encourage active transportation.

Quantitative isomer-specific N-glycan fingerprinting using isotope coded labeling and high performance liquid chromatography-electrospray ionization-mass spectrometry with graphitic carbon stationary phase.

PubMed

Michael, Claudia; Rizzi, Andreas M

2015-02-27

Glycan reductive isotope labeling (GRIL) using (12)C6-/(13)C6-aniline as labeling reagent is reported with the aim of quantitative N-glycan fingerprinting. Porous graphitized carbon (PGC) as stationary phase in capillary scale HPLC coupled to electrospray mass spectrometry with time of flight analyzer was applied for the determination of labeled N-glycans released from glycoproteins. The main benefit of using stable isotope-coding in the context of comparative glycomics lies in the improved accuracy and precision of the quantitative analysis in combined samples and in the potential of correcting for structure-dependent incomplete enzymatic release of oligosaccharides when comparing identical target proteins. The method was validated with respect to mobile phase parameters, reproducibility, accuracy, linearity and limit of detection/quantification (LOD/LOQ) using test glycoproteins. It is shown that the developed method is capable of determining relative amounts of N-glycans (including isomers) comparing two samples in one single HPLC-MS run. The analytical potential and usefulness of GRIL in combination with PGC-ESI-TOF-MS is demonstrated comparing glycosylation in human monoclonal antibodies produced in Chinese hamster ovary cells (CHO) and hybridoma cell lines. Copyright © 2015 Elsevier B.V. All rights reserved.

Isotopic anomalies from neutron reactions during explosive carbon burning

NASA Technical Reports Server (NTRS)

Lee, T.; Schramm, D. N.; Wefel, J. P.; Blake, J. B.

1978-01-01

The possibility that the newly discovered correlated isotopic anomalies for heavy elements in the Allende meteorite were synthesized in the secondary neutron capture episode during the explosive carbon burning, the possible source of the O-16 and Al-26 anomalies, is examined. Explosive carbon burning calculations under typical conditions were first performed to generate time profiles of temperature, density, and free particle concentrations. These quantities were inputted into a general neutron capture code which calculates the resulting isotopic pattern from exposing the preexisting heavy seed nuclei to these free particles during the explosive carbon burning conditions. The interpretation avoids the problem of the Sr isotopic data and may resolve the conflict between the time scales inferred from 1-129, Pu-244, and Al-26.

Isotopic Effects in Nuclear Fragmentation and GCR Transport Problems

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.

2002-01-01

Improving the accuracy of the galactic cosmic ray (GCR) environment and transport models is an important goal in preparing for studies of the projected risks and the efficiency of potential mitigations methods for space exploration. In this paper we consider the effects of the isotopic composition of the primary cosmic rays and the isotopic dependence of nuclear fragmentation cross sections on GCR transport models. Measurements are used to describe the isotopic composition of the GCR including their modulation throughout the solar cycle. The quantum multiple-scattering approach to nuclear fragmentation (QMSFRG) is used as the data base generator in order to accurately describe the odd-even effect in fragment production. Using the Badhwar and O'Neill GCR model, the QMSFRG model and the HZETRN transport code, the effects of the isotopic dependence of the primary GCR composition and on fragment production for transport problems is described for a complete GCR isotopic-grid. The principle finding of this study is that large errors ( 100%) will occur in the mass-flux spectra when comparing the complete isotopic-grid (141 ions) to a reduced isotopic-grid (59 ions), however less significant errors 30%) occur in the elemental-flux spectra. Because the full isotopic-grid is readily handled on small computer work-stations, it is recommended that they be used for future GCR studies.

Cleavable DNA-protein hybrid molecular beacon: A novel efficient signal translator for sensitive fluorescence anisotropy bioassay.

PubMed

Hu, Pan; Yang, Bin

2016-01-15

Due to its unique features such as high sensitivity, homogeneous format, and independence on fluorescent intensity, fluorescence anisotropy (FA) assay has become a hotspot of study in oligonucleotide-based bioassays. However, until now most FA probes require carefully customized structure designs, and thus are neither generalizable for different sensing systems nor effective to obtain sufficient signal response. To address this issue, a cleavable DNA-protein hybrid molecular beacon was successfully engineered for signal amplified FA bioassay, via combining the unique stable structure of molecular beacon and the large molecular mass of streptavidin. Compared with single DNA strand probe or conventional molecular beacon, the DNA-protein hybrid molecular beacon exhibited a much higher FA value, which was potential to obtain high signal-background ratio in sensing process. As proof-of-principle, this novel DNA-protein hybrid molecular beacon was further applied for FA bioassay using DNAzyme-Pb(2+) as a model sensing system. This FA assay approach could selectively detect as low as 0.5nM Pb(2+) in buffer solution, and also be successful for real samples analysis with good recovery values. Compatible with most of oligonucleotide probes' designs and enzyme-based signal amplification strategies, the molecular beacon can serve as a novel signal translator to expand the application prospect of FA technology in various bioassays. Copyright © 2015 Elsevier B.V. All rights reserved.

New nonbinary quantum codes with larger distance constructed from BCH codes over 𝔽q2

NASA Astrophysics Data System (ADS)

Xu, Gen; Li, Ruihu; Fu, Qiang; Ma, Yuena; Guo, Luobin

2017-03-01

This paper concentrates on construction of new nonbinary quantum error-correcting codes (QECCs) from three classes of narrow-sense imprimitive BCH codes over finite field 𝔽q2 (q ≥ 3 is an odd prime power). By a careful analysis on properties of cyclotomic cosets in defining set T of these BCH codes, the improved maximal designed distance of these narrow-sense imprimitive Hermitian dual-containing BCH codes is determined to be much larger than the result given according to Aly et al. [S. A. Aly, A. Klappenecker and P. K. Sarvepalli, IEEE Trans. Inf. Theory 53, 1183 (2007)] for each different code length. Thus families of new nonbinary QECCs are constructed, and the newly obtained QECCs have larger distance than those in previous literature.

A genetic scale of reading frame coding.

PubMed

Michel, Christian J

2014-08-21

The reading frame coding (RFC) of codes (sets) of trinucleotides is a genetic concept which has been largely ignored during the last 50 years. A first objective is the definition of a new and simple statistical parameter PrRFC for analysing the probability (efficiency) of reading frame coding (RFC) of any trinucleotide code. A second objective is to reveal different classes and subclasses of trinucleotide codes involved in reading frame coding: the circular codes of 20 trinucleotides and the bijective genetic codes of 20 trinucleotides coding the 20 amino acids. This approach allows us to propose a genetic scale of reading frame coding which ranges from 1/3 with the random codes (RFC probability identical in the three frames) to 1 with the comma-free circular codes (RFC probability maximal in the reading frame and null in the two shifted frames). This genetic scale shows, in particular, the reading frame coding probabilities of the 12,964,440 circular codes (PrRFC=83.2% in average), the 216 C(3) self-complementary circular codes (PrRFC=84.1% in average) including the code X identified in eukaryotic and prokaryotic genes (PrRFC=81.3%) and the 339,738,624 bijective genetic codes (PrRFC=61.5% in average) including the 52 codes without permuted trinucleotides (PrRFC=66.0% in average). Otherwise, the reading frame coding probabilities of each trinucleotide code coding an amino acid with the universal genetic code are also determined. The four amino acids Gly, Lys, Phe and Pro are coded by codes (not circular) with RFC probabilities equal to 2/3, 1/2, 1/2 and 2/3, respectively. The amino acid Leu is coded by a circular code (not comma-free) with a RFC probability equal to 18/19. The 15 other amino acids are coded by comma-free circular codes, i.e. with RFC probabilities equal to 1. The identification of coding properties in some classes of trinucleotide codes studied here may bring new insights in the origin and evolution of the genetic code. Copyright © 2014 Elsevier

C++ Coding Standards and Style Guide

NASA Technical Reports Server (NTRS)

Hughes, Steven; Jun, Linda; Shoan, Wendy

2005-01-01

This document is based on the "C Style Guide" (SEL-94-003). It contains recommendations for C++ implementations that build on, or in some cases replace, the style described in the C style guide. Style guidelines on any topics that are not covered in this document can be found in the "C Style Guide." An attempt has been made to indicate when these recommendations are just guidelines or suggestions versus when they are more strongly encouraged. Using coding standards makes code easier to read and maintain. General principles that maximize the readability and maintainability of C++ are: (1) Organize classes using encapsulation and information hiding techniques. (2) Enhance readability through the use of indentation and blank lines. (3) Add comments to header files to help users of classes. (4) Add comments to implementation files to help maintainers of classes. (5) Create names that are meaningful and readable.

MARC Coding of DDC for Subject Retrieval.

ERIC Educational Resources Information Center

Wajenberg, Arnold S.

1983-01-01

Recommends an expansion of MARC codes for decimal class numbers to enhance automated subject retrieval. Five values for a second indicator and two new subfields are suggested for encoding hierarchical relationships among decimal class numbers. Additional subfields are suggested to enhance retrieval through analysis of synthesized numbers in…

Distinct Pseudomonas type-III effectors use a cleavable transit peptide to target chloroplasts.

PubMed

Li, Guangyong; Froehlich, John E; Elowsky, Christian; Msanne, Joseph; Ostosh, Andrew C; Zhang, Chi; Awada, Tala; Alfano, James R

2014-01-01

The pathogen Pseudomonas syringae requires a type-III protein secretion system and the effector proteins it injects into plant cells for pathogenesis. The primary role for P. syringae type-III effectors is the suppression of plant immunity. The P. syringae pv. tomato DC3000 HopK1 type-III effector was known to suppress the hypersensitive response (HR), a programmed cell death response associated with effector-triggered immunity. Here we show that DC3000 hopK1 mutants are reduced in their ability to grow in Arabidopsis, and produce reduced disease symptoms. Arabidopsis transgenically expressing HopK1 are reduced in PAMP-triggered immune responses compared with wild-type plants. An N-terminal region of HopK1 shares similarity with the corresponding region in the well-studied type-III effector AvrRps4; however, their C-terminal regions are dissimilar, indicating that they have different effector activities. HopK1 is processed in planta at the same processing site found in AvrRps4. The processed forms of HopK1 and AvrRps4 are chloroplast localized, indicating that the shared N-terminal regions of these type-III effectors represent a chloroplast transit peptide. The HopK1 contribution to virulence and the ability of HopK1 and AvrRps4 to suppress immunity required their respective transit peptides, but the AvrRps4-induced HR did not. Our results suggest that a primary virulence target of these type-III effectors resides in chloroplasts, and that the recognition of AvrRps4 by the plant immune system occurs elsewhere. Moreover, our results reveal that distinct type-III effectors use a cleavable transit peptide to localize to chloroplasts, and that targets within this organelle are important for immunity. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Comparison of deterministic and stochastic approaches for isotopic concentration and decay heat uncertainty quantification on elementary fission pulse

NASA Astrophysics Data System (ADS)

Lahaye, S.; Huynh, T. D.; Tsilanizara, A.

2016-03-01

Uncertainty quantification of interest outputs in nuclear fuel cycle is an important issue for nuclear safety, from nuclear facilities to long term deposits. Most of those outputs are functions of the isotopic vector density which is estimated by fuel cycle codes, such as DARWIN/PEPIN2, MENDEL, ORIGEN or FISPACT. CEA code systems DARWIN/PEPIN2 and MENDEL propagate by two different methods the uncertainty from nuclear data inputs to isotopic concentrations and decay heat. This paper shows comparisons between those two codes on a Uranium-235 thermal fission pulse. Effects of nuclear data evaluation's choice (ENDF/B-VII.1, JEFF-3.1.1 and JENDL-2011) is inspected in this paper. All results show good agreement between both codes and methods, ensuring the reliability of both approaches for a given evaluation.

School Dress Codes and Uniform Policies.

ERIC Educational Resources Information Center

Anderson, Wendell

2002-01-01

Opinions abound on what students should wear to class. Some see student dress as a safety issue; others see it as a student-rights issue. The issue of dress codes and uniform policies has been tackled in the classroom, the boardroom, and the courtroom. This Policy Report examines the whole fabric of the debate on dress codes and uniform policies…

Progress in tropical isotope dendroclimatology

NASA Astrophysics Data System (ADS)

Evans, M. N.; Schrag, D. P.; Poussart, P. F.; Anchukaitis, K. J.

2005-12-01

The terrestrial tropics remain an important gap in the growing high resolution proxy network used to characterize the mean state and variability of the hydrological cycle. Here we review early efforts to develop a new class of proxy paleorainfall/humidity indicators using intraseasonal to interannual-resolution stable isotope data from tropical trees. The approach invokes a recently published model of oxygen isotopic composition of alpha-cellulose, rapid methods for cellulose extraction from raw wood, and continuous flow isotope ratio mass spectrometry to develop proxy chronological, rainfall and growth rate estimates from tropical trees, even those lacking annual rings. Isotopically-derived age models may be confirmed for modern intervals using trees of known age, radiocarbon measurements, direct measurements of tree diameter, and time series replication. Studies are now underway at a number of laboratories on samples from Costa Rica, northwestern coastal Peru, Indonesia, Thailand, New Guinea, Paraguay, Brazil, India, and the South American Altiplano. Improved sample extraction chemistry and online pyrolysis techniques should increase sample throughput, precision, and time series replication. Statistical calibration together with simple forward modeling based on the well-observed modern period can provide for objective interpretation of the data. Ultimately, replicated data series with well-defined uncertainties can be entered into multiproxy efforts to define aspects of tropical hydrological variability associated with ENSO, the meridional overturning circulation, and the monsoon systems.

A new algorithm to handle finite nuclear mass effects in electronic calculations: the ISOTOPE program.

PubMed

Gonçalves, Cristina P; Mohallem, José R

2004-11-15

We report the development of a simple algorithm to modify quantum chemistry codes based on the LCAO procedure, to account for the isotope problem in electronic structure calculations. No extra computations are required compared to standard Born-Oppenheimer calculations. An upgrade of the Gamess package called ISOTOPE is presented, and its applicability is demonstrated in some examples.

Detection of adenoviruses in shellfish by means of conventional-PCR, nested-PCR, and integrated cell culture PCR (ICC/PCR).

PubMed

Rigotto, C; Sincero, T C M; Simões, C M O; Barardi, C R M

2005-01-01

We tested three PCR based methodologies to detect adenoviruses associated with cultivated oysters. Conventional-PCR, nested-PCR, and integrated cell culture-PCR (ICC/PCR) were first optimized using oysters seeded with know amounts of Adenovirus serotype 5 (Ad5). The maximum sensitivity for Ad5 detection was determined for each method, and then used to detect natural adenovirus contamination in oysters from three aquiculture farms in Florianopolis, Santa Catarina State, Brazil, over a period of 6 months. The results showed that the nested-PCR was more sensitive (limit of detection: 1.2 PFU/g of tissue) than conventional-PCR and ICC-PCR (limit of detection for both: 1.2 x 10(2)PFU/g of tissue) for detection of Ad5 in oyster extracts. Nested-PCR was able to detect 90% of Ad5 contamination in harvested oyster samples, while conventional-PCR was unable to detect Ad5 in any of the samples. The present work suggests that detection of human adenoviruses can be used as a tool to monitor the presence of human viruses in marine environments where shellfish grow, and that nested-PCR is the method of choice.

Geochemically distinct carbon isotope distributions in Allochromatium vinosum DSM 180T grown photoautotrophically and photoheterotrophically.

PubMed

Tang, T; Mohr, W; Sattin, S R; Rogers, D R; Girguis, P R; Pearson, A

2017-03-01

Anoxygenic, photosynthetic bacteria are common at redox boundaries. They are of interest in microbial ecology and geosciences through their role in linking the carbon, sulfur, and iron cycles, yet much remains unknown about how their flexible carbon metabolism-permitting either autotrophic or heterotrophic growth-is recorded in the bulk sedimentary and lipid biomarker records. Here, we investigated patterns of carbon isotope fractionation in a model photosynthetic sulfur-oxidizing bacterium, Allochromatium vinosum DSM180 T . In one treatment, A. vinosum was grown with CO 2 as the sole carbon source, while in a second treatment, it was grown on acetate. Different intracellular isotope patterns were observed for fatty acids, phytol, individual amino acids, intact proteins, and total RNA between the two experiments. Photoautotrophic CO 2 fixation yielded typical isotopic ordering for the lipid biomarkers: δ 13 C values of phytol > n-alkyl lipids. In contrast, growth on acetate greatly suppressed intracellular isotopic heterogeneity across all molecular classes, except for a marked 13 C-depletion in phytol. This caused isotopic "inversion" in the lipids (δ 13 C values of phytol < n-alkyl lipids). The finding suggests that inverse δ 13 C patterns of n-alkanes and pristane/phytane in the geologic record may be at least in part a signal for photoheterotrophy. In both experimental scenarios, the relative isotope distributions could be predicted from an isotope flux-balance model, demonstrating that microbial carbon metabolisms can be interrogated by combining compound-specific stable isotope analysis with metabolic modeling. Isotopic differences among molecular classes may be a means of fingerprinting microbial carbon metabolism, both in the modern environment and the geologic record. © 2017 John Wiley & Sons Ltd.

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications.

PubMed

Shaul, Shaul; Berel, Dror; Benjamini, Yoav; Graur, Dan

2010-01-01

It has been suggested that tRNA acceptor stems specify an operational RNA code for amino acids. In the last 20 years several attributes of the putative code have been elucidated for a small number of model organisms. To gain insight about the ensemble attributes of the code, we analyzed 4925 tRNA sequences from 102 bacterial and 21 archaeal species. Here, we used a classification and regression tree (CART) methodology, and we found that the degrees of degeneracy or specificity of the RNA codes in both Archaea and Bacteria differ from those of the genetic code. We found instances of taxon-specific alternative codes, i.e., identical acceptor stem determinants encrypting different amino acids in different species, as well as instances of ambiguity, i.e., identical acceptor stem determinants encrypting two or more amino acids in the same species. When partitioning the data by class of synthetase, the degree of code ambiguity was significantly reduced. In cryptographic terms, a plausible interpretation of this result is that the class distinction in synthetases is an essential part of the decryption rules for resolving the subset of RNA code ambiguities enciphered by identical acceptor stem determinants of tRNAs acylated by enzymes belonging to the two classes. In evolutionary terms, our findings lend support to the notion that in the pre-DNA world, interactions between tRNA acceptor stems and synthetases formed the basis for the distinction between the two classes; hence, ambiguities in the ancient RNA code were pivotal for the fixation of these enzymes in the genomes of ancestral prokaryotes.

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications

PubMed Central

Shaul, Shaul; Berel, Dror; Benjamini, Yoav; Graur, Dan

2010-01-01

It has been suggested that tRNA acceptor stems specify an operational RNA code for amino acids. In the last 20 years several attributes of the putative code have been elucidated for a small number of model organisms. To gain insight about the ensemble attributes of the code, we analyzed 4925 tRNA sequences from 102 bacterial and 21 archaeal species. Here, we used a classification and regression tree (CART) methodology, and we found that the degrees of degeneracy or specificity of the RNA codes in both Archaea and Bacteria differ from those of the genetic code. We found instances of taxon-specific alternative codes, i.e., identical acceptor stem determinants encrypting different amino acids in different species, as well as instances of ambiguity, i.e., identical acceptor stem determinants encrypting two or more amino acids in the same species. When partitioning the data by class of synthetase, the degree of code ambiguity was significantly reduced. In cryptographic terms, a plausible interpretation of this result is that the class distinction in synthetases is an essential part of the decryption rules for resolving the subset of RNA code ambiguities enciphered by identical acceptor stem determinants of tRNAs acylated by enzymes belonging to the two classes. In evolutionary terms, our findings lend support to the notion that in the pre-DNA world, interactions between tRNA acceptor stems and synthetases formed the basis for the distinction between the two classes; hence, ambiguities in the ancient RNA code were pivotal for the fixation of these enzymes in the genomes of ancestral prokaryotes. PMID:19952117

Code-Mixing as a Bilingual Instructional Strategy

ERIC Educational Resources Information Center

Jiang, Yih-Lin Belinda; García, Georgia Earnest; Willis, Arlette Ingram

2014-01-01

This study investigated code-mixing practices, specifically the use of L2 (English) in an L1 (Chinese) class in a U.S. bilingual program. Our findings indicate that the code-mixing practices made and prompted by the teacher served five pedagogical functions: (a) to enhance students' bilingualism and bilingual learning, (b) to review and…

Data-driven Approaches to Teaching Stable Isotopes in Hydrology and Environmental Geochemistry

NASA Astrophysics Data System (ADS)

Jefferson, A.; Merchant, W. R.; Dees, D.; Griffith, E. M.; Ortiz, J. D.

2016-12-01

Stable isotopes have revolutionized our understanding of watershed hydrology and other earth science processes. However, students may struggle to correctly interpret isotope ratios and few students understand how isotope measurements are made. New laser-based technologies lower the barrier to entry for giving students hands on experience with isotope measurements and data analysis. We hypothesizedthat integrating such activities into the curriculum would increase student content knowledge, perceptions, and motivation to learn. This project assessed the impact that different pedagogical approaches have on student learning of stable isotope concepts in upper-division geoscience courses. An isotope hydrograph separation module was developed and taught for a Watershed Hydrology course, and a Rayleigh distillation activity was developed and deployed for Environmental Geochemistry and Sedimentology/Stratigraphy classes. Groups of students were exposed to this content via (1) a lecture-only format; (2) a paper-based data analysis activity; and (3) hands-on data collection, sometimes including spectrometer analysis. Pre- and post-tests measured gains in content knowledge while approaches to learning and motivational questionnaires instruments were used to identify the effects of the classroom environment on learning approaches and motivation. Focus group interviews were also conducted to verify the quantitative data. All instructional styles appear to be equally effective at increasing student content knowledge of stable isotopes in the geosciences, but future studies need to move beyond "exam question" style assessment of learning. Our results may reflect that hands-on experiences are not new to upper-level geosciences students, because this is the way that many classes are taught in the geosciences (labs, field trips). Thus, active learning approaches may not have had the impact they would with other groups. The "messiness" of hands-on activities and authentic research

A unified model of the standard genetic code.

PubMed

José, Marco V; Zamudio, Gabriel S; Morgado, Eberto R

2017-03-01

The Rodin-Ohno (RO) and the Delarue models divide the table of the genetic code into two classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the tRNA acceptor stem, respectively. These models are asymmetric but they are biologically meaningful. On the other hand, the standard genetic code (SGC) can be derived from the primeval RNY code (R stands for purines, Y for pyrimidines and N any of them). In this work, the RO-model is derived by means of group actions, namely, symmetries represented by automorphisms, assuming that the SGC originated from a primeval RNY code. It turns out that the RO-model is symmetric in a six-dimensional (6D) hypercube. Conversely, using the same automorphisms, we show that the RO-model can lead to the SGC. In addition, the asymmetric Delarue model becomes symmetric by means of quotient group operations. We formulate isometric functions that convert the class aaRS I into the class aaRS II and vice versa. We show that the four polar requirement categories display a symmetrical arrangement in our 6D hypercube. Altogether these results cannot be attained, neither in two nor in three dimensions. We discuss the present unified 6D algebraic model, which is compatible with both the SGC (based upon the primeval RNY code) and the RO-model.

Biological Information Transfer Beyond the Genetic Code: The Sugar Code

NASA Astrophysics Data System (ADS)

Gabius, H.-J.

In the era of genetic engineering, cloning, and genome sequencing the focus of research on the genetic code has received an even further accentuation in the public eye. In attempting, however, to understand intra- and intercellular recognition processes comprehensively, the two biochemical dimensions established by nucleic acids and proteins are not sufficient to satisfactorily explain all molecular events in, for example, cell adhesion or routing. The consideration of further code systems is essential to bridge this gap. A third biochemical alphabet forming code words with an information storage capacity second to no other substance class in rather small units (words, sentences) is established by monosaccharides (letters). As hardware oligosaccharides surpass peptides by more than seven orders of magnitude in the theoretical ability to build isomers, when the total of conceivable hexamers is calculated. In addition to the sequence complexity, the use of magnetic resonance spectroscopy and molecular modeling has been instrumental in discovering that even small glycans can often reside in not only one but several distinct low-energy conformations (keys). Intriguingly, conformers can display notably different capacities to fit snugly into the binding site of nonhomologous receptors (locks). This process, experimentally verified for two classes of lectins, is termed "differential conformer selection." It adds potential for shifts of the conformer equilibrium to modulate ligand properties dynamically and reversibly to the well-known changes in sequence (including anomeric positioning and linkage points) and in pattern of substitution, for example, by sulfation. In the intimate interplay with sugar receptors (lectins, enzymes, and antibodies) the message of coding units of the sugar code is deciphered. Their recognition will trigger postbinding signaling and the intended biological response. Knowledge about the driving forces for the molecular rendezvous, i

Combinatorial effects on clumped isotopes and their significance in biogeochemistry

NASA Astrophysics Data System (ADS)

Yeung, Laurence Y.

2016-01-01

The arrangement of isotopes within a collection of molecules records their physical and chemical histories. Clumped-isotope analysis interrogates these arrangements, i.e., how often rare isotopes are bound together, which in many cases can be explained by equilibrium and/or kinetic isotope fractionation. However, purely combinatorial effects, rooted in the statistics of pairing atoms in a closed system, are also relevant, and not well understood. Here, I show that combinatorial isotope effects are most important when two identical atoms are neighbors on the same molecule (e.g., O2, N2, and D-D clumping in CH4). When the two halves of an atom pair are either assembled with different isotopic preferences or drawn from different reservoirs, combinatorial effects cause depletions in clumped-isotope abundance that are most likely between zero and -1‰, although they could potentially be -10‰ or larger for D-D pairs. These depletions are of similar magnitude, but of opposite sign, to low-temperature equilibrium clumped-isotope effects for many small molecules. Enzymatic isotope-pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect, although it is not limited to biological reactions. Chemical-kinetic isotope effects, which are related to a bond-forming transition state, arise independently and express second-order combinatorial effects related to the abundance of the rare isotope. Heteronuclear moeties (e.g., Csbnd O and Csbnd H), are insensitive to direct combinatorial influences, but secondary combinatorial influences are evident. In general, both combinatorial and chemical-kinetic factors are important for calculating and interpreting clumped-isotope signatures of kinetically controlled reactions. I apply this analytical framework to isotope-pairing reactions relevant to geochemical oxygen, carbon, and nitrogen cycling that may be influenced by combinatorial

pH-Cleavable Nucleoside Lipids: A New Paradigm for Controlling the Stability of Lipid-Based Delivery Systems.

PubMed

Oumzil, Khalid; Benizri, Sébastien; Tonelli, Giovanni; Staedel, Cathy; Appavoo, Ananda; Chaffanet, Max; Navailles, Laurence; Barthélémy, Philippe

2015-11-01

Lipid-based delivery systems are an established technology with considerable clinical acceptance and several applications in human. Herein, we report the design, synthesis and evaluation of novel orthoester nucleoside lipids (ONLs) for the modulation of liposome stability. The ONLs contain head groups with 3'-orthoester nucleoside derivatives featuring positive or negative charges. The insertion of the orthoester function in the NL structures allows the formation of pH-sensitive liposomes. ONL-based liposomes can be hydrolyzed to provide nontoxic products, including nucleoside derivatives and hexadecanol. To allow the release to be tunable at different hydrolysis rates, the charge of the polar head structure is modulated, and the head group can be released at a biologically relevant pH. Crucially, when ONLs are mixed with natural phosphocholine lipids (PC), the resultant liposome evolves toward the formation of a hexadecanol/PC lamellar system. Biological evaluation shows that stable nucleic acid lipid particles (SNALPs) formulated with ONLs and siRNAs can effectively enter into tumor cells and release their nucleic acid payload in response to an intracellular acidic environment. This results in a much higher antitumor activity than conventional SNALPs. The ability to use pH-cleavable nucleolipids to control the stability of lipid-based delivery systems represents a promising approach for the intracellular delivery of drug cargos. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides*

PubMed Central

Giese, Sven H.; Fischer, Lutz; Rappsilber, Juri

2016-01-01

Cross-linking/mass spectrometry resolves protein–protein interactions or protein folds by help of distance constraints. Cross-linkers with specific properties such as isotope-labeled or collision-induced dissociation (CID)-cleavable cross-linkers are in frequent use to simplify the identification of cross-linked peptides. Here, we analyzed the mass spectrometric behavior of 910 unique cross-linked peptides in high-resolution MS1 and MS2 from published data and validate the observation by a ninefold larger set from currently unpublished data to explore if detailed understanding of their fragmentation behavior would allow computational delivery of information that otherwise would be obtained via isotope labels or CID cleavage of cross-linkers. Isotope-labeled cross-linkers reveal cross-linked and linear fragments in fragmentation spectra. We show that fragment mass and charge alone provide this information, alleviating the need for isotope-labeling for this purpose. Isotope-labeled cross-linkers also indicate cross-linker-containing, albeit not specifically cross-linked, peptides in MS1. We observed that acquisition can be guided to better than twofold enrich cross-linked peptides with minimal losses based on peptide mass and charge alone. By help of CID-cleavable cross-linkers, individual spectra with only linear fragments can be recorded for each peptide in a cross-link. We show that cross-linked fragments of ordinary cross-linked peptides can be linearized computationally and that a simplified subspectrum can be extracted that is enriched in information on one of the two linked peptides. This allows identifying candidates for this peptide in a simplified database search as we propose in a search strategy here. We conclude that the specific behavior of cross-linked peptides in mass spectrometers can be exploited to relax the requirements on cross-linkers. PMID:26719564

Reactive transport modeling of Li isotope fractionation

NASA Astrophysics Data System (ADS)

Wanner, C.; Sonnenthal, E. L.

2013-12-01

The fractionation of Li isotopes has been used as a proxy for interaction processes between silicate rocks and any kind of fluids. In particular, Li isotope measurements are powerful because Li is almost exclusively found in silicate minerals. Moreover, the two stable Li isotopes, 6Li and 7Li, differ by 17% in mass introducing a large mass dependent isotope fractionation even at high temperature. Typical applications include Li isotope measurements along soil profiles and of river waters to track silicate weathering patterns and Li isotope measurements of geothermal wells and springs to assess water-rock interaction processes in geothermal systems. For this contribution we present a novel reactive transport modeling approach for the simulation of Li isotope fractionation using the code TOUGHREACT [1]. It is based on a 6Li-7Li solid solution approach similar to the one recently described for simulating Cr isotope fractionation [2]. Model applications include the simulation of granite weathering along a 1D flow path as well as the simulation of a column experiment related to an enhanced geothermal system. Results show that measured δ7Li values are mainly controlled by (i) the degree of interaction between Li bearing primary silicate mineral phases (e.g., micas, feldspars) and the corresponding fluid, (ii) the Li isotope fractionation factor during precipitation of secondary mineral phases (e.g., clays), (iii) the Li concentration in primary and secondary Li bearing mineral phases and (iv) the proportion of dissolved Li that adsorbs to negatively charged surfaces (e.g., clays, Fe/Al-hydroxides). To date, most of these parameters are not very well constrained. Reactive transport modeling thus currently has to rely on many assumptions. Nevertheless, such models are powerful because they are the only viable option if individual contributions of all potential processes on the resulting (i.e., measured) Li isotopic ratio have to be quantitatively assessed. Accordingly, we

Low Density Parity Check Codes Based on Finite Geometries: A Rediscovery and More

NASA Technical Reports Server (NTRS)

Kou, Yu; Lin, Shu; Fossorier, Marc

1999-01-01

Low density parity check (LDPC) codes with iterative decoding based on belief propagation achieve astonishing error performance close to Shannon limit. No algebraic or geometric method for constructing these codes has been reported and they are largely generated by computer search. As a result, encoding of long LDPC codes is in general very complex. This paper presents two classes of high rate LDPC codes whose constructions are based on finite Euclidean and projective geometries, respectively. These classes of codes a.re cyclic and have good constraint parameters and minimum distances. Cyclic structure adows the use of linear feedback shift registers for encoding. These finite geometry LDPC codes achieve very good error performance with either soft-decision iterative decoding based on belief propagation or Gallager's hard-decision bit flipping algorithm. These codes can be punctured or extended to obtain other good LDPC codes. A generalization of these codes is also presented.

Isotope-coded, iodoacetamide-based reagent to determine individual cysteine pKa values by MALDI-TOF mass spectrometry

PubMed Central

Nelson, Kimberly J.; Day, Amanda E.; Zeng, Bubing B.; King, S. Bruce; Poole, Leslie B.

