[Expression, purification and activity analysis of GGDEF and EAL domain-containing proteins from Lactobacillus acidophilus].

PubMed

He, Jia-Hui; Sun, Jie-Li; Yan, Wen-Juan; Wang, Fang

2017-05-20

To identify the functions of the proteins containing the GGDEF or EAL domain in Lactobacillus acidophilus for investigation of the regulatory mechanism of c-di-GMP in this strain. The DNA fragments of NH13_07045-GGDEF, NH13_07050 and NH13_07055 from Lactobacillus acidophilus ATCC4356 were amplified by PCR and cloned into the expression vector pMAL-His-c2. After sequencing, the recombinant plasmids were transformed into competent Escherichia coli cells, which were induced by IPTG to express the recombinant proteins fused with maltose binding protein (MBP). The fusion proteins were purified using amylose resin column for diguanylate cyclase (DGC) or phosphodiesterase (PDE) activity assays in vitro followed by analysis with high-performance liquid chromatography (HPLC). The target DNA fragments were obtained by PCR, and their sequences were all identical to that in GenBank. The purified and concentrated fusion proteins, which were identified by SDS-PAGE and Western blotting, had relative molecular masses of 59 kD, 67 kD and 72 kD. HPLC analysis showed no DGC activity in NH13_07045-GGDEF, while PDE activity was found in NH13_07050 but not in NH13_07055. We obtained the protein encoded by NH13_07050 that possesses PDE activity in vitro. This protein may facilitate the evaluation of the regulatory function of c-di-GMP in Lactobacillus acidophilus.

Procedure for implementation of temperature-dependent mechanical property capability in the Engineering Analysis Language (EAL) system

NASA Technical Reports Server (NTRS)

Glass, David E.; Robinson, James C.

1990-01-01

A procedure is presented to allow the use of temperature dependent mechanical properties in the Engineering Analysis Language (EAL) System for solid structural elements. This is accomplished by including a modular runstream in the main EAL runstream. The procedure is applicable for models with multiple materials and with anisotropic properties, and can easily be incorporated into an existing EAL runstream. The procedure (which is applicable for EAL elastic solid elements) is described in detail, followed by a description of the validation of the routine. A listing of the EAL runstream used to validate the procedure is included in the Appendix.

Estimation of Cyclic Shift with Delayed Correlation and Matched Filtering in Time Domain Cyclic-SLM for PAPR Reduction

PubMed Central

2016-01-01

Time domain cyclic-selective mapping (TDC-SLM) reduces the peak-to-average power ratio (PAPR) in OFDM systems while the amounts of cyclic shifts are required to recover the transmitted signal in a receiver. One of the critical issues of the SLM scheme is sending the side information (SI) which reduces the throughputs in wireless OFDM systems. The proposed scheme implements delayed correlation and matched filtering (DC-MF) to estimate the amounts of the cyclic shifts in the receiver. In the proposed scheme, the DC-MF is placed after the frequency domain equalization (FDE) to improve the accuracy of cyclic shift estimation. The accuracy rate of the propose scheme reaches 100% at E b/N 0 = 5 dB and the bit error rate (BER) improves by 0.2 dB as compared with the conventional TDC-SLM. The BER performance of the proposed scheme is also better than that of the conventional TDC-SLM even though a nonlinear high power amplifier is assumed. PMID:27752539

2015 EAL evidence-based nutrition practice guildeline for the management of hypertension in adults

USDA-ARS?s Scientific Manuscript database

Hypertension (HTN) or high blood pressure (BP) is one of the most prevalent forms of cardiovascular disease and occurs in approximately one of every three adults in the United States. Nutrition therapy is an important component of treatment. The purpose of this Evidence Analysis Library (EAL) gui...

Narrative Learning, EAL and Metacognitive Development

ERIC Educational Resources Information Center

Cortazzi, Martin; Jin, Lixian

2007-01-01

This paper elaborates some aspects of narrative learning--defined here as learning to tell stories and learning from, about and through narratives--in the context of primary-age pupils who use English as an Additional Language (EAL). The paper introduces some principles to support their language development in classroom interaction. We argue that…

Plan Aggregation for Strong Cyclic Planning in Nondeterministic Domains

DTIC Science & Technology

2014-07-02

Plan Aggregation for Strong Cyclic Planning in Nondeterministic Domains Ron Alforda, Ugur Kuterc, Dana Naub, Robert P. Goldmanc aASEE/NRL...addresses: ronald.alford.ctr@nrl.navy.mil (Ron Alford), ukuter@sift.net ( Ugur Kuter), nau@cs.umd.edu (Dana Nau), rpgoldman@sift.net (Robert P. Goldman

Plan Aggregation for Strong Cyclic Planning in Nondeterministic Domains

DTIC Science & Technology

2014-07-23

ACRONYM(S) ARO 8. PERFORMING ORGANIZATION REPORT NUMBER 19a. NAME OF RESPONSIBLE PERSON 19b. TELEPHONE NUMBER Michael Cox Ron Alford, Ugur Kuter...ScienceDirect Artificial Intelligence www.elsevier.com/locate/artint Plan aggregation for strong cyclic planning in nondeterministic domains Ron Alford a,∗, Ugur

A systematic analysis of the in vitro and in vivo functions of the HD-GYP domain proteins of Vibrio cholerae.

PubMed

McKee, Robert W; Kariisa, Ankunda; Mudrak, Benjamin; Whitaker, Courtney; Tamayo, Rita

2014-10-25

The second messenger cyclic diguanylate (c-di-GMP) plays a central role in bacterial adaptation to extracellular stimuli, controlling processes such as motility, biofilm development, cell development and, in some pathogens, virulence. The intracellular level of c-di-GMP is controlled by the complementary activities of diguanylate cyclases containing a GGDEF domain and two classes of c-di-GMP phosphodiesterases containing an EAL or HD-GYP hydrolytic domain. Compared to the GGDEF and EAL domains, the functions of HD-GYP domain family proteins are poorly characterized. The human diarrheal pathogen Vibrio cholerae encodes nine putative HD-GYP domain proteins. To determine the contributions of HD-GYP domain proteins to c-di-GMP signaling in V. cholerae, we systematically analyzed the enzymatic functionality of each protein and their involvement in processes known to be regulated by c-di-GMP: motility, biofilm development and virulence. Complementary in vitro and in vivo experiments showed that four HD-GYP domain proteins are active c-di-GMP phosphodiesterases: VC1295, VC1348, VCA0210 and VCA0681. Mutation of individual HD-GYP domain genes, as well as combinatorial mutations of multiple HD-GYP domain genes, had no effect on motility or biofilm formation of V. cholerae under the conditions tested. Furthermore, no single HD-GYP domain gene affected intestinal colonization by V. cholerae in an infant mouse model. However, inactivation of multiple HD-GYP domain genes, including the four encoding functional phosphodiesterases, significantly attenuated colonization. These results indicate that the HD-GYP family of c-di-GMP phosphodiesterases impacts signaling by this second messenger during infection. Altogether, this work greatly furthers the understanding of this important family of c-di-GMP metabolic enzymes and demonstrates a role for HD-GYP domain proteins in the virulence of V. cholerae.