2008-01-01

Cysteine reactivity in enzymes is imparted to a large extent by the stabilization of the deprotonated form of the reduced cysteine (i.e. the thiolate) within the active site. While this is likely to be an important chemical attribute of many thiol-based enzymes including cysteine-dependent peroxidases (peroxiredoxins) and proteases, only relatively few pKa values have been determined experimentally. Presented here is a new technique for determining the pKa value of cysteine residues through quantitative mass spectrometry following chemical modification with an iodoacetamide-based reagent over a range of pH buffers. This isotope-coded reagent, N-phenyl iodoacetamide (iodoacetanilide), is readily prepared in deuterated (d5) and protiated (d0) versions and is more reactive toward free cysteine than is iodoacetamide. Using this approach, the pKa values for the two cysteine residues in Escherichia coli thioredoxin were determined to be 6.5 and > 10, in good agreement with previous reports using chemical modification approaches. This technique allows the pKa of specific cysteine residues to be determined in a clear, fast, and simple manner and, because cysteine residues on separate tryptic peptides are measured separately, is not complicated by the presence of multiple cysteines within the protein of interest. PMID:18162165

A novel class sensitive hashing technique for large-scale content-based remote sensing image retrieval

NASA Astrophysics Data System (ADS)

Reato, Thomas; Demir, Begüm; Bruzzone, Lorenzo

2017-10-01

This paper presents a novel class sensitive hashing technique in the framework of large-scale content-based remote sensing (RS) image retrieval. The proposed technique aims at representing each image with multi-hash codes, each of which corresponds to a primitive (i.e., land cover class) present in the image. To this end, the proposed method consists of a three-steps algorithm. The first step is devoted to characterize each image by primitive class descriptors. These descriptors are obtained through a supervised approach, which initially extracts the image regions and their descriptors that are then associated with primitives present in the images. This step requires a set of annotated training regions to define primitive classes. A correspondence between the regions of an image and the primitive classes is built based on the probability of each primitive class to be present at each region. All the regions belonging to the specific primitive class with a probability higher than a given threshold are highly representative of that class. Thus, the average value of the descriptors of these regions is used to characterize that primitive. In the second step, the descriptors of primitive classes are transformed into multi-hash codes to represent each image. This is achieved by adapting the kernel-based supervised locality sensitive hashing method to multi-code hashing problems. The first two steps of the proposed technique, unlike the standard hashing methods, allow one to represent each image by a set of primitive class sensitive descriptors and their hash codes. Then, in the last step, the images in the archive that are very similar to a query image are retrieved based on a multi-hash-code-matching scheme. Experimental results obtained on an archive of aerial images confirm the effectiveness of the proposed technique in terms of retrieval accuracy when compared to the standard hashing methods.

Analysis on applicable error-correcting code strength of storage class memory and NAND flash in hybrid storage

NASA Astrophysics Data System (ADS)

Matsui, Chihiro; Kinoshita, Reika; Takeuchi, Ken

2018-04-01

A hybrid of storage class memory (SCM) and NAND flash is a promising technology for high performance storage. Error correction is inevitable on SCM and NAND flash because their bit error rate (BER) increases with write/erase (W/E) cycles, data retention, and program/read disturb. In addition, scaling and multi-level cell technologies increase BER. However, error-correcting code (ECC) degrades storage performance because of extra memory reading and encoding/decoding time. Therefore, applicable ECC strength of SCM and NAND flash is evaluated independently by fixing ECC strength of one memory in the hybrid storage. As a result, weak BCH ECC with small correctable bit is recommended for the hybrid storage with large SCM capacity because SCM is accessed frequently. In contrast, strong and long-latency LDPC ECC can be applied to NAND flash in the hybrid storage with large SCM capacity because large-capacity SCM improves the storage performance.

Benchmarking of Neutron Production of Heavy-Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

The chloroplast tRNALys(UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide.

PubMed

Neuhaus, H; Link, G

1987-01-01

The trnK gene endocing the tRNALys(UUU) has been located on mustard (Sinapis alba) chloroplast DNA, 263 bp upstream of the psbA gene on the same strand. The nucleotide sequence of the trnK gene and its flanking regions as well as the putative transcription start and termination sites are shown. The 5' end of the transcript lies 121 bp upstream of the 5' tRNA coding region and is preceded by procaryotic-type "-10" and "-35" sequence elements, while the 3' end maps 2.77 kb downstream to a DNA region with possible stemloop secondary structure. The anticodon loop of the tRNALys is interrupted by a 2,574 bp intron containing a long open reading frame, which codes for 524 amino acids. Based on conserved stem and loop structures, this intron has characteristic features of a class II intron. A region near the carboxyl terminus of the derived polypeptide appears structurally related to maturases.

Quantitative profiling of O-glycans by electrospray ionization- and matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry after in-gel derivatization with isotope-coded 1-phenyl-3-methyl-5-pyrazolone.

PubMed

Sić, Siniša; Maier, Norbert M; Rizzi, Andreas M

2016-09-07

The potential and benefits of isotope-coded labeling in the context of MS-based glycan profiling are evaluated focusing on the analysis of O-glycans. For this purpose, a derivatization strategy using d0/d5-1-phenyl-3-methyl-5-pyrazolone (PMP) is employed, allowing O-glycan release and derivatization to be achieved in one single step. The paper demonstrates that this release and derivatization reaction can be carried out also in-gel with only marginal loss in sensitivity compared to in-solution derivatization. Such an effective in-gel reaction allows one to extend this release/labeling method also to glycoprotein/glycoform samples pre-separated by gel-electrophoresis without the need of extracting the proteins/digested peptides from the gel. With highly O-glycosylated proteins (e.g. mucins) LODs in the range of 0.4 μg glycoprotein (100 fmol) loaded onto the electrophoresis gel can be attained, with minor glycosylated proteins (like IgAs, FVII, FIX) the LODs were in the range of 80-100 μg (250 pmol-1.5 nmol) glycoprotein loaded onto the gel. As second aspect, the potential of isotope coded labeling as internal standardization strategy for the reliable determination of quantitative glycan profiles via MALDI-MS is investigated. Towards this goal, a number of established and emerging MALDI matrices were tested for PMP-glycan quantitation, and their performance is compared with that of ESI-based measurements. The crystalline matrix 2,6-dihydroxyacetophenone (DHAP) and the ionic liquid matrix N,N-diisopropyl-ethyl-ammonium 2,4,6-trihydroxyacetophenone (DIEA-THAP) showed potential for MALDI-based quantitation of PMP-labeled O-glycans. We also provide a comprehensive overview on the performance of MS-based glycan quantitation approaches by comparing sensitivity, LOD, accuracy and repeatability data obtained with RP-HPLC-ESI-MS, stand-alone nano-ESI-MS with a spray-nozzle chip, and MALDI-MS. Finally, the suitability of the isotope-coded PMP labeling strategy for O

Codes, Code-Switching, and Context: Style and Footing in Peer Group Bilingual Play

ERIC Educational Resources Information Center

Kyratzis, Amy; Tang, Ya-Ting; Koymen, S. Bahar

2009-01-01

According to Bernstein (A sociolinguistic approach to socialization; with some reference to educability, Basil Blackwell Ltd., 1972), middle-class parents transmit an elaborated code to their children that relies on verbal means, rather than paralinguistic devices or shared assumptions, to express meanings. Bernstein's ideas were used to argue…

Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast

PubMed Central

Muto, Machiko; Henry, Ryan E; Mayfield, Stephen P

2009-01-01

Background Expression of recombinant proteins in green algal chloroplast holds substantial promise as a platform for the production of human therapeutic proteins. A number of proteins have been expressed in the chloroplast of Chlamydomonas reinhardtii, including complex mammalian proteins, but many of these proteins accumulate to significantly lower levels than do endogenous chloroplast proteins. We examined if recombinant protein accumulation could be enhanced by genetically fusing the recombinant reporter protein, luciferase, to the carboxy-terminal end of an abundant endogenous protein, the large subunit of ribulose bisphosphate carboxylase (Rubisco LSU). Additionally, as recombinant proteins fused to endogenous proteins are of little clinical or commercial value, we explored the possibility of engineering our recombinant protein to be cleavable from the endogenous protein in vivo. This strategy would obviate the need for further in vitro processing steps in order to produce the desired recombinant protein. To achieve this, a native protein-processing site from preferredoxin (preFd) was placed between the Rubisco LSU and luciferase coding regions in the fusion protein construct. Results The luciferase from the fusion protein accumulated to significantly higher levels than luciferase expressed alone. By eliminating the endogenous Rubisco large subunit gene (rbcL), we achieved a further increase in luciferase accumulation with respect to luciferase expression in the WT background. Importantly, near-wild type levels of functional Rubisco holoenzyme were generated following the proteolytic removal of the fused luciferase, while luciferase activity for the fusion protein was almost ~33 times greater than luciferase expressed alone. These data demonstrate the utility of using fusion proteins to enhance recombinant protein accumulation in algal chloroplasts, and also show that engineered proteolytic processing sites can be used to liberate the exogenous protein from

Isotopic composition analysis and age dating of uranium samples by high resolution gamma ray spectrometry

NASA Astrophysics Data System (ADS)

Apostol, A. I.; Pantelica, A.; Sima, O.; Fugaru, V.

2016-09-01

Non-destructive methods were applied to determine the isotopic composition and the time elapsed since last chemical purification of nine uranium samples. The applied methods are based on measuring gamma and X radiations of uranium samples by high resolution low energy gamma spectrometric system with planar high purity germanium detector and low background gamma spectrometric system with coaxial high purity germanium detector. The ;Multigroup γ-ray Analysis Method for Uranium; (MGAU) code was used for the precise determination of samples' isotopic composition. The age of the samples was determined from the isotopic ratio 214Bi/234U. This ratio was calculated from the analyzed spectra of each uranium sample, using relative detection efficiency. Special attention is paid to the coincidence summing corrections that have to be taken into account when performing this type of analysis. In addition, an alternative approach for the age determination using full energy peak efficiencies obtained by Monte Carlo simulations with the GESPECOR code is described.

75 FR 39145 - Amendment of Class C Airspace; Flint, MI

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-08

...-0599; Airspace Docket No. 10-AWA-3] RIN 2120-AA66 Amendment of Class C Airspace; Flint, MI AGENCY... description of the Bishop International Airport, Flint, MI, Class C airspace area by amending the airport... defines the Class C airspace area's center point. The Rule This action amends Title 14 Code of Federal...

Locality-preserving logical operators in topological stabilizer codes

NASA Astrophysics Data System (ADS)

Webster, Paul; Bartlett, Stephen D.

2018-01-01

Locality-preserving logical operators in topological codes are naturally fault tolerant, since they preserve the correctability of local errors. Using a correspondence between such operators and gapped domain walls, we describe a procedure for finding all locality-preserving logical operators admitted by a large and important class of topological stabilizer codes. In particular, we focus on those equivalent to a stack of a finite number of surface codes of any spatial dimension, where our procedure fully specifies the group of locality-preserving logical operators. We also present examples of how our procedure applies to codes with different boundary conditions, including color codes and toric codes, as well as more general codes such as Abelian quantum double models and codes with fermionic excitations in more than two dimensions.

Deterministic quantum dense coding networks

NASA Astrophysics Data System (ADS)

Roy, Saptarshi; Chanda, Titas; Das, Tamoghna; Sen(De), Aditi; Sen, Ujjwal

2018-07-01

We consider the scenario of deterministic classical information transmission between multiple senders and a single receiver, when they a priori share a multipartite quantum state - an attempt towards building a deterministic dense coding network. Specifically, we prove that in the case of two or three senders and a single receiver, generalized Greenberger-Horne-Zeilinger (gGHZ) states are not beneficial for sending classical information deterministically beyond the classical limit, except when the shared state is the GHZ state itself. On the other hand, three- and four-qubit generalized W (gW) states with specific parameters as well as the four-qubit Dicke states can provide a quantum advantage of sending the information in deterministic dense coding. Interestingly however, numerical simulations in the three-qubit scenario reveal that the percentage of states from the GHZ-class that are deterministic dense codeable is higher than that of states from the W-class.

Short-Block Protograph-Based LDPC Codes

NASA Technical Reports Server (NTRS)

Divsalar, Dariush; Dolinar, Samuel; Jones, Christopher

2010-01-01

Short-block low-density parity-check (LDPC) codes of a special type are intended to be especially well suited for potential applications that include transmission of command and control data, cellular telephony, data communications in wireless local area networks, and satellite data communications. [In general, LDPC codes belong to a class of error-correcting codes suitable for use in a variety of wireless data-communication systems that include noisy channels.] The codes of the present special type exhibit low error floors, low bit and frame error rates, and low latency (in comparison with related prior codes). These codes also achieve low maximum rate of undetected errors over all signal-to-noise ratios, without requiring the use of cyclic redundancy checks, which would significantly increase the overhead for short blocks. These codes have protograph representations; this is advantageous in that, for reasons that exceed the scope of this article, the applicability of protograph representations makes it possible to design highspeed iterative decoders that utilize belief- propagation algorithms.

Finite mixture models for the computation of isotope ratios in mixed isotopic samples

NASA Astrophysics Data System (ADS)

Koffler, Daniel; Laaha, Gregor; Leisch, Friedrich; Kappel, Stefanie; Prohaska, Thomas

2013-04-01

parameters of the algorithm, i.e. the maximum count of ratios, the minimum relative group-size of data points belonging to each ratio has to be defined. Computation of the models can be done with statistical software. In this study Leisch and Grün's flexmix package [2] for the statistical open-source software R was applied. A code example is available in the electronic supplementary material of Kappel et al. [1]. In order to demonstrate the usefulness of finite mixture models in fields dealing with the computation of multiple isotope ratios in mixed samples, a transparent example based on simulated data is presented and problems regarding small group-sizes are illustrated. In addition, the application of finite mixture models to isotope ratio data measured in uranium oxide particles is shown. The results indicate that finite mixture models perform well in computing isotope ratios relative to traditional estimation procedures and can be recommended for more objective and straightforward calculation of isotope ratios in geochemistry than it is current practice. [1] S. Kappel, S. Boulyga, L. Dorta, D. Günther, B. Hattendorf, D. Koffler, G. Laaha, F. Leisch and T. Prohaska: Evaluation Strategies for Isotope Ratio Measurements of Single Particles by LA-MC-ICPMS, Analytical and Bioanalytical Chemistry, 2013, accepted for publication on 2012-12-18 (doi: 10.1007/s00216-012-6674-3) [2] B. Grün and F. Leisch: Fitting finite mixtures of generalized linear regressions in R. Computational Statistics & Data Analysis, 51(11), 5247-5252, 2007. (doi:10.1016/j.csda.2006.08.014)

New double-byte error-correcting codes for memory systems

NASA Technical Reports Server (NTRS)

Feng, Gui-Liang; Wu, Xinen; Rao, T. R. N.

1996-01-01

Error-correcting or error-detecting codes have been used in the computer industry to increase reliability, reduce service costs, and maintain data integrity. The single-byte error-correcting and double-byte error-detecting (SbEC-DbED) codes have been successfully used in computer memory subsystems. There are many methods to construct double-byte error-correcting (DBEC) codes. In the present paper we construct a class of double-byte error-correcting codes, which are more efficient than those known to be optimum, and a decoding procedure for our codes is also considered.

Low-Density Parity-Check (LDPC) Codes Constructed from Protographs

NASA Astrophysics Data System (ADS)

Thorpe, J.

2003-08-01

We introduce a new class of low-density parity-check (LDPC) codes constructed from a template called a protograph. The protograph serves as a blueprint for constructing LDPC codes of arbitrary size whose performance can be predicted by analyzing the protograph. We apply standard density evolution techniques to predict the performance of large protograph codes. Finally, we use a randomized search algorithm to find good protographs.

A guide for the laboratory information management system (LIMS) for light stable isotopes--Versions 7 and 8

USGS Publications Warehouse

Coplen, Tyler B.

2000-01-01

The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program, the Laboratory Information Management System (LIMS) for Light Stable Isotopes, is presented herein. Major benefits of this system include (i) a dramatic improvement in quality assurance, (ii) an increase in laboratory efficiency, (iii) a reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) a decrease in errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for laboratories. LIMS for Light Stable Isotopes is available for both Microsoft Office 97 Professional and Microsoft Office 2000 Professional as versions 7 and 8, respectively. Both source code (mdb file) and precompiled executable files (mde) are available. Numerous improvements have been made for continuous flow isotopic analysis in this version (specifically 7.13 for Microsoft Access 97 and 8.13 for Microsoft Access 2000). It is much easier to import isotopic results from Finnigan ISODAT worksheets, even worksheets on which corrections for amount of sample (linearity corrections) have been added. The capability to determine blank corrections using isotope mass balance from analyses of elemental analyzer samples has been added. It is now possible to calculate and apply drift corrections to isotopic

Non-lethal sampling of walleye for stable isotope analysis: a comparison of three tissues

USGS Publications Warehouse

Chipps, Steven R.; VanDeHey, J.A.; Fincel, M.J.

2012-01-01

Stable isotope analysis of fishes is often performed using muscle or organ tissues that require sacrificing animals. Non-lethal sampling provides an alternative for evaluating isotopic composition for species of concern or individuals of exceptional value. Stable isotope values of white muscle (lethal) were compared with those from fins and scales (non-lethal) in walleye, Sander vitreus (Mitchill), from multiple systems, size classes and across a range of isotopic values. Isotopic variability was also compared among populations to determine the potential of non-lethal tissues for diet-variability analyses. Muscle-derived isotope values were enriched compared with fins and depleted relative to scales. A split-sample validation technique and linear regression found that isotopic composition of walleye fins and scales was significantly related to that in muscle tissue for both δ13C and δ15N (r2 = 0.79–0.93). However, isotopic variability was significantly different between tissue types in two of six populations for δ15N and three of six populations for δ13C. Although species and population specific, these findings indicate that isotopic measures obtained from non-lethal tissues are indicative of those obtained from muscle.

CNO isotopes in red giant stars

NASA Technical Reports Server (NTRS)

Wannier, P. G.

1985-01-01

The production and distribution of the CNO nuclides is discussed in light of observed abundance ratios in red giants and in the interstellar medium. Isotope abundances have been measured in the atmospheres and in the recent ejecta of cool giants, including carbon stars, S-type stars and red supergiants as well as in oxygen-rich giants making their first ascent of the giant branch. Several of the observations suggest revision of currently accepted nuclear cross-sections and of the mixing processes operating in giant envelopes. By comparing red giant abundances with high-quality observations of the interstellar medium, conclusions are reached about the contribution of intermediate-mass stars to galactic nuclear evolution. The three oxygen isotopes, O-16, -17 and -18, are particularly valuable for such comparison because they reflect three different stages of stellar nucleosynthesis. One remarkable result comes from observations of O-17/O-18 in several classes of red giant stars. The observed range of values for red giants excludes the entire range of values seen in interstellar molecular clouds. Furthermore, both the observations of stars and interstellar clouds exclude the isotopic ratio found in the solar system.

76 FR 39038 - Proposed Establishment of Class E Airspace; Lebanon, PA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-05

...-0558; Airspace Docket No. 11-AEA-13] Proposed Establishment of Class E Airspace; Lebanon, PA AGENCY... action proposes to establish Class E Airspace at Lebanon, PA, to accommodate new Standard Instrument... amendment to Title 14, Code of Federal Regulations (14 CFR) part 71 to establish Class E airspace at Lebanon...

Benchmarking of neutron production of heavy-ion transport codes

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

Remec, I.; Ronningen, R. M.; Heilbronn, L.

Document available in abstract form only, full text of document follows: Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondarymore » neutron production. Results are encouraging; however, further improvements in models and codes and additional benchmarking are required. (authors)« less

"Anticlumping" and Other Combinatorial Effects on Clumped Isotopes: Implications for Tracing Biogeochemical Cycling

NASA Astrophysics Data System (ADS)

Yeung, L.

2015-12-01

I present a mode of isotopic ordering that has purely combinatorial origins. It can be important when identical rare isotopes are paired by coincidence (e.g., they are neighbors on the same molecule), or when extrinsic factors govern the isotopic composition of the two atoms that share a chemical bond. By itself, combinatorial isotope pairing yields products with isotopes either randomly distributed or with a deficit relative to a random distribution of isotopes. These systematics arise because of an unconventional coupling between the formation of singly- and multiply-substituted isotopic moieties. In a random distribution, rare isotopes are symmetrically distributed: Single isotopic substitutions (e.g., H‒D and D‒H in H2) occur with equal probability, and double isotopic substitutions (e.g., D2) occur according to random chance. The absence of symmetry in a bond-making complex can yield unequal numbers of singly-substituted molecules (e.g., more H‒D than D‒H in H2), which is recorded in the product molecule as a deficit in doubly-substituted moieties and an "anticlumped" isotope distribution (i.e., Δn < 0). Enzymatic isotope pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect. Chemical-kinetic isotope effects, which are related to the bond-forming transition state, arise independently and express second-order combinatorial effects. In general, both combinatorial and chemical factors are important for calculating and interpreting clumped-isotope signatures of individual reactions. In many reactions relevant to geochemical oxygen, carbon, and nitrogen cycling, combinatorial isotope pairing likely plays a strong role in the clumped isotope distribution of the products. These isotopic signatures, manifest as either directly bound isotope clumps or as features of a molecule's isotopic anatomy, could be exploited as tracers of biogeochemistry that can

Validation of cell-based fluorescence assays: practice guidelines from the ICSH and ICCS - part IV - postanalytic considerations.

PubMed

Barnett, David; Louzao, Raaul; Gambell, Peter; De, Jitakshi; Oldaker, Teri; Hanson, Curtis A

2013-01-01

Flow cytometry and other technologies of cell-based fluorescence assays are as a matter of good laboratory practice required to validate all assays, which when in clinical practice may pass through regulatory review processes using criteria often defined with a soluble analyte in plasma or serum samples in mind. Recently the U.S. Food and Drug Administration (FDA) has entered into a public dialogue in the U.S. regarding their regulatory interest in laboratory developed tests (LDTs) or so-called home brew assays performed in clinical laboratories. The absence of well-defined guidelines for validation of cell-based assays using fluorescence detection has thus become a subject of concern for the International Council for Standardization of Haematology (ICSH) and International Clinical Cytometry Society (ICCS). Accordingly, a group of over 40 international experts in the areas of test development, test validation, and clinical practice of a variety of assay types using flow cytometry and/or morphologic image analysis were invited to develop a set of practical guidelines useful to in vitro diagnostic (IVD) innovators, clinical laboratories, regulatory scientists, and laboratory inspectors. The focus of the group was restricted to fluorescence reporter reagents, although some common principles are shared by immunohistochemistry or immunocytochemistry techniques and noted where appropriate. The work product of this two year effort is the content of this special issue of this journal, which is published as 5 separate articles, this being Validation of Cell-based Fluorescence Assays: Practice Guidelines from the ICSH and ICCS - Part IV - Postanalytic considerations. © 2013 International Clinical Cytometry Society.

Validation of cell-based fluorescence assays: practice guidelines from the ICSH and ICCS - part II - preanalytical issues.

PubMed

Davis, Bruce H; Dasgupta, Amar; Kussick, Steven; Han, Jin-Yeong; Estrellado, Annalee

2013-01-01

Flow cytometry and other technologies of cell-based fluorescence assays are as a matter of good laboratory practice required to validate all assays, which when in clinical practice may pass through regulatory review processes using criteria often defined with a soluble analyte in plasma or serum samples in mind. Recently the U.S. Food and Drug Administration (FDA) has entered into a public dialogue in the U.S. regarding their regulatory interest in laboratory developed tests (LDTs) or so-called "home brew" assays performed in clinical laboratories. The absence of well-defined guidelines for validation of cell-based assays using fluorescence detection has thus become a subject of concern for the International Council for Standardization of Haematology (ICSH) and International Clinical Cytometry Society (ICCS). Accordingly, a group of over 40 international experts in the areas of test development, test validation, and clinical practice of a variety of assay types using flow cytometry and/or morphologic image analysis were invited to develop a set of practical guidelines useful to in vitro diagnostic (IVD) innovators, clinical laboratories, regulatory scientists, and laboratory inspectors. The focus of the group was restricted to fluorescence reporter reagents, although some common principles are shared by immunohistochemistry or immunocytochemistry techniques and noted where appropriate. The work product of this two year effort is the content of this special issue of this journal, which is published as 5 separate articles, this being Validation of Cell-based Fluorescence Assays: Practice Guidelines from the ICSH and ICCS - Part II - Preanalytical issues. © 2013 International Clinical Cytometry Society. © 2013 International Clinical Cytometry Society.

Simulation of multi-photon emission isotopes using time-resolved SimSET multiple photon history generator

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

Chiang, Chih-Chieh; Lin, Hsin-Hon; Lin, Chang-Shiun

Abstract-Multiple-photon emitters, such as In-111 or Se-75, have enormous potential in the field of nuclear medicine imaging. For example, Se-75 can be used to investigate the bile acid malabsorption and measure the bile acid pool loss. The simulation system for emission tomography (SimSET) is a well-known Monte Carlo simulation (MCS) code in nuclear medicine for its high computational efficiency. However, current SimSET cannot simulate these isotopes due to the lack of modeling of complex decay scheme and the time-dependent decay process. To extend the versatility of SimSET for simulation of those multi-photon emission isotopes, a time-resolved multiple photon history generatormore » based on SimSET codes is developed in present study. For developing the time-resolved SimSET (trSimSET) with radionuclide decay process, the new MCS model introduce new features, including decay time information and photon time-of-flight information, into this new code. The half-life of energy states were tabulated from the Evaluated Nuclear Structure Data File (ENSDF) database. The MCS results indicate that the overall percent difference is less than 8.5% for all simulation trials as compared to GATE. To sum up, we demonstrated that time-resolved SimSET multiple photon history generator can have comparable accuracy with GATE and keeping better computational efficiency. The new MCS code is very useful to study the multi-photon imaging of novel isotopes that needs the simulation of lifetime and the time-of-fight measurements. (authors)« less

Enantiomeric and Isotopic Analysis of Organic Compounds in Carbonaceous Meteorites

NASA Technical Reports Server (NTRS)

Cooper, George

2004-01-01

Carbonaceous meteorites are relatively enriched in soluble organic compounds. The Murchison and Murray meteorites contain numerous compounds of interest in the study of early solar system organic chemistry and organic compounds of potential importance for the origin of life. These include: amino acids, amides, carboxylic acids, and polyols. This talk will focus on the enantiomeric and isotopic analysis of individual meteoritic compounds - primarily polyol acids. The analyses will determine if, in addition to certain amino acids from Murchison, another potentially important class of prebiotic compounds also contains enantiomeric excesses, i.e., excesses that could have contributed to the current homochirality of life. Preliminary enantiomeric and isotopic (C- 13) measurements of Murchison glyceric acid show that it is indeed extraterrestrial. C-13 and D isotope analysis of meteoritic sugar alcohols (glycerol, threitol, ribitol, etc.) has shown that they are also indigenous to the meteorite.

Error-trellis Syndrome Decoding Techniques for Convolutional Codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1984-01-01

An error-trellis syndrome decoding technique for convolutional codes is developed. This algorithm is then applied to the entire class of systematic convolutional codes and to the high-rate, Wyner-Ash convolutional codes. A special example of the one-error-correcting Wyner-Ash code, a rate 3/4 code, is treated. The error-trellis syndrome decoding method applied to this example shows in detail how much more efficient syndrome decoding is than Viterbi decoding if applied to the same problem. For standard Viterbi decoding, 64 states are required, whereas in the example only 7 states are needed. Also, within the 7 states required for decoding, many fewer transitions are needed between the states.

Error-trellis syndrome decoding techniques for convolutional codes

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1985-01-01

An error-trellis syndrome decoding technique for convolutional codes is developed. This algorithm is then applied to the entire class of systematic convolutional codes and to the high-rate, Wyner-Ash convolutional codes. A special example of the one-error-correcting Wyner-Ash code, a rate 3/4 code, is treated. The error-trellis syndrome decoding method applied to this example shows in detail how much more efficient syndrome decordig is than Viterbi decoding if applied to the same problem. For standard Viterbi decoding, 64 states are required, whereas in the example only 7 states are needed. Also, within the 7 states required for decoding, many fewer transitions are needed between the states.

A Modern Analogue for Proterozoic Inverse Carbon Isotope Signatures

NASA Astrophysics Data System (ADS)

Close, H. G.; Diefendorf, A. F.; Freeman, K. H.; Pearson, A.

2008-12-01

The carbon isotope distribution preserved in sedimentary lipids changes near the Neoproterozoic-Cambrian boundary. In older samples, n-alkyl lipids contain more 13C than both isoprenoid lipids and kerogen [1]. In younger samples, the opposite prevails. Although extreme heterotrophy has been invoked as a mechanism to explain the enrichment in 13C [2], here we suggest another explanation. The switch may reflect a fundamental transition from an oligotrophic ocean dominated by prokaryotic biomass, to an ocean in which carbon fixation is more intensive and burial is dominated by eukaryotic biomass. An analogue for Proterozoic ordering is found in the modern, oligotrophic Pacific Ocean, where n-alkyl lipids of picoplankton (0.2-0.5 μm particulate matter) contain excess 13C relative to the same lipids found in larger size classes (> 0.5 μm). Picoplanktonic lipids are heavier isotopically (-18 ‰) than both the sterols of eukaryotes (-23 ‰ to -26 ‰) and the total organic matter (-20 ‰; TOM). The 0.2-0.5 μm size class also has a distinct chain-length abundance profile. Although large particles must be the vehicle for total carbon export, paradoxically the lipid component of export production appears to be dominated by the 0.2-0.5 μm source. The picoplanktonic chain lengths and isotopic composition dominate lipids of TOM at 670 meters. When the ratio of prokaryotic to eukaryotic production is high, as in the modern central Pacific Ocean, it appears that exported material has an inverse carbon isotope signature similar to that preserved in Precambrian samples. [1] Logan, G. A. et al., Nature 376:53-56 (1995). [2] Rothman, D. H. et al., PNAS 100:8124-8129 (2003).

Brush border enzyme-cleavable linkers: Evaluation for reducing renal uptake of radiolabeled prostate-specific membrane antigen inhibitors.

PubMed

Vaidyanathan, Ganesan; Kang, Choong Mo; McDougald, Darryl; Minn, Il; Brummet, Mary; Pomper, Martin G; Zalutsky, Michael R

2018-05-05

Radiolabeled, low-molecular-weight prostate-specific membrane antigen (PSMA) inhibitors based on the Glu-ureido pharmacophore show promise for the detection and treatment of castration-resistant prostate cancer; however, high renal retention of activity, related in part to overexpression of PSMA in kidneys can be problematic. The goal of the current study was to investigate the use of brush border enzyme-cleavable linkers as a strategy for reducing kidney activity levels from radiolabeled PSMA inhibitors. PSMA-769 (6), a derivative of the prototypical PSMA inhibitor (((S)‑1‑carboxy‑5‑(4‑iodobenzamido)pentyl)carbamoyl)glutamate (12) modified to contain a Gly-Tyr linker, and its protected tin precursor (11) were synthesized starting from the basic pharmacophore molecule Lys-urea-Glu. An analogue of 6 containing d‑tyrosine in lieu of l‑tyrosine (PSMA-769-d-tyrosine) and the corresponding tin precursor (d-11) also were synthesized. Both radioiodinated and 211 At-labeled 6 were synthesized by radiohalogenation of 11 and deprotection in situ. Similarly, radioiodinated d-6 was synthesized from d-11. Paired label biodistribution of [ 125 I]12 and [ 131 I]6 was performed in normal mice and in SCID mice bearing both PC3 PIP (PSMA+) and PC3 flu (PSMA-) subcutaneous prostate carcinoma xenografts. The biodistribution of [ 131 I]6 and [ 211 At]6 was also evaluated in this tumor model. Biodistribution of the two radioiodinated diastereomers of 6 was evaluated in normal mice and urine samples were analyzed for the presence of 4‑iodohippuric acid. Compounds [ 131 I]6 and [ 211 At]6 were synthesized from 11 in overall radiochemical yields of 32.5 ± 0.1% (n = 4) and 22% (n = 1), respectively; radiochemical purity was >95%. In normal mice, renal uptake of [ 131 I]6 was 1.4-, 2.8- and 161-fold lower than that seen for co-injected [ 125 I]12 at 1 h, 4 h and 21 h, respectively. In tumor-bearing mice, kidney uptake of [ 131 I]6 was similar to that for

76 FR 66662 - Proposed Amendment of Class D Airspace; Santa Monica, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-27

...-0611; Airspace Docket No. 11-AWP-11] Proposed Amendment of Class D Airspace; Santa Monica, CA AGENCY... action proposes to modify Class D airspace at Santa Monica Municipal Airport, CA, to accommodate aircraft... an amendment to Title 14 Code of Federal Regulations (14 CFR) Part 71 by modifying Class D airspace...

Final Technical Report for GO17004 Regulatory Logic: Codes and Standards for the Hydrogen Economy

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

Nakarado, Gary L.

The objectives of this project are to: develop a robust supporting research and development program to provide critical hydrogen behavior data and a detailed understanding of hydrogen combustion and safety across a range of scenarios, needed to establish setback distances in building codes and minimize the overall data gaps in code development; support and facilitate the completion of technical specifications by the International Organization for Standardization (ISO) for gaseous hydrogen refueling (TS 20012) and standards for on-board liquid (ISO 13985) and gaseous or gaseous blend (ISO 15869) hydrogen storage by 2007; support and facilitate the effort, led by the NFPA,more » to complete the draft Hydrogen Technologies Code (NFPA 2) by 2008; with experimental data and input from Technology Validation Program element activities, support and facilitate the completion of standards for bulk hydrogen storage (e.g., NFPA 55) by 2008; facilitate the adoption of the most recently available model codes (e.g., from the International Code Council [ICC]) in key regions; complete preliminary research and development on hydrogen release scenarios to support the establishment of setback distances in building codes and provide a sound basis for model code development and adoption; support and facilitate the development of Global Technical Regulations (GTRs) by 2010 for hydrogen vehicle systems under the United Nations Economic Commission for Europe, World Forum for Harmonization of Vehicle Regulations and Working Party on Pollution and Energy Program (ECE-WP29/GRPE); and to Support and facilitate the completion by 2012 of necessary codes and standards needed for the early commercialization and market entry of hydrogen energy technologies.« less

Bounds on Block Error Probability for Multilevel Concatenated Codes

NASA Technical Reports Server (NTRS)

Lin, Shu; Moorthy, Hari T.; Stojanovic, Diana

1996-01-01

Maximum likelihood decoding of long block codes is not feasable due to large complexity. Some classes of codes are shown to be decomposable into multilevel concatenated codes (MLCC). For these codes, multistage decoding provides good trade-off between performance and complexity. In this paper, we derive an upper bound on the probability of block error for MLCC. We use this bound to evaluate difference in performance for different decompositions of some codes. Examples given show that a significant reduction in complexity can be achieved when increasing number of stages of decoding. Resulting performance degradation varies for different decompositions. A guideline is given for finding good m-level decompositions.

Stable Isotope Identification of Nitrogen Sources for United ...

EPA Pesticide Factsheets

We used natural abundance stable isotope data to evaluate nitrogen sources to U.S. west coast estuaries. We collected δ15N of macroalgae data and supplemented this with available data from the literature for estuaries from Mexico to Alaska. Stable isotope ratios of green macroalgae were compared to δ15N of dissolved inorganic nitrogen of oceanic and watershed end members. There was a latitudinal gradient in δ15N of macroalgae with southern estuaries being 7 per mil heavier than northern estuaries. Gradients in isotope data were compared to nitrogen sources estimated by the USGS using the SPARROW model. In California estuaries, the elevation of isotope data appeared to be related to anthropogenic nitrogen sources. In Oregon systems, the nitrogen levels of streams flowing into the estuaries are related to forest cover, rather than to developed land classes. In addition, the δ15N of macroalgae suggested that the ocean and nitrogen-fixing trees in the watersheds were the dominant nitrogen sources. There was also a strong gradient in δ15N of macroalgae with heavier sites located near the estuary mouth. In some Oregon estuaries, there was an elevation an elevation of δ15N above marine end members in the vicinity of wastewater treatment facility discharge locations, suggesting isotopes may be useful for distinguishing inputs along an estuarine gradient. Nutrients are the leading cause of water quality impairments in the United States, and as a result too

Validation of cell-based fluorescence assays: practice guidelines from the ICSH and ICCS - part I - rationale and aims.

PubMed

Davis, Bruce H; Wood, Brent; Oldaker, Teri; Barnett, David

2013-01-01

Flow cytometry and other technologies of cell-based fluorescence assays are as a matter of good laboratory practice required to validate all assays, which when in clinical practice may pass through regulatory review processes using criteria often defined with a soluble analyte in plasma or serum samples in mind. Recently the U.S. Food and Drug Administration (FDA) has entered into a public dialogue in the U.S. regarding their regulatory interest in laboratory developed tests (LDTs) or so-called "home brew" assays performed in clinical laboratories. The absence of well-defined guidelines for validation of cell-based assays using fluorescence detection has thus become a subject of concern for the International Council for Standardization of Haematology (ICSH) and International Clinical Cytometry Society (ICCS). Accordingly, a group of over 40 international experts in the areas of test development, test validation, and clinical practice of a variety of assay types using flow cytometry and/or morphologic image analysis were invited to develop a set of practical guidelines useful to in vitro diagnostic (IVD) innovators, clinical laboratories, regulatory scientists, and laboratory inspectors. The focus of the group was restricted to fluorescence reporter reagents, although some common principles are shared by immunohistochemistry or immunocytochemistry techniques and noted where appropriate. The work product of this two year effort is the content of this special issue of this journal, which is published as 5 separate articles, this being Validation of Cell-based Fluorescence Assays: Practice Guidelines from the ICSH and ICCS - Part I - Rationale and aims. © 2013 International Clinical Cytometry Society. © 2013 International Clinical Cytometry Society.

Multipath search coding of stationary signals with applications to speech

NASA Astrophysics Data System (ADS)

Fehn, H. G.; Noll, P.

1982-04-01

This paper deals with the application of multipath search coding (MSC) concepts to the coding of stationary memoryless and correlated sources, and of speech signals, at a rate of one bit per sample. Use is made of three MSC classes: (1) codebook coding, or vector quantization, (2) tree coding, and (3) trellis coding. This paper explains the performances of these coders and compares them both with those of conventional coders and with rate-distortion bounds. The potentials of MSC coding strategies are demonstrated by illustrations. The paper reports also on results of MSC coding of speech, where both the strategy of adaptive quantization and of adaptive prediction were included in coder design.

Quantitative proteomic analysis of human breast epithelial cells with differential telomere length

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

Yu, Li-Rong; Chan, King C.; Tahara, Hidetoshi

Telomeres play important functional roles in cell proliferation, cell cycle regulation, and genetic stability, in which telomere length is critical. In this study, quantitative proteome comparisons for the human breast epithelial cells with short and long telomeres (184-hTERT{sub L} vs. 184-hTERT{sub S} and 90P-hTERT{sub L} vs. 90P-hTERT{sub S}), resulting from transfection of the human telomerase reverse transcriptase (hTERT) gene, were performed using cleavable isotope-coded affinity tags. More than 2000 proteins were quantified in each comparative experiment, with approximately 77% of the proteins identified in both analyses. In the cells with long telomeres, significant and consistent alterations were observed in metabolismmore » (amino acid, nucleotide, and lipid metabolism), genetic information transmission (transcription and translation regulation, spliceosome and ribosome complexes), and cell signaling. Interestingly, the DNA excision repair pathway is enhanced, while integrin and its ligands are downregulated in the cells with long telomeres. These results may provide valuable information related to telomere functions.« less

New Site Coefficients and Site Classification System Used in Recent Building Seismic Code Provisions

USGS Publications Warehouse

Dobry, R.; Borcherdt, R.D.; Crouse, C.B.; Idriss, I.M.; Joyner, W.B.; Martin, G.R.; Power, M.S.; Rinne, E.E.; Seed, R.B.

2000-01-01

Recent code provisions for buildings and other structures (1994 and 1997 NEHRP Provisions, 1997 UBC) have adopted new site amplification factors and a new procedure for site classification. Two amplitude-dependent site amplification factors are specified: Fa for short periods and Fv for longer periods. Previous codes included only a long period factor S and did not provide for a short period amplification factor. The new site classification system is based on definitions of five site classes in terms of a representative average shear wave velocity to a depth of 30 m (V?? s). This definition permits sites to be classified unambiguously. When the shear wave velocity is not available, other soil properties such as standard penetration resistance or undrained shear strength can be used. The new site classes denoted by letters A - E, replace site classes in previous codes denoted by S1 - S4. Site classes A and B correspond to hard rock and rock, Site Class C corresponds to soft rock and very stiff / very dense soil, and Site Classes D and E correspond to stiff soil and soft soil. A sixth site class, F, is defined for soils requiring site-specific evaluations. Both Fa and Fv are functions of the site class, and also of the level of seismic hazard on rock, defined by parameters such as Aa and Av (1994 NEHRP Provisions), Ss and S1 (1997 NEHRP Provisions) or Z (1997 UBC). The values of Fa and Fv decrease as the seismic hazard on rock increases due to soil nonlinearity. The greatest impact of the new factors Fa and Fv as compared with the old S factors occurs in areas of low-to-medium seismic hazard. This paper summarizes the new site provisions, explains the basis for them, and discusses ongoing studies of site amplification in recent earthquakes that may influence future code developments.

Phases of match-play in professional Australian Football: Descriptive analysis and reliability assessment.

PubMed

Rennie, Michael J; Watsford, Mark L; Spurrs, Robert W; Kelly, Stephen J; Pine, Matthew J

2018-06-01

To examine the frequency and time spent in the phases of Australian Football (AF) match-play and to assess the intra-assessor reliability of coding these phases of match-play. Observational, intra-reliability assessment. Video footage of 10 random quarters of AF match-play were coded by a single researcher. Phases of offence, defence, contested play, umpire stoppage, set shot and goal reset were coded using a set of operational definitions. Descriptive statistics were provided for all phases of match-play. Following a 6-month washout period, intra-coder reliability was assessed using typical error of measurement (TEM) and intra-class correlation coefficients (ICC). A quarter of AF match-play involved 128±20 different phases of match-play. The highest proportion of match-play involved contested play (25%), followed by offence (18%), defence (18%) and umpire stoppages (18%). The mean duration of offence, defence, contested play, umpire stoppage, set shot and goal reset were 14, 14, 10, 11, 28 and 47s, respectively. No differences were found between the two coding assessments (p>0.05). ICCs for coding the phases of play demonstrated very high reliability (r=0.902-0.992). TEM of the total time spent in each phase of play represented moderate to good reliability (TEM=1.8-9.3%). Coding of offence, defence and contested play tended to display slightly poorer TEMs than umpire stoppages, set shots and goal resets (TEM=8.1 vs 4.5%). Researchers can reliably code the phases of AF match-play which may permit the analysis of specific elements of competition. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

The CRONOS Code for Astrophysical Magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Kissmann, R.; Kleimann, J.; Krebl, B.; Wiengarten, T.

2018-06-01

We describe the magnetohydrodynamics (MHD) code CRONOS, which has been used in astrophysics and space-physics studies in recent years. CRONOS has been designed to be easily adaptable to the problem in hand, where the user can expand or exchange core modules or add new functionality to the code. This modularity comes about through its implementation using a C++ class structure. The core components of the code include solvers for both hydrodynamical (HD) and MHD problems. These problems are solved on different rectangular grids, which currently support Cartesian, spherical, and cylindrical coordinates. CRONOS uses a finite-volume description with different approximate Riemann solvers that can be chosen at runtime. Here, we describe the implementation of the code with a view toward its ongoing development. We illustrate the code’s potential through several (M)HD test problems and some astrophysical applications.

Circular codes revisited: a statistical approach.

PubMed

Gonzalez, D L; Giannerini, S; Rosa, R

2011-04-21

In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C(3) maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization. Copyright © 2011 Elsevier Ltd. All rights reserved.

Enzyme-Cleavable Polymeric Micelles for the Intracellular Delivery of Proapoptotic Peptides.

PubMed

Kern, Hanna B; Srinivasan, Selvi; Convertine, Anthony J; Hockenbery, David; Press, Oliver W; Stayton, Patrick S

2017-05-01

red blood cell lysis assay showed a corresponding increase in membrane destabilizing activity (<1% lysis at pH 7.4 versus 95% lysis at pH 6.6). The full carrier-drug system successfully induced apoptosis in SKOV3 ovarian cancer cells in a dose-dependent manner, in comparison to a control polymer containing a scrambled BIM peptide sequence. Mechanistic analysis verified target-dependent activation of caspase 3/7 activity (8.1-fold increase), and positive annexin V staining (72% increase). The increased blood stability of this enzyme-cleavable peptide polymer design, together with the direct polymerization approach that eliminated postsynthetic conjugation steps, suggests that this new carrier design could provide important benefits for intracellular peptide drug delivery.

Automatic Certification of Kalman Filters for Reliable Code Generation

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd; Schumann, Johann; Richardson, Julian

2005-01-01

AUTOFILTER is a tool for automatically deriving Kalman filter code from high-level declarative specifications of state estimation problems. It can generate code with a range of algorithmic characteristics and for several target platforms. The tool has been designed with reliability of the generated code in mind and is able to automatically certify that the code it generates is free from various error classes. Since documentation is an important part of software assurance, AUTOFILTER can also automatically generate various human-readable documents, containing both design and safety related information. We discuss how these features address software assurance standards such as DO-178B.

On codes with multi-level error-correction capabilities

NASA Technical Reports Server (NTRS)

Lin, Shu

1987-01-01

In conventional coding for error control, all the information symbols of a message are regarded equally significant, and hence codes are devised to provide equal protection for each information symbol against channel errors. However, in some occasions, some information symbols in a message are more significant than the other symbols. As a result, it is desired to devise codes with multilevel error-correcting capabilities. Another situation where codes with multi-level error-correcting capabilities are desired is in broadcast communication systems. An m-user broadcast channel has one input and m outputs. The single input and each output form a component channel. The component channels may have different noise levels, and hence the messages transmitted over the component channels require different levels of protection against errors. Block codes with multi-level error-correcting capabilities are also known as unequal error protection (UEP) codes. Structural properties of these codes are derived. Based on these structural properties, two classes of UEP codes are constructed.

76 FR 38580 - Proposed Amendment of Class D Airspace; Eglin AFB, FL

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-01

...-0087; Airspace Docket No. 11-ASO-12] Proposed Amendment of Class D Airspace; Eglin AFB, FL AGENCY... action proposes to amend Class D Airspace in the Eglin Air Force Base (AFB), FL airspace area. The Destin... amendment to Title 14, Code of Federal Regulations (14 CFR) part 71 to amend Class D airspace in the Eglin...

Probabilistic seismic hazard zonation for the Cuban building code update

NASA Astrophysics Data System (ADS)

Garcia, J.; Llanes-Buron, C.

2013-05-01

A probabilistic seismic hazard assessment has been performed in response to a revision and update of the Cuban building code (NC-46-99) for earthquake-resistant building construction. The hazard assessment have been done according to the standard probabilistic approach (Cornell, 1968) and importing the procedures adopted by other nations dealing with the problem of revising and updating theirs national building codes. Problems of earthquake catalogue treatment, attenuation of peak and spectral ground acceleration, as well as seismic source definition have been rigorously analyzed and a logic-tree approach was used to represent the inevitable uncertainties encountered through the whole seismic hazard estimation process. The seismic zonation proposed here, is formed by a map where it is reflected the behaviour of the spectral acceleration values for short (0.2 seconds) and large (1.0 seconds) periods on rock conditions with a 1642 -year return period, which being considered as maximum credible earthquake (ASCE 07-05). In addition, other three design levels are proposed (severe earthquake: with a 808 -year return period, ordinary earthquake: with a 475 -year return period and minimum earthquake: with a 225 -year return period). The seismic zonation proposed here fulfils the international standards (IBC-ICC) as well as the world tendencies in this thematic.

NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans*

PubMed Central

Rhoads, Timothy W.; Prasad, Aman; Kwiecien, Nicholas W.; Merrill, Anna E.; Zawack, Kelson; Westphall, Michael S.; Schroeder, Frank C.; Kimble, Judith; Coon, Joshua J.

2015-01-01

The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress. PMID:26392051

49 CFR 173.52 - Classification codes and compatibility groups of explosives.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 2 2014-10-01 2014-10-01 false Classification codes and compatibility groups of... Class 1 § 173.52 Classification codes and compatibility groups of explosives. (a) The classification..., consists of the division number followed by the compatibility group letter. Compatibility group letters are...

Single-tube, non-isotopic, multiplex PCR/OLA assay and sequence-coded separation for simultaneous screening of 31 cystic fibrosis mutations

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

Brinson, E.C.; Adriano, T.; Bloch, W.

1994-09-01

We have developed a rapid, single-tube, non-isotopic assay that screens a patient sample for the presence of 31 cystic fibrosis (CF) mutations. This assay can identify these mutations in a single reaction tube and a single electrophoresis run. Sample preparation is a simple, boil-and-go procedure, completed in less than an hour. The assay is composed of a 15-plex PCR, followed by a 61-plex oligonucleotide ligation assay (OLA), and incorporates a novel detection scheme, Sequence Coded Separation. Initially, the multiplex PCR amplifies 15 relevant segments of the CFTR gene, simultaneously. These PCR amplicons serve as templates for the multiplex OLA, whichmore » detects the normal or mutant allele at all loci, simultaneously. Each polymorphic site is interrogated by three oligonucleotide probes, a common probe and two allele-specific probes. Each common probe is tagged with a fluorescent dye, and the competing normal and mutant allelic probes incorporate different, non-nucleotide, mobility modifiers. These modifiers are composed of hexaethylene oxide (HEO) units, incorporated as HEO phosphoramidite monomers during automated DNA synthesis. The OLA is based on both probe hybridization and the ability of DNA ligase to discriminate single base mismatches at the junction between paired probes. Each single tube assay is electrophoresed in a single gel lane of a 4-color fluorescent DNA sequencer (Applied Biosystems, Model 373A). Each of the ligation products is identified by its unique combination of electrophoretic mobility and one of three colors. The fourth color is reserved for the in-lane size standard, used by GENESCAN{sup TM} software (Applied Biosystems) to size the OLA electrophoresis products. The Genotyper{sub TM} software (Applied Biosystems) decodes these Sequence-Coded-Separation data to create a patient summary report for all loci tested.« less

A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci.

PubMed

Qian, Jing; Nunez, Sara; Reed, Eric; Reilly, Muredach P; Foulkes, Andrea S

2016-01-01

Characterizing the genetic determinants of complex diseases can be further augmented by incorporating knowledge of underlying structure or classifications of the genome, such as newly developed mappings of protein-coding genes, epigenetic marks, enhancer elements and non-coding RNAs. We apply a simple class-level testing framework, termed Genetic Class Association Testing (GenCAT), to identify protein-coding gene association with 14 cardiometabolic (CMD) related traits across 6 publicly available genome wide association (GWA) meta-analysis data resources. GenCAT uses SNP-level meta-analysis test statistics across all SNPs within a class of elements, as well as the size of the class and its unique correlation structure, to determine if the class is statistically meaningful. The novelty of findings is evaluated through investigation of regional signals. A subset of findings are validated using recently updated, larger meta-analysis resources. A simulation study is presented to characterize overall performance with respect to power, control of family-wise error and computational efficiency. All analysis is performed using the GenCAT package, R version 3.2.1. We demonstrate that class-level testing complements the common first stage minP approach that involves individual SNP-level testing followed by post-hoc ascribing of statistically significant SNPs to genes and loci. GenCAT suggests 54 protein-coding genes at 41 distinct loci for the 13 CMD traits investigated in the discovery analysis, that are beyond the discoveries of minP alone. An additional application to biological pathways demonstrates flexibility in defining genetic classes. We conclude that it would be prudent to include class-level testing as standard practice in GWA analysis. GenCAT, for example, can be used as a simple, complementary and efficient strategy for class-level testing that leverages existing data resources, requires only summary level data in the form of test statistics, and adds

Isotope and mixture effects on neoclassical transport in the pedestal

NASA Astrophysics Data System (ADS)

Pusztai, Istvan; Buller, Stefan; Omotani, John T.; Newton, Sarah L.

2017-10-01

The isotope mass scaling of the energy confinement time in tokamak plasmas differs from gyro-Bohm estimates, with implications for the extrapolation from current experiments to D-T reactors. Differences in mass scaling in L-mode and various H-mode regimes suggest that the isotope effect may originate from the pedestal. In the pedestal, sharp gradients render local diffusive estimates invalid, and global effects due to orbit-width scale profile variations have to be taken into account. We calculate neoclassical cross-field fluxes from a radially global drift-kinetic equation using the PERFECT code, to study isotope composition effects in density pedestals. The relative reduction to the peak heat flux due to global effects as a function of the density scale length is found to saturate at an isotope-dependent value that is larger for heavier ions. We also consider D-T and H-D mixtures with a focus on isotope separation. The ability to reproduce the mixture results via single-species simulations with artificial ``DT'' and ``HD'' species has been considered. These computationally convenient single ion simulations give a good estimate of the total ion heat flux in corresponding mixtures. Funding received from the International Career Grant of Vetenskapsradet (VR) (330-2014-6313) with Marie Sklodowska Curie Actions, Cofund, Project INCA 600398, and Framework Grant for Strategic Energy Research of VR (2014-5392).

Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled High-Resolution Gamma Spectrometry Systems Final Report

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

Dreyer, Jonathan G.; Wang, Tzu-Fang; Vo, Duc T.

Under a 2006 agreement between the Department of Energy (DOE) of the United States of America and the Institut de Radioprotection et de Sûreté Nucléaire (IRSN) of France, the National Nuclear Security Administration (NNSA) within DOE and IRSN initiated a collaboration to improve isotopic identification and analysis of nuclear material [i.e., plutonium (Pu) and uranium (U)]. The specific aim of the collaborative project was to develop new versions of two types of isotopic identification and analysis software: (1) the fixed-energy response-function analysis for multiple energies (FRAM) codes and (2) multi-group analysis (MGA) codes. The project is entitled Action Sheet 4more » – Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled, High-Resolution Gamma Spectrometry Systems (Action Sheet 4). FRAM and MGA/U235HI are software codes used to analyze isotopic ratios of U and Pu. FRAM is an application that uses parameter sets for the analysis of U or Pu. MGA and U235HI are two separate applications that analyze Pu or U, respectively. They have traditionally been used by safeguards practitioners to analyze gamma spectra acquired with high-resolution gamma spectrometry (HRGS) systems that are cooled by liquid nitrogen. However, it was discovered that these analysis programs were not as accurate when used on spectra acquired with a newer generation of more portable, electrically cooled HRGS (ECHRGS) systems. In response to this need, DOE/NNSA and IRSN collaborated to update the FRAM and U235HI codes to improve their performance with newer ECHRGS systems. Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL) performed this work for DOE/NNSA.« less

Applicability of integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) for the simultaneous detection of the four human enteric enterovirus species in disinfection studies

EPA Science Inventory

A newly developed integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) method and its applicability in UV disinfection studies is described. This method utilizes a singular cell culture system coupled with four RTqPCR assays to detect infectious serotypes t...

Evolution of major histocompatibility complex class I and class II genes in the brown bear

PubMed Central

2012-01-01

Background Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae. Results We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (dN) exceeded the rate of synonymous substitutions (dS) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca. Conclusions Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South–north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia. PMID:23031405

Evolution of major histocompatibility complex class I and class II genes in the brown bear.

PubMed

Kuduk, Katarzyna; Babik, Wiesław; Bojarska, Katarzyna; Sliwińska, Ewa B; Kindberg, Jonas; Taberlet, Pierre; Swenson, Jon E; Radwan, Jacek

2012-10-02

Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae. We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (dN) exceeded the rate of synonymous substitutions (dS) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca. Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South-north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia.

Proteomic validation of protease drug targets: pharmacoproteomics of matrix metalloproteinase inhibitor drugs using isotope-coded affinity tag labelling and tandem mass spectrometry.

PubMed

Butler, G S; Overall, C M

2007-01-01

We illustrate the use of quantitative proteomics, namely isotope-coded affinity tag labelling and tandem mass spectrometry, to assess the targets and effects of the blockade of matrix metalloproteinases by an inhibitor drug in a breast cancer cell culture system. Treatment of MT1-MMP-transfected MDA-MB-231 cells with AG3340 (Prinomastat) directly affected the processing a multitude of matrix metalloproteinase substrates, and indirectly altered the expression of an array of other proteins with diverse functions. Therefore, broad spectrum blockade of MMPs has wide-ranging biological consequences. In this human breast cancer cell line, secreted substrates accumulated uncleaved in the conditioned medium and plasma membrane protein substrates were retained on the cell surface, due to reduced processing and shedding of these proteins (cell surface receptors, growth factors and bioactive molecules) to the medium in the presence of the matrix metalloproteinase inhibitor. Hence, proteomic investigation of drug-perturbed cellular proteomes can identify new protease substrates and at the same time provides valuable information for target validation, drug efficacy and potential side effects prior to commitment to clinical trials.

A New Class of Pulse Compression Codes and Techniques.

DTIC Science & Technology

1980-03-26

04 11 01 12 02 13 03 14 OA DIALFL I NOTE’ BO𔃾T TRANSFORM AND DIGITAL FILTER NETWORK INVERSE TRANSFORM DRIVE FRANK CODE SAME DIGITAL FILTER ; ! ! I I...function from circuit of Fig. I with N =9 TRANSFORM INVERSE TRANSFORM SINGLE _WORD S1A ~b,.ISR -.- ISR I- SR I--~ SR SIC-- I1GENERATOR 0 fJFJ $ J$ .. J...FOR I 1 1 13 11 12 13 FROM RECEIVER TRANSMIT Q- j ~ ~ 01 02 03 0, 02 03 11 01 12 02 13 03 4 1 1 ~ 4 NOTrE: BOTH TRANSFORM ANDI I I I INVERSE TRANSFORM DRIVE

Rates for neutron-capture reactions on tungsten isotopes in iron meteorites. [Abstract only

NASA Technical Reports Server (NTRS)

Masarik, J.; Reedy, R. C.

1994-01-01

High-precision W isotopic analyses by Harper and Jacobsen indicate the W-182/W-183 ratio in the Toluca iron meteorite is shifted by -(3.0 +/- 0.9) x 10(exp -4) relative to a terrestrial standard. Possible causes of this shift are neutron-capture reactions on W during Toluca's approximately 600-Ma exposure to cosmic ray particles or radiogenic growth of W-182 from 9-Ma Hf-182 in the silicate portion of the Earth after removal of W to the Earth's core. Calculations for the rates of neutron-capture reactions on W isotopes were done to study the first possibility. The LAHET Code System (LCS) which consists of the Los Alamos High Energy Transport (LAHET) code and the Monte Carlo N-Particle(MCNP) transport code was used to numerically simulate the irradiation of the Toluca iron meteorite by galactic-cosmic-ray (GCR) particles and to calculate the rates of W(n, gamma) reactions. Toluca was modeled as a 3.9-m-radius sphere with the composition of a typical IA iron meteorite. The incident GCR protons and their interactions were modeled with LAHET, which also handled the interactions of neutrons with energies above 20 MeV. The rates for the capture of neutrons by W-182, W-183, and W-186 were calculated using the detailed library of (n, gamma) cross sections in MCNP. For this study of the possible effect of W(n, gamma) reactions on W isotope systematics, we consider the peak rates. The calculated maximum change in the normalized W-182/W-183 ratio due to neutron-capture reactions cannot account for more than 25% of the mass 182 deficit observed in Toluca W.

Isotopic Biogeochemistry

NASA Technical Reports Server (NTRS)

Hayes, J. M.

1985-01-01

An overview is provided of the biogeochemical research. The funding, productivity, personnel and facilities are reviewed. Some of the technical areas covered are: carbon isotopic records; isotopic studies of banded iron formations; isotope effects in microbial systems; studies of organic compounds in ancient sediments; and development in isotopic geochemistry and analysis.

(U) Ristra Next Generation Code Report

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

Hungerford, Aimee L.; Daniel, David John

LANL’s Weapons Physics management (ADX) and ASC program office have defined a strategy for exascale-class application codes that follows two supportive, and mutually risk-mitigating paths: evolution for established codes (with a strong pedigree within the user community) based upon existing programming paradigms (MPI+X); and Ristra (formerly known as NGC), a high-risk/high-reward push for a next-generation multi-physics, multi-scale simulation toolkit based on emerging advanced programming systems (with an initial focus on data-flow task-based models exemplified by Legion [5]). Development along these paths is supported by the ATDM, IC, and CSSE elements of the ASC program, with the resulting codes forming amore » common ecosystem, and with algorithm and code exchange between them anticipated. Furthermore, solution of some of the more challenging problems of the future will require a federation of codes working together, using established-pedigree codes in partnership with new capabilities as they come on line. The role of Ristra as the high-risk/high-reward path for LANL’s codes is fully consistent with its role in the Advanced Technology Development and Mitigation (ATDM) sub-program of ASC (see Appendix C), in particular its emphasis on evolving ASC capabilities through novel programming models and data management technologies.« less

On models of the genetic code generated by binary dichotomic algorithms.

PubMed

Gumbel, Markus; Fimmel, Elena; Danielli, Alberto; Strüngmann, Lutz

2015-02-01

In this paper we introduce the concept of a BDA-generated model of the genetic code which is based on binary dichotomic algorithms (BDAs). A BDA-generated model is based on binary dichotomic algorithms (BDAs). Such a BDA partitions the set of 64 codons into two disjoint classes of size 32 each and provides a generalization of known partitions like the Rumer dichotomy. We investigate what partitions can be generated when a set of different BDAs is applied sequentially to the set of codons. The search revealed that these models are able to generate code tables with very different numbers of classes ranging from 2 to 64. We have analyzed whether there are models that map the codons to their amino acids. A perfect matching is not possible. However, we present models that describe the standard genetic code with only few errors. There are also models that map all 64 codons uniquely to 64 classes showing that BDAs can be used to identify codons precisely. This could serve as a basis for further mathematical analysis using coding theory, for example. The hypothesis that BDAs might reflect a molecular mechanism taking place in the decoding center of the ribosome is discussed. The scan demonstrated that binary dichotomic partitions are able to model different aspects of the genetic code very well. The search was performed with our tool Beady-A. This software is freely available at http://mi.informatik.hs-mannheim.de/beady-a. It requires a JVM version 6 or higher. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

77 FR 35617 - Amendment of Class C Airspace; Colorado Springs, CO

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-14

... 44 U.S.C. 1510. #0; #0;The Code of Federal Regulations is sold by the Superintendent of Documents. #0...; Airspace Docket No. 12-AWA-4] Amendment of Class C Airspace; Colorado Springs, CO AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Final rule. SUMMARY: This action modifies the Colorado Springs, CO, Class C...

Quantitative Determination of Isotope Ratios from Experimental Isotopic Distributions

PubMed Central

Kaur, Parminder; O’Connor, Peter B.

2008-01-01

Isotope variability due to natural processes provides important information for studying a variety of complex natural phenomena from the origins of a particular sample to the traces of biochemical reaction mechanisms. These measurements require high-precision determination of isotope ratios of a particular element involved. Isotope Ratio Mass Spectrometers (IRMS) are widely employed tools for such a high-precision analysis, which have some limitations. This work aims at overcoming the limitations inherent to IRMS by estimating the elemental isotopic abundance from the experimental isotopic distribution. In particular, a computational method has been derived which allows the calculation of 13C/12C ratios from the whole isotopic distributions, given certain caveats, and these calculations are applied to several cases to demonstrate their utility. The limitations of the method in terms of the required number of ions and S/N ratio are discussed. For high-precision estimates of the isotope ratios, this method requires very precise measurement of the experimental isotopic distribution abundances, free from any artifacts introduced by noise, sample heterogeneity, or other experimental sources. PMID:17263354

EASY-II Renaissance: n, p, d, α, γ-induced Inventory Code System

NASA Astrophysics Data System (ADS)

Sublet, J.-Ch.; Eastwood, J. W.; Morgan, J. G.

2014-04-01

The European Activation SYstem has been re-engineered and re-written in modern programming languages so as to answer today's and tomorrow's needs in terms of activation, transmutation, depletion, decay and processing of radioactive materials. The new FISPACT-II inventory code development project has allowed us to embed many more features in terms of energy range: up to GeV; incident particles: alpha, gamma, proton, deuteron and neutron; and neutron physics: self-shielding effects, temperature dependence and covariance, so as to cover all anticipated application needs: nuclear fission and fusion, accelerator physics, isotope production, stockpile and fuel cycle stewardship, materials characterization and life, and storage cycle management. In parallel, the maturity of modern, truly general purpose libraries encompassing thousands of target isotopes such as TENDL-2012, the evolution of the ENDF-6 format and the capabilities of the latest generation of processing codes PREPRO, NJOY and CALENDF have allowed the activation code to be fed with more robust, complete and appropriate data: cross sections with covariance, probability tables in the resonance ranges, kerma, dpa, gas and radionuclide production and 24 decay types. All such data for the five most important incident particles (n, p, d, α, γ), are placed in evaluated data files up to an incident energy of 200 MeV. The resulting code system, EASY-II is designed as a functional replacement for the previous European Activation System, EASY-2010. It includes many new features and enhancements, but also benefits already from the feedback from extensive validation and verification activities performed with its predecessor.