Complexity, Accuracy, Fluency and Lexis in Task-Based Performance: A Synthesis of the Ealing Research

ERIC Educational Resources Information Center

Skehan, Peter; Foster, Pauline

2012-01-01

This chapter will present a research synthesis of a series of studies, termed here the Ealing research. The studies use the same general framework to conceptualise tasks and task performance, enabling easier comparability. The different studies, although each is self-contained, build into a wider picture of task performance. The major point of…

Resilience through Storytelling in the EAL Classroom

ERIC Educational Resources Information Center

Geres, Koreen

2016-01-01

English as an Additional Language (EAL) teachers often become the trusted confidants of students who experienced forced migration. Although teachers are not typically trained to be counsellors or encouraged to take that role, what they do in the classroom can have a great influence on their students' well-being (Pipher, 2002). In fact, teachers…

Hybrid Raman/Brillouin-optical-time-domain-analysis-distributed optical fiber sensors based on cyclic pulse coding.

PubMed

Taki, M; Signorini, A; Oton, C J; Nannipieri, T; Di Pasquale, F

2013-10-15

We experimentally demonstrate the use of cyclic pulse coding for distributed strain and temperature measurements in hybrid Raman/Brillouin optical time-domain analysis (BOTDA) optical fiber sensors. The highly integrated proposed solution effectively addresses the strain/temperature cross-sensitivity issue affecting standard BOTDA sensors, allowing for simultaneous meter-scale strain and temperature measurements over 10 km of standard single mode fiber using a single narrowband laser source only.

The Use of Makaton for Supporting Talk, through Play, for Pupils Who have English as an Additional Language (EAL) in the Foundation Stage

ERIC Educational Resources Information Center

Mistry, Malini; Barnes, Danielle

2013-01-01

This study examines the use of Makaton® , a language programme based on the use of signing, symbols and speech, as a pedagogic tool to support the development of talk for pupils learning English as an Additional Language (EAL). The research setting was a Reception class with a high percentage of pupils who have EAL in the initial stages of…

Joint Frequency-Domain Equalization and Despreading for Multi-Code DS-CDMA Using Cyclic Delay Transmit Diversity

NASA Astrophysics Data System (ADS)

Yamamoto, Tetsuya; Takeda, Kazuki; Adachi, Fumiyuki

Frequency-domain equalization (FDE) based on the minimum mean square error (MMSE) criterion can provide a better bit error rate (BER) performance than rake combining. To further improve the BER performance, cyclic delay transmit diversity (CDTD) can be used. CDTD simultaneously transmits the same signal from different antennas after adding different cyclic delays to increase the number of equivalent propagation paths. Although a joint use of CDTD and MMSE-FDE for direct sequence code division multiple access (DS-CDMA) achieves larger frequency diversity gain, the BER performance improvement is limited by the residual inter-chip interference (ICI) after FDE. In this paper, we propose joint FDE and despreading for DS-CDMA using CDTD. Equalization and despreading are simultaneously performed in the frequency-domain to suppress the residual ICI after FDE. A theoretical conditional BER analysis is presented for the given channel condition. The BER analysis is confirmed by computer simulation.

Scaffolding during the Formal Assessment of Young EAL Learners: A New Zealand Case Study

ERIC Educational Resources Information Center

Booth, Dawn

2012-01-01

Despite growing interest in the theorisation of teacher-based assessment (TBA), very little research has paid close attention to how teachers practice assessment embedded in real classroom contexts. This longitudinal study over one school term reports on the TBA of young learners with English as an additional language (EAL) in New Zealand primary…

Complex regulatory network encompassing the Csr, c-di-GMP and motility systems of Salmonella Typhimurium.

PubMed

Jonas, Kristina; Edwards, Adrianne N; Ahmad, Irfan; Romeo, Tony; Römling, Ute; Melefors, Ojar

2010-02-01

Bacterial survival depends on the ability to switch between sessile and motile lifestyles in response to changing environmental conditions. In many species, this switch is governed by (3'-5')-cyclic-diguanosine monophosphate (c-di-GMP), a signalling molecule, which is metabolized by proteins containing GGDEF and/or EAL domains. Salmonella Typhimurium contains 20 such proteins. Here, we show that the RNA-binding protein CsrA regulates the expression of eight genes encoding GGDEF, GGDEF-EAL and EAL domain proteins. CsrA bound directly to the mRNA leaders of five of these genes, suggesting that it may regulate these genes post-transcriptionally. The c-di-GMP-specific phosphodiesterase STM3611, which reciprocally controls flagella function and production of biofilm matrix components, was regulated by CsrA binding to the mRNA, but was also indirectly regulated by CsrA through the FlhDC/FliA flagella cascade and STM1344. STM1344 is an unconventional (c-di-GMP-inactive) EAL domain protein, recently identified as a negative regulator of flagella gene expression. Here, we demonstrate that CsrA directly downregulates expression of STM1344, which in turn regulates STM3611 through fliA and thus reciprocally controls motility and biofilm factors. Altogether, our data reveal that the concerted and complex regulation of several genes encoding GGDEF/EAL domain proteins allows CsrA to control the motility-sessility switch in S. Typhimurium at multiple levels.

Occurrence of Cyclic di-GMP-Modulating Output Domains in Cyanobacteria: an Illuminating Perspective

PubMed Central

Agostoni, Marco; Koestler, Benjamin J.; Waters, Christopher M.; Williams, Barry L.; Montgomery, Beronda L.

2013-01-01

ABSTRACT Microorganisms use a variety of metabolites to respond to external stimuli, including second messengers that amplify primary signals and elicit biochemical changes in a cell. Levels of the second messenger cyclic dimeric GMP (c-di-GMP) are regulated by a variety of environmental stimuli and play a critical role in regulating cellular processes such as biofilm formation and cellular motility. Cyclic di-GMP signaling systems have been largely characterized in pathogenic bacteria; however, proteins that can impact the synthesis or degradation of c-di-GMP are prominent in cyanobacterial species and yet remain largely underexplored. In cyanobacteria, many putative c-di-GMP synthesis or degradation domains are found in genes that also harbor light-responsive signal input domains, suggesting that light is an important signal for altering c-di-GMP homeostasis. Indeed, c-di-GMP-associated domains are often the second most common output domain in photoreceptors—outnumbered only by a histidine kinase output domain. Cyanobacteria differ from other bacteria regarding the number and types of photoreceptor domains associated with c-di-GMP domains. Due to the widespread distribution of c-di-GMP domains in cyanobacteria, we investigated the evolutionary origin of a subset of genes. Phylogenetic analyses showed that c-di-GMP signaling systems were present early in cyanobacteria and c-di-GMP genes were both vertically and horizontally inherited during their evolution. Finally, we compared intracellular levels of c-di-GMP in two cyanobacterial species under different light qualities, confirming that light is an important factor for regulating this second messenger in vivo. PMID:23943760

Developing EAL Learners' Intercultural Sensitivity through a Digital Literacy Project

ERIC Educational Resources Information Center

Galante, Angelica

2014-01-01

Language and culture are informally integrated in many English as an Additional Language (EAL) programs, but cultural discussions are often regarded from the perspective of a particular dominant culture. Although this integration is crucial for the development of communicative competence, practical applications are still challenging as language…

Developing EAL Learners' Science Conceptual Understanding through Visualisation

ERIC Educational Resources Information Center

Hainsworth, Mark

2017-01-01

Science can be a difficult subject for EAL (English as an Additional Language) learners to master, mainly because of the prominent role that language plays in the acquisition of scientific concepts. Language is essential to science because it is the means by which we envisage and communicate new ideas. Teaching this new language to pupils involves…

Different roles for the cyclic nucleotide binding domain and amino terminus in assembly and expression of hyperpolarization-activated, cyclic nucleotide-gated channels.