Cathepsin S-cleavable, multi-block HPMA copolymers for improved SPECT/CT imaging of pancreatic cancer.

PubMed

Fan, Wei; Shi, Wen; Zhang, Wenting; Jia, Yinnong; Zhou, Zhengyuan; Brusnahan, Susan K; Garrison, Jered C

2016-10-01

This work continues our efforts to improve the diagnostic and radiotherapeutic effectiveness of nanomedicine platforms by developing approaches to reduce the non-target accumulation of these agents. Herein, we developed multi-block HPMA copolymers with backbones that are susceptible to cleavage by cathepsin S, a protease that is abundantly expressed in tissues of the mononuclear phagocyte system (MPS). Specifically, a bis-thiol terminated HPMA telechelic copolymer containing 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) was synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization. Three maleimide modified linkers with different sequences, including cathepsin S degradable oligopeptide, scramble oligopeptide and oligo ethylene glycol, were subsequently synthesized and used for the extension of the HPMA copolymers by thiol-maleimide click chemistry. All multi-block HPMA copolymers could be labeled by (177)Lu with high labeling efficiency and exhibited high serum stability. In vitro cleavage studies demonstrated highly selective and efficient cathepsin S mediated cleavage of the cathepsin S-susceptible multi-block HPMA copolymer. A modified multi-block HPMA copolymer series capable of Förster Resonance Energy Transfer (FRET) was utilized to investigate the rate of cleavage of the multi-block HPMA copolymers in monocyte-derived macrophages. Confocal imaging and flow cytometry studies revealed substantially higher rates of cleavage for the multi-block HPMA copolymers containing the cathepsin S-susceptible linker. The efficacy of the cathepsin S-cleavable multi-block HPMA copolymer was further examined using an in vivo model of pancreatic ductal adenocarcinoma. Based on the biodistribution and SPECT/CT studies, the copolymer extended with the cathepsin S susceptible linker exhibited significantly faster clearance and lower non-target retention without compromising tumor targeting. Overall, these results indicate that

Shell-model-based deformation analysis of light cadmium isotopes

NASA Astrophysics Data System (ADS)

Schmidt, T.; Heyde, K. L. G.; Blazhev, A.; Jolie, J.

2017-07-01

Large-scale shell-model calculations for the even-even cadmium isotopes 98Cd-108Cd have been performed with the antoine code in the π (2 p1 /2;1 g9 /2) ν (2 d5 /2;3 s1 /2;2 d3 /2;1 g7 /2;1 h11 /2) model space without further truncation. Known experimental energy levels and B (E 2 ) values could be well reproduced. Taking these calculations as a starting ground we analyze the deformation parameters predicted for the Cd isotopes as a function of neutron number N and spin J using the methods of model independent invariants introduced by Kumar [Phys. Rev. Lett. 28, 249 (1972), 10.1103/PhysRevLett.28.249] and Cline [Annu. Rev. Nucl. Part. Sci. 36, 683 (1986), 10.1146/annurev.ns.36.120186.003343].

A New Class of Pandiagonal Squares

ERIC Educational Resources Information Center

Loly, P. D.; Steeds, M. J.

2005-01-01

An interesting class of purely pandiagonal, i.e. non-magic, whole number (integer) squares of orders (row/column dimension) of the powers of two which are related to Gray codes and square Karnaugh maps has been identified. Treated as matrices these squares possess just two non-zero eigenvalues. The construction of these squares has been automated…

Constrained coding for the deep-spaced optical channel

NASA Technical Reports Server (NTRS)

Moision, B.; Hamkins, J.

2002-01-01

In this paper, we demonstrate a class of low-complexity modulation codes satisfying the (d,k) constraint that offer throughput gains over M-PPM on the order of 10-15%, which translate into SNR gains of .4 - .6 dB.

Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes.

PubMed

Oren, Aharon; da Costa, Milton S; Garrity, George M; Rainey, Fred A; Rosselló-Móra, Ramon; Schink, Bernhard; Sutcliffe, Iain; Trujillo, Martha E; Whitman, William B

2015-11-01

The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.

Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA).

PubMed

Guo, Guangyu; Li, Ning

2011-07-01

In the quantitative proteomic studies, numerous in vitro and in vivo peptide labeling strategies have been successfully applied to measure differentially regulated protein and peptide abundance. These approaches have been proven to be versatile and repeatable in biological discoveries. (15)N metabolic labeling is one of these widely adopted and economical methods. However, due to the differential incorporation rates of (15)N or (14)N, the labeling results produce imperfectly matched isotopic envelopes between the heavy and light nitrogen-labeled peptides. In the present study, we have modified the solid Arabidopsis growth medium to standardize the (15)N supply, which led to a uniform incorporation of (15)N into the whole plant protein complement. The incorporation rate (97.43±0.11%) of (15)N into (15)N-coded peptides was determined by correlating the intensities of peptide ions with the labeling efficiencies according to Gaussian distribution. The resulting actual incorporation rate (97.44%) and natural abundance of (15)N/(14)N-coded peptides are used to re-calculate the intensities of isotopic envelopes of differentially labeled peptides, respectively. A modified (15)N/(14)N stable isotope labeling strategy, SILIA, is assessed and the results demonstrate that this approach is able to differentiate the fold change in protein abundance down to 10%. The machine dynamic range limitation and purification step will make the precursor ion ratio deriving from the actual ratio fold change. It is suggested that the differentially mixed (15)N-coded and (14)N-coded plant protein samples that are used to establish the protein abundance standard curve should be prepared following a similar protein isolation protocol used to isolate the proteins to be quantitated. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Genomic localization of the human gene encoding Dr1, a negative modulator of transcription of class II and class III genes.

PubMed

Purrello, M; Di Pietro, C; Rapisarda, A; Viola, A; Corsaro, C; Motta, S; Grzeschik, K H; Sichel, G

1996-01-01

Dr1 is a nuclear protein of 19 kDa that exists in the nucleoplasm as a homotetramer. By binding to TBP (the DNA-binding subunit of TFIID, and also a subunit of SL1 and TFIIIB), the protein blocks class II and class III preinitiation complex assembly, thus repressing the activity of the corresponding promoters. Since transcription of class I genes is unaffected by Dr1. it has been proposed that the protein may coordinate the expression of class I, class II and class III genes. By somatic cell genetics and fluorescence in situ hybridization, we have localized the gene (DR1), present in the genome of higher eukaryotes as a single copy, to human chromosome region 1p21-->p13. The nucleotide sequence conservation of the coding segment of the gene, as determined by Noah's ark blot analysis, and its ubiquitous transcription suggest that Dr1 has an important biological role, which could be related to the negative control of cell proliferation.

Production of medical isotopes from a thorium target irradiated by light charged particles up to 70 MeV

NASA Astrophysics Data System (ADS)

Duchemin, C.; Guertin, A.; Haddad, F.; Michel, N.; Métivier, V.

2015-02-01

The irradiation of a thorium target by light charged particles (protons and deuterons) leads to the production of several isotopes of medical interest. Direct nuclear reaction allows the production of Protactinium-230 which decays to Uranium-230 the mother nucleus of Thorium-226, a promising isotope for alpha radionuclide therapy. The fission of Thorium-232 produces fragments of interest like Molybdenum-99, Iodine-131 and Cadmium-115g. We focus our study on the production of these isotopes, performing new cross section measurements and calculating production yields. Our new sets of data are compared with the literature and the last version of the TALYS code.

Production of medical isotopes from a thorium target irradiated by light charged particles up to 70 MeV.

PubMed

Duchemin, C; Guertin, A; Haddad, F; Michel, N; Métivier, V

2015-02-07

The irradiation of a thorium target by light charged particles (protons and deuterons) leads to the production of several isotopes of medical interest. Direct nuclear reaction allows the production of Protactinium-230 which decays to Uranium-230 the mother nucleus of Thorium-226, a promising isotope for alpha radionuclide therapy. The fission of Thorium-232 produces fragments of interest like Molybdenum-99, Iodine-131 and Cadmium-115g. We focus our study on the production of these isotopes, performing new cross section measurements and calculating production yields. Our new sets of data are compared with the literature and the last version of the TALYS code.

Nonlinear viscoplasticity in class="text smallcaps">ASPECT: benchmarking and applications to subduction

NASA Astrophysics Data System (ADS)

Glerum, Anne; Thieulot, Cedric; Fraters, Menno; Blom, Constantijn; Spakman, Wim

2018-03-01

class="text smallcaps">ASPECT (Advanced Solver for Problems in Earth's ConvecTion) is a massively parallel finite element code originally designed for modeling thermal convection in the mantle with a Newtonian rheology. The code is characterized by modern numerical methods, high-performance parallelism and extensibility. This last characteristic is illustrated in this work: we have extended the use of class="text smallcaps">ASPECT from global thermal convection modeling to upper-mantle-scale applications of subduction.

class="p">Subduction modeling generally requires the tracking of multiple materials with different properties and with nonlinear viscous and viscoplastic rheologies. To this end, we implemented a frictional plasticity criterion that is combined with a viscous diffusion and dislocation creep rheology. Because class="text smallcaps">ASPECT uses compositional fields to represent different materials, all material parameters are made dependent on a user-specified number of fields.

class="p">The goal of this paper is primarily to describe and verify our implementations of complex, multi-material rheology by reproducing the results of four well-known two-dimensional benchmarks: the indentor benchmark, the brick experiment, the sandbox experiment and the slab detachment benchmark. Furthermore, we aim to provide hands-on examples for prospective users by demonstrating the use of multi-material viscoplasticity with three-dimensional, thermomechanical models of oceanic subduction, putting class="text smallcaps">ASPECT on the map as a community code for high-resolution, nonlinear rheology subduction modeling.

Color Coded Cards for Student Behavior Management in Higher Education Environments

ERIC Educational Resources Information Center

Alhalabi, Wadee; Alhalabi, Mobeen

2017-01-01

The Color Coded Cards system as a possibly effective class management tool is the focus of this research. The Color Coded Cards system involves each student being given a card with a specific color based on his or her behavior. The main objective of the research is to find out whether this system effectively improves students' behavior, thus…

Using Abbreviated Injury Scale (AIS) codes to classify Computed Tomography (CT) features in the Marshall System.

PubMed

Lesko, Mehdi M; Woodford, Maralyn; White, Laura; O'Brien, Sarah J; Childs, Charmaine; Lecky, Fiona E

2010-08-06

The purpose of Abbreviated Injury Scale (AIS) is to code various types of Traumatic Brain Injuries (TBI) based on their anatomical location and severity. The Marshall CT Classification is used to identify those subgroups of brain injured patients at higher risk of deterioration or mortality. The purpose of this study is to determine whether and how AIS coding can be translated to the Marshall Classification Initially, a Marshall Class was allocated to each AIS code through cross-tabulation. This was agreed upon through several discussion meetings with experts from both fields (clinicians and AIS coders). Furthermore, in order to make this translation possible, some necessary assumptions with regards to coding and classification of mass lesions and brain swelling were essential which were all approved and made explicit. The proposed method involves two stages: firstly to determine all possible Marshall Classes which a given patient can attract based on allocated AIS codes; via cross-tabulation and secondly to assign one Marshall Class to each patient through an algorithm. This method can be easily programmed in computer softwares and it would enable future important TBI research programs using trauma registry data.

Using Abbreviated Injury Scale (AIS) codes to classify Computed Tomography (CT) features in the Marshall System

PubMed Central

2010-01-01

Background The purpose of Abbreviated Injury Scale (AIS) is to code various types of Traumatic Brain Injuries (TBI) based on their anatomical location and severity. The Marshall CT Classification is used to identify those subgroups of brain injured patients at higher risk of deterioration or mortality. The purpose of this study is to determine whether and how AIS coding can be translated to the Marshall Classification Methods Initially, a Marshall Class was allocated to each AIS code through cross-tabulation. This was agreed upon through several discussion meetings with experts from both fields (clinicians and AIS coders). Furthermore, in order to make this translation possible, some necessary assumptions with regards to coding and classification of mass lesions and brain swelling were essential which were all approved and made explicit. Results The proposed method involves two stages: firstly to determine all possible Marshall Classes which a given patient can attract based on allocated AIS codes; via cross-tabulation and secondly to assign one Marshall Class to each patient through an algorithm. Conclusion This method can be easily programmed in computer softwares and it would enable future important TBI research programs using trauma registry data. PMID:20691038

Carbon isotope composition of low molecular weight hydrocarbons and monocarboxylic acids from Murchison meteorite

NASA Technical Reports Server (NTRS)

Yuen, G.; Blair, N.; Des Marais, D. J.; Chang, S.

1984-01-01

Carbon isotopic compositions have been measured for individual hydrocarbons and monocarboxylic acids from the Murchison meteorite, a C2 carbonaceous chondrite which fell in Australia in 1969. With few exceptions, notably benzene, the volatile products are substantially isotopically heavier than their terrestrial counterparts, signifying their extraterrestrial origin. For both classes of compounds, the ratio of C-13 to C-12 decreases with increasing carbon number in a roughly parallel manner, and each carboxylic acid exhibits a higher isotopic ratio than the hydrocarbon containing the same number of carbon atoms. These trends are consistent with the kinetically controlled synthesis of higher homologues from lower ones. The results suggest the possibility that the production mechanisms for hydrocarbons and carboxylic acids may be similar, and impose constraints on the identity of the reactant species.

R classes and methods for SNP array data.

PubMed

Scharpf, Robert B; Ruczinski, Ingo

2010-01-01

The Bioconductor project is an "open source and open development software project for the analysis and comprehension of genomic data" (1), primarily based on the R programming language. Infrastructure packages, such as Biobase, are maintained by Bioconductor core developers and serve several key roles to the broader community of Bioconductor software developers and users. In particular, Biobase introduces an S4 class, the eSet, for high-dimensional assay data. Encapsulating the assay data as well as meta-data on the samples, features, and experiment in the eSet class definition ensures propagation of the relevant sample and feature meta-data throughout an analysis. Extending the eSet class promotes code reuse through inheritance as well as interoperability with other R packages and is less error-prone. Recently proposed class definitions for high-throughput SNP arrays extend the eSet class. This chapter highlights the advantages of adopting and extending Biobase class definitions through a working example of one implementation of classes for the analysis of high-throughput SNP arrays.

The trellis complexity of convolutional codes

NASA Technical Reports Server (NTRS)

Mceliece, R. J.; Lin, W.

1995-01-01

It has long been known that convolutional codes have a natural, regular trellis structure that facilitates the implementation of Viterbi's algorithm. It has gradually become apparent that linear block codes also have a natural, though not in general a regular, 'minimal' trellis structure, which allows them to be decoded with a Viterbi-like algorithm. In both cases, the complexity of the Viterbi decoding algorithm can be accurately estimated by the number of trellis edges per encoded bit. It would, therefore, appear that we are in a good position to make a fair comparison of the Viterbi decoding complexity of block and convolutional codes. Unfortunately, however, this comparison is somewhat muddled by the fact that some convolutional codes, the punctured convolutional codes, are known to have trellis representations that are significantly less complex than the conventional trellis. In other words, the conventional trellis representation for a convolutional code may not be the minimal trellis representation. Thus, ironically, at present we seem to know more about the minimal trellis representation for block than for convolutional codes. In this article, we provide a remedy, by developing a theory of minimal trellises for convolutional codes. (A similar theory has recently been given by Sidorenko and Zyablov). This allows us to make a direct performance-complexity comparison for block and convolutional codes. A by-product of our work is an algorithm for choosing, from among all generator matrices for a given convolutional code, what we call a trellis-minimal generator matrix, from which the minimal trellis for the code can be directly constructed. Another by-product is that, in the new theory, punctured convolutional codes no longer appear as a special class, but simply as high-rate convolutional codes whose trellis complexity is unexpectedly small.

PatternCoder: A Programming Support Tool for Learning Binary Class Associations and Design Patterns

ERIC Educational Resources Information Center

Paterson, J. H.; Cheng, K. F.; Haddow, J.

2009-01-01

PatternCoder is a software tool to aid student understanding of class associations. It has a wizard-based interface which allows students to select an appropriate binary class association or design pattern for a given problem. Java code is then generated which allows students to explore the way in which the class associations are implemented in a…

The extent of aqueous alteration in C-class asteroids, and the survival of presolar isotopic signatures in chondrites

NASA Astrophysics Data System (ADS)

Trigo-Rodriguez, J. M.

2011-05-01

Several sample return missions are being planned by different space agencies for in situ sampling of undifferentiated bodies. Such missions wish to bring back to Earth pristine samples from C-class asteroids and comets to obtain clues on solar system formation conditions. A careful selection of targeted areas is required as many C-class asteroids and periodic comets have been subjected to collisional and space weathering processing since their formation. Their surfaces have been reworked by impacts as pointed out by the brecciated nature of many chondrites arrived to Earth, exhibiting different levels of thermal and aqueous alteration. It is not surprising that pristine chondrites can be considered quite rare in meteorite collections because they were naturally sampled in collisions, but several groups of carbonaceous chondrites contain a few members with promising unaltered properties. The CI and CM groups suffered extensive aqueous alteration [1], but for the most part escaped thermal metamorphism (only a few CMs evidence heating temperature over several hundred K). Both chondrite groups are water-rich, containing secondary minerals as consequence of the pervasive alteration of their primary mineral phases [2]. CO, CV, and CR chondrite groups suffered much less severe aqueous alteration, but some CRs are moderately aqueously altered. All five groups are good candidates to find unequilibrated materials between samples unaffected by aqueous alteration or metamorphism. The water was incorporated during accretion, and was released as consequence of shock after impact compaction, and/or by mild radiogenic heating. Primary minerals were transformed by water into secondary ones. Water soaking the bodies participated in chemical homogenization of the different components [1]. Hydrothermal alteration and collisional metamorphism changed the abundances of isotopically distinguishable presolar silicates [3]. Additional instruments in the landers to identify aqueous

Some practical universal noiseless coding techniques

NASA Technical Reports Server (NTRS)

Rice, R. F.

1979-01-01

Some practical adaptive techniques for the efficient noiseless coding of a broad class of such data sources are developed and analyzed. Algorithms are designed for coding discrete memoryless sources which have a known symbol probability ordering but unknown probability values. A general applicability of these algorithms to solving practical problems is obtained because most real data sources can be simply transformed into this form by appropriate preprocessing. These algorithms have exhibited performance only slightly above all entropy values when applied to real data with stationary characteristics over the measurement span. Performance considerably under a measured average data entropy may be observed when data characteristics are changing over the measurement span.

Cooperative optimization and their application in LDPC codes

NASA Astrophysics Data System (ADS)

Chen, Ke; Rong, Jian; Zhong, Xiaochun

2008-10-01

Cooperative optimization is a new way for finding global optima of complicated functions of many variables. The proposed algorithm is a class of message passing algorithms and has solid theory foundations. It can achieve good coding gains over the sum-product algorithm for LDPC codes. For (6561, 4096) LDPC codes, the proposed algorithm can achieve 2.0 dB gains over the sum-product algorithm at BER of 4×10-7. The decoding complexity of the proposed algorithm is lower than the sum-product algorithm can do; furthermore, the former can achieve much lower error floor than the latter can do after the Eb / No is higher than 1.8 dB.

Isotope chirality in long-armed multifunctional organosilicon ("Cephalopod") molecules.

PubMed

Barabás, Béla; Kurdi, Róbert; Zucchi, Claudia; Pályi, Gyula

2018-07-01

Long-armed multifunctional organosilicon molecules display self-replicating and self-perfecting behavior in asymmetric autocatalysis (Soai reaction). Two representatives of this class were studied by statistical methods aiming at determination of probabilities of natural abundance chiral isotopomers. The results, reported here, show an astonishing richness of possibilities of the formation of chiral isotopically substituted derivatives. This feature could serve as a model for the evolution of biological chirality in prebiotic and early biotic stereochemistry. © 2018 Wiley Periodicals, Inc.

Stable hydrogen and carbon isotope ratios of extractable hydrocarbons in the Murchison meteorite

NASA Technical Reports Server (NTRS)

Krishnamurthy, R. V.; Epstein, S.; Pizzarello, S.; Cronin, J. R.; Yuen, G. U.

1991-01-01

A fairly fool-proof method to ensure that the compounds isolated from meteorites are truly part of the meteorites and not an artifact introduced by exposure to the terrestrial environment, storage, or handling is presented. The stable carbon and hydrogen isotope ratios in several of the chemical compounds extracted from the Murchison meteorite were measured. The results obtained by studying the amino acids in this meteorite gave very unusual hydrogen and carbon isotope ratios. The technique was extended to the different classes of hydrocarbons and the hydrocarbons were isolated using a variety of separation techniques. The results and methods used in this investigation are described in this two page paper.

Trellis phase codes for power-bandwith efficient satellite communications

NASA Technical Reports Server (NTRS)

Wilson, S. G.; Highfill, J. H.; Hsu, C. D.; Harkness, R.

1981-01-01

Support work on improved power and spectrum utilization on digital satellite channels was performed. Specific attention is given to the class of signalling schemes known as continuous phase modulation (CPM). The specific work described in this report addresses: analytical bounds on error probability for multi-h phase codes, power and bandwidth characterization of 4-ary multi-h codes, and initial results of channel simulation to assess the impact of band limiting filters and nonlinear amplifiers on CPM performance.

Methane clumped isotopes: Progress and potential for a new isotopic tracer

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

Douglas, Peter M. J.; Stolper, Daniel A.; Eiler, John M.

The isotopic composition of methane is of longstanding geochemical interest, with important implications for understanding hydrocarbon systems, atmospheric greenhouse gas concentrations, the global carbon cycle, and life in extreme environments. Recent analytical developments focusing on multiply substituted isotopologues (‘clumped isotopes’) are opening a potentially valuable new window into methane geochemistry. When methane forms in internal isotopic equilibrium, clumped isotopes can provide a direct record of formation temperature, making this property particularly valuable for identifying different methane origins. However, it has also become clear that in certain settings methane clumped isotope measurements record kinetic rather than equilibrium isotope effects. Here wemore » present a substantially expanded dataset of methane clumped isotope analyses, and provide a synthesis of the current interpretive framework for this parameter. We review different processes affecting methane clumped isotope compositions, describe the relationships between conventional isotope and clumped isotope data, and summarize the types of information that this measurement can provide in different Earth and planetary environments.« less

Temperature dependence of the symmetry energy and neutron skins in Ni, Sn, and Pb isotopic chains

NASA Astrophysics Data System (ADS)

Antonov, A. N.; Kadrev, D. N.; Gaidarov, M. K.; Sarriguren, P.; de Guerra, E. Moya

2017-02-01

The temperature dependence of the symmetry energy for isotopic chains of even-even Ni, Sn, and Pb nuclei is investigated in the framework of the local density approximation (LDA). The Skyrme energy density functional with two Skyrme-class effective interactions, SkM* and SLy4, is used in the calculations. The temperature-dependent proton and neutron densities are calculated through the hfbtho code that solves the nuclear Skyrme-Hartree-Fock-Bogoliubov problem by using the cylindrical transformed deformed harmonic-oscillator basis. In addition, two other density distributions of 208Pb, namely the Fermi-type density determined within the extended Thomas-Fermi (TF) method and symmetrized-Fermi local density obtained within the rigorous density functional approach, are used. The kinetic energy densities are calculated either by the hfbtho code or, for a comparison, by the extended TF method up to second order in temperature (with T2 term). Alternative ways to calculate the symmetry energy coefficient within the LDA are proposed. The results for the thermal evolution of the symmetry energy coefficient in the interval T =0 -4 MeV show that its values decrease with temperature. The temperature dependence of the neutron and proton root-mean-square radii and corresponding neutron skin thickness is also investigated, showing that the effect of temperature leads mainly to a substantial increase of the neutron radii and skins, especially in the more neutron-rich nuclei, a feature that may have consequences on astrophysical processes and neutron stars.

77 FR 40492 - Revocation of Class D Airspace; Andalusia, AL; and Amendment of Class E Airspace; Fort Rucker, AL

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-10

... Alabama Regional Airport at Bill Benton Field has closed, and amends Class E Airspace at Fort Rucker, AL, by recognizing the airport's name change to South Alabama Regional Airport at Bill Benton Field. This... reference action under title 1, Code of Federal Regulations, part 51, subject to the annual revision of FAA...

Effective modification of cell death-inducing intracellular peptides by means of a photo-cleavable peptide array-based screening system.

PubMed

Kozaki, Ikko; Shimizu, Kazunori; Honda, Hiroyuki

2017-08-01

Intracellular functional peptides that play a significant role inside cells have been receiving a lot of attention as regulators of cellular activity. Previously, we proposed a novel screening system for intracellular functional peptides; it combined a photo-cleavable peptide array system with cell-penetrating peptides (CPPs). Various peptides can be delivered into cells and intracellular functions of the peptides can be assayed by means of our system. The aim of the present study was to demonstrate that the proposed screening system can be used for assessing the intracellular activity of peptides. The cell death-inducing peptide (LNLISKLF) identified in a mitochondria-targeting domain (MTD) of the Noxa protein served as an original peptide sequence for screening of peptides with higher activity via modification of the peptide sequence. We obtained 4 peptides with higher activity, in which we substituted serine (S) at the fifth position with phenylalanine (F), valine (V), tryptophan (W), or tyrosine (Y). During analysis of the mechanism of action, the modified peptides induced an increase in intracellular calcium concentration, which was caused by the treatment with the original peptide. Higher capacity for cell death induction by the modified peptides may be caused by increased hydrophobicity or an increased number of aromatic residues. Thus, the present work suggests that the intracellular activity of peptides can be assessed using the proposed screening system. It could be used for identifying intracellular functional peptides with higher activity through comprehensive screening. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Intrasystem Analysis Program (IAP) code summaries

NASA Astrophysics Data System (ADS)

Dobmeier, J. J.; Drozd, A. L. S.; Surace, J. A.

1983-05-01

This report contains detailed descriptions and capabilities of the codes that comprise the Intrasystem Analysis Program. The four codes are: Intrasystem Electromagnetic Compatibility Analysis Program (IEMCAP), General Electromagnetic Model for the Analysis of Complex Systems (GEMACS), Nonlinear Circuit Analysis Program (NCAP), and Wire Coupling Prediction Models (WIRE). IEMCAP is used for computer-aided evaluation of electromagnetic compatibility (ECM) at all stages of an Air Force system's life cycle, applicable to aircraft, space/missile, and ground-based systems. GEMACS utilizes a Method of Moments (MOM) formalism with the Electric Field Integral Equation (EFIE) for the solution of electromagnetic radiation and scattering problems. The code employs both full matrix decomposition and Banded Matrix Iteration solution techniques and is expressly designed for large problems. NCAP is a circuit analysis code which uses the Volterra approach to solve for the transfer functions and node voltage of weakly nonlinear circuits. The Wire Programs deal with the Application of Multiconductor Transmission Line Theory to the Prediction of Cable Coupling for specific classes of problems.

Performance Theories for Sentence Coding: Some Quantitative Models

ERIC Educational Resources Information Center

Aaronson, Doris; And Others

1977-01-01

This study deals with the patterns of word-by-word reading times over a sentence when the subject must code the linguistic information sufficiently for immediate verbatim recall. A class of quantitative models is considered that would account for reading times at phrase breaks. (Author/RM)

On the Effects of Social Class on Language Use: A Fresh Look at Bernstein's Theory

ERIC Educational Resources Information Center

Aliakbari, Mohammad; Allahmoradi, Nazal

2014-01-01

Basil Bernstein (1971) introduced the notion of the Restricted and the Elaborated code, claiming that working-class speakers have access only to the former but middle-class members to both. In an attempt to test this theory in the Iranian context and to investigate the effect of social class on the quality of students language use, we examined the…

Laser isotope separation of erbium and other isotopes

DOEpatents

Haynam, Christopher A.; Worden, Earl F.

1995-01-01

Laser isotope separation is accomplished using at least two photoionization pathways of an isotope simultaneously, where each pathway comprises two or more transition steps. This separation method has been applied to the selective photoionization of erbium isotopes, particularly for the enrichment of .sup.167 Er. The hyperfine structure of .sup.167 Er was used to find two three-step photoionization pathways having a common upper energy level.

Determination of the delta(2H/1H)of Water: RSIL Lab Code 1574

USGS Publications Warehouse

Revesz, Kinga; Coplen, Tyler B.

2008-01-01

Reston Stable Isotope Laboratory (RSIL) lab code 1574 describes a method used to determine the relative hydrogen isotope-ratio delta(2H,1H), abbreviated hereafter as d2H of water. The d2H measurement of water also is a component of the National Water Quality Laboratory (NWQL) schedules 1142 and 1172. The water is collected unfiltered in a 60-mL glass bottle and capped with a Polyseal cap. In the laboratory, the water sample is equilibrated with gaseous hydrogen using a platinum catalyst (Horita, 1988; Horita and others, 1989; Coplen and others, 1991). The reaction for the exchange of one hydrogen atom is shown in equation 1.

Error threshold for color codes and random three-body Ising models.

PubMed

Katzgraber, Helmut G; Bombin, H; Martin-Delgado, M A

2009-08-28

We study the error threshold of color codes, a class of topological quantum codes that allow a direct implementation of quantum Clifford gates suitable for entanglement distillation, teleportation, and fault-tolerant quantum computation. We map the error-correction process onto a statistical mechanical random three-body Ising model and study its phase diagram via Monte Carlo simulations. The obtained error threshold of p(c) = 0.109(2) is very close to that of Kitaev's toric code, showing that enhanced computational capabilities do not necessarily imply lower resistance to noise.

Network coding based joint signaling and dynamic bandwidth allocation scheme for inter optical network unit communication in passive optical networks

NASA Astrophysics Data System (ADS)

Wei, Pei; Gu, Rentao; Ji, Yuefeng

2014-06-01

As an innovative and promising technology, network coding has been introduced to passive optical networks (PON) in recent years to support inter optical network unit (ONU) communication, yet the signaling process and dynamic bandwidth allocation (DBA) in PON with network coding (NC-PON) still need further study. Thus, we propose a joint signaling and DBA scheme for efficiently supporting differentiated services of inter ONU communication in NC-PON. In the proposed joint scheme, the signaling process lays the foundation to fulfill network coding in PON, and it can not only avoid the potential threat to downstream security in previous schemes but also be suitable for the proposed hybrid dynamic bandwidth allocation (HDBA) scheme. In HDBA, a DBA cycle is divided into two sub-cycles for applying different coding, scheduling and bandwidth allocation strategies to differentiated classes of services. Besides, as network traffic load varies, the entire upstream transmission window for all REPORT messages slides accordingly, leaving the transmission time of one or two sub-cycles to overlap with the bandwidth allocation calculation time at the optical line terminal (the OLT), so that the upstream idle time can be efficiently eliminated. Performance evaluation results validate that compared with the existing two DBA algorithms deployed in NC-PON, HDBA demonstrates the best quality of service (QoS) support in terms of delay for all classes of services, especially guarantees the end-to-end delay bound of high class services. Specifically, HDBA can eliminate queuing delay and scheduling delay of high class services, reduce those of lower class services by at least 20%, and reduce the average end-to-end delay of all services over 50%. Moreover, HDBA also achieves the maximum delay fairness between coded and uncoded lower class services, and medium delay fairness for high class services.

Hydrogen Isotopes in Amino Acids and Soils Offer New Potential to Study Complex Processes

NASA Astrophysics Data System (ADS)

Fogel, M. L.; Newsome, S. D.; Williams, E. K.; Bradley, C. J.; Griffin, P.; Nakamoto, B. J.

2016-12-01

Hydrogen isotopes have been analyzed extensively in the earth and biogeosciences to trace water through various environmental systems. The majority of the measurements have been made on water in rocks and minerals (inorganic) or non-exchangeable H in lipids (organic), important biomarkers that represent a small fraction of the organic molecules synthesized by living organisms. Our lab has been investigating hydrogen isotopes in amino acids and complex soil organic matter, which have traditionally been thought to be too complex to interpret owing to complications from potentially exchangeable hydrogen. For the amino acids, we show how hydrogen in amino acids originates from two sources, food and water, and demonstrate that hydrogen isotopes can be routed directly between organisms. Amino acid hydrogen isotopes may unravel cycling in extremophiles in order to discover novel biochemical pathways central to the organism. For soil organic matter, recent approaches to understanding the origin of soil organic matter are pointing towards root exudates along with microbial biomass as the source, rather than aboveground leaf litter. Having an isotope tracer in very complex, potentially exchangeable organic matter can be handled with careful experimentation. Although no new instrumentation is being used per se, extension of classes of organic matter to isotope measurements has potential to open up new doors for understanding organic matter cycling on earth and in planetary materials.

Laser isotope separation of erbium and other isotopes

DOEpatents

Haynam, C.A.; Worden, E.F.

1995-08-22

Laser isotope separation is accomplished using at least two photoionization pathways of an isotope simultaneously, where each pathway comprises two or more transition steps. This separation method has been applied to the selective photoionization of erbium isotopes, particularly for the enrichment of {sup 167}Er. The hyperfine structure of {sup 167}Er was used to find two three-step photoionization pathways having a common upper energy level. 3 figs.

The Reliability of Pharyngeal High Resolution Manometry with Impedance for Derivation of Measures of Swallowing Function in Healthy Volunteers

PubMed Central

Omari, Taher I.; Savilampi, Johanna; Kokkinn, Karmen; Schar, Mistyka; Lamvik, Kristin; Doeltgen, Sebastian; Cock, Charles

2016-01-01

Purpose. We evaluated the intra- and interrater agreement and test-retest reliability of analyst derivation of swallow function variables based on repeated high resolution manometry with impedance measurements. Methods. Five subjects swallowed 10 × 10 mL saline on two occasions one week apart producing a database of 100 swallows. Swallows were repeat-analysed by six observers using software. Swallow variables were indicative of contractility, intrabolus pressure, and flow timing. Results. The average intraclass correlation coefficients (ICC) for intra- and interrater comparisons of all variable means showed substantial to excellent agreement (intrarater ICC 0.85–1.00; mean interrater ICC 0.77–1.00). Test-retest results were less reliable. ICC for test-retest comparisons ranged from slight to excellent depending on the class of variable. Contractility variables differed most in terms of test-retest reliability. Amongst contractility variables, UES basal pressure showed excellent test-retest agreement (mean ICC 0.94), measures of UES postrelaxation contractile pressure showed moderate to substantial test-retest agreement (mean Interrater ICC 0.47–0.67), and test-retest agreement of pharyngeal contractile pressure ranged from slight to substantial (mean Interrater ICC 0.15–0.61). Conclusions. Test-retest reliability of HRIM measures depends on the class of variable. Measures of bolus distension pressure and flow timing appear to be more test-retest reliable than measures of contractility. PMID:27190520

Raman scattering method and apparatus for measuring isotope ratios and isotopic abundances

DOEpatents

Harney, Robert C.; Bloom, Stewart D.

1978-01-01

Raman scattering is used to measure isotope ratios and/or isotopic abundances. A beam of quasi-monochromatic photons is directed onto the sample to be analyzed, and the resulting Raman-scattered photons are detected and counted for each isotopic species of interest. These photon counts are treated mathematically to yield the desired isotope ratios or isotopic abundances.

A Learner-Centered Spiral Knowledge Approach to Teaching Isotope Geology

NASA Astrophysics Data System (ADS)

Reid, M. R.

2006-12-01

Aided by the insights I gained by participation in the Arizona Board of Regents Tri-University Collaboration on Learner-Centered Practice, I made major changes to a graduate course in isotope geology (GLG617), including: 1) implementation of a spiral knowledge approach (e.g., Bruner, 1990; Dyar et al., 2004); 2) incorporation of more learner-centered in-class activities; and 3) more explicit emphasis on skills that I regarded as important for success in geochemistry. In the geosciences, the field of isotope geology is now an essential area of inquiry with implications for geologic timescales, climate information, tracing geochemical processes, and biological evolution, to name a few. The traditional approach to teaching isotope geology suffers from the fact that learning tends to be compartmentalized by technique/approach and one subfield (e.g., stable or radiogenic isotopes) is usually favored by appearing earlier in semester. To make learning more integrated, I employed a simplified spiral learning approach so that common principles could be revisited several times over the course of the semester and, in so doing, students' grasp of the fundamental principles could be scaffolded into greater understanding. Other learner-centered changes to the course included more explicit emphasis on helping students become comfortable with interpreting data displayed graphically and explicit emphasis on helping students give and evaluate oral presentations that rely on isotope data. I also developed a detailed grading rubric for the final paper and allowed students to have a draft of their final papers evaluated and graded (guided by Huba and Freed, 2000) A number of cooperative learning activities developed specifically for this course (19 in all) enabled me to gain a better appreciation for students' learning. Activities included pair share, round-robin, small group explorations of techniques and case studies (sometimes as introduction to, sometimes as review of material

Effect Of Substrates On The Fractionation Of Hydrogen Isotopes During Lipid-Biosynthesis By Haloarcula marismortui

NASA Astrophysics Data System (ADS)

Dirghangi, S. S.; Pagani, M.

2010-12-01

Lipids form an important class of proxies for paleoclimatological research, and hydrogen isotope ratios of lipids are being increasingly used for understanding changes in the hydrological system. Proper understanding of hydrogen isotope fractionation during lipid biosynthesis is therefore important and attention has been directed toward understanding the magnitude of hydrogen isotope fractionation that occurs during lipid biosynthesis in various organisms. Hydrogen isotope ratios of lipids depend on the hydrogen isotopic composition of the ambient water, hydrogen isotopic composition of NADPH used during biosynthesis, growth conditions, pathways of lipid biosynthesis, and substrates in the case of heterotrophic organisms. Recently it has been observed that NADPH contributes a significant part of the hydrogen in fatty acids synthesized by bacteria during heterotrophic growth (Zhang et al, 2009). As NADPH is formed by reduction of NADP+ during metabolism of substrates, different metabolic pathways form NADPH with different D/H ratios, which in turn results in variation in D/H ratios of lipids (Zhang et al, 2009). Therefore, substrates play a significant role in hydrogen isotopic compositions of lipids. For this study, we are investigating the effects of substrates on hydrogen isotope fractionation during biosynthesis of isoprenoidal lipids by heterotrophically growing halophilic archaea. Haloarcula marismortui is a halophilic archaea which synthesizes Archaeol (a diether lipid) and other isoprenoidal lipids. We have grown Haloarcula marismortui in pure cultures on three different substrates and are in the process of evaluating isotopic variability of Archaeol and other lipids associated with substrate and the D/H composition of ambient water. Our results will be helpful for a better understanding of hydrogen isotope fractionations during lipid synthesis by archaea. Also, halophilic archaea are the only source of archaeol in hypersaline environments. Therefore, our

Statistical clumped isotope signatures

PubMed Central

Röckmann, T.; Popa, M. E.; Krol, M. C.; Hofmann, M. E. G.

2016-01-01

High precision measurements of molecules containing more than one heavy isotope may provide novel constraints on element cycles in nature. These so-called clumped isotope signatures are reported relative to the random (stochastic) distribution of heavy isotopes over all available isotopocules of a molecule, which is the conventional reference. When multiple indistinguishable atoms of the same element are present in a molecule, this reference is calculated from the bulk (≈average) isotopic composition of the involved atoms. We show here that this referencing convention leads to apparent negative clumped isotope anomalies (anti-clumping) when the indistinguishable atoms originate from isotopically different populations. Such statistical clumped isotope anomalies must occur in any system where two or more indistinguishable atoms of the same element, but with different isotopic composition, combine in a molecule. The size of the anti-clumping signal is closely related to the difference of the initial isotope ratios of the indistinguishable atoms that have combined. Therefore, a measured statistical clumped isotope anomaly, relative to an expected (e.g. thermodynamical) clumped isotope composition, may allow assessment of the heterogeneity of the isotopic pools of atoms that are the substrate for formation of molecules. PMID:27535168

Sea surface salinity of the Eocene Arctic Azolla event using innovative isotope modeling

NASA Astrophysics Data System (ADS)

Speelman, E. N.; Sewall, J. O.; Noone, D.; Huber, M.; Sinninghe Damste, J. S.; Reichart, G. J.

2009-04-01

With the realization that the Eocene Arctic Ocean was covered with enormous quantities of the free floating freshwater fern Azolla, new questions regarding Eocene conditions facilitating these blooms arose. Our present research focuses on constraining the actual salinity of, and water sources for, the Eocene Arctic basin through the application of stable water isotope tracers. Precipitation pathways potentially strongly affect the final isotopic composition of water entering the Arctic Basin. Therefore we use the Community Atmosphere Model (CAM3), developed by NCAR, combined with a recently developed integrated isotope tracer code to reconstruct the isotopic composition of global Eocene precipitation and run-off patterns. We further addressed the sensitivity of the modeled hydrological cycle to changes in boundary conditions, such as pCO2, sea surface temperatures (SSTs) and sea ice formation. In this way it is possible to assess the effect of uncertainties in proxy estimates of these parameters. Overall, results of all runs with Eocene boundary conditions, including Eocene topography, bathymetry, vegetation patterns, TEX86 derived SSTs and pCO2 estimates, show the presence of an intensified hydrological cycle with precipitation exceeding evaporation in the Arctic region. Enriched, precipitation weighted, isotopic values of around -120‰ are reported for the Arctic region. Combining new results obtained from compound specific isotope analyses (δD) on terrestrially derived n-alkanes extracted from Eocene sediments, and model outcomes make it possible to verify climate reconstructions for the middle Eocene Arctic. Furthermore, recently, characteristic long-chain mid-chain ω20 hydroxy wax constituents of Azolla were found in ACEX sediments. δD values of these C32 - C36 diols provide insight into the isotopic composition of the Eocene Arctic surface water. As the isotopic signature of the runoff entering the Arctic is modelled, and the final isotopic composition of

The Impact of Codes of Conduct on Stakeholders

ERIC Educational Resources Information Center

Newman, Wayne R.

2015-01-01

The purpose of this study was to determine how an urban school district's code of conduct aligned with actual school/class behaviors, and how stakeholders perceived the ability of this document to achieve its number one goal: safe and productive learning environments. Twenty participants including students, teachers, parents, and administrators…

Metal-ferroelectric-metal capacitor based persistent memory for electronic product code class-1 generation-2 uhf passive radio-frequency identification tag

NASA Astrophysics Data System (ADS)

Yoon, Bongno; Sung, Man Young; Yeon, Sujin; Oh, Hyun S.; Kwon, Yoonjoo; Kim, Chuljin; Kim, Kyung-Ho

2009-03-01

With the circuits using metal-ferroelectric-metal (MFM) capacitor, rf operational signal properties are almost the same or superior to those of polysilicon-insulator-polysilicon, metal-insulator-metal, and metal-oxide-semiconductor (MOS) capacitors. In electronic product code global class-1 generation-2 uhf radio-frequency identification (RFID) protocols, the MFM can play a crucial role in satisfying the specifications of the inventoried flag's persistence times (Tpt) for each session (S0-S3, SL). In this paper, we propose and design a new MFM capacitor based memory scheme of which persistence time for S1 flag is measured at 2.2 s as well as indefinite for S2, S3, and SL flags during the period of power-on. A ferroelectric random access memory embedded RFID tag chip is fabricated with an industry-standard complementary MOS process. The chip size is around 500×500 μm2 and the measured power consumption is about 10 μW.

Molecular and isotopic analyses of the hydroxy acids, dicarboxylic acids, and hydroxydicarboxylic acids of the Murchison meteorite

NASA Astrophysics Data System (ADS)

Cronin, J. R.; Pizzarello, S.; Epstein, S.; Krishnamurthy, R. V.

1993-10-01

The hydroxymonocarboxylic acids, dicarboxylic acids, and hydroxydicarboxylic acids of the Murchison meteorite were analyzed as their tert-butyldimethylsilyl derivatives using combined gas chromatography-mass spectrometry. The hydroxydicarboxylic acids have not been found previously in meteorites. Each class of compounds is numerous with carbon chains up to C8 or C9 and many, if not all, chain and substitution position isomers represented at each carbon number. The alpha-hydroxycarboxylic acids and alpha-hydroxydicarboxylic acids correspond structurally to many of the known meteoritic alpha-aminocarboxylic acids and alpha-aminodicarboxylic acids, a fact that supports the proposal that a Strecker synthesis was involved in the formation of both classes of compounds. Isotopic analyses show these acids to be D-rich relative to terrestrial organic compounds, as expected; however, the hydroxy acids appear to be isotopically lighter than the amino acids with respect to both carbon and hydrogen.

A high burnup model developed for the DIONISIO code

NASA Astrophysics Data System (ADS)

Soba, A.; Denis, A.; Romero, L.; Villarino, E.; Sardella, F.

2013-02-01

A group of subroutines, designed to extend the application range of the fuel performance code DIONISIO to high burn up, has recently been included in the code. The new calculation tools, which are tuned for UO2 fuels in LWR conditions, predict the radial distribution of power density, burnup, and concentration of diverse nuclides within the pellet. The balance equations of all the isotopes involved in the fission process are solved in a simplified manner, and the one-group effective cross sections of all of them are obtained as functions of the radial position in the pellet, burnup, and enrichment in 235U. In this work, the subroutines are described and the results of the simulations performed with DIONISIO are presented. The good agreement with the data provided in the FUMEX II/III NEA data bank can be easily recognized.

Isotopic niche partitioning between two apex predators over time.

PubMed

Drago, Massimiliano; Cardona, Luis; Franco-Trecu, Valentina; Crespo, Enrique A; Vales, Damián G; Borella, Florencia; Zenteno, Lisette; Gonzáles, Enrique M; Inchausti, Pablo

2017-07-01

Stable isotope analyses have become an important tool in reconstructing diets, analysing resource use patterns, elucidating trophic relations among predators and understanding the structure of food webs. Here, we use stable carbon and nitrogen isotope ratios in bone collagen to reconstruct and compare the isotopic niches of adult South American fur seals (Arctocephalus australis; n = 86) and sea lions (Otaria flavescens; n = 49) - two otariid species with marked morphological differences - in the Río de la Plata estuary (Argentina - Uruguay) and the adjacent Atlantic Ocean during the second half of the 20th century and the beginning of the 21st century. Samples from the middle Holocene (n = 7 fur seals and n = 5 sea lions) are also included in order to provide a reference point for characterizing resource partitioning before major anthropogenic modifications of the environment. We found that the South American fur seals and South American sea lions had distinct isotopic niches during the middle Holocene. Isotopic niche segregation was similar at the beginning of the second half of the 20th century, but has diminished over time. The progressive convergence of the isotopic niches of these two otariids during the second half of the 20th century and the beginning of the 21st century is most likely due to the increased reliance of South American fur seals on demersal prey. This recent dietary change in South American fur seals can be explained by at least two non-mutually exclusive mechanisms: (i) the decrease in the abundance of sympatric South American sea lions as a consequence of small colony size and high pup mortality resulting from commercial sealing; and (ii) the decrease in the average size of demersal fishes due to intense fishing of the larger class sizes, which may have increased their accessibility to those eared seals with a smaller mouth gape, that is, South American fur seals of both sexes and female South American sea lions. © 2017 The Authors

Development of Parallel Computing Framework to Enhance Radiation Transport Code Capabilities for Rare Isotope Beam Facility Design

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

Kostin, Mikhail; Mokhov, Nikolai; Niita, Koji

A parallel computing framework has been developed to use with general-purpose radiation transport codes. The framework was implemented as a C++ module that uses MPI for message passing. It is intended to be used with older radiation transport codes implemented in Fortran77, Fortran 90 or C. The module is significantly independent of radiation transport codes it can be used with, and is connected to the codes by means of a number of interface functions. The framework was developed and tested in conjunction with the MARS15 code. It is possible to use it with other codes such as PHITS, FLUKA andmore » MCNP after certain adjustments. Besides the parallel computing functionality, the framework offers a checkpoint facility that allows restarting calculations with a saved checkpoint file. The checkpoint facility can be used in single process calculations as well as in the parallel regime. The framework corrects some of the known problems with the scheduling and load balancing found in the original implementations of the parallel computing functionality in MARS15 and PHITS. The framework can be used efficiently on homogeneous systems and networks of workstations, where the interference from the other users is possible.« less

Isotopic, Chemical and Mineralogical Investigation's of Extraterrestrial Materials

NASA Technical Reports Server (NTRS)

Lugmair, G. W.

2003-01-01

During the grant period we have concentrated on the following main topics: 1. Enstatite meteorites and original heterogeneity of Mn-53 distribution in the solar nebula. We have completed our studies of the enstatite chondrites. 2. Processes of planetary differentiation. We have completed our study of silicate clasts from the mesosiderite Vaca Muerta and found that the global Mn/Cr fractionation event that established mantle source reservoirs on the parent body of the Vaca Muerta silicate clasts occurred approx. 2 Ma after a similar event on the howardite-eucrite-diogenite (HED) parent body. 3. Carbonaceous chondrites. Much effort has been devoted during the last three years to the investigation of this important class of meteorites. 4. Early solar system timescales. Based on the studies of the Mn-53 - Cr-53 isotope system in various meteorites and using results obtained with other isotope chronometers we constructed an absolute time-scale for events in the early solar system. 5.Unusual meteorites. We have studied the anomalous pallasite Eagle Station. 6. The chromium isotopic composition as a tracer for extraterrestrial material on Earth. Based on the observed difference in the Cr-53/Cr-52 ratios between Earth and the other solar system objects we developed a method for detecting cosmic materials on Earth using the Cr-53/Cr-52 ratio as a tracer.

Is a Genome a Codeword of an Error-Correcting Code?

PubMed Central

Kleinschmidt, João H.; Silva-Filho, Márcio C.; Bim, Edson; Herai, Roberto H.; Yamagishi, Michel E. B.; Palazzo, Reginaldo

2012-01-01

Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction. PMID:22649495

EVALUATION OF AN INDIVIDUALLY PACED COURSE FOR AIRBORNE RADIO CODE OPERATORS. FINAL REPORT.

ERIC Educational Resources Information Center

BALDWIN, ROBERT O.; JOHNSON, KIRK A.

IN THIS STUDY COMPARISONS WERE MADE BETWEEN AN INDIVIDUALLY PACED VERSION OF THE AIRBORNE RADIO CODE OPERATOR (ARCO) COURSE AND TWO VERSIONS OF THE COURSE IN WHICH THE STUDENTS PROGRESSED AT A FIXED PACE. THE ARCO COURSE IS A CLASS C SCHOOL IN WHICH THE STUDENT LEARNS TO SEND AND RECEIVE MILITARY MESSAGES USING THE INTERNATIONAL MORSE CODE. THE…

ISOTOPE CONVERSION DEVICE

DOEpatents

Wigner, E.P.; Young, G.J.; Ohlinger, L.A.

1957-12-01

This patent relates to nuclear reactors of tbe type utilizing a liquid fuel and designed to convert a non-thermally fissionable isotope to a thermally fissionable isotope by neutron absorption. A tank containing a reactive composition of a thermally fissionable isotope dispersed in a liquid moderator is disposed within an outer tank containing a slurry of a non-thermally fissionable isotope convertible to a thermally fissionable isotope by neutron absorption. A control rod is used to control the chain reaction in the reactive composition and means are provided for circulating and cooling the reactive composition and slurry in separate circuits.

Modeling Subsurface Reactive Flows Using Leadership-Class Computing

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

Mills, Richard T; Hammond, Glenn; Lichtner, Peter

2009-01-01

We describe our experiences running PFLOTRAN - a code for simulation of coupled hydro-thermal-chemical processes in variably saturated, non-isothermal, porous media - on leadership-class supercomputers, including initial experiences running on the petaflop incarnation of Jaguar, the Cray XT5 at the National Center for Computational Sciences at Oak Ridge National Laboratory. PFLOTRAN utilizes fully implicit time-stepping and is built on top of the Portable, Extensible Toolkit for Scientific Computation (PETSc). We discuss some of the hurdles to 'at scale' performance with PFLOTRAN and the progress we have made in overcoming them on leadership-class computer architectures.

Compound-specific Isotope Analysis of Cyanobacterial Pure cultures and Microbial Mats: Effects of Photorespiration?

NASA Technical Reports Server (NTRS)

Jahnke, L. L.; Summons, R. E.

2006-01-01

Microbial mats are considered modern homologs of Precambrian stromatolites. The carbon isotopic compositions of organic matter and biomarker lipids provide clues to the depositional environments of ancient mat ecosystems. As the source of primary carbon fixation for over two billion years, an understanding of cyanobacterial lipid biosynthesis, associated isotopic discriminations, and the influence of physiological factors on growth and isotope expression is essential to help us compare modern microbial ecosystems to their ancient counterparts. Here, we report on the effects of photorespiration (PR) on the isotopic composition of cyanobacteria and biomarker lipids, and on potential PR effects associated with the composition of various microbial mats. The high light, high O2 and limiting CO2 conditions often present at the surface of microbial mats are known to support PR in cyanobacteria. The oxygenase function of ribulose bisphosphate carboxylase/oxygenase can result in photoexcretion of glycolate and subsequent degration by heterotrophic bacteria. We have found evidence which supports an isotopic depletion (increased apparent E) scaled to O2 level associated with growth of Phormidium luridum at low CO2 concentrations (less than 0.04%). Similar to previous studies, isotopic differences between biomass and lipid biomarkers, and between lipid classes were positively correlated with overall fractionation, and should provide a means of estimating the influence of PR on overall isotopic composition of microbial mats. Several examples of microbial mats growing in the hydrothermal waters of Yellowstone National Park and the hypersaline marine evaporation ponds at Guerrero Negro, Baja Sur Mexico will be compared with a view to PR as a possible explanation of the relatively heavy C-isotope composition of hypersaline mats.

Electron linac for medical isotope production with improved energy efficiency and isotope recovery

DOEpatents

Noonan, John; Walters, Dean; Virgo, Matt; Lewellen, John

2015-09-08

A method and isotope linac system are provided for producing radio-isotopes and for recovering isotopes. The isotope linac is an energy recovery linac (ERL) with an electron beam being transmitted through an isotope-producing target. The electron beam energy is recollected and re-injected into an accelerating structure. The ERL provides improved efficiency with reduced power requirements and provides improved thermal management of an isotope target and an electron-to-x-ray converter.

On the optimality of code options for a universal noiseless coder

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu; Rice, Robert F.; Miller, Warner

1991-01-01

A universal noiseless coding structure was developed that provides efficient performance over an extremely broad range of source entropy. This is accomplished by adaptively selecting the best of several easily implemented variable length coding algorithms. Custom VLSI coder and decoder modules capable of processing over 20 million samples per second are currently under development. The first of the code options used in this module development is shown to be equivalent to a class of Huffman code under the Humblet condition, other options are shown to be equivalent to the Huffman codes of a modified Laplacian symbol set, at specified symbol entropy values. Simulation results are obtained on actual aerial imagery, and they confirm the optimality of the scheme. On sources having Gaussian or Poisson distributions, coder performance is also projected through analysis and simulation.

High compression image and image sequence coding

NASA Technical Reports Server (NTRS)

Kunt, Murat

1989-01-01

The digital representation of an image requires a very large number of bits. This number is even larger for an image sequence. The goal of image coding is to reduce this number, as much as possible, and reconstruct a faithful duplicate of the original picture or image sequence. Early efforts in image coding, solely guided by information theory, led to a plethora of methods. The compression ratio reached a plateau around 10:1 a couple of years ago. Recent progress in the study of the brain mechanism of vision and scene analysis has opened new vistas in picture coding. Directional sensitivity of the neurones in the visual pathway combined with the separate processing of contours and textures has led to a new class of coding methods capable of achieving compression ratios as high as 100:1 for images and around 300:1 for image sequences. Recent progress on some of the main avenues of object-based methods is presented. These second generation techniques make use of contour-texture modeling, new results in neurophysiology and psychophysics and scene analysis.

Evaluation of an Online Instructional Database Accessed by QR Codes to Support Biochemistry Practical Laboratory Classes

ERIC Educational Resources Information Center

Yip, Tor; Melling, Louise; Shaw, Kirsty J.

2016-01-01

An online instructional database containing information on commonly used pieces of laboratory equipment was created. In order to make the database highly accessible and to promote its use, QR codes were utilized. The instructional materials were available anytime and accessed using QR codes located on the equipment itself and within undergraduate…

The functional spectrum of low-frequency coding variation.

PubMed

Marth, Gabor T; Yu, Fuli; Indap, Amit R; Garimella, Kiran; Gravel, Simon; Leong, Wen Fung; Tyler-Smith, Chris; Bainbridge, Matthew; Blackwell, Tom; Zheng-Bradley, Xiangqun; Chen, Yuan; Challis, Danny; Clarke, Laura; Ball, Edward V; Cibulskis, Kristian; Cooper, David N; Fulton, Bob; Hartl, Chris; Koboldt, Dan; Muzny, Donna; Smith, Richard; Sougnez, Carrie; Stewart, Chip; Ward, Alistair; Yu, Jin; Xue, Yali; Altshuler, David; Bustamante, Carlos D; Clark, Andrew G; Daly, Mark; DePristo, Mark; Flicek, Paul; Gabriel, Stacey; Mardis, Elaine; Palotie, Aarno; Gibbs, Richard

2011-09-14

Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency. The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants. This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.

High-precision optical measurements of 13C/12C isotope ratios in organic compounds at natural abundance

PubMed Central

Zare, Richard N.; Kuramoto, Douglas S.; Haase, Christa; Tan, Sze M.; Crosson, Eric R.; Saad, Nabil M. R.

2009-01-01

A continuous-flow cavity ring-down spectroscopy (CRDS) system integrating a chromatographic separation technique, a catalytic combustor, and an isotopic 13C/12C optical analyzer is described for the isotopic analysis of a mixture of organic compounds. A demonstration of its potential is made for the geochemically important class of short-chain hydrocarbons. The system proved to be linear over a 3-fold injection volume dynamic range with an average precision of 0.95‰ and 0.67‰ for ethane and propane, respectively. The calibrated accuracy for methane, ethane, and propane is within 3‰ of the values determined using isotope ratio mass spectrometry (IRMS), which is the current method of choice for compound-specific isotope analysis. With anticipated improvements, the low-cost, portable, and easy-to-use CRDS-based instrumental setup is poised to evolve into a credible challenge to the high-cost and complex IRMS-based technique. PMID:19564619

Testing the Late-Veneer hypothesis with selenium isotopes

NASA Astrophysics Data System (ADS)

Labidi, J.; Koenig, S.; Bennett, N.; Kurzawa, T.; Aierken, E.; Shahar, A.; Schoenberg, R.

2016-12-01

Selenium (Se) is a siderophile element displaying an excess abundance in Earth's mantle compared to experimental predictions [1], which may be attributed to the Late-Veneer. As Se is also volatile, testing the late-veneer addition of Se can constrain the origin of other volatile elements on Earth. Here we combine high-precision Se isotope measurements of metal-silicate partitioning experiments and chondrites to assess whether planetary differentiation could leave a measurable Se isotopic signature on planetary mantles. We performed Se isotopic measurements of 5 metal-silicate partitioning experiments and 20 chondrites of all major classes. Experiments were conducted at 1 GPa and 1650 C for 1 to 4 hours using the piston-cylinder apparatus at Carnegie's Geophysical Laboratory. After wet chemistry, data were obtained on a ThermoFisher Scientific™ NeptunePlus MC-ICP-MS at the University of Tübingen with a 74Se/77Se double spike technique. δ82/76Se values are given relative to NIST SRM-3149 and the external reproducibility calculated from duplicate meteorite analyses is ≤ 0.1‰ (2 s.d.). Chondrites vary over a 0.8‰ range of δ82/76Se values. CIs and CMs show evidence for heavier 82Se/76Se ratios, likely due to mixing processes in the proto-planetary nebula. When these isotopically heavier meteorites are excluded, remaining chondrites have δ82/76Se values varying over a 0.3‰ range, within uncertainty of previous results [2]. We suggest that these chondrites may be used to estimate a δ82/76Se value of bulk planets. At the conditions of our experiments, the partition coefficients for Se log Dmetal-silicate range from 0.7±0.1 to 1.9±0.1, consistent with previous work [1]. A small but resolvable Se isotopic fractionation was observed: 82Se/76Se ratios were enriched by ≤ 0.5‰ in the silicates relative to the metals. Thus, given current uncertainties for Se isotopic measurements, marginal differences between planetary mantles and chondrites may be resolved

Unitals and ovals of symmetric block designs in LDPC and space-time coding

NASA Astrophysics Data System (ADS)

Andriamanalimanana, Bruno R.

2004-08-01

An approach to the design of LDPC (low density parity check) error-correction and space-time modulation codes involves starting with known mathematical and combinatorial structures, and deriving code properties from structure properties. This paper reports on an investigation of unital and oval configurations within generic symmetric combinatorial designs, not just classical projective planes, as the underlying structure for classes of space-time LDPC outer codes. Of particular interest are the encoding and iterative (sum-product) decoding gains that these codes may provide. Various small-length cases have been numerically implemented in Java and Matlab for a number of channel models.

LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature.

PubMed

Pian, Cong; Zhang, Guangle; Chen, Zhi; Chen, Yuanyuan; Zhang, Jin; Yang, Tao; Zhang, Liangyun

2016-01-01

As a novel class of noncoding RNAs, long noncoding RNAs (lncRNAs) have been verified to be associated with various diseases. As large scale transcripts are generated every year, it is significant to accurately and quickly identify lncRNAs from thousands of assembled transcripts. To accurately discover new lncRNAs, we develop a classification tool of random forest (RF) named LncRNApred based on a new hybrid feature. This hybrid feature set includes three new proposed features, which are MaxORF, RMaxORF and SNR. LncRNApred is effective for classifying lncRNAs and protein coding transcripts accurately and quickly. Moreover,our RF model only requests the training using data on human coding and non-coding transcripts. Other species can also be predicted by using LncRNApred. The result shows that our method is more effective compared with the Coding Potential Calculate (CPC). The web server of LncRNApred is available for free at http://mm20132014.wicp.net:57203/LncRNApred/home.jsp.

Oxygen Isotopic Compositions of Solar Corundum Grains

NASA Astrophysics Data System (ADS)

Makide, Kentaro; Nagashima, Kazuhide; Krot, Alexander N.; Huss, Gary R.

2009-11-01

Oxygen is one of the major rock-forming elements in the solar system and the third most abundant element of the Sun. Oxygen isotopic composition of the Sun, however, is not known due to a poor resolution of astronomical spectroscopic measurements. Several Δ17O values have been proposed for the composition of the Sun based on (1) the oxygen isotopic measurements of the solar wind implanted into metallic particles in lunar soil (< -20‰ by Hashizume & Chaussidon and ~ +26‰ by Ireland et al.), (2) the solar wind returned by the Genesis spacecraft (-27‰ ± 6‰ by McKeegan et al.), and (3) the mineralogically pristine calcium-aluminum-rich inclusions (CAIs) (-23.3‰ ± 1.9‰ by Makide et al. and -35‰ by Gounelle et al.). CAIs are the oldest solar system solids, and are believed to have formed by evaporation, condensation, and melting processes in hot nebular region(s) when the Sun was infalling (Class 0) or evolved (Class 1) protostar. Corundum (Al2O3) is thermodynamically the first condensate from a cooling gas of solar composition. Corundum-bearing CAIs, however, are exceptionally rare, suggesting either continuous reaction of the corundum condensates with a cooling nebular gas and their replacement by hibonite (CaAl12O19) or their destruction by melting together with less refractory condensates during formation of igneous CAIs. In contrast to the corundum-bearing CAIs, isolated micrometer-sized corundum grains are common in the acid-resistant residues from unmetamorphosed chondrites. These grains could have avoided multistage reprocessing during CAI formation and, therefore, can potentially provide constraints on the initial oxygen isotopic composition of the solar nebula, and, hence, of the Sun. Here we report oxygen isotopic compositions of ~60 micrometer-sized corundum grains in the acid-resistant residues from unequilibrated ordinary chondrites (Semarkona (LL3.0), Bishunpur (LL3.1), Roosevelt County 075 (H3.2)) and unmetamorphosed carbonaceous

Confidence Intervals and "F" Tests for Intraclass Correlation Coefficients Based on Three-Way Mixed Effects Models

ERIC Educational Resources Information Center

Zhou, Hong; Muellerleile, Paige; Ingram, Debra; Wong, Seok P.

2011-01-01

Intraclass correlation coefficients (ICCs) are commonly used in behavioral measurement and psychometrics when a researcher is interested in the relationship among variables of a common class. The formulas for deriving ICCs, or generalizability coefficients, vary depending on which models are specified. This article gives the equations for…

Changes in mitochondrial genetic codes as phylogenetic characters: Two examples from the flatworms

PubMed Central

Telford, Maximilian J.; Herniou, Elisabeth A.; Russell, Robert B.; Littlewood, D. Timothy J.