PubMed

Proenza, Catherine; Tran, Neil; Angoli, Damiano; Zahynacz, Kristin; Balcar, Petr; Accili, Eric A

2002-08-16

In mammalian heart and brain, pacemaker currents are produced by hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels, which probably exist as heteromeric assemblies of different subunit isoforms. To investigate the molecular domains that participate in assembly and membrane trafficking of HCN channels, we have used the yeast two-hybrid system, patch clamp electrophysiology, and confocal microscopy. We show here that the N termini of the HCN1 and HCN2 isoforms interacted and were essential for expression of functional homo- or heteromeric channels on the plasma membrane of Chinese hamster ovary cells. We also show that the cyclic nucleotide binding domain (CNBD) of HCN2 was required for the expression of functional homomeric channels. This expression was dependent on a 12-amino acid domain corresponding to the B-helix in the CNBD of the catabolite activator protein. However, co-expression with HCN1 of an HCN2 deletion mutant lacking the CNBD rescued surface immunofluorescence and currents, indicating that a CNBD need not be present in each subunit of a heteromeric HCN channel. Furthermore, neither CNBDs nor other COOH-terminal domains of HCN1 and HCN2 interacted in yeast two-hybrid assays. Thus, interaction between NH(2)-terminal domains is important for HCN subunit assembly, whereas the CNBD is important for functional expression, but its absence from some subunits will still allow for the assembly of functional channels.

Observation on the transformation domains of super-elastic NiTi shape memory alloy and their evolutions during cyclic loading

NASA Astrophysics Data System (ADS)

Xie, Xi; Kan, Qianhua; Kang, Guozheng; Li, Jian; Qiu, Bo; Yu, Chao

2016-04-01

The strain field of a super-elastic NiTi shape memory alloy (SMA) and its variation during uniaxial cyclic tension-unloading were observed by a non-contact digital image correlation method, and then the transformation domains and their evolutions were indirectly investigated and discussed. It is seen that the super-elastic NiTi (SMA) exhibits a remarkable localized deformation and the transformation domains evolve periodically with the repeated cyclic tension-unloading within the first several cycles. However, the evolutions of transformation domains at the stage of stable cyclic transformation depend on applied peak stress: when the peak stress is low, no obvious transformation band is observed and the strain field is nearly uniform; when the peak stress is large enough, obvious transformation bands occur due to the residual martensite caused by the prevention of enriched dislocations to the reverse transformation from induced martensite to austenite. Temperature variations measured by an infrared thermal imaging method further verifies the formation and evolution of transformation domains.

A Healing Space: The Experiences of First Nations and Inuit Youth with Equine-Assisted Learning (EAL)

ERIC Educational Resources Information Center

Dell, Colleen Anne; Chalmers, Darlene; Bresette, Nora; Swain, Sue; Rankin, Deb; Hopkins, Carol

2011-01-01

The Nimkee NupiGawagan Healing Centre (NNHC) in Muncey, ON provides residential treatment to First Nations and Inuit youth who abuse solvents. As a complement to its culture-based programming, in 2008 the centre began offering weekly equine-assisted learning (EAL) curriculum to its clients in partnership with the Keystone Equine Centre and the…

How Does the Use of Role-Play Affect the Learning of Year 4 Children in a Predominately EAL Class?

ERIC Educational Resources Information Center

Grant, Katrina; Mistry, Malini Tina

2010-01-01

This paper investigates role-play activities and how they can be used within learning for English as an Additional Language (EAL) pupils in a Key Stage 2 setting in England. Through observations, results showed effective role-play activities can be beneficial to EAL pupils, allowing them to practice words and phrases in a relaxed atmosphere…

A novel dimerization interface of cyclic nucleotide binding domain, which is disrupted in presence of cAMP: implications for CNG channels gating.

PubMed

Gushchin, Ivan Y; Gordeliy, Valentin I; Grudinin, Sergei

2012-09-01

Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cation channels. Despite the availability of CNBD crystal structures of bacterial cyclic nucleotide-gated (CNG) and mammalian hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels in presence and absence of the cNMP, the full understanding of CNBD conformational changes during activation is lacking. Here, we describe a novel CNBD dimerization interface found in crystal structures of bacterial CNG channel MlotiK1 and mammalian cAMP-activated guanine nucleotide-exchange factor Epac2. Molecular dynamics simulations show that the found interface is stable on the studied timescale of 100 ns, in contrast to the dimerization interface, reported previously. Comparisons with cN-bound structures of CNBD show that the dimerization is incompatible with cAMP binding. Thus, the cAMP-dependent monomerization of CNBD may be an alternative mechanism of the cAMP sensing. Based on these findings, we propose a model of the bacterial CNG channel modulation by cAMP.

The cyclic-di-GMP phosphodiesterase BinA negatively regulates cellulose-containing biofilms in Vibrio fischeri.

PubMed

Bassis, Christine M; Visick, Karen L

2010-03-01

Bacteria produce different types of biofilms under distinct environmental conditions. Vibrio fischeri has the capacity to produce at least two distinct types of biofilms, one that relies on the symbiosis polysaccharide Syp and another that depends upon cellulose. A key regulator of biofilm formation in bacteria is the intracellular signaling molecule cyclic diguanylate (c-di-GMP). In this study, we focused on a predicted c-di-GMP phosphodiesterase encoded by the gene binA, located directly downstream of syp, a cluster of 18 genes critical for biofilm formation and the initiation of symbiotic colonization of the squid Euprymna scolopes. Disruption or deletion of binA increased biofilm formation in culture and led to increased binding of Congo red and calcofluor, which are indicators of cellulose production. Using random transposon mutagenesis, we determined that the phenotypes of the DeltabinA mutant strain could be disrupted by insertions in genes in the bacterial cellulose biosynthesis cluster (bcs), suggesting that cellulose production is negatively regulated by BinA. Replacement of critical amino acids within the conserved EAL residues of the EAL domain disrupted BinA activity, and deletion of binA increased c-di-GMP levels in the cell. Together, these data support the hypotheses that BinA functions as a phosphodiesterase and that c-di-GMP activates cellulose biosynthesis. Finally, overexpression of the syp regulator sypG induced binA expression. Thus, this work reveals a mechanism by which V. fischeri inhibits cellulose-dependent biofilm formation and suggests that the production of two different polysaccharides may be coordinated through the action of the cellulose inhibitor BinA.

C-Terminal β9-Strand of the Cyclic Nucleotide-Binding Homology Domain Stabilizes Activated States of Kv11.1 Channels

PubMed Central

Ng, Chai Ann; Ke, Ying; Perry, Matthew D.; Tan, Peter S.; Hill, Adam P.; Vandenberg, Jamie I.

2013-01-01

Kv11.1 potassium channels are important for regulation of the normal rhythm of the heartbeat. Reduced activity of Kv11.1 channels causes long QT syndrome type 2, a disorder that increases the risk of cardiac arrhythmias and sudden cardiac arrest. Kv11.1 channels are members of the KCNH subfamily of voltage-gated K+ channels. However, they also share many similarities with the cyclic nucleotide gated ion channel family, including having a cyclic nucleotide-binding homology (cNBH) domain. Kv11.1 channels, however, are not directly regulated by cyclic nucleotides. Recently, crystal structures of the cNBH domain from mEAG and zELK channels, both members of the KCNH family of voltage-gated potassium channels, revealed that a C-terminal β9-strand in the cNBH domain occupied the putative cyclic nucleotide-binding site thereby precluding binding of cyclic nucleotides. Here we show that mutations to residues in the β9-strand affect the stability of the open state relative to the closed state of Kv11.1 channels. We also show that disrupting the structure of the β9-strand reduces the stability of the inactivated state relative to the open state. Clinical mutations located in this β9-strand result in reduced trafficking efficiency, which suggests that binding of the C-terminal β9-strand to the putative cyclic nucleotide-binding pocket is also important for assembly and trafficking of Kv11.1 channels. PMID:24204727

Documentation for a Structural Optimization Procedure Developed Using the Engineering Analysis Language (EAL)

NASA Technical Reports Server (NTRS)

Martin, Carl J., Jr.

1996-01-01

This report describes a structural optimization procedure developed for use with the Engineering Analysis Language (EAL) finite element analysis system. The procedure is written primarily in the EAL command language. Three external processors which are written in FORTRAN generate equivalent stiffnesses and evaluate stress and local buckling constraints for the sections. Several built-up structural sections were coded into the design procedures. These structural sections were selected for use in aircraft design, but are suitable for other applications. Sensitivity calculations use the semi-analytic method, and an extensive effort has been made to increase the execution speed and reduce the storage requirements. There is also an approximate sensitivity update method included which can significantly reduce computational time. The optimization is performed by an implementation of the MINOS V5.4 linear programming routine in a sequential liner programming procedure.

Negotiating Contradictions in Developing Teacher Identity during the EAL Practicum in Australia

ERIC Educational Resources Information Center

Nguyen, Minh Hue

2017-01-01

This paper reports on how Maria (pseudonym), a non-native English speaker (NNES) and preservice teacher (PST) of English as an additional language (EAL), developed her professional identity during the practicum in an Australian secondary school. Drawing on activity theory, the study identified contradictions in Maria's practicum activity and…

Creating Inclusive EAL Classrooms: How Language Instruction for Newcomers to Canada (LINC) Instructors Understand and Mitigate Barriers for Students Who Have Experienced Trauma

ERIC Educational Resources Information Center

Wilbur, Amea

2016-01-01

This article draws on my dissertation, "Creating Inclusive EAL Classrooms: How LINC Instructors Understand and Mitigate Barriers for Students Who Have Experienced Trauma." The article explores some assumptions and understandings that English as an Additional Language (EAL) teachers bring to teaching students believed to have experienced…

Comparative analysis of diguanylate cyclase and phosphodiesterase genes in Klebsiella pneumoniae.

PubMed

Cruz, Diana P; Huertas, Mónica G; Lozano, Marcela; Zárate, Lina; Zambrano, María Mercedes

2012-07-09

Klebsiella pneumoniae can be found in environmental habitats as well as in hospital settings where it is commonly associated with nosocomial infections. One of the factors that contribute to virulence is its capacity to form biofilms on diverse biotic and abiotic surfaces. The second messenger Bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) is a ubiquitous signal in bacteria that controls biofilm formation as well as several other cellular processes. The cellular levels of this messenger are controlled by c-di-GMP synthesis and degradation catalyzed by diguanylate cyclase (DGC) and phophodiesterase (PDE) enzymes, respectively. Many bacteria contain multiple copies of these proteins with diverse organizational structure that highlight the complex regulatory mechanisms of this signaling network. This work was undertaken to identify DGCs and PDEs and analyze the domain structure of these proteins in K. pneumoniae. A search for conserved GGDEF and EAL domains in three sequenced K. pneumoniae genomes showed that there were multiple copies of GGDEF and EAL containing proteins. Both single domain and hybrid GGDEF proteins were identified: 21 in K. pneumoniae Kp342, 18 in K. pneumoniae MGH 78578 and 17 in K. pneumoniae NTUH-K2044. The majority had only the GGDEF domain, most with the GGEEF motif, and hybrid proteins containing both GGDEF and EAL domains were also found. The I site for allosteric control was identified only in single GGDEF domain proteins and not in hybrid proteins. EAL-only proteins, containing either intact or degenerate domains, were also identified: 15 in Kp342, 15 in MGH 78578 and 10 in NTUH-K2044. Several input sensory domains and transmembrane segments were identified, which together indicate complex regulatory circuits that in many cases can be membrane associated. The comparative analysis of proteins containing GGDEF/EAL domains in K. pneumoniae showed that most copies were shared among the three strains and that some were unique to a particular strain

Cyclic coding for Brillouin optical time-domain analyzers using probe dithering.

PubMed

Iribas, Haritz; Loayssa, Alayn; Sauser, Florian; Llera, Miguel; Le Floch, Sébastien

2017-04-17

We study the performance limits of mono-color cyclic coding applied to Brillouin optical time-domain analysis (BOTDA) sensors that use probe wave dithering. BOTDA analyzers with dithering of the probe use a dual-probe-sideband setup in which an optical frequency modulation of the probe waves along the fiber is introduced. This avoids non-local effects while keeping the Brillouin threshold at its highest level, thus preventing the spontaneous Brillouin scattering from generating noise in the deployed sensing fiber. In these conditions, it is possible to introduce an unprecedented high probe power into the sensing fiber, which leads to an enhancement of the signal-to-noise ratio (SNR) and consequently to a performance improvement of the analyzer. The addition of cyclic coding in these set-ups can further increase the SNR and accordingly enhance the performance. However, this unprecedented probe power levels that can be employed result in the appearance of detrimental effects in the measurement that had not previously been observed in other BOTDA set-ups. In this work, we analyze the distortion in the decoding process and the errors in the measurement that this distortion causes, due to three factors: the power difference of the successive pulses of a code sequence, the appearance of first-order non-local effects and the non-linear amplification of the probe wave that results when using mono-color cyclic coding of the pump pulses. We apply the results of this study to demonstrate the performance enhancement that can be achieved in a long-range dithered dual-probe BOTDA. A 164-km fiber-loop is measured with 1-m spatial resolution, obtaining 3-MHz Brillouin frequency shift measurement precision at the worst contrast location. To the best of our knowledge, this is the longest sensing distance achieved with a BOTDA sensor using mono-color cyclic coding.

Applied Linguistics Project: Student-Led Computer Assisted Research in High School EAL/EAP

ERIC Educational Resources Information Center

Bohát, Róbert; Rödlingová, Beata; Horáková, Nina

2015-01-01

The Applied Linguistics Project (ALP) started at the International School of Prague (ISP) in 2013. Every year, Grade 9 English as an Additional Language (EAL) students identify an area of learning in need of improvement and design a research method followed by data collection and analysis using basic computer software tools or online corpora.…

Static and dynamic structural-sensitivity derivative calculations in the finite-element-based Engineering Analysis Language (EAL) system

NASA Technical Reports Server (NTRS)

Camarda, C. J.; Adelman, H. M.