2000-01-01

Shared molecular genetic characteristics other than DNA and protein sequences can provide excellent sources of phylogenetic information, particularly if they are complex and rare and are consequently unlikely to have arisen by chance convergence. We have used two such characters, arising from changes in mitochondrial genetic code, to define a clade within the Platyhelminthes (flatworms), the Rhabditophora. We have sampled 10 distinct classes within the Rhabditophora and find that all have the codon AAA coding for the amino acid Asn rather than the usual Lys and AUA for Ile rather than the usual Met. We find no evidence to support claims that the codon UAA codes for Tyr in the Platyhelminthes rather than the standard stop codon. The Rhabditophora are a very diverse group comprising the majority of the free-living turbellarian taxa and the parasitic Neodermata. In contrast, three other classes of turbellarian flatworm, the Acoela, Nemertodermatida, and Catenulida, have the standard invertebrate assignments for these codons and so are convincingly excluded from the rhabditophoran clade. We have developed a rapid computerized method for analyzing genetic codes and demonstrate the wide phylogenetic distribution of the standard invertebrate code as well as confirming already known metazoan deviations from it (ascidian, vertebrate, echinoderm/hemichordate). PMID:11027335

Simultaneous analysis of multiple classes of antimicrobials in environmental water samples using SPE coupled with UHPLC-ESI-MS/MS and isotope dilution.

PubMed

Tran, Ngoc Han; Chen, Hongjie; Do, Thanh Van; Reinhard, Martin; Ngo, Huu Hao; He, Yiliang; Gin, Karina Yew-Hoong

2016-10-01

A robust and sensitive analytical method was developed for the simultaneous analysis of 21 target antimicrobials in different environmental water samples. Both single SPE and tandem SPE cartridge systems were investigated to simultaneously extract multiple classes of antimicrobials. Experimental results showed that good extraction efficiencies (84.5-105.6%) were observed for the vast majority of the target analytes when extraction was performed using the tandem SPE cartridge (SB+HR-X) system under an extraction pH of 3.0. HPLC-MS/MS parameters were optimized for simultaneous analysis of all the target analytes in a single injection. Quantification of target antimicrobials in water samples was accomplished using 15 isotopically labeled internal standards (ILISs), which allowed the efficient compensation of the losses of target analytes during sample preparation and correction of matrix effects during UHPLC-MS/MS as well as instrument fluctuations in MS/MS signal intensity. Method quantification limit (MQL) for most target analytes based on SPE was below 5ng/L for surface waters, 10ng/L for treated wastewater effluents, and 15ng/L for raw wastewater. The method was successfully applied to detect and quantify the occurrence of the target analytes in raw influent, treated effluent and surface water samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Large-scale shell-model calculations for 32-39P isotopes

NASA Astrophysics Data System (ADS)

Srivastava, P. C.; Hirsch, J. G.; Ermamatov, M. J.; Kota, V. K. B.

2012-10-01

In this work, the structure of 32-39P isotopes is described in the framework of stateof-the-art large-scale shell-model calculations, employing the code ANTOINE with three modern effective interactions: SDPF-U, SDPF-NR and the extended pairing plus quadrupole-quadrupoletype forces with inclusion of monopole interaction (EPQQM). Protons are restricted to fill the sd shell, while neutrons are active in the sd - pf valence space. Results for positive and negative level energies and electromagnetic observables are compared with the available experimental data.

Isotope separation by photochromatography

DOEpatents

Suslick, Kenneth S.

1977-01-01

An isotope separation method which comprises physically adsorbing an isotopically mixed molecular species on an adsorptive surface and irradiating the adsorbed molecules with radiation of a predetermined wavelength which will selectively excite a desired isotopic species. Sufficient energy is transferred to the excited molecules to desorb them from the surface and thereby separate them from the unexcited undesired isotopic species. The method is particularly applicable to the separation of hydrogen isotopes.

Rare isotope accelerator project in Korea and its application to high energy density sciences

NASA Astrophysics Data System (ADS)

Chung, M.; Chung, Y. S.; Kim, S. K.; Lee, B. J.; Hoffmann, D. H. H.

2014-01-01

As a national science project, the Korean government has recently established the Institute for Basic Science (IBS) with the goal of conducting world-class research in basic sciences. One of the core facilities for the IBS will be the rare isotope accelerator which can produce high-intensity rare isotope beams to investigate the fundamental properties of nature, and also to support a broad research program in material sciences, medical and biosciences, and future nuclear energy technologies. The construction of the accelerator is scheduled to be completed by approximately 2017. The design of the accelerator complex is optimized to deliver high average beam current on targets, and to maximize the production of rare isotope beams through the simultaneous use of Isotope Separation On-Line (ISOL) and In-Flight Fragmentation (IFF) methods. The proposed accelerator is, however, not optimal for high energy density science, which usually requires very high peak currents on the target. In this study, we present possible beam-plasma experiments that can be done within the scope of the current accelerator design, and we also investigate possible future extension paths that may enable high energy density science with intense pulsed heavy ion beams.

78 FR 23550 - Department of Energy's (DOE) Participation in Development of the International Energy...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-19

...: Notice. SUMMARY: The DOE participates in the code development process of the International Code Council... notice outlines the process by which DOE produces code change proposals, and participates in the ICC code development process. FOR FURTHER INFORMATION CONTACT: Jeremiah Williams, U.S. Department of Energy, Office of...

Using the verona coding definitions of emotional sequences (VR-CoDES) and health provider responses (VR-CoDES-P) in the dental context.

PubMed

Wright, Alice; Humphris, Gerry; Wanyonyi, Kristina L; Freeman, Ruth

2012-10-01

To show if cues, concerns and provider responses (defined in VR-CoDES and VR-CoDES-P manuals) are present, can be reliably coded and require additional advice for adoption in a dental context. Thirteen patients in a dental practice setting were videoed with either their dentist or hygienist and dental nurse present in routine treatment sessions. All utterances were coded using the Verona systems: VR-CoDES and the VR-CoDES-P. Rates of cue, concerns and provider responses described and reliability tested. The VR-CoDES and VR-CoDES-P were successfully applied in the dental context. The intra-rater ICCs for the detection of cues and concerns and provider response were acceptable and above 0.75. A similar satisfactory result was found for the inter-rater reliability. The VR-CoDES and the VR-CoDES-P are applicable in the dental setting with minor supporting guidelines and show evidence of reliable coding. The VR-CoDES and the VR-CoDES-P may be helpful tools for analysing patient cues and concerns and the dental professionals' responses in the dental context. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Exploring University Teacher Perceptions about Out-of-Class Teamwork

ERIC Educational Resources Information Center

Ruiz-Esparza Barajas, Elizabeth; Medrano Vela, Cecilia Araceli; Zepeda Huerta, Jesús Helbert Karim

2016-01-01

This study reports on the first stage of a larger joint research project undertaken by five universities in Mexico to explore university teachers' thinking about out-of-class teamwork. Data from interviews were analyzed using open and axial coding. Although results suggest a positive perception towards teamwork, the study unveiled important…

Color management in the real world: sRGB, ICM2, ICC, ColorSync, and other attempts to make color management transparent

NASA Astrophysics Data System (ADS)

Stokes, Michael

1998-07-01

A uniformly adopted color standards infrastructure has a dramatic impact on any color imaging industry and technology. This presentation begins by framing the current color standards situation in a historical context. A series of similar appearing infrastructure adoptions in color publishing during the last fifty years are reviewed and compared to the current events. This historical review is followed by brief technical, business and marketing reviews of two of the more popular recent color standards proposals, sRGB and ICC, along with their operating system implementations in the Microsoft and Apple operating systems. The paper concludes with a summary of Hewlett- Packard Company's and Microsoft's proposed future direction.

Validation of personal digital photography to assess dietary quality among people with intellectual disabilities.

PubMed

Elinder, L S; Brunosson, A; Bergström, H; Hagströmer, M; Patterson, E

2012-02-01

Dietary assessment is a challenge in general, and specifically in individuals with intellectual disabilities (ID). This study aimed to evaluate personal digital photography as a method of assessing different aspects of dietary quality in this target group. Eighteen adults with ID were recruited from community residences and activity centres in Stockholm County. Participants were instructed to photograph all foods and beverages consumed during 1 day, while observed. Photographs were coded by two raters. Observations and photographs of meal frequency, intake occasions of four specific food and beverage items, meal quality and dietary diversity were compared. Evaluation of inter-rater reliability and validity of the method was performed by intra-class correlation analysis. With reminders from staff, 85% of all observed eating or drinking occasions were photographed. The inter-rater reliability was excellent for all assessed variables (ICC ≥ 0.88), except for meal quality where ICC was 0.66. The correlations between items assessed in photos and observations were strong to almost perfect with ICC values ranging from 0.71 to 0.92 and all were statistically significant. Personal digital photography appears to be a feasible, reliable and valid method for assessing dietary quality in people with mild to moderate ID, who have daily staff support. © 2011 The Authors. Journal of Intellectual Disability Research © 2011 Blackwell Publishing Ltd.

The Educational and Moral Significance of the American Chemical Society's The Chemist's Code of Conduct

NASA Astrophysics Data System (ADS)

Bruton, Samuel V.

2003-05-01

While the usefulness of the case study method in teaching research ethics is frequently emphasized, less often noted is the educational value of professional codes of ethics. Much can be gained by having students examine codes and reflect on their significance. This paper argues that codes such as the American Chemical Society‘s The Chemist‘s Code of Conduct are an important supplement to the use of cases and describes one way in which they can be integrated profitably into a class discussion of research ethics.

Techniques for the analysis of data from coded-mask X-ray telescopes

NASA Technical Reports Server (NTRS)

Skinner, G. K.; Ponman, T. J.; Hammersley, A. P.; Eyles, C. J.

1987-01-01

Several techniques useful in the analysis of data from coded-mask telescopes are presented. Methods of handling changes in the instrument pointing direction are reviewed and ways of using FFT techniques to do the deconvolution considered. Emphasis is on techniques for optimally-coded systems, but it is shown that the range of systems included in this class can be extended through the new concept of 'partial cycle averaging'.

Performance Comparison of Orthogonal and Quasi-orthogonal Codes in Quasi-Synchronous Cellular CDMA Communication

NASA Astrophysics Data System (ADS)

Jos, Sujit; Kumar, Preetam; Chakrabarti, Saswat

Orthogonal and quasi-orthogonal codes are integral part of any DS-CDMA based cellular systems. Orthogonal codes are ideal for use in perfectly synchronous scenario like downlink cellular communication. Quasi-orthogonal codes are preferred over orthogonal codes in the uplink communication where perfect synchronization cannot be achieved. In this paper, we attempt to compare orthogonal and quasi-orthogonal codes in presence of timing synchronization error. This will give insight into the synchronization demands in DS-CDMA systems employing the two classes of sequences. The synchronization error considered is smaller than chip duration. Monte-Carlo simulations have been carried out to verify the analytical and numerical results.

Projectile fragmentation of 40,48Ca and isotopic scaling in a transport approach

NASA Astrophysics Data System (ADS)

Mikhailova, T. I.; Erdemchimeg, B.; Artukh, A. G.; Di Toro, M.; Wolter, H. H.

2016-07-01

We investigate theoretically projectile fragmentation in reactions of 40,48Ca on 9Be and 181Ta targets using a Boltzmann-type transport approach, which is supplemented by a statistical decay code to describe the de-excitation of the hot primary fragments. We determine the thermodynamical properties of the primary fragments and calculate the isotope distributions of the cold final fragments. These describe the data reasonably well. For the pairs of projectiles with different isotopic content we analyze the isotopic scaling (or isoscaling) of the final fragment distributions, which has been used to extract the symmetry energy of the primary source. The calculation exhibits isoscaling behavior for the total yields as do the experiments. We also perform an impact-parameter-dependent isoscaling analysis in view of the fact that the primary systems at different impact parameters have very different properties. Then the isoscaling behavior is less stringent, which we can attribute to specific structure effects of the 40,48Ca pair. The symmetry energy determined in this way depends on these structure effects.

An Approach for Validating Actinide and Fission Product Burnup Credit Criticality Safety Analyses-Isotopic Composition Predictions

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

Radulescu, Georgeta; Gauld, Ian C; Ilas, Germina

2011-01-01

The expanded use of burnup credit in the United States (U.S.) for storage and transport casks, particularly in the acceptance of credit for fission products, has been constrained by the availability of experimental fission product data to support code validation. The U.S. Nuclear Regulatory Commission (NRC) staff has noted that the rationale for restricting the Interim Staff Guidance on burnup credit for storage and transportation casks (ISG-8) to actinide-only is based largely on the lack of clear, definitive experiments that can be used to estimate the bias and uncertainty for computational analyses associated with using burnup credit. To address themore » issues of burnup credit criticality validation, the NRC initiated a project with the Oak Ridge National Laboratory to (1) develop and establish a technically sound validation approach for commercial spent nuclear fuel (SNF) criticality safety evaluations based on best-available data and methods and (2) apply the approach for representative SNF storage and transport configurations/conditions to demonstrate its usage and applicability, as well as to provide reference bias results. The purpose of this paper is to describe the isotopic composition (depletion) validation approach and resulting observations and recommendations. Validation of the criticality calculations is addressed in a companion paper at this conference. For isotopic composition validation, the approach is to determine burnup-dependent bias and uncertainty in the effective neutron multiplication factor (keff) due to bias and uncertainty in isotopic predictions, via comparisons of isotopic composition predictions (calculated) and measured isotopic compositions from destructive radiochemical assay utilizing as much assay data as is available, and a best-estimate Monte Carlo based method. This paper (1) provides a detailed description of the burnup credit isotopic validation approach and its technical bases, (2) describes the application of the

Isotope separation by photochromatography

DOEpatents

Suslick, K.S.

1975-10-03

A photochromatographic method for isotope separation is described. An isotopically mixed molecular species is adsorbed on an adsorptive surface, and the adsorbed molecules are irradiated with radiation of a predetermined wavelength which will selectively excite desired isotopic species. Sufficient energy is transferred to the excited molecules to desorb them from the surface and thus separate them from the undesired isotopic species. The method is particularly applicable to the separation of hydrogen isotopes. (BLM)

49 CFR Appendix E to Part 512 - Consumer Assistance to Recycle and Save (CARS) Class Determinations

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 6 2012-10-01 2012-10-01 false Consumer Assistance to Recycle and Save (CARS... Save (CARS) Class Determinations (a) The Chief Counsel has determined that the following information... (3) CARS Dealer Code and Authorization Code. (b) The Chief Counsel has determined that the disclosure...

49 CFR Appendix E to Part 512 - Consumer Assistance to Recycle and Save (CARS) Class Determinations

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 6 2014-10-01 2014-10-01 false Consumer Assistance to Recycle and Save (CARS... Save (CARS) Class Determinations (a) The Chief Counsel has determined that the following information... (3) CARS Dealer Code and Authorization Code. (b) The Chief Counsel has determined that the disclosure...

49 CFR Appendix E to Part 512 - Consumer Assistance to Recycle and Save (CARS) Class Determinations

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 6 2010-10-01 2010-10-01 false Consumer Assistance to Recycle and Save (CARS... Save (CARS) Class Determinations (a) The Chief Counsel has determined that the following information... (3) CARS Dealer Code and Authorization Code. (b) The Chief Counsel has determined that the disclosure...

49 CFR Appendix E to Part 512 - Consumer Assistance to Recycle and Save (CARS) Class Determinations

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 6 2011-10-01 2011-10-01 false Consumer Assistance to Recycle and Save (CARS... Save (CARS) Class Determinations (a) The Chief Counsel has determined that the following information... (3) CARS Dealer Code and Authorization Code. (b) The Chief Counsel has determined that the disclosure...

Synthetic isotope mixtures for the calibration of isotope amount ratio measurements of carbon

NASA Astrophysics Data System (ADS)

Russe, K.; Valkiers, S.; Taylor, P. D. P.

2004-07-01

Synthetic isotope mixtures for the calibration of carbon isotope amount ratio measurements have been prepared by mixing carbon tetrafluoride highly enriched in 13C with carbon tetrafluoride depleted in 13C. Mixing procedures based on volumetry and gravimetry are described. The mixtures served as primary measurement standards for the calibration of isotope amount ratio measurements of the Isotopic Reference Materials PEF1, NBS22 and USGS24. Thus SI-traceable measurements of absolute carbon isotope amount ratios have been performed for the first time without any hypothesis needed for a correction of oxygen isotope abundances, such as is the case for measurements on carbon dioxide. As a result, "absolute" carbon isotope amount ratios determined via carbon tetrafluoride have smaller uncertainties than those published for carbon dioxide. From the measurements of the Reference Materials concerned, the absolute carbon isotope amount ratio of Vienna Pee Dee Belemnite (VPDB)--the hypothetical material upon which the scale for relative carbon isotope ratio measurements is based--was calculated to be R13(VPDB) = (11 101 +/- 16) × 10-6.

Method for separating isotopes

DOEpatents

Jepson, B.E.

1975-10-21

Isotopes are separated by contacting a feed solution containing the isotopes with a cyclic polyether wherein a complex of one isotope is formed with the cyclic polyether, the cyclic polyether complex is extracted from the feed solution, and the isotope is thereafter separated from the cyclic polyether.

Teacher-Child Dyadic Interaction: A Manual for Coding Classroom Behavior. Report Series No. 27.

ERIC Educational Resources Information Center

Brophy, Jere E.; Good, Thomas L.

This manual presents the rationale and coding system for the study of dyadic interaction between teachers and children in classrooms. The introduction notes major differences between this system and others in common use: 1) it is not a universal system that attempts to code all classroom behavior, and 2) the teacher's interactions in his class are…

LEGO: A modular accelerator design code

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

Cai, Y.; Donald, M.; Irwin, J.

1997-08-01

An object-oriented accelerator design code has been designed and implemented in a simple and modular fashion. It contains all major features of its predecessors: TRACY and DESPOT. All physics of single-particle dynamics is implemented based on the Hamiltonian in the local frame of the component. Components can be moved arbitrarily in the three dimensional space. Several symplectic integrators are used to approximate the integration of the Hamiltonian. A differential algebra class is introduced to extract a Taylor map up to arbitrary order. Analysis of optics is done in the same way both for the linear and nonlinear case. Currently, themore » code is used to design and simulate the lattices of the PEP-II. It will also be used for the commissioning.« less

Photochemical isotope separation

DOEpatents

Robinson, C. Paul; Jensen, Reed J.; Cotter, Theodore P.; Greiner, Norman R.; Boyer, Keith

1987-01-01

A process for separating isotopes by selective excitation of isotopic species of a volatile compound by tuned laser light. A highly cooled gas of the volatile compound is produced in which the isotopic shift is sharpened and defined. Before substantial condensation occurs, the cooled gas is irradiated with laser light precisely tuned to a desired wavelength to selectively excite a particular isotopic species in the cooled gas. The laser light may impart sufficient energy to the excited species to cause it to undergo photochemical reaction or even to photoionize. Alternatively, a two-photon irradiation may be applied to the cooled gas to induce photochemical reaction or photoionization. The process is particularly applicable to the separation of isotopes of uranium and plutonium.

Laser isotope separation

DOEpatents

Robinson, C.P.; Reed, J.J.; Cotter, T.P.; Boyer, K.; Greiner, N.R.

1975-11-26

A process and apparatus for separating isotopes by selective excitation of isotopic species of a volatile compound by tuned laser light is described. A highly cooled gas of the volatile compound is produced in which the isotopic shift is sharpened and defined. Before substantial condensation occurs, the cooled gas is irradiated with laser light precisely tuned to a desired wavelength to selectively excite a particular isotopic species in the cooled gas. The laser light may impart sufficient energy to the excited species to cause it to undergo photolysis, photochemical reaction or even to photoionize. Alternatively, a two-photon irradiation may be applied to the cooled gas to induce photolysis, photochemical reaction or photoionization. The process is particularly applicable to the separation of isotopes of uranium.

Laser isotope separation

DOEpatents

Robinson, C. Paul; Jensen, Reed J.; Cotter, Theodore P.; Boyer, Keith; Greiner, Norman R.

1988-01-01

A process and apparatus for separating isotopes by selective excitation of isotopic species of a volatile compound by tuned laser light. A highly cooled gas of the volatile compound is produced in which the isotopic shift is sharpened and defined. Before substantial condensation occurs, the cooled gas is irradiated with laser light precisely tuned to a desired wavelength to selectively excite a particular isotopic species in the cooled gas. The laser light may impart sufficient energy to the excited species to cause it to undergo photolysis, photochemical reaction or even to photoionize. Alternatively, a two-photon irradiation may be applied to the cooled gas to induce photolysis, photochemical reaction or photoionization. The process is particularly applicable to the separation of isotopes of uranium.

Photochemical isotope separation

DOEpatents

Robinson, C.P.; Jensen, R.J.; Cotter, T.P.; Greiner, N.R.; Boyer, K.

1987-04-28

A process is described for separating isotopes by selective excitation of isotopic species of a volatile compound by tuned laser light. A highly cooled gas of the volatile compound is produced in which the isotopic shift is sharpened and defined. Before substantial condensation occurs, the cooled gas is irradiated with laser light precisely tuned to a desired wavelength to selectively excite a particular isotopic species in the cooled gas. The laser light may impart sufficient energy to the excited species to cause it to undergo photochemical reaction or even to photoionize. Alternatively, a two-photon irradiation may be applied to the cooled gas to induce photochemical reaction or photoionization. The process is particularly applicable to the separation of isotopes of uranium and plutonium. 8 figs.

The Numerical Electromagnetics Code (NEC) - A Brief History

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

Burke, G J; Miller, E K; Poggio, A J

The Numerical Electromagnetics Code, NEC as it is commonly known, continues to be one of the more widely used antenna modeling codes in existence. With several versions in use that reflect different levels of capability and availability, there are now 450 copies of NEC4 and 250 copies of NEC3 that have been distributed by Lawrence Livermore National Laboratory to a limited class of qualified recipients, and several hundred copies of NEC2 that had a recorded distribution by LLNL. These numbers do not account for numerous copies (perhaps 1000s) that were acquired through other means capitalizing on the open source code,more » the absence of distribution controls prior to NEC3 and the availability of versions on the Internet. In this paper we briefly review the history of the code that is concisely displayed in Figure 1. We will show how it capitalized on the research of prominent contributors in the early days of computational electromagnetics, how a combination of events led to the tri-service-supported code development program that ultimately led to NEC and how it evolved to the present day product. The authors apologize that space limitations do not allow us to provide a list of references or to acknowledge the numerous contributors to the code both of which can be found in the code documents.« less

A discriminative test among the different theories proposed to explain the origin of the genetic code: the coevolution theory finds additional support.

PubMed

Giulio, Massimo Di

2018-05-19

A discriminative statistical test among the different theories proposed to explain the origin of the genetic code is presented. Gathering the amino acids into polarity and biosynthetic classes that are the first expression of the physicochemical theory of the origin of the genetic code and the second expression of the coevolution theory, these classes are utilized in the Fisher's exact test to establish their significance within the genetic code table. Linking to the rows and columns of the genetic code of probabilities that express the statistical significance of these classes, I have finally been in the condition to be able to calculate a χ value to link to both the physicochemical theory and to the coevolution theory that would express the corroboration level referred to these theories. The comparison between these two χ values showed that the coevolution theory is able to explain - in this strictly empirical analysis - the origin of the genetic code better than that of the physicochemical theory. Copyright © 2018 Elsevier B.V. All rights reserved.

Recent developments in the use of isotope ratio mass spectrometry in sports drug testing.

PubMed

Piper, Thomas; Emery, Caroline; Saugy, Martial

2011-08-01

According to the annual report of the World Anti-Doping Agency, steroids are the most frequently detected class of doping agents. Detecting the misuse of endogenously occurring steroids, i.e. steroids such as testosterone that are produced naturally by humans, is one of the most challenging issues in doping control analysis. The established thresholds for urinary concentrations or concentration ratios such as the testosterone/epitestosterone quotient are sometimes inconclusive owing to the large biological variation in these parameters.For more than 15 years, doping control laboratories focused on the carbon isotope ratios of endogenous steroids to distinguish between naturally elevated steroid profile parameters and illicit administration of steroids. A variety of different methods has been developed throughout the last decade and the number of different steroids under investigation by isotope ratio mass spectrometry has recently grown considerably. Besides norandrosterone, boldenone was found to occur endogenously in rare cases and the misuse of corticosteroids or epitestosterone can now be detected with the aid of carbon isotope ratios as well. In addition, steroids excreted as sulfoconjugates were investigated, and the first results regarding hydrogen isotope ratios recently became available.All of these will be presented in detail within this review together with some considerations on validation issues and on identification of parameters influencing steroidal isotope ratios in urine.

Re-evaluation of Spent Nuclear Fuel Assay Data for the Three Mile Island Unit 1 Reactor and Application to Code Validation

DOE PAGES

Gauld, Ian C.; Giaquinto, J. M.; Delashmitt, J. S.; ...

2016-01-01

Destructive radiochemical assay measurements of spent nuclear fuel rod segments from an assembly irradiated in the Three Mile Island unit 1 (TMI-1) pressurized water reactor have been performed at Oak Ridge National Laboratory (ORNL). Assay data are reported for five samples from two fuel rods of the same assembly. The TMI-1 assembly was a 15 X 15 design with an initial enrichment of 4.013 wt% 235U, and the measured samples achieved burnups between 45.5 and 54.5 gigawatt days per metric ton of initial uranium (GWd/t). Measurements were performed mainly using inductively coupled plasma mass spectrometry after elemental separation via highmore » performance liquid chromatography. High precision measurements were achieved using isotope dilution techniques for many of the lanthanides, uranium, and plutonium isotopes. Measurements are reported for more than 50 different isotopes and 16 elements. One of the two TMI-1 fuel rods measured in this work had been measured previously by Argonne National Laboratory (ANL), and these data have been widely used to support code and nuclear data validation. Recently, ORNL provided an important opportunity to independently cross check results against previous measurements performed at ANL. The measured nuclide concentrations are used to validate burnup calculations using the SCALE nuclear systems modeling and simulation code suite. These results show that the new measurements provide reliable benchmark data for computer code validation.« less

Isotope reference materials

USGS Publications Warehouse

Coplen, Tyler B.

2010-01-01

Measurement of the same isotopically homogeneous sample by any laboratory worldwide should yield the same isotopic composition within analytical uncertainty. International distribution of light element isotopic reference materials by the International Atomic Energy Agency and the U.S. National Institute of Standards and Technology enable laboratories to achieve this goal.

nRC: non-coding RNA Classifier based on structural features.

PubMed

Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

2017-01-01

Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

Vibrationally averaged post Born-Oppenheimer isotopic dipole moment calculations approaching spectroscopic accuracy.

PubMed

Arapiraca, A F C; Jonsson, Dan; Mohallem, J R

2011-12-28

We report an upgrade of the Dalton code to include post Born-Oppenheimer nuclear mass corrections in the calculations of (ro-)vibrational averages of molecular properties. These corrections are necessary to achieve an accuracy of 10(-4) debye in the calculations of isotopic dipole moments. Calculations on the self-consistent field level present this accuracy, while numerical instabilities compromise correlated calculations. Applications to HD, ethane, and ethylene isotopologues are implemented, all of them approaching the experimental values.

Short-lived non-coding transcripts (SLiTs): Clues to regulatory long non-coding RNA.

PubMed

Tani, Hidenori

2017-03-22

Whole transcriptome analyses have revealed a large number of novel long non-coding RNAs (lncRNAs). Although the importance of lncRNAs has been documented in previous reports, the biological and physiological functions of lncRNAs remain largely unknown. The role of lncRNAs seems an elusive problem. Here, I propose a clue to the identification of regulatory lncRNAs. The key point is RNA half-life. RNAs with a long half-life (t 1/2 > 4 h) contain a significant proportion of ncRNAs, as well as mRNAs involved in housekeeping functions, whereas RNAs with a short half-life (t 1/2 < 4 h) include known regulatory ncRNAs and regulatory mRNAs. This novel class of ncRNAs with a short half-life can be categorized as Short-Lived non-coding Transcripts (SLiTs). I consider that SLiTs are likely to be rich in functionally uncharacterized regulatory RNAs. This review describes recent progress in research into SLiTs.

MHC class I diversity in chimpanzees and bonobos.

PubMed

Maibach, Vincent; Hans, Jörg B; Hvilsom, Christina; Marques-Bonet, Tomas; Vigilant, Linda

2017-10-01

Major histocompatibility complex (MHC) class I genes are critically involved in the defense against intracellular pathogens. MHC diversity comparisons among samples of closely related taxa may reveal traces of past or ongoing selective processes. The bonobo and chimpanzee are the closest living evolutionary relatives of humans and last shared a common ancestor some 1 mya. However, little is known concerning MHC class I diversity in bonobos or in central chimpanzees, the most numerous and genetically diverse chimpanzee subspecies. Here, we used a long-read sequencing technology (PacBio) to sequence the classical MHC class I genes A, B, C, and A-like in 20 and 30 wild-born bonobos and chimpanzees, respectively, with a main focus on central chimpanzees to assess and compare diversity in those two species. We describe in total 21 and 42 novel coding region sequences for the two species, respectively. In addition, we found evidence for a reduced MHC class I diversity in bonobos as compared to central chimpanzees as well as to western chimpanzees and humans. The reduced bonobo MHC class I diversity may be the result of a selective process in their evolutionary past since their split from chimpanzees.

Transcriptome-wide Analysis of Exosome Targets

PubMed Central

Schneider, Claudia; Kudla, Grzegorz; Wlotzka, Wiebke; Tuck, Alex; Tollervey, David

2012-01-01

Summary The exosome plays major roles in RNA processing and surveillance but the in vivo target range and substrate acquisition mechanisms remain unclear. Here we apply in vivo RNA crosslinking (CRAC) to the nucleases (Rrp44, Rrp6), two structural subunits (Rrp41, Csl4) and a cofactor (Trf4) of the yeast exosome. Analysis of wild-type Rrp44 and catalytic mutants showed that both the CUT and SUT classes of non-coding RNA, snoRNAs and, most prominently, pre-tRNAs and other Pol III transcripts are targeted for oligoadenylation and exosome degradation. Unspliced pre-mRNAs were also identified as targets for Rrp44 and Rrp6. CRAC performed using cleavable proteins (split-CRAC) revealed that Rrp44 endonuclease and exonuclease activities cooperate on most substrates. Mapping oligoadenylated reads suggests that the endonuclease activity may release stalled exosome substrates. Rrp6 was preferentially associated with structured targets, which frequently did not associate with the core exosome indicating that substrates follow multiple pathways to the nucleases. PMID:23000172

ICD-10 procedure codes produce transition challenges

PubMed Central

Boyd, Andrew D.; Li, Jianrong ‘John’; Kenost, Colleen; Zaim, Samir Rachid; Krive, Jacob; Mittal, Manish; Satava, Richard A.; Burton, Michael; Smith, Jacob; Lussier, Yves A.

2018-01-01

The transition of procedure coding from ICD-9-CM-Vol-3 to ICD-10-PCS has generated problems for the medical community at large resulting from the lack of clarity required to integrate two non-congruent coding systems. We hypothesized that quantifying these issues with network topology analyses offers a better understanding of the issues, and therefore we developed solutions (online tools) to empower hospital administrators and researchers to address these challenges. Five topologies were identified: “identity”(I), “class-to-subclass”(C2S), “subclass-toclass”(S2C), “convoluted(C)”, and “no mapping”(NM). The procedure codes in the 2010 Illinois Medicaid dataset (3,290 patients, 116 institutions) were categorized as C=55%, C2S=40%, I=3%, NM=2%, and S2C=1%. Majority of the problematic and ambiguous mappings (convoluted) pertained to operations in ophthalmology cardiology, urology, gyneco-obstetrics, and dermatology. Finally, the algorithms were expanded into a user-friendly tool to identify problematic topologies and specify lists of procedural codes utilized by medical professionals and researchers for mitigating error-prone translations, simplifying research, and improving quality.http://www.lussiergroup.org/transition-to-ICD10PCS PMID:29888037

ICD-10 procedure codes produce transition challenges.

PubMed

Boyd, Andrew D; Li, Jianrong 'John'; Kenost, Colleen; Zaim, Samir Rachid; Krive, Jacob; Mittal, Manish; Satava, Richard A; Burton, Michael; Smith, Jacob; Lussier, Yves A

2018-01-01

The transition of procedure coding from ICD-9-CM-Vol-3 to ICD-10-PCS has generated problems for the medical community at large resulting from the lack of clarity required to integrate two non-congruent coding systems. We hypothesized that quantifying these issues with network topology analyses offers a better understanding of the issues, and therefore we developed solutions (online tools) to empower hospital administrators and researchers to address these challenges. Five topologies were identified: "identity"(I), "class-to-subclass"(C2S), "subclass-toclass"(S2C), "convoluted(C)", and "no mapping"(NM). The procedure codes in the 2010 Illinois Medicaid dataset (3,290 patients, 116 institutions) were categorized as C=55%, C2S=40%, I=3%, NM=2%, and S2C=1%. Majority of the problematic and ambiguous mappings (convoluted) pertained to operations in ophthalmology cardiology, urology, gyneco-obstetrics, and dermatology. Finally, the algorithms were expanded into a user-friendly tool to identify problematic topologies and specify lists of procedural codes utilized by medical professionals and researchers for mitigating error-prone translations, simplifying research, and improving quality.http://www.lussiergroup.org/transition-to-ICD10PCS.

DNA rearrangements directed by non-coding RNAs in ciliates

PubMed Central

Mochizuki, Kazufumi

2013-01-01

Extensive programmed rearrangement of DNA, including DNA elimination, chromosome fragmentation, and DNA descrambling, takes place in the newly developed macronucleus during the sexual reproduction of ciliated protozoa. Recent studies have revealed that two distant classes of ciliates use distinct types of non-coding RNAs to regulate such DNA rearrangement events. DNA elimination in Tetrahymena is regulated by small non-coding RNAs that are produced and utilized in an RNAi-related process. It has been proposed that the small RNAs produced from the micronuclear genome are used to identify eliminated DNA sequences by whole-genome comparison between the parental macronucleus and the micronucleus. In contrast, DNA descrambling in Oxytricha is guided by long non-coding RNAs that are produced from the parental macronuclear genome. These long RNAs are proposed to act as templates for the direct descrambling events that occur in the developing macronucleus. Both cases provide useful examples to study epigenetic chromatin regulation by non-coding RNAs. PMID:21956937

Establishing confidence in complex physics codes: Art or science?

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

Trucano, T.

1997-12-31

The ALEGRA shock wave physics code, currently under development at Sandia National Laboratories and partially supported by the US Advanced Strategic Computing Initiative (ASCI), is generic to a certain class of physics codes: large, multi-application, intended to support a broad user community on the latest generation of massively parallel supercomputer, and in a continual state of formal development. To say that the author has ``confidence`` in the results of ALEGRA is to say something different than that he believes that ALEGRA is ``predictive.`` It is the purpose of this talk to illustrate the distinction between these two concepts. The authormore » elects to perform this task in a somewhat historical manner. He will summarize certain older approaches to code validation. He views these methods as aiming to establish the predictive behavior of the code. These methods are distinguished by their emphasis on local information. He will conclude that these approaches are more art than science.« less

Attenuation of drug-stimulated topoisomerase II-DNA cleavable complex formation in wild-type HL-60 cells treated with an intracellular calcium buffer is correlated with decreased cytotoxicity and site-specific hypophosphorylation of topoisomerase IIalpha.

PubMed Central

Aoyama, M; Grabowski, D R; Dubyak, G R; Constantinou, A I; Rybicki, L A; Bukowski, R M; Ganapathi, M K; Hickson, I D; Ganapathi, R

1998-01-01

Topoisomerase II (topo II), an essential enzyme for cell viability, is also the target for clinically important anti-neoplastic agents that stimulate topo II-mediated DNA scission. The role of alterations in topo IIalpha phosphorylation and its effect on drug-induced DNA damage and cytotoxicity were investigated. Following loading of HL-60 cells with the calcium buffer 1, 2-bis-(o-aminophenoxy)ethane-N,N,N',N'-tetra-acetic acid tetra(acetoxymethyl) ester (BAPTA-AM), which abrogates intracellular Ca2+ transients, a significant decrease in etoposide (VP-16)- or amsacrine (m-AMSA)-stabilized topo II-DNA cleavable complex formation and a corresponding decrease in cytotoxicity was observed. In a cell-free system, nuclear extracts from BAPTA-AM-treated cells exhibited markedly less activity when assayed for VP-16-stabilized topo II-DNA complex formation, but not decatenation of kinetoplast DNA. In contrast, the loading of HL-60 cells with N,N,N', N'-tetrakis-(2-pyridyl)ethylenediamine (TPEN), which binds heavy metals without disturbing calcium or magnesium concentrations, did not significantly affect VP-16-stimulated topo II-DNA cleavable complex formation or cytotoxicity. In HL-60 cells the accumulation of BAPTA, but not TPEN, also led to the hypophosphorylation of topo IIalpha. Tryptic phosphopeptide mapping of topo IIalpha protein from HL-60 cells revealed: (a) eight major phosphorylation sites in untreated cells; (b) hypophosphorylation of two out of eight sites in BAPTA-AM-treated cells; and (c) hypophosphorylation of between two and four out of eight sites in topo II-poison-resistant HL-60 cells. The two hypophosphorylated sites present following BAPTA-AM treatment of wild-type cells were identical with the hypophosphorylated sites in the resistant cells, but were not the same as the sites that are substrates for casein kinase II [Wells, Addison, Fry, Ganapathi and Hickson (1994) J. Biol. Chem. 269, 29746-29751]. In summary, changes in intracellular Ca2+ transients

Context-aware and locality-constrained coding for image categorization.

PubMed

Xiao, Wenhua; Wang, Bin; Liu, Yu; Bao, Weidong; Zhang, Maojun

2014-01-01

Improving the coding strategy for BOF (Bag-of-Features) based feature design has drawn increasing attention in recent image categorization works. However, the ambiguity in coding procedure still impedes its further development. In this paper, we introduce a context-aware and locality-constrained Coding (CALC) approach with context information for describing objects in a discriminative way. It is generally achieved by learning a word-to-word cooccurrence prior to imposing context information over locality-constrained coding. Firstly, the local context of each category is evaluated by learning a word-to-word cooccurrence matrix representing the spatial distribution of local features in neighbor region. Then, the learned cooccurrence matrix is used for measuring the context distance between local features and code words. Finally, a coding strategy simultaneously considers locality in feature space and context space, while introducing the weight of feature is proposed. This novel coding strategy not only semantically preserves the information in coding, but also has the ability to alleviate the noise distortion of each class. Extensive experiments on several available datasets (Scene-15, Caltech101, and Caltech256) are conducted to validate the superiority of our algorithm by comparing it with baselines and recent published methods. Experimental results show that our method significantly improves the performance of baselines and achieves comparable and even better performance with the state of the arts.

Stable Isotope Identification of Nitrogen Sources for United States (U.S.) Pacific Coast Estuaries

NASA Astrophysics Data System (ADS)

Brown, C. A.; Kaldy, J. E.; Fong, P.; Fong, C.; Mochon Collura, T.; Clinton, P.

2016-02-01

Nutrients are the leading cause of water quality impairments in the United States, and as a result tools are needed to identify the sources of nutrients. We used natural abundance stable isotope data to evaluate nitrogen sources to U.S. west coast estuaries. We collected macroalgae and analyzed these samples for natural abundance of stable isotopes (δ15N) and supplemented this with available data from the literature for estuaries from Mexico to Alaska. Stable isotope ratios of green macroalgae were compared to δ15N of dissolved inorganic nitrogen of oceanic and watershed end members. There was a latitudinal gradient in δ15N of macroalgae with southern estuaries being 7 per mil heavier than northern estuaries. Gradients in isotope data were compared to nitrogen sources estimated by the USGS using the SPARROW model. In California estuaries, the elevation of isotope data appeared to be related to anthropogenic nitrogen sources. In Oregon systems, the nitrogen levels of streams flowing into the estuaries are related to forest cover, rather than to developed land classes. In Oregon estuaries, the δ15N of macroalgae suggested that the ocean and nitrogen-fixing trees in the watersheds were the dominant nitrogen sources with heavier sites located near the estuary mouth. In California estuaries, the gradient was reversed with heavier sites located upriver. In some Oregon estuaries, there was an elevation an elevation of δ15N above marine end members in the vicinity of wastewater treatment facility discharge locations, suggesting isotopes may be useful for distinguishing inputs along an estuarine gradient.

The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

PubMed

Di Giulio, Massimo

2017-11-07

The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal

Long non-coding RNAs in cancer metabolism.

PubMed

Xiao, Zhen-Dong; Zhuang, Li; Gan, Boyi

2016-10-01

Altered cellular metabolism is an emerging hallmark of cancer. Accumulating recent evidence links long non-coding RNAs (lncRNAs), a still poorly understood class of non-coding RNAs, to cancer metabolism. Here we review the emerging findings on the functions of lncRNAs in cancer metabolism, with particular emphasis on how lncRNAs regulate glucose and glutamine metabolism in cancer cells, discuss how lncRNAs regulate various aspects of cancer metabolism through their cross-talk with other macromolecules, explore the mechanistic conceptual framework of lncRNAs in reprogramming metabolism in cancers, and highlight the challenges in this field. A more in-depth understanding of lncRNAs in cancer metabolism may enable the development of novel and effective therapeutic strategies targeting cancer metabolism. © 2016 WILEY Periodicals, Inc.

Optimization of on-line hydrogen stable isotope ratio measurements of halogen- and sulfur-bearing organic compounds using elemental analyzer–chromium/high-temperature conversion isotope ratio mass spectrometry (EA-Cr/HTC-IRMS)

USGS Publications Warehouse

Gehre, Matthias; Renpenning, Julian; Geilmann, Heike; Qi, Haiping; Coplen, Tyler B.; Kümmel, Steffen; Ivdra, Natalija; Brand, Willi A.; Schimmelmann, Arndt

2017-01-01

Conclusions: The optimized EA-Cr/HTC reactor design can be implemented in existing analytical equipment using commercially available material and is universally applicable for both heteroelement-bearing and heteroelement-free organic-compound classes. The sensitivity and simplicity of the on-line EA-Cr/HTC-IRMS technique provide a much needed tool for routine hydrogen-isotope source tracing of organic contaminants in the environment. Copyright © 2016 John Wiley & Sons, Ltd.

Adjusting for case mix and social class in examining variation in home visits between practices.

PubMed

Sullivan, Caoimhe O; Omar, Rumana Z; Forrest, Christopher B; Majeed, Azeem

2004-08-01

The purpose of this study was to investigate whether adjusting for clinical case mix and social class explains more of the variation in home visits between general practices than adjusting for age and sex alone. The setting was 60 general practices in England and Wales taking part in the 1 year Fourth National Morbidity Survey. The participants comprised 349 505 patients who were registered with one of the participating general practices for at least 180 days, and who had at least one consultation during the period. The outcome measure is whether or not a patient received a home visit in that year. A clinical case mix category (morbidity class) based on 1 year's diagnostic information was assigned to each patient using the Johns Hopkins Adjusted Clinical Groups (ACG) Case Mix System. The social class measure was derived from occupation and employment status and is similar to that of the 1991 UK census. Variations in home visits between practices were examined using multilevel logistic regression models. The variability between practices before and after adjusting for clinical case mix and social class was estimated using the intracluster correlation coefficient (ICC). The overall percentage of patients receiving a home visit over the 1 year study period was 17%, and this varied from 7 to 31% across the 60 practices. The percentage of the total variation in home visits attributable to differences between practices was 2.5% [95% confidence interval (CI) 1.4-3.2%] after adjusting for age and sex. This reduced to 1.6% (95% CI 1.1-2.4%) after taking into account morbidity class. The results were similar when social class was included instead of morbidity class. Morbidity and social class together reduced variation in home visits between practices to 1.5% (95% CI 1.1-2.2%). Age, sex, social class and clinical case mix are strong determinants of home visits in the UK. Adjusting for morbidity and social class results in a small improvement in explaining the variability in

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments.

PubMed

Moulder, Robert; Filén, Jan-Jonas; Salmi, Jussi; Katajamaa, Mikko; Nevalainen, Olli S; Oresic, Matej; Aittokallio, Tero; Lahesmaa, Riitta; Nyman, Tuula A

2005-07-01

The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However, recent developments with data format conversion have subsequently increased such processing opportunities. In the present study, data sets from ICAT experiments, analysed with liquid chromatography/tandem mass spectrometry (MS/MS), using an Applied Biosystems QSTAR Pulsar quadrupole-TOF mass spectrometer, were processed in triplicate using separate mass spectrometry software packages. The programs Pro ICAT, Spectrum Mill and SEQUEST with XPRESS were employed. Attention was paid towards the extent of common identification and agreement of quantitative results, with additional interest in the flexibility and productivity of these programs. The comparisons were made with data from the analysis of a specifically prepared test mixture, nine proteins at a range of relative concentration ratios from 0.1 to 10 (light to heavy labelled forms), as a known control, and data selected from an ICAT study involving the measurement of cytokine induced protein expression in human lymphoblasts, as an applied example. Dissimilarities were detected in peptide identification that reflected how the associated scoring parameters favoured information from the MS/MS data sets. Accordingly, there were differences in the numbers of peptides and protein identifications, although from these it was apparent that both confirmatory and complementary information was present. In the quantitative results from the three programs, no statistically significant differences were observed.

Telecollaborative Desktop-Videoconferencing Exchange: The Case of Mark

ERIC Educational Resources Information Center

Martin, Véronique

2014-01-01

This presentation is a case study of the Intercultural Communicative Competence (ICC) development of Mark, one of ten American students engaged in a desktop-videoconferencing telecollaborative exchange with a class of French students. Due in part to its inherent complexity, this context has not been widely researched. To observe ICC development, I…

Controlling Energy Radiations of Electromagnetic Waves via Frequency Coding Metamaterials.

PubMed

Wu, Haotian; Liu, Shuo; Wan, Xiang; Zhang, Lei; Wang, Dan; Li, Lianlin; Cui, Tie Jun

2017-09-01

Metamaterials are artificial structures composed of subwavelength unit cells to control electromagnetic (EM) waves. The spatial coding representation of metamaterial has the ability to describe the material in a digital way. The spatial coding metamaterials are typically constructed by unit cells that have similar shapes with fixed functionality. Here, the concept of frequency coding metamaterial is proposed, which achieves different controls of EM energy radiations with a fixed spatial coding pattern when the frequency changes. In this case, not only different phase responses of the unit cells are considered, but also different phase sensitivities are also required. Due to different frequency sensitivities of unit cells, two units with the same phase response at the initial frequency may have different phase responses at higher frequency. To describe the frequency coding property of unit cell, digitalized frequency sensitivity is proposed, in which the units are encoded with digits "0" and "1" to represent the low and high phase sensitivities, respectively. By this merit, two degrees of freedom, spatial coding and frequency coding, are obtained to control the EM energy radiations by a new class of frequency-spatial coding metamaterials. The above concepts and physical phenomena are confirmed by numerical simulations and experiments.

Controlling Energy Radiations of Electromagnetic Waves via Frequency Coding Metamaterials

PubMed Central

Wu, Haotian; Liu, Shuo; Wan, Xiang; Zhang, Lei; Wang, Dan; Li, Lianlin

2017-01-01

Metamaterials are artificial structures composed of subwavelength unit cells to control electromagnetic (EM) waves. The spatial coding representation of metamaterial has the ability to describe the material in a digital way. The spatial coding metamaterials are typically constructed by unit cells that have similar shapes with fixed functionality. Here, the concept of frequency coding metamaterial is proposed, which achieves different controls of EM energy radiations with a fixed spatial coding pattern when the frequency changes. In this case, not only different phase responses of the unit cells are considered, but also different phase sensitivities are also required. Due to different frequency sensitivities of unit cells, two units with the same phase response at the initial frequency may have different phase responses at higher frequency. To describe the frequency coding property of unit cell, digitalized frequency sensitivity is proposed, in which the units are encoded with digits “0” and “1” to represent the low and high phase sensitivities, respectively. By this merit, two degrees of freedom, spatial coding and frequency coding, are obtained to control the EM energy radiations by a new class of frequency‐spatial coding metamaterials. The above concepts and physical phenomena are confirmed by numerical simulations and experiments. PMID:28932671

Projectile fragmentation of {sup 40,48}Ca and isotopic scaling in a transport approach

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

Mikhailova, T. I., E-mail: tmikh@jinr.ru; Erdemchimeg, B.; Artukh, A. G.

2016-07-15

We investigate theoretically projectile fragmentation in reactions of {sup 40,48}Ca on {sup 9}Be and {sup 181}Ta targets using a Boltzmann-type transport approach, which is supplemented by a statistical decay code to describe the de-excitation of the hot primary fragments. We determine the thermodynamical properties of the primary fragments and calculate the isotope distributions of the cold final fragments. These describe the data reasonably well. For the pairs of projectiles with different isotopic content we analyze the isotopic scaling (or isoscaling) of the final fragment distributions, which has been used to extract the symmetry energy of the primary source. The calculationmore » exhibits isoscaling behavior for the total yields as do the experiments. We also perform an impact-parameter-dependent isoscaling analysis in view of the fact that the primary systems at different impact parameters have very different properties. Then the isoscaling behavior is less stringent, which we can attribute to specific structure effects of the {sup 40,48}Ca pair. The symmetry energy determined in this way depends on these structure effects.« less

Generating code adapted for interlinking legacy scalar code and extended vector code

DOEpatents

Gschwind, Michael K

2013-06-04

Mechanisms for intermixing code are provided. Source code is received for compilation using an extended Application Binary Interface (ABI) that extends a legacy ABI and uses a different register configuration than the legacy ABI. First compiled code is generated based on the source code, the first compiled code comprising code for accommodating the difference in register configurations used by the extended ABI and the legacy ABI. The first compiled code and second compiled code are intermixed to generate intermixed code, the second compiled code being compiled code that uses the legacy ABI. The intermixed code comprises at least one call instruction that is one of a call from the first compiled code to the second compiled code or a call from the second compiled code to the first compiled code. The code for accommodating the difference in register configurations is associated with the at least one call instruction.

Assessing the inter-observer variability of Computer-Aided Nodule Assessment and Risk Yield (CANARY) to characterize lung adenocarcinomas.

PubMed

Nakajima, Erica C; Frankland, Michael P; Johnson, Tucker F; Antic, Sanja L; Chen, Heidi; Chen, Sheau-Chiann; Karwoski, Ronald A; Walker, Ronald; Landman, Bennett A; Clay, Ryan D; Bartholmai, Brian J; Rajagopalan, Srinivasan; Peikert, Tobias; Massion, Pierre P; Maldonado, Fabien

2018-01-01

Lung adenocarcinoma (ADC), the most common lung cancer type, is recognized increasingly as a disease spectrum. To guide individualized patient care, a non-invasive means of distinguishing indolent from aggressive ADC subtypes is needed urgently. Computer-Aided Nodule Assessment and Risk Yield (CANARY) is a novel computed tomography (CT) tool that characterizes early ADCs by detecting nine distinct CT voxel classes, representing a spectrum of lepidic to invasive growth, within an ADC. CANARY characterization has been shown to correlate with ADC histology and patient outcomes. This study evaluated the inter-observer variability of CANARY analysis. Three novice observers segmented and analyzed independently 95 biopsy-confirmed lung ADCs from Vanderbilt University Medical Center/Nashville Veterans Administration Tennessee Valley Healthcare system (VUMC/TVHS) and the Mayo Clinic (Mayo). Inter-observer variability was measured using intra-class correlation coefficient (ICC). The average ICC for all CANARY classes was 0.828 (95% CI 0.76, 0.895) for the VUMC/TVHS cohort, and 0.852 (95% CI 0.804, 0.901) for the Mayo cohort. The most invasive voxel classes had the highest ICC values. To determine whether nodule size influenced inter-observer variability, an additional cohort of 49 sub-centimeter nodules from Mayo were also segmented by three observers, with similar ICC results. Our study demonstrates that CANARY ADC classification between novice CANARY users has an acceptably low degree of variability, and supports the further development of CANARY for clinical application.

Intracellular Cadmium Isotope Fractionation

NASA Astrophysics Data System (ADS)

Horner, T. J.; Lee, R. B.; Henderson, G. M.; Rickaby, R. E.

2011-12-01

Recent stable isotope studies into the biological utilization of transition metals (e.g. Cu, Fe, Zn, Cd) suggest several stepwise cellular processes can fractionate isotopes in both culture and nature. However, the determination of fractionation factors is often unsatisfactory, as significant variability can exist - even between different organisms with the same cellular functions. Thus, it has not been possible to adequately understand the source and mechanisms of metal isotopic fractionation. In order to address this problem, we investigated the biological fractionation of Cd isotopes within genetically-modified bacteria (E. coli). There is currently only one known biological use or requirement of Cd, a Cd/Zn carbonic anhydrase (CdCA, from the marine diatom T. weissfloggii), which we introduce into the E. coli genome. We have also developed a cleaning procedure that allows for the treating of bacteria so as to study the isotopic composition of different cellular components. We find that whole cells always exhibit a preference for uptake of the lighter isotopes of Cd. Notably, whole cells appear to have a similar Cd isotopic composition regardless of the expression of CdCA within the E. coli. However, isotopic fractionation can occur within the genetically modified E. coli during Cd use, such that Cd bound in CdCA can display a distinct isotopic composition compared to the cell as a whole. Thus, the externally observed fractionation is independent of the internal uses of Cd, with the largest Cd isotope fractionation occurring during cross-membrane transport. A general implication of these experiments is that trace metal isotopic fractionation most likely reflects metal transport into biological cells (either actively or passively), rather than relating to expression of specific physiological function and genetic expression of different metalloenzymes.

A carbon isotope mass balance for an anoxic marine sediment: Isotopic signatures of diagenesis

NASA Technical Reports Server (NTRS)

Boehme, Susan E.

1993-01-01

A carbon isotope mass balance was determined for the sediments of Cape Lookout Bight, NC to constrain the carbon budgets published previously. The diffusive, ebullitive and burial fluxes of sigma CO2 and CH4, as well as the carbon isotope signatures of these fluxes, were measured. The flux-weighted isotopic signature of the remineralized carbon (-18.9 plus or minus 2.7 per mil) agreed with the isotopic composition of the remineralized organic carbon determined from the particulate organic carbon (POC) delta(C-13) profiles (-19.2 plus or minus 0.2), verifying the flux and isotopic signature estimates. The measured delta(C-13) values of the sigma CO2 and CH4 diffusive fluxes were significantly different from those calculated from porewater gradients. The differences appear to be influenced by methane oxidation at the sediment-water interface, although other potential processes cannot be excluded. The isotope mass balance provides important information concerning the locations of potential diagenetic isotope effects. Specifically, the absence of downcore change in the delta(C-13) value of the POC fraction and the identical isotopic composition of the POC and the products of remineralization indicate that no isotopic fractionation is expressed during the initial breakdown of the POC, despite its isotopically heterogeneous composition.

Carbon isotopic composition of forest soil respiration in the decade following bark beetle and stem girdling disturbances in the Rocky Mountains: Carbon isotopes of soil respiration following disturbance

DOE PAGES

Maurer, Gregory E.; Chan, Allison M.; Trahan, Nicole A.; ...

2016-04-26

Bark beetle outbreaks are widespread in western North American forests, reducing primary productivity and transpiration, leading to forest mortality across large areas and altering ecosystem carbon cycling. Here the carbon isotope composition (δ13C) of soil respiration (δJ) was monitored in the decade after disturbance for forests affected naturally by mountain pine beetle infestation and artificially by stem girdling. The seasonal mean δJ changed along both chronosequences. We found (a) enrichment of δJ relative to controls (<1 ‰) in near-surface soils in the first 2 years after disturbance; (b) depletion (1‰ or no change) during years 3–7; and (c) a secondmore » period of enrichment (1–2‰) in years 8–10. Results were consistent with isotopic patterns associated with the gradual death and decomposition of rhizosphere organisms, fine roots, conifer needles and woody roots and debris over the course of a decade after mortality. Finally, δJ was progressively more 13C-depleted deeper in the soil than near the surface, while the bulk soil followed the well-established pattern of 13C-enrichment at depth. Overall, differences in δJ between mortality classes (<1‰) and soil depths (<3‰) were smaller than variability within a class or depth over a season (up to 6‰).« less

40 CFR 147.300 - State-administered program-Class II wells.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr... Colorado Assistant Attorney General to the Acting Regional Counsel, EPA Region VIII, “Re: Class II Well...) Letter from Colorado Assistant Attorney General to the Acting Regional Counsel, EPA Region VIII, “Re...

40 CFR 147.300 - State-administered program-Class II wells.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr... Colorado Assistant Attorney General to the Acting Regional Counsel, EPA Region VIII, “Re: Class II Well...) Letter from Colorado Assistant Attorney General to the Acting Regional Counsel, EPA Region VIII, “Re...

40 CFR 147.300 - State-administered program-Class II wells.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr... Colorado Assistant Attorney General to the Acting Regional Counsel, EPA Region VIII, “Re: Class II Well...) Letter from Colorado Assistant Attorney General to the Acting Regional Counsel, EPA Region VIII, “Re...

40 CFR 147.300 - State-administered program-Class II wells.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr... Colorado Assistant Attorney General to the Acting Regional Counsel, EPA Region VIII, “Re: Class II Well...) Letter from Colorado Assistant Attorney General to the Acting Regional Counsel, EPA Region VIII, “Re...

Assessment and Mitigation of Radiation, EMP, Debris & Shrapnel Impacts at Megajoule-Class Laser Facilities

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

Eder, D C; Anderson, R W; Bailey, D S

2009-10-05

The generation of neutron/gamma radiation, electromagnetic pulses (EMP), debris and shrapnel at mega-Joule class laser facilities (NIF and LMJ) impacts experiments conducted at these facilities. The complex 3D numerical codes used to assess these impacts range from an established code that required minor modifications (MCNP - calculates neutron and gamma radiation levels in complex geometries), through a code that required significant modifications to treat new phenomena (EMSolve - calculates EMP from electrons escaping from laser targets), to a new code, ALE-AMR, that is being developed through a joint collaboration between LLNL, CEA, and UC (UCSD, UCLA, and LBL) for debrismore » and shrapnel modelling.« less

Treatment with chemotherapy and dendritic cells pulsed with multiple Wilms' tumor 1 (WT1)-specific MHC class I/II-restricted epitopes for pancreatic cancer.

PubMed

Koido, Shigeo; Homma, Sadamu; Okamoto, Masato; Takakura, Kazuki; Mori, Masako; Yoshizaki, Shinji; Tsukinaga, Shintaro; Odahara, Shunichi; Koyama, Seita; Imazu, Hiroo; Uchiyama, Kan; Kajihara, Mikio; Arakawa, Hiroshi; Misawa, Takeyuki; Toyama, Yoichi; Yanagisawa, Satoru; Ikegami, Masahiro; Kan, Shin; Hayashi, Kazumi; Komita, Hideo; Kamata, Yuko; Ito, Masaki; Ishidao, Takefumi; Yusa, Sei-Ichi; Shimodaira, Shigetaka; Gong, Jianlin; Sugiyama, Haruo; Ohkusa, Toshifumi; Tajiri, Hisao

2014-08-15

We performed a phase I trial to investigate the safety, clinical responses, and Wilms' tumor 1 (WT1)-specific immune responses following treatment with dendritic cells (DC) pulsed with a mixture of three types of WT1 peptides, including both MHC class I and II-restricted epitopes, in combination with chemotherapy. Ten stage IV patients with pancreatic ductal adenocarcinoma (PDA) and 1 patient with intrahepatic cholangiocarcinoma (ICC) who were HLA-positive for A*02:01, A*02:06, A*24:02, DRB1*04:05, DRB1*08:03, DRB1*15:01, DRB1*15:02, DPB1*05:01, or DPB1*09:01 were enrolled. The patients received one course of gemcitabine followed by biweekly intradermal vaccinations with mature DCs pulsed with MHC class I (DC/WT1-I; 2 PDA and 1 ICC), II (DC/WT1-II; 1 PDA), or I/II-restricted WT1 peptides (DC/WT1-I/II; 7 PDA), and gemcitabine. The combination therapy was well tolerated. WT1-specific IFNγ-producing CD4(+) T cells were significantly increased following treatment with DC/WT1-I/II. WT1 peptide-specific delayed-type hypersensitivity (DTH) was detected in 4 of the 7 patients with PDA vaccinated with DC/WT1-I/II and in 0 of the 3 patients with PDA vaccinated with DC/WT1-I or DC/WT1-II. The WT1-specific DTH-positive patients showed significantly improved overall survival (OS) and progression-free survival (PFS) compared with the negative control patients. In particular, all 3 patients with PDA with strong DTH reactions had a median OS of 717 days. The activation of WT1-specific immune responses by DC/WT1-I/II combined with chemotherapy may be associated with disease stability in advanced pancreatic cancer. ©2014 American Association for Cancer Research.

Benchmark Problems of the Geothermal Technologies Office Code Comparison Study

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

White, Mark D.; Podgorney, Robert; Kelkar, Sharad M.

A diverse suite of numerical simulators is currently being applied to predict or understand the performance of enhanced geothermal systems (EGS). To build confidence and identify critical development needs for these analytical tools, the United States Department of Energy, Geothermal Technologies Office has sponsored a Code Comparison Study (GTO-CCS), with participants from universities, industry, and national laboratories. A principal objective for the study was to create a community forum for improvement and verification of numerical simulators for EGS modeling. Teams participating in the study were those representing U.S. national laboratories, universities, and industries, and each team brought unique numerical simulationmore » capabilities to bear on the problems. Two classes of problems were developed during the study, benchmark problems and challenge problems. The benchmark problems were structured to test the ability of the collection of numerical simulators to solve various combinations of coupled thermal, hydrologic, geomechanical, and geochemical processes. This class of problems was strictly defined in terms of properties, driving forces, initial conditions, and boundary conditions. Study participants submitted solutions to problems for which their simulation tools were deemed capable or nearly capable. Some participating codes were originally developed for EGS applications whereas some others were designed for different applications but can simulate processes similar to those in EGS. Solution submissions from both were encouraged. In some cases, participants made small incremental changes to their numerical simulation codes to address specific elements of the problem, and in other cases participants submitted solutions with existing simulation tools, acknowledging the limitations of the code. The challenge problems were based on the enhanced geothermal systems research conducted at Fenton Hill, near Los Alamos, New Mexico, between 1974 and 1995. The

An FPGA design of generalized low-density parity-check codes for rate-adaptive optical transport networks

NASA Astrophysics Data System (ADS)

Zou, Ding; Djordjevic, Ivan B.

2016-02-01

Forward error correction (FEC) is as one of the key technologies enabling the next-generation high-speed fiber optical communications. In this paper, we propose a rate-adaptive scheme using a class of generalized low-density parity-check (GLDPC) codes with a Hamming code as local code. We show that with the proposed unified GLDPC decoder architecture, a variable net coding gains (NCGs) can be achieved with no error floor at BER down to 10-15, making it a viable solution in the next-generation high-speed fiber optical communications.

Isotope pattern deconvolution as rising tool for isotope tracer studies in environmental research

NASA Astrophysics Data System (ADS)

Irrgeher, Johanna; Zitek, Andreas; Prohaska, Thomas

2014-05-01

During the last decade stable isotope tracers have emerged as versatile tool in ecological research. Besides 'intrinsic' isotope tracers caused by the natural variation of isotopes, the intentional introduction of 'extrinsic' enriched stable isotope tracers into biological systems has gained significant interest. Hereby the induced change in the natural isotopic composition of an element allows amongst others for studying the fate and fluxes of metals, trace elements and species in organisms or provides an intrinsic marker or tag of particular biological samples. Due to the shoreless potential of this methodology, the number of publications dealing with applications of isotope (double) spikes as tracers to address research questions in 'real world systems' is constantly increasing. However, some isotope systems like the natural Sr isotopic system, although potentially very powerful for this type of application, are still rarely used, mainly because their adequate measurement/determination poses major analytical challenges; as e.g. Sr is available in significant amounts in natural samples. In addition, biological systems underlie complex processes such as metabolism, adsorption/desorption or oxidation/reduction. As a consequence, classic evaluation approaches such as the isotope dilution mass spectrometry equation are often not applicable because of the unknown amount of tracer finally present in the sample. Isotope pattern deconvolution (IPD), based on multiple linear regression, serves as simplified alternative data processing strategy to double spike isotope dilution calculations. The outstanding advantage of this mathematical tool lies in the possibility of deconvolving the isotope pattern in a spiked sample without knowing the quantities of enriched isotope tracer being incorporated into the natural sample matrix as well as the degree of impurities and species-interconversion (e.g. from sample preparation). Here, the potential of IPD for environmental tracer

Meteoritic Sulfur Isotopic Analysis

NASA Technical Reports Server (NTRS)

Thiemens, Mark H.

1996-01-01

Funds were requested to continue our program in meteoritic sulfur isotopic analysis. We have recently detected a potential nucleosynthetic sulfur isotopic anomaly. We will search for potential carriers. The documentation of bulk systematics and the possible relation to nebular chemistry and oxygen isotopes will be explored. Analytical techniques for delta(sup 33), delta(sup 34)S, delta(sup 36)S isotopic analysis were improved. Analysis of sub milligram samples is now possible. A possible relation between sulfur isotopes and oxygen was detected, with similar group systematics noted, particularly in the case of aubrites, ureilites and entstatite chondrites. A possible nucleosynthetic excess S-33 has been noted in bulk ureilites and an oldhamite separate from Norton County. High energy proton (approximately 1 GeV) bombardments of iron foils were done to experimentally determine S-33, S-36 spallogenic yields for quantitation of isotopic measurements in iron meteorites. Techniques for measurement of mineral separates were perfected and an analysis program initiated. The systematic behavior of bulk sulfur isotopes will continue to be explored.