1984-01-01

The implementation of static and dynamic structural-sensitivity derivative calculations in a general purpose, finite-element computer program denoted the Engineering Analysis Language (EAL) System is described. Derivatives are calculated with respect to structural parameters, specifically, member sectional properties including thicknesses, cross-sectional areas, and moments of inertia. Derivatives are obtained for displacements, stresses, vibration frequencies and mode shapes, and buckling loads and mode shapes. Three methods for calculating derivatives are implemented (analytical, semianalytical, and finite differences), and comparisons of computer time and accuracy are made. Results are presented for four examples: a swept wing, a box beam, a stiffened cylinder with a cutout, and a space radiometer-antenna truss.

Programs for transferring data between a relational data base and a finite element structural analysis program

NASA Technical Reports Server (NTRS)

Johnson, S. C.

1982-01-01

An interface system for passing data between a relational information management (RIM) data base complex and engineering analysis language (EAL), a finite element structural analysis program is documented. The interface system, implemented on a CDC Cyber computer, is composed of two FORTRAN programs called RIM2EAL and EAL2RIM. The RIM2EAL reads model definition data from RIM and creates a file of EAL commands to define the model. The EAL2RIM reads model definition and EAL generated analysis data from EAL's data library and stores these data dirctly in a RIM data base. These two interface programs and the format for the RIM data complex are described.

Structure of a eukaryotic cyclic nucleotide-gated channel

PubMed Central

Li, Minghui; Zhou, Xiaoyuan; Wang, Shu; Michailidis, Ioannis; Gong, Ye; Su, Deyuan; Li, Huan; Li, Xueming; Yang, Jian

2018-01-01

Summary Cyclic nucleotide-gated (CNG) channels are essential for vision and olfaction. They belong to the voltage-gated ion channel superfamily but their activities are controlled by intracellular cyclic nucleotides instead of transmembrane voltage. Here we report a 3.5 Å-resolution single-particle electron cryomicroscopy structure of a CNG channel from C. elegans in the cGMP-bound open state. The channel has an unusual voltage-sensor-like domain (VSLD), accounting for its deficient voltage dependence. A C-terminal linker connecting S6 and the cyclic nucleotide-binding domain interacts directly with both the VSLD and pore domain, forming a gating ring that couples conformational changes triggered by cyclic nucleotide binding to the gate. The selectivity filter is lined by the carboxylate side chains of a functionally important glutamate and three rings of backbone carbonyls. This structure provides a new framework for understanding mechanisms of ion permeation, gating and channelopathy of CNG channels and cyclic nucleotide modulation of related channels. PMID:28099415

Structural analysis of an oxygen-regulated diguanylate cyclase.

PubMed

Tarnawski, Miroslaw; Barends, Thomas R M; Schlichting, Ilme

2015-11-01

Cyclic di-GMP is a bacterial second messenger that is involved in switching between motile and sessile lifestyles. Given the medical importance of biofilm formation, there has been increasing interest in understanding the synthesis and degradation of cyclic di-GMPs and their regulation in various bacterial pathogens. Environmental cues are detected by sensing domains coupled to GGDEF and EAL or HD-GYP domains that have diguanylate cyclase and phosphodiesterase activities, respectively, producing and degrading cyclic di-GMP. The Escherichia coli protein DosC (also known as YddV) consists of an oxygen-sensing domain belonging to the class of globin sensors that is coupled to a C-terminal GGDEF domain via a previously uncharacterized middle domain. DosC is one of the most strongly expressed GGDEF proteins in E. coli, but to date structural information on this and related proteins is scarce. Here, the high-resolution structural characterization of the oxygen-sensing globin domain, the middle domain and the catalytic GGDEF domain in apo and substrate-bound forms is described. The structural changes between the iron(III) and iron(II) forms of the sensor globin domain suggest a mechanism for oxygen-dependent regulation. The structural information on the individual domains is combined into a model of the dimeric DosC holoprotein. These findings have direct implications for the oxygen-dependent regulation of the activity of the cyclase domain.

An Exploration of School Communication Approaches for Newly Arrived EAL Students: Applying Three Dimensions of Organisational Communication Theory

ERIC Educational Resources Information Center

Schneider, Claudia; Arnot, Madeleine

2018-01-01

This article explores the modes of school communication associated with language and cultural diversity, demonstrating how organisational communication theory can be applied to the analysis of schools' communication responses to the presence of pupils who have English as an additional language (EAL). The article highlights three analytical…

Bis-(3'-5')-cyclic dimeric GMP-linked quorum sensing controls swarming in Vibrio parahaemolyticus.

PubMed

Trimble, Michael J; McCarter, Linda L

2011-11-01

Movement over and colonization of surfaces are important survival strategies for bacteria, and many find it advantageous to perform these activities as a group, using quorum sensing to sample population size and synchronize behavior. It is puzzling however, that swarming-proficient and virulent strains of Vibrio parahaemolyticus are silenced for the vibrio archetypal pathway of quorum sensing. Here we describe the S-signal, a pheromone that can be communicated between cells in coculture to regulate surface colonization. This signal was harvested in cell-free supernatants and demonstrated to stimulate swarming gene expression at low cell density. The S-signal was generated by the pyridoxal phosphate-dependent aminotransferase ScrA; signal reception required the periplasmic binding protein ScrB and the membrane-bound GGDEF-EAL domain-containing protein ScrC. ScrC is a bifunctional enzyme that has the ability to form and degrade the second messenger bis-(3'-5') cyclic dimeric GMP (c-di-GMP). ScrA in neighboring cells was able to alter the activity of ScrC in a ScrB-dependent manner, transforming ScrC's repressing ability to inducing activity with respect to swarming. Conversely, cell-cell signaling repressed capsule gene expression. In summary, we report that quorum sensing can stimulate swarming in V. parahaemolyticus; it does so via an alternative pathway capable of generating an autoinducing signal that influences c-di-GMP, thereby expanding the lexicon and language of cell-cell communication.

The GDP-switched GAF domain of DcpA modulates the concerted synthesis/hydrolysis of c-di-GMP in Mycobacterium smegmatis.

PubMed

Chen, Hui-Jie; Li, Na; Luo, Ye; Jiang, Yong-Liang; Zhou, Cong-Zhao; Chen, Yuxing; Li, Qiong

2018-04-09

The second messenger c-di-GMP [bis-(3'-5')-cyclic dimeric guanosine monophosphate] plays a key role in bacterial growth, survival and pathogenesis, and thus its intracellular homeostasis should be finely maintained. Mycobacterium smegmatis encodes a GAF (mammalian c G MP-regulated phosphodiesterases, Anabaena a denylyl cyclases and Escherichia coli transcription activator F hlA) domain containing bifunctional enzyme DcpA ( d iguanylate c yclase and p hosphodiesterase A ) that catalyzes the synthesis and hydrolysis of c-di-GMP . Here, we found that M. smegmatis DcpA catalyzes the hydrolysis of c-di-GMP at a higher velocity, compared with synthetic activity, resulting in a sum reaction from the ultimate substrate GTP to the final product pGpG [5'-phosphoguanylyl-(3'-5')-guanosine]. Fusion with the N-terminal GAF domain enables the GGDEF (Gly-Gly-Asp-Glu-Phe) domain of DcpA to dimerize and accordingly gain synthetic activity. Screening of putative metabolites revealed that GDP is the ligand of the GAF domain. Binding of GDP to the GAF domain down-regulates synthetic activity, but up-regulates hydrolytic activity, which, in consequence, might enable a timely response to the transient accumulation of c-di-GMP at the stationary phase or under stresses. Combined with the crystal structure of the EAL (Glu-Ala-Leu) domain and the small-angle X-ray scattering data, we propose a putative regulatory model of the GAF domain finely tuned by the intracellular GTP/GDP ratio. These findings help us to better understand the concerted control of the synthesis and hydrolysis of c-di-GMP in M. smegmatis in various microenvironments. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Estimation of exciton reverse transfer for variable spectra and high efficiency in interlayer-based organic light-emitting devices

NASA Astrophysics Data System (ADS)

Liu, Shengqiang; Zhao, Juan; Huang, Jiang; Yu, Junsheng

2016-12-01

Organic light-emitting devices (OLEDs) with three different exciton adjusting interlayers (EALs), which are inserted between two complementary blue and yellow emitting layers, are fabricated to demonstrate the relationship between the EAL and device performance. The results show that the variations of type and thickness of EAL have different adjusting capability and distribution control on excitons. However, we also find that the reverse Dexter transfer of triplet exciton from the light-emitting layer to the EAL is an energy loss path, which detrimentally affects electroluminescent (EL) spectral performance and device efficiency in different EAL-based devices. Based on exciton distribution and integration, an estimation of exciton reverse transfer is developed through a triplet energy level barrier to simulate the exciton behavior. Meanwhile, the estimation results also demonstrate the relationship between the EAL and device efficiency by a parameter of exciton reverse transfer probability. The estimation of exciton reverse transfer discloses a crucial role of the EALs in the interlayer-based OLEDs to achieve variable EL spectra and high efficiency.

Cyclic density functional theory: A route to the first principles simulation of bending in nanostructures

NASA Astrophysics Data System (ADS)

Banerjee, Amartya S.; Suryanarayana, Phanish

2016-11-01

We formulate and implement Cyclic Density Functional Theory (Cyclic DFT) - a self-consistent first principles simulation method for nanostructures with cyclic symmetries. Using arguments based on Group Representation Theory, we rigorously demonstrate that the Kohn-Sham eigenvalue problem for such systems can be reduced to a fundamental domain (or cyclic unit cell) augmented with cyclic-Bloch boundary conditions. Analogously, the equations of electrostatics appearing in Kohn-Sham theory can be reduced to the fundamental domain augmented with cyclic boundary conditions. By making use of this symmetry cell reduction, we show that the electronic ground-state energy and the Hellmann-Feynman forces on the atoms can be calculated using quantities defined over the fundamental domain. We develop a symmetry-adapted finite-difference discretization scheme to obtain a fully functional numerical realization of the proposed approach. We verify that our formulation and implementation of Cyclic DFT is both accurate and efficient through selected examples. The connection of cyclic symmetries with uniform bending deformations provides an elegant route to the ab-initio study of bending in nanostructures using Cyclic DFT. As a demonstration of this capability, we simulate the uniform bending of a silicene nanoribbon and obtain its energy-curvature relationship from first principles. A self-consistent ab-initio simulation of this nature is unprecedented and well outside the scope of any other systematic first principles method in existence. Our simulations reveal that the bending stiffness of the silicene nanoribbon is intermediate between that of graphene and molybdenum disulphide - a trend which can be ascribed to the variation in effective thickness of these materials. We describe several future avenues and applications of Cyclic DFT, including its extension to the study of non-uniform bending deformations and its possible use in the study of the nanoscale flexoelectric effect.

Simulation-based Discovery of Cyclic Peptide Nanotubes

NASA Astrophysics Data System (ADS)

Ruiz Pestana, Luis A.

Today, there is a growing need for environmentally friendly synthetic membranes with selective transport capabilities to address some of society's most pressing issues, such as carbon dioxide pollution, or access to clean water. While conventional membranes cannot stand up to the challenge, thin nanocomposite membranes, where vertically aligned subnanometer pores (e.g. nanotubes) are embedded in a thin polymeric film, promise to overcome some of the current limitations, namely, achieving a monodisperse distribution of subnanometer size pores, vertical pore alignment across the membrane thickness, and tunability of the pore surface chemistry. Self-assembled cyclic peptide nanotubes (CPNs), are particularly promising as selective nanopores because the pore size can be controlled at the subnanometer level, exhibit high chemical design flexibility, and display remarkable mechanical stability. In addition, when conjugated with polymer chains, the cyclic peptides can co-assemble in block copolymer domains to form nanoporous thin films. CPNs are thus well positioned to tackle persistent challenges in molecular separation applications. However, our poor understanding of the physics underlying their remarkable properties prevents the rational design and implementation of CPNs in technologically relevant membranes. In this dissertation, we use a simulation-based approach, in particular molecular dynamics (MD) simulations, to investigate the critical knowledge gaps hindering the implementation of CPNs. Computational mechanical tests show that, despite the weak nature of the stabilizing hydrogen bonds and the small cross section, CPNs display a Young's modulus of approximately 20 GPa and a maximum strength of around 1 GPa, placing them among the strongest proteinaceous materials known. Simulations of the self-assembly process reveal that CPNs grow by self-similar coarsening, contrary to other low-dimensional peptide systems, such as amyloids, that are believed to grow through

Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes

PubMed Central

Bridges, Dave; Fraser, Marie E; Moorhead, Greg BG

2005-01-01

Background Cyclic nucleotides are ubiquitous intracellular messengers. Until recently, the roles of cyclic nucleotides in plant cells have proven difficult to uncover. With an understanding of the protein domains which can bind cyclic nucleotides (CNB and GAF domains) we scanned the completed genomes of the higher plants Arabidopsis thaliana (mustard weed) and Oryza sativa (rice) for the effectors of these signalling molecules. Results Our analysis found that several ion channels and a class of thioesterases constitute the possible cyclic nucleotide binding proteins in plants. Contrary to some reports, we found no biochemical or bioinformatic evidence for a plant cyclic nucleotide regulated protein kinase, suggesting that cyclic nucleotide functions in plants have evolved differently than in mammals. Conclusion This paper provides a molecular framework for the discussion of cyclic nucleotide function in plants, and resolves a longstanding debate about the presence of a cyclic nucleotide dependent kinase in plants. PMID:15644130

Colour cyclic code for Brillouin distributed sensors

NASA Astrophysics Data System (ADS)

Le Floch, Sébastien; Sauser, Florian; Llera, Miguel; Rochat, Etienne

2015-09-01

For the first time, a colour cyclic coding (CCC) is theoretically and experimentally demonstrated for Brillouin optical time-domain analysis (BOTDA) distributed sensors. Compared to traditional intensity-modulated cyclic codes, the code presents an additional gain of √2 while keeping the same number of sequences as for a colour coding. A comparison with a standard BOTDA sensor is realized and validates the theoretical coding gain.

CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel

PubMed Central

James, Zachary M.; Borst, Andrew J.; Haitin, Yoni; Frenz, Brandon; DiMaio, Frank; Zagotta, William N.; Veesler, David

2017-01-01

Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. These channels are characterized by the presence of a carboxyl-terminal cyclic nucleotide-binding domain (CNBD) that connects to the channel pore via a C-linker domain. Although cyclic nucleotide binding has been shown to promote CNG and HCN channel opening, the precise mechanism underlying gating remains poorly understood. Here we used cryoEM to determine the structure of the intact LliK CNG channel isolated from Leptospira licerasiae—which shares sequence similarity to eukaryotic CNG and HCN channels—in the presence of a saturating concentration of cAMP. A short S4–S5 linker connects nearby voltage-sensing and pore domains to produce a non–domain-swapped transmembrane architecture, which appears to be a hallmark of this channel family. We also observe major conformational changes of the LliK C-linkers and CNBDs relative to the crystal structures of isolated C-linker/CNBD fragments and the cryoEM structures of related CNG, HCN, and KCNH channels. The conformation of our LliK structure may represent a functional state of this channel family not captured in previous studies. PMID:28396445

Mesodomain and Protein-Associated Solvent Phases with Temperature-Tunable (200-265 K) Dynamics Surround Ethanolamine Ammonia-Lyase in Globally Polycrystalline Aqueous Solution Containing Dimethyl Sulfoxide.

PubMed

Nforneh, Benjamen; Warncke, Kurt

2017-12-14

Electron paramagnetic resonance spectroscopy of the spin probe, TEMPOL, is used to resolve solvent phases that surround the ethanolamine ammonia-lyase (EAL) protein from Salmonella typhimurium at low temperature (T) in frozen, globally polycrystalline aqueous solution and to report on the T dependence of their detectably rigid and fluid states. EAL plays a role in human gut microbiome-based disease conditions, and physicochemical studies provide insight into protein structure and mechanism, toward potential therapeutics. Temperature dependences of the rotational correlation times (τ c ; detection range, 10 -11 ≤ τ c ≤ 10 -7 s) and the corresponding weights of TEMPOL tumbling components from 200 to 265 K in the presence of EAL are measured in two frozen systems: (1) water-only and (2) 1% v/v dimethyl sulfoxide (DMSO). In the water-only condition, a protein-vicinal solvent component detectably fluidizes at 230 K and melts the surrounding ice-crystalline region with increasing T, creating a bounded, relatively high-viscosity aqueous solvent domain, up to 265 K. In the EAL, 1% v/v DMSO condition, two distinct concentric solvent phases are resolved around EAL: protein-associated domain (PAD) and mesodomain. The DMSO aqueous mesodomain fluidizes at 200 K, followed by PAD fluidization at 210 K. The interphase dynamical coupling is consistent with the spatial arrangement and significant contact areas of the phases, indicated by the experimentally determined mean volume ratio, V(mesodomain)/V(PAD)/V(protein) = 0.5:0.3:1.0. The results provide a rationale for native chemical reactions of EAL at T < 250 K and an advance toward precise control of solvent dynamics as a tunable parameter for quantifying the coupling between solvent and protein fluctuations and chemical reaction steps in EAL and other enzymes.

On cyclic yield strength in definition of limits for characterisation of fatigue and creep behaviour

NASA Astrophysics Data System (ADS)

Gorash, Yevgen; MacKenzie, Donald

2017-06-01

This study proposes cyclic yield strength as a potential characteristic of safe design for structures operating under fatigue and creep conditions. Cyclic yield strength is defined on a cyclic stress-strain curve, while monotonic yield strength is defined on a monotonic curve. Both values of strengths are identified using a two-step procedure of the experimental stress-strain curves fitting with application of Ramberg-Osgood and Chaboche material models. A typical S-N curve in stress-life approach for fatigue analysis has a distinctive minimum stress lower bound, the fatigue endurance limit. Comparison of cyclic strength and fatigue limit reveals that they are approximately equal. Thus, safe fatigue design is guaranteed in the purely elastic domain defined by the cyclic yielding. A typical long-term strength curve in time-to-failure approach for creep analysis has two inflections corresponding to the cyclic and monotonic strengths. These inflections separate three domains on the long-term strength curve, which are characterised by different creep fracture modes and creep deformation mechanisms. Therefore, safe creep design is guaranteed in the linear creep domain with brittle failure mode defined by the cyclic yielding. These assumptions are confirmed using three structural steels for normal and high-temperature applications. The advantage of using cyclic yield strength for characterisation of fatigue and creep strength is a relatively quick experimental identification. The total duration of cyclic tests for a cyclic stress-strain curve identification is much less than the typical durations of fatigue and creep rupture tests at the stress levels around the cyclic yield strength.

Cyclic axial-torsional deformation behavior of a cobalt-base superalloy

NASA Technical Reports Server (NTRS)

Bonacuse, Peter J.; Kalluri, Sreeramesh

1992-01-01

Multiaxial loading, especially at elevated temperature, can cause the inelastic response of a material to differ significantly from that predicted by simple flow rules, i.e., von Mises or Tresca. To quantify some of these differences, the cyclic high-temperature, deformation behavior of a wrought cobalt-based superalloy, Haynes 188, is investigated under combined axial and torsional loads. Haynes 188 is currently used in many aerospace gas turbine and rocket engine applications, e.g., the combustor liner for the T800 turboshaft engine for the RAH-66 Comanche helicopter and the liquid oxygen posts in the main injector of the space shuttle main engine. The deformation behavior of this material is assessed through the examination of hysteresis loops generated from a biaxial fatigue test program. A high-temperature axial, torsional, and combined axial-torsional fatigue data base has been generated on Haynes 188 at 760 C. Cyclic loading tests have been conducted on uniform gauge section tubular specimens in a servohydraulic axial-torsional test rig. Test control and data acquisition were accomplished with a minicomputer. In this paper, the cyclic hardening characteristics and typical hysteresis loops in the axial stress versus axial strain, shear stress versus engineering shear strain, axial strain versus engineering shear strain, and axial stress versus shear stress spaces are presented for cyclic, in-phase and out-of-phase, axial torsional tests. For in-phase tests three different values of the proportionality constant, lambda (ratio of engineering shear strain amplitude to axial strain amplitude), are examined, viz., 0.86, 1.73, and 3.46. In the out-of-phase tests, three different values of the phase angle, phi (between the axial and engineering shear strain waveforms), are studied, viz., 30, 60, and 90 deg with lambda = 1.73. The cyclic hardening behaviors of all the tests conducted on Haynes 188 at 760 C are evaluated using the von Mises equivalent stress

Cyclic Axial-Torsional Deformation Behavior of a Cobalt-Base Superalloy

NASA Technical Reports Server (NTRS)

Bonacuse, Peter J.; Kalluri, Sreeramesh

1995-01-01

The cyclic, high-temperature deformation behavior of a wrought cobalt-base super-alloy, Haynes 188, is investigated under combined axial and torsional loads. This is accomplished through the examination of hysteresis loops generated from a biaxial fatigue test program. A high-temperature axial, torsional, and combined axial-torsional fatigue database has been generated on Haynes 188 at 760 C. Cyclic loading tests have been conducted on uniform gage section tubular specimens in a servohydraulic axial-torsional test rig. Test control and data acquisition were accomplished with a minicomputer. The fatigue behavior of Haynes 188 at 760 C under axial, torsional, and combined axial-torsional loads and the monotonic and cyclic deformation behaviors under axial and torsional loads have been previously reported. In this paper, the cyclic hardening characteristics and typical hysteresis loops in the axial stress versus axial strain, shear stress ,versus engineering shear strain, axial strain versus engineering shear strain. and axial stress versus shear stress spaces are presented for cyclic in-phase and out-of-phase axial-torsional tests. For in-phase tests, three different values of the proportionality constant lambda (the ratio of engineering shear strain amplitude to axial strain amplitude, are examined, viz. 0.86, 1.73, and 3.46. In the out-of-phase tests, three different values of the phase angle, phi (between the axial and engineering shear strain waveforms), are studied, viz., 30, 60, and 90 degrees with lambda equals 1.73. The cyclic hardening behaviors of all the tests conducted on Haynes 188 at 760 C are evaluated using the von Mises equivalent stress-strain and the maximum shear stress-maximum engineering shear strain (Tresca) curves. Comparisons are also made between the hardening behaviors of cyclic axial, torsional, and combined in-phase (lambda = 1.73 and phi = 0) and out-of-phase (lambda = 1.73 and phi = 90') axial-torsional fatigue tests. These comparisons

Experimental demonstration of wavelength domain rogue-free ONU based on wavelength-pairing for TDM/WDM optical access networks.

PubMed

Lee, Jie Hyun; Park, Heuk; Kang, Sae-Kyoung; Lee, Joon Ki; Chung, Hwan Seok

2015-11-30

In this study, we propose and experimentally demonstrate a wavelength domain rogue-free ONU based on wavelength-pairing of downstream and upstream signals for time/wavelength division-multiplexed optical access networks. The wavelength-pairing tunable filter is aligned to the upstream wavelength channel by aligning it to one of the downstream wavelength channels. Wavelength-pairing is implemented with a compact and cyclic Si-AWG integrated with a Ge-PD. The pairing filter covered four 100 GHz-spaced wavelength channels. The feasibility of the wavelength domain rogue-free operation is investigated by emulating malfunction of the misaligned laser. The wavelength-pairing tunable filter based on the Si-AWG blocks the upstream signal in the non-assigned wavelength channel before data collision with other ONUs.

New findings on phosphodiesterases, MoPdeH and MoPdeL, in Magnaporthe oryzae revealed by structural analysis.

PubMed

Yang, Li-Na; Yin, Ziyi; Zhang, Xi; Feng, Wanzhen; Xiao, Yuhan; Zhang, Haifeng; Zheng, Xiaobo; Zhang, Zhengguang

2018-05-01

The cyclic adenosine monophosphate (cAMP) signalling pathway mediates signal communication and sensing during infection-related morphogenesis in eukaryotes. Many studies have implicated cAMP as a critical mediator of appressorium development in the rice blast fungus, Magnaporthe oryzae. The cAMP phosphodiesterases, MoPdeH and MoPdeL, as key regulators of intracellular cAMP levels, play pleiotropic roles in cell wall integrity, cellular morphology, appressorium formation and infectious growth in M. oryzae. Here, we analysed the roles of domains of MoPdeH and MoPdeL separately or in chimeras. The results indicated that the HD and EAL domains of MoPdeH are indispensable for its phosphodiesterase activity and function. Replacement of the MoPdeH HD domain with the L1 and L2 domains of MoPdeL, either singly or together, resulted in decreased cAMP hydrolysis activity of MoPdeH. All of the transformants exhibited phenotypes similar to that of the ΔMopdeH mutant, but also revealed that EAL and L1 play additional roles in conidiation, and that L1 is involved in infectious growth. We further found that the intracellular cAMP level is important for surface signal recognition and hyphal autolysis. The intracellular cAMP level negatively regulates Mps1-MAPK and positively regulates Pmk1-MAPK in the rice blast fungus. Our results provide new information to better understand the cAMP signalling pathway in the development, differentiation and plant infection of the fungus. © 2017 BSPP AND JOHN WILEY & SONS LTD.

Compressed sensing with cyclic-S Hadamard matrix for terahertz imaging applications

NASA Astrophysics Data System (ADS)

Ermeydan, Esra Şengün; ćankaya, Ilyas

2018-01-01

Compressed Sensing (CS) with Cyclic-S Hadamard matrix is proposed for single pixel imaging applications in this study. In single pixel imaging scheme, N = r . c samples should be taken for r×c pixel image where . denotes multiplication. CS is a popular technique claiming that the sparse signals can be reconstructed with samples under Nyquist rate. Therefore to solve the slow data acquisition problem in Terahertz (THz) single pixel imaging, CS is a good candidate. However, changing mask for each measurement is a challenging problem since there is no commercial Spatial Light Modulators (SLM) for THz band yet, therefore circular masks are suggested so that for each measurement one or two column shifting will be enough to change the mask. The CS masks are designed using cyclic-S matrices based on Hadamard transform for 9 × 7 and 15 × 17 pixel images within the framework of this study. The %50 compressed images are reconstructed using total variation based TVAL3 algorithm. Matlab simulations demonstrates that cyclic-S matrices can be used for single pixel imaging based on CS. The circular masks have the advantage to reduce the mechanical SLMs to a single sliding strip, whereas the CS helps to reduce acquisition time and energy since it allows to reconstruct the image from fewer samples.

Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II

DOE PAGES

Campbell, James C.; Kim, Jeong Joo; Li, Kevin Y.; ...

2016-01-14

Membrane-bound cGMP-dependent protein kinase (PKG) II is an important regulator of bone growth, renin secretion, and memory formation. Despite its crucial physiological roles, little is known about its cyclic nucleotide selectivity mechanism due to a lack of structural information. Here, we find that the C-terminal cyclic nucleotide binding (CNB-B) domain of PKGII binds cGMP with higher affinity and selectivity when compared with its N-terminal CNB (CNB-A) domain. To understand the structural basis of cGMP selectivity, we solved co-crystal structures of the CNB domains with cyclic nucleotides. Our structures combined with mutagenesis demonstrate that the guanine-specific contacts at Asp-412 and Arg-415more » of the αC-helix of CNB-B are crucial for cGMP selectivity and activation of PKG II. Structural comparison with the cGMP selective CNB domains of human PKG I and Plasmodium falciparum PKG (PfPKG) shows different contacts with the guanine moiety, revealing a unique cGMP selectivity mechanism for PKG II.« less

Adverse childhood experiences are associated with irritable bowel syndrome and gastrointestinal symptom severity.

PubMed

Park, S H; Videlock, E J; Shih, W; Presson, A P; Mayer, E A; Chang, L

2016-08-01

Early adverse life events (EALs) are associated with irritable bowel syndrome (IBS). Exposure to EALs as assessed by the Adverse Childhood Experiences (ACE) questionnaire is associated with greater disease prevalence, but ACE has not been studied in gastrointestinal disorders. Study aims were to: (i) Estimate the prevalence of EALs in the IBS patients using the ACE questionnaire; (ii) Determine correlations between ACE and Early Trauma Inventory Self Report-Short Form (ETI-SR) scores to confirm its validity in IBS; and (iii) Correlate ACE scores with IBS symptom severity. A total of 148 IBS (73% women, mean