7 CFR 1792.103 - Seismic design and construction standards for new buildings.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Seismic Regulation for New Buildings. (b) Each of the following model codes or standards provides a level...) 548-2723. Fax: (703) 295-6211. (3) 2003 International Code Council (ICC) International Building Code... buildings. 1792.103 Section 1792.103 Agriculture Regulations of the Department of Agriculture (Continued...

7 CFR 1792.103 - Seismic design and construction standards for new buildings.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Seismic Regulation for New Buildings. (b) Each of the following model codes or standards provides a level...) 548-2723. Fax: (703) 295-6211. (3) 2003 International Code Council (ICC) International Building Code... buildings. 1792.103 Section 1792.103 Agriculture Regulations of the Department of Agriculture (Continued...

7 CFR 1792.103 - Seismic design and construction standards for new buildings.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Seismic Regulation for New Buildings. (b) Each of the following model codes or standards provides a level...) 548-2723. Fax: (703) 295-6211. (3) 2003 International Code Council (ICC) International Building Code... buildings. 1792.103 Section 1792.103 Agriculture Regulations of the Department of Agriculture (Continued...

7 CFR 1792.103 - Seismic design and construction standards for new buildings.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Seismic Regulation for New Buildings. (b) Each of the following model codes or standards provides a level...) 548-2723. Fax: (703) 295-6211. (3) 2003 International Code Council (ICC) International Building Code... buildings. 1792.103 Section 1792.103 Agriculture Regulations of the Department of Agriculture (Continued...

Simulations of linear and Hamming codes using SageMath

NASA Astrophysics Data System (ADS)

Timur, Tahta D.; Adzkiya, Dieky; Soleha

2018-03-01

Digital data transmission over a noisy channel could distort the message being transmitted. The goal of coding theory is to ensure data integrity, that is, to find out if and where this noise has distorted the message and what the original message was. Data transmission consists of three stages: encoding, transmission, and decoding. Linear and Hamming codes are codes that we discussed in this work, where encoding algorithms are parity check and generator matrix, and decoding algorithms are nearest neighbor and syndrome. We aim to show that we can simulate these processes using SageMath software, which has built-in class of coding theory in general and linear codes in particular. First we consider the message as a binary vector of size k. This message then will be encoded to a vector with size n using given algorithms. And then a noisy channel with particular value of error probability will be created where the transmission will took place. The last task would be decoding, which will correct and revert the received message back to the original message whenever possible, that is, if the number of error occurred is smaller or equal to the correcting radius of the code. In this paper we will use two types of data for simulations, namely vector and text data.

Computer codes for checking, plotting and processing of neutron cross-section covariance data and their application

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

Sartori, E.; Roussin, R.W.

This paper presents a brief review of computer codes concerned with checking, plotting, processing and using of covariances of neutron cross-section data. It concentrates on those available from the computer code information centers of the United States and the OECD/Nuclear Energy Agency. Emphasis will be placed also on codes using covariances for specific applications such as uncertainty analysis, data adjustment and data consistency analysis. Recent evaluations contain neutron cross section covariance information for all isotopes of major importance for technological applications of nuclear energy. It is therefore important that the available software tools needed for taking advantage of this informationmore » are widely known as hey permit the determination of better safety margins and allow the optimization of more economic, I designs of nuclear energy systems.« less

Learning Low-Rank Class-Specific Dictionary and Sparse Intra-Class Variant Dictionary for Face Recognition.

PubMed

Tang, Xin; Feng, Guo-Can; Li, Xiao-Xin; Cai, Jia-Xin

2015-01-01

Face recognition is challenging especially when the images from different persons are similar to each other due to variations in illumination, expression, and occlusion. If we have sufficient training images of each person which can span the facial variations of that person under testing conditions, sparse representation based classification (SRC) achieves very promising results. However, in many applications, face recognition often encounters the small sample size problem arising from the small number of available training images for each person. In this paper, we present a novel face recognition framework by utilizing low-rank and sparse error matrix decomposition, and sparse coding techniques (LRSE+SC). Firstly, the low-rank matrix recovery technique is applied to decompose the face images per class into a low-rank matrix and a sparse error matrix. The low-rank matrix of each individual is a class-specific dictionary and it captures the discriminative feature of this individual. The sparse error matrix represents the intra-class variations, such as illumination, expression changes. Secondly, we combine the low-rank part (representative basis) of each person into a supervised dictionary and integrate all the sparse error matrix of each individual into a within-individual variant dictionary which can be applied to represent the possible variations between the testing and training images. Then these two dictionaries are used to code the query image. The within-individual variant dictionary can be shared by all the subjects and only contribute to explain the lighting conditions, expressions, and occlusions of the query image rather than discrimination. At last, a reconstruction-based scheme is adopted for face recognition. Since the within-individual dictionary is introduced, LRSE+SC can handle the problem of the corrupted training data and the situation that not all subjects have enough samples for training. Experimental results show that our method achieves the

Learning Low-Rank Class-Specific Dictionary and Sparse Intra-Class Variant Dictionary for Face Recognition

PubMed Central

Tang, Xin; Feng, Guo-can; Li, Xiao-xin; Cai, Jia-xin

2015-01-01

Face recognition is challenging especially when the images from different persons are similar to each other due to variations in illumination, expression, and occlusion. If we have sufficient training images of each person which can span the facial variations of that person under testing conditions, sparse representation based classification (SRC) achieves very promising results. However, in many applications, face recognition often encounters the small sample size problem arising from the small number of available training images for each person. In this paper, we present a novel face recognition framework by utilizing low-rank and sparse error matrix decomposition, and sparse coding techniques (LRSE+SC). Firstly, the low-rank matrix recovery technique is applied to decompose the face images per class into a low-rank matrix and a sparse error matrix. The low-rank matrix of each individual is a class-specific dictionary and it captures the discriminative feature of this individual. The sparse error matrix represents the intra-class variations, such as illumination, expression changes. Secondly, we combine the low-rank part (representative basis) of each person into a supervised dictionary and integrate all the sparse error matrix of each individual into a within-individual variant dictionary which can be applied to represent the possible variations between the testing and training images. Then these two dictionaries are used to code the query image. The within-individual variant dictionary can be shared by all the subjects and only contribute to explain the lighting conditions, expressions, and occlusions of the query image rather than discrimination. At last, a reconstruction-based scheme is adopted for face recognition. Since the within-individual dictionary is introduced, LRSE+SC can handle the problem of the corrupted training data and the situation that not all subjects have enough samples for training. Experimental results show that our method achieves the

Platinum isotopes in iron meteorites: Galactic cosmic ray effects and nucleosynthetic homogeneity in the p-process isotope 190Pt and the other platinum isotopes

NASA Astrophysics Data System (ADS)

Hunt, Alison C.; Ek, Mattias; Schönbächler, Maria

2017-11-01

Platinum isotopes are sensitive to the effects of galactic cosmic rays (GCR), which can alter isotope ratios and mask nucleosynthetic isotope variations. Platinum also features one p-process isotope, 190Pt, which is very low abundance and therefore challenging to analyse. Platinum-190 is relevant for early solar-system chronology because of its decay to 186Os. Here, we present new Pt isotope data for five iron meteorite groups (IAB, IIAB, IID, IIIAB and IVA), including high-precision measurements of 190Pt for the IAB, IIAB and IIIAB irons, determined by multi-collector ICPMS. New data are in good agreement with previous studies and display correlations between different Pt isotopes. The slopes of these correlations are well-reproduced by the available GCR models. We report Pt isotope ratios for the IID meteorite Carbo that are consistently higher than the predicted effects from the GCR model. This suggests that the model predictions do not fully account for all the GCR effects on Pt isotopes, but also that the pre-atmospheric radii and exposure times calculated for Carbo may be incorrect. Despite this, the good agreement of relative effects in Pt isotopes with the predicted GCR trends confirms that Pt isotopes are a useful in-situ neutron dosimeter. Once GCR effects are accounted for, our new dataset reveals s- and r-process homogeneity between the iron meteorite groups studied here and the Earth. New 190Pt data for the IAB, IIAB and IIIAB iron meteorites indicate the absence of GCR effects and homogeneity in the p-process isotope between these groups and the Earth. This corresponds well with results from other heavy p-process isotopes and suggests their homogenous distribution in the inner solar system, although it does not exclude that potential p-process isotope variations are too diluted to be currently detectable.

The fourfold way of the genetic code.

PubMed

Jiménez-Montaño, Miguel Angel

2009-11-01

We describe a compact representation of the genetic code that factorizes the table in quartets. It represents a "least grammar" for the genetic language. It is justified by the Klein-4 group structure of RNA bases and codon doublets. The matrix of the outer product between the column-vector of bases and the corresponding row-vector V(T)=(C G U A), considered as signal vectors, has a block structure consisting of the four cosets of the KxK group of base transformations acting on doublet AA. This matrix, translated into weak/strong (W/S) and purine/pyrimidine (R/Y) nucleotide classes, leads to a code table with mixed and unmixed families in separate regions. A basic difference between them is the non-commuting (R/Y) doublets: AC/CA, GU/UG. We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé [Jestin, J.-L., Soulé, C., 2007. Symmetries by base substitutions in the genetic code predict 2' or 3' aminoacylation of tRNAs. J. Theor. Biol. 247, 391-394], and the rearrangements of the table by Delarue [Delarue, M., 2007. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13, 161-169] and Rodin and Rodin [Rodin, S.N., Rodin, A.S., 2008. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100, 341-355], respectively.

Magnetic-Fe/Fe(3)O(4)-nanoparticle-bound SN38 as carboxylesterase-cleavable prodrug for the delivery to tumors within monocytes/macrophages.

PubMed

Wang, Hongwang; Shrestha, Tej B; Basel, Matthew T; Dani, Raj Kumar; Seo, Gwi-Moon; Balivada, Sivasai; Pyle, Marla M; Prock, Heidy; Koper, Olga B; Thapa, Prem S; Moore, David; Li, Ping; Chikan, Viktor; Troyer, Deryl L; Bossmann, Stefan H

2012-01-01

The targeted delivery of therapeutics to the tumor site is highly desirable in cancer treatment, because it is capable of minimizing collateral damage. Herein, we report the synthesis of a nanoplatform, which is composed of a 15 ± 1 nm diameter core/shell Fe/Fe(3)O(4) magnetic nanoparticles (MNPs) and the topoisomerase I blocker SN38 bound to the surface of the MNPs via a carboxylesterase cleavable linker. This nanoplatform demonstrated high heating ability (SAR = 522 ± 40 W/g) in an AC-magnetic field. For the purpose of targeted delivery, this nanoplatform was loaded into tumor-homing double-stable RAW264.7 cells (mouse monocyte/macrophage-like cells (Mo/Ma)), which have been engineered to express intracellular carboxylesterase (InCE) upon addition of doxycycline by a Tet-On Advanced system. The nanoplatform was taken up efficiently by these tumor-homing cells. They showed low toxicity even at high nanoplatform concentration. SN38 was released successfully by switching on the Tet-On Advanced system. We have demonstrated that this nanoplatform can be potentially used for thermochemotherapy. We will be able to achieve the following goals: (1) Specifically deliver the SN38 prodrug and magnetic nanoparticles to the cancer site as the payload of tumor-homing double-stable RAW264.7 cells; (2) Release of chemotherapeutic SN38 at the cancer site by means of the self-containing Tet-On Advanced system; (3) Provide localized magnetic hyperthermia to enhance the cancer treatment, both by killing cancer cells through magnetic heating and by activating the immune system.

Magnetic-Fe/Fe3O4-nanoparticle-bound SN38 as carboxylesterase-cleavable prodrug for the delivery to tumors within monocytes/macrophages

PubMed Central

Shrestha, Tej B; Basel, Matthew T; Dani, Raj Kumar; Seo, Gwi-Moon; Balivada, Sivasai; Pyle, Marla M; Prock, Heidy; Koper, Olga B; Thapa, Prem S; Moore, David; Li, Ping; Chikan, Viktor

2012-01-01

Summary The targeted delivery of therapeutics to the tumor site is highly desirable in cancer treatment, because it is capable of minimizing collateral damage. Herein, we report the synthesis of a nanoplatform, which is composed of a 15 ± 1 nm diameter core/shell Fe/Fe3O4 magnetic nanoparticles (MNPs) and the topoisomerase I blocker SN38 bound to the surface of the MNPs via a carboxylesterase cleavable linker. This nanoplatform demonstrated high heating ability (SAR = 522 ± 40 W/g) in an AC-magnetic field. For the purpose of targeted delivery, this nanoplatform was loaded into tumor-homing double-stable RAW264.7 cells (mouse monocyte/macrophage-like cells (Mo/Ma)), which have been engineered to express intracellular carboxylesterase (InCE) upon addition of doxycycline by a Tet-On Advanced system. The nanoplatform was taken up efficiently by these tumor-homing cells. They showed low toxicity even at high nanoplatform concentration. SN38 was released successfully by switching on the Tet-On Advanced system. We have demonstrated that this nanoplatform can be potentially used for thermochemotherapy. We will be able to achieve the following goals: (1) Specifically deliver the SN38 prodrug and magnetic nanoparticles to the cancer site as the payload of tumor-homing double-stable RAW264.7 cells; (2) Release of chemotherapeutic SN38 at the cancer site by means of the self-containing Tet-On Advanced system; (3) Provide localized magnetic hyperthermia to enhance the cancer treatment, both by killing cancer cells through magnetic heating and by activating the immune system. PMID:23016149

CO2-dependent carbon isotope fractionation in the dinoflagellate Alexandrium tamarense

NASA Astrophysics Data System (ADS)

Wilkes, Elise B.; Carter, Susan J.; Pearson, Ann

2017-09-01

The carbon isotopic composition of marine sedimentary organic matter is used to resolve long-term histories of pCO2 based on studies indicating a CO2-dependence of photosynthetic carbon isotope fractionation (εP). It recently was proposed that the δ13C values of dinoflagellates, as recorded in fossil dinocysts, might be used as a proxy for pCO2. However, significant questions remain regarding carbon isotope fractionation in dinoflagellates and how such fractionation may impact sedimentary records throughout the Phanerozoic. Here we investigate εP as a function of CO2 concentration and growth rate in the dinoflagellate Alexandrium tamarense. Experiments were conducted in nitrate-limited chemostat cultures. Values of εP were measured on cells having growth rates (μ) of 0.14-0.35 d-1 and aqueous carbon dioxide concentrations of 10.2-63 μmol kg-1 and were found to correlate linearly with μ/[CO2(aq)] (r2 = 0.94) in accord with prior, analogous chemostat investigations with eukaryotic phytoplankton. A maximum fractionation (εf) value of 27‰ was characterized from the intercept of the experiments, representing the first value of εf determined for an algal species employing Form II RubisCO-a structurally and catalytically distinct form of the carbon-fixing enzyme. This value is larger than theoretical predictions for Form II RubisCO and not significantly different from the ∼25‰ εf values observed for taxa employing Form ID RubisCO. We also measured the carbon isotope contents of dinosterol, hexadecanoic acid, and phytol from each experiment, finding that each class of biomarker exhibits different isotopic behavior. The apparent CO2-dependence of εP values in our experiments strengthens the proposal to use dinocyst δ13C values as a pCO2 proxy. Moreover, the similarity between the εf value for A. tamarense and the consensus value of ∼25‰ indicates that the CO2-sensitivity of carbon isotope fractionation saturates at similar CO2 levels across all three

Proxies of Tropical Cyclone Isotope Spikes in Precipitation: Landfall Site Selection

NASA Astrophysics Data System (ADS)

Lawrence, J. R.; Maddocks, R.

2011-12-01

The human experience of climate change is not one of gradual changes in seasonal or yearly changes in temperature or rainfall. Despite that most paleoclimatic reconstructions attempt to provide just such information. Humans experience climate change on much shorter time scales. We remember hurricanes, weeks of drought or overwhelming rainy periods. Tropical cyclones produce very low isotope ratios in both rainfall and in atmospheric water vapor. Thus, climate proxies that potentially record these low isotope ratios offer the most concrete record of climate change to which humans can relate. The oxygen isotopic composition of tropical cyclone rainfall has the potential to be recorded in fresh water carbonate fossil material, cave deposits and corals. The hydrogen isotopic composition of tropical cyclone rainfall has the potential to be recorded in tree ring cellulose and organic matter in fresh water bodies. The Class of carbonate organisms known as Ostracoda form their carapaces very rapidly. Thus fresh water ephemeral ponds in the subtropics are ideal locations for isotopic studies because they commonly are totally dry when tropical cyclones make landfall. The other proxies suffer primarily from a dilution effect. The water from tropical cyclones is mixed with pre-existing water. In cave deposits tropical cyclone rains mix with soil and ground waters. In the near shore coral environment the rain mixes with seawater. For tree rings there are three sources of water: soil water, atmospheric water vapor that exchanges with leaf water and tropical cyclone rain. In lakes because of their large size rainfall runoff mixes with ground water and preexisting water in the lake. A region that shows considerable promise is Texas / Northeast Mexico. In a study of surface waters that developed from the passage of Tropical Storm Allison (2001) in SE Texas both the pond water and Ostracoda that bloomed recorded the low oxygen isotope signal of that storm (Lawrence et al, 2008). In

The synthesis of tritium, carbon-14 and stable isotope labelled selective estrogen receptor degraders.

PubMed

Bragg, Ryan A; Bushby, Nick; Ericsson, Cecilia; Kingston, Lee P; Ji, Hailong; Elmore, Charles S

2016-09-01

As part of a Medicinal Chemistry program aimed at developing an orally bioavailable selective estrogen receptor degrader, a number of tritium, carbon-14, and stable isotope labelled (E)-3-[4-(2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indol-1-yl)phenyl]prop-2-enoic acids were required. This paper discusses 5 synthetic approaches to this compound class. Copyright © 2016 John Wiley & Sons, Ltd.

The Classification of Tongue Colors with Standardized Acquisition and ICC Profile Correction in Traditional Chinese Medicine

PubMed Central

Tu, Li-ping; Chen, Jing-bo; Hu, Xiao-juan; Zhang, Zhi-feng

2016-01-01

Background and Goal. The application of digital image processing techniques and machine learning methods in tongue image classification in Traditional Chinese Medicine (TCM) has been widely studied nowadays. However, it is difficult for the outcomes to generalize because of lack of color reproducibility and image standardization. Our study aims at the exploration of tongue colors classification with a standardized tongue image acquisition process and color correction. Methods. Three traditional Chinese medical experts are chosen to identify the selected tongue pictures taken by the TDA-1 tongue imaging device in TIFF format through ICC profile correction. Then we compare the mean value of L * a * b * of different tongue colors and evaluate the effect of the tongue color classification by machine learning methods. Results. The L * a * b * values of the five tongue colors are statistically different. Random forest method has a better performance than SVM in classification. SMOTE algorithm can increase classification accuracy by solving the imbalance of the varied color samples. Conclusions. At the premise of standardized tongue acquisition and color reproduction, preliminary objectification of tongue color classification in Traditional Chinese Medicine (TCM) is feasible. PMID:28050555

The Classification of Tongue Colors with Standardized Acquisition and ICC Profile Correction in Traditional Chinese Medicine.

PubMed

Qi, Zhen; Tu, Li-Ping; Chen, Jing-Bo; Hu, Xiao-Juan; Xu, Jia-Tuo; Zhang, Zhi-Feng

2016-01-01

Background and Goal . The application of digital image processing techniques and machine learning methods in tongue image classification in Traditional Chinese Medicine (TCM) has been widely studied nowadays. However, it is difficult for the outcomes to generalize because of lack of color reproducibility and image standardization. Our study aims at the exploration of tongue colors classification with a standardized tongue image acquisition process and color correction. Methods . Three traditional Chinese medical experts are chosen to identify the selected tongue pictures taken by the TDA-1 tongue imaging device in TIFF format through ICC profile correction. Then we compare the mean value of L * a * b * of different tongue colors and evaluate the effect of the tongue color classification by machine learning methods. Results . The L * a * b * values of the five tongue colors are statistically different. Random forest method has a better performance than SVM in classification. SMOTE algorithm can increase classification accuracy by solving the imbalance of the varied color samples. Conclusions . At the premise of standardized tongue acquisition and color reproduction, preliminary objectification of tongue color classification in Traditional Chinese Medicine (TCM) is feasible.

Estimating lifetime risk from spot biomarker data and intra‐class correlation coefficients (ICC)

EPA Science Inventory

Human biomarker measurements in tissues including blood, breath, and urine can serve as efficient surrogates for environmental monitoring because a single biological sample integrates personal exposure across all environmental media and uptake pathways. However, biomarkers repres...

Oxygen isotope analysis of bacterial and fungal manganese oxidation.

PubMed

Sutherland, K M; Wankel, S D; Hansel, C M

2018-07-01

The ability of micro-organisms to oxidize manganese (Mn) from Mn(II) to Mn(III/IV) oxides transcends boundaries of biological clade or domain. Many bacteria and fungi oxidize Mn(II) to Mn(III/IV) oxides directly through enzymatic activity or indirectly through the production of reactive oxygen species. Here, we determine the oxygen isotope fractionation factors associated with Mn(II) oxidation via various biotic (bacteria and fungi) and abiotic Mn(II) reaction pathways. As oxygen in Mn(III/IV) oxides may be derived from precursor water and molecular oxygen, we use a twofold approach to determine the isotope fractionation with respect to each oxygen source. Using both 18 O-labeled water and closed-system Rayleigh distillation approaches, we constrain the kinetic isotope fractionation factors associated with O atom incorporation during Mn(II) oxidation to -17.3‰ to -25.9‰ for O 2 and -1.9‰ to +1.8‰ for water. Results demonstrate that stable oxygen isotopes of Mn(III/IV) oxides have potential to distinguish between two main classes of biotic Mn(II) oxidation: direct enzymatic oxidation in which O 2 is the oxidant and indirect enzymatic oxidation in which superoxide is the oxidant. The fraction of Mn(III/IV) oxide-associated oxygen derived from water varies significantly (38%-62%) among these bio-oxides with only weak relationship to Mn oxidation state, suggesting Mn(III) disproportionation may account for differences in the fraction of mineral-bound oxygen from water and O 2 . Additionally, direct incorporation of molecular O 2 suggests that Mn(III/IV) oxides contain a yet untapped proxy of δ18OO2 of environmental O 2 , a parameter reflecting the integrated influence of global respiration, photorespiration, and several other biogeochemical reactions of global significance. © 2018 John Wiley & Sons Ltd.

The Landscape of long non-coding RNA classification

PubMed Central

St Laurent, Georges; Wahlestedt, Claes; Kapranov, Philipp

2015-01-01

Advances in the depth and quality of transcriptome sequencing have revealed many new classes of long non-coding RNAs (lncRNAs). lncRNA classification has mushroomed to accommodate these new findings, even though the real dimensions and complexity of the non-coding transcriptome remain unknown. Although evidence of functionality of specific lncRNAs continues to accumulate, conflicting, confusing, and overlapping terminology has fostered ambiguity and lack of clarity in the field in general. The lack of fundamental conceptual un-ambiguous classification framework results in a number of challenges in the annotation and interpretation of non-coding transcriptome data. It also might undermine integration of the new genomic methods and datasets in an effort to unravel function of lncRNA. Here, we review existing lncRNA classifications, nomenclature, and terminology. Then we describe the conceptual guidelines that have emerged for their classification and functional annotation based on expanding and more comprehensive use of large systems biology-based datasets. PMID:25869999

Electrochemically controlled iron isotope fractionation

NASA Astrophysics Data System (ADS)

Black, Jay R.; Young, Edward D.; Kavner, Abby

2010-02-01

Variations in the stable isotope abundances of transition metals have been observed in the geologic record and trying to understand and reconstruct the physical/environmental conditions that produced these signatures is an area of active research. It is clear that changes in oxidation state lead to large fractionations of the stable isotopes of many transition metals such as iron, suggesting that transition metal stable isotope signatures could be used as a paleo-redox proxy. However, the factors contributing to these observed stable isotope variations are poorly understood. Here we investigate how the kinetics of iron redox electrochemistry generates isotope fractionation. Through a combination of electrodeposition experiments and modeling of electrochemical processes including mass-transport, we show that electron transfer reactions are the cause of a large isotope separation, while mass transport-limited supply of reactant to the electrode attenuates the observed isotopic fractionation. Furthermore, the stable isotope composition of electroplated transition metals can be tuned in the laboratory by controlling parameters such as solution chemistry, reaction overpotential, and solution convection. These methods are potentially useful for generating isotopically-marked metal surfaces for tracking and forensic purposes. In addition, our studies will help interpret stable isotope data in terms of identifying underlying electron transfer processes in laboratory and natural samples.

Hybrid concatenated codes and iterative decoding

NASA Technical Reports Server (NTRS)

Divsalar, Dariush (Inventor); Pollara, Fabrizio (Inventor)

2000-01-01

Several improved turbo code apparatuses and methods. The invention encompasses several classes: (1) A data source is applied to two or more encoders with an interleaver between the source and each of the second and subsequent encoders. Each encoder outputs a code element which may be transmitted or stored. A parallel decoder provides the ability to decode the code elements to derive the original source information d without use of a received data signal corresponding to d. The output may be coupled to a multilevel trellis-coded modulator (TCM). (2) A data source d is applied to two or more encoders with an interleaver between the source and each of the second and subsequent encoders. Each of the encoders outputs a code element. In addition, the original data source d is output from the encoder. All of the output elements are coupled to a TCM. (3) At least two data sources are applied to two or more encoders with an interleaver between each source and each of the second and subsequent encoders. The output may be coupled to a TCM. (4) At least two data sources are applied to two or more encoders with at least two interleavers between each source and each of the second and subsequent encoders. (5) At least one data source is applied to one or more serially linked encoders through at least one interleaver. The output may be coupled to a TCM. The invention includes a novel way of terminating a turbo coder.

Fractionation of Nitrogen and Oxygen Isotopes and Roles of Bacteria during Denitrification

NASA Astrophysics Data System (ADS)

Kang, J.; Buyanjargal, A.; Jeen, S. W.

2017-12-01

Nitrate in groundwater can cause health and environmental problems when not properly treated. The purpose of this study was to develop a treatment method for nitrate in groundwater using organic carbon-based reactive mixtures (i.e., wood chips and gravel) through column experiments and to evaluate reaction mechanisms responsible for the treatment. The column experiments were operated for a total of 19 months. The results from the geochemical analyses for the experiments suggest that cultures of denitrifying bacteria used organic carbon while utilizing nitrate as their electron acceptor via denitrification process. Proteobacteria was the most abundant phylum in all samples, accounting for 45.7% of the bacterial reads, followed by Firmicutes (22.6%) and Chlorobi (10.6%). Bacilli, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Actinobacteria_c consisted of 32, 30, 23, 11, and 2% of denitrifying bacteria class. The denitrification process caused fractionation of nitrogen and oxygen isotopes of nitrate while nitrate concentration decreased. When fitted to the Rayleigh's fractionation model, enrichment factors (ɛ) were 11.5‰ and 5.6‰ for 15N and 18O isotopes, respectively. Previous studies suggested that nitrogen isotope enrichment factors of denitrification are within the range of 4.7 to 40‰ and oxygen isotopic enrichment factors are between 8 and 18.3‰. This study shows that nitrate in groundwater can be effectively treated using passive treatment systems, such as permeable reactive barriers (PRBs), and denitrificaton is the dominant process reponsible for the removal of nitrate.

The origin of volatile element depletion in early solar system material: Clues from Zn isotopes in chondrules

NASA Astrophysics Data System (ADS)

Pringle, Emily A.; Moynier, Frédéric; Beck, Pierre; Paniello, Randal; Hezel, Dominik C.

2017-06-01

Volatile lithophile elements are depleted in the different planetary materials to various degrees, but the origin of these depletions is still debated. Stable isotopes of moderately volatile elements such as Zn can be used to understand the origin of volatile element depletions. Samples with significant volatile element depletions, including the Moon and terrestrial tektites, display heavy Zn isotope compositions (i.e. enrichment of 66Zn vs. 64Zn), consistent with kinetic Zn isotope fractionation during evaporation. However, Luck et al. (2005) found a negative correlation between δ66Zn and 1/[Zn] between CI, CM, CO, and CV chondrites, opposite to what would be expected if evaporation caused the Zn abundance variations among chondrite groups. We have analyzed the Zn isotope composition of multiple samples of the major carbonaceous chondrite classes: CI (1), CM (4), CV (2), CO (4), CB (2), CH (2), CK (4), and CK/CR (1). The bulk chondrites define a negative correlation in a plot of δ66Zn vs 1/[Zn], confirming earlier results that Zn abundance variations among carbonaceous chondrites cannot be explained by evaporation. Exceptions are CB and CH chondrites, which display Zn systematics consistent with a collisional formation mechanism that created enrichment in heavy Zn isotopes relative to the trend defined by CI-CK. We further report Zn isotope analyses of chondrite components, including chondrules from Allende (CV3) and Mokoia (CV3), as well as an aliquot of Allende matrix. All chondrules are enriched in light Zn isotopes (∼500 ppm on 66Zn/64Zn) relative to the bulk, contrary to what would be expected if Zn were depleted during evaporation, on the other hand the matrix has a complementary heavy isotope composition. We report sequential leaching experiments in un-equilibrated ordinary chondrites, which show sulfides are isotopically heavy compared to silicates and the bulk meteorite by ca. +0.65 per mil on 66Zn/64Zn. We suggest isotopically heavy sulfides were

Abundances in red giant stars - Carbon and oxygen isotopes in carbon-rich molecular envelopes

NASA Technical Reports Server (NTRS)

Wannier, P. G.; Sahai, R.

1987-01-01

Millimeter-wave observations have been made of isotopically substituted CO toward the envelopes of 11 carbon-rich stars. In every case, C-13O was detected and model calculations were used to estimate the C-12/C-13 abundance ratio. C-17O was detected toward three, and possibly four, envelopes, with sensitive upper limits for two others. The CO-18 variant was detected in two envelopes. New results include determinations of oxygen isotopic ratios in the two carbon-rich protoplanetary nebulae CRL 26688 and CRL 618. As with other classes of red giant stars, the carbon-rich giants seem to be significantly, though variably, enriched in O-17. These results, in combination with observations in interstellar molecular clouds, indicate that current knowledge of stellar production of the CNO nuclides is far from satisfactory.

Dynamic fracture toughness of ASME SA508 Class 2a ASME SA533 grade A Class 2 base and heat affected zone material and applicable weld metals

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

Logsdon, W.A.; Begley, J.A.; Gottshall, C.L.

1978-03-01

The ASME Boiler and Pressure Vessel Code, Section III, Article G-2000, requires that dynamic fracture toughness data be developed for materials with specified minimum yield strengths greater than 50 ksi to provide verification and utilization of the ASME specified minimum reference toughness K/sub IR/ curve. In order to qualify ASME SA508 Class 2a and ASME SA533 Grade A Class 2 pressure vessel steels (minimum yield strengths equal 65 kip/in./sup 2/ and 70 kip/in./sup 2/, respectively) per this requirement, dynamic fracture toughness tests were performed on these materials. All dynamic fracture toughness values of SA508 Class 2a base and HAZ material,more » SA533 Grade A Class 2 base and HAZ material, and applicable weld metals exceeded the ASME specified minimum reference toughness K/sub IR/ curve.« less

40 CFR 147.2551 - State-administered program-Class II wells.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr..., “Re: Application for Primacy in the Regulation of Class II Injection Wells,” March 8, 1982; (5) Letter from State Oil and Gas Supervisor, Wyoming Oil and Gas Conservation Commission, to EPA Region VIII, “Re...

40 CFR 147.2551 - State-administered program-Class II wells.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr..., “Re: Application for Primacy in the Regulation of Class II Injection Wells,” March 8, 1982; (5) Letter from State Oil and Gas Supervisor, Wyoming Oil and Gas Conservation Commission, to EPA Region VIII, “Re...

40 CFR 147.2551 - State-administered program-Class II wells.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., call 202-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr..., “Re: Application for Primacy in the Regulation of Class II Injection Wells,” March 8, 1982; (5) Letter from State Oil and Gas Supervisor, Wyoming Oil and Gas Conservation Commission, to EPA Region VIII, “Re...

40 CFR 147.2551 - State-administered program-Class II wells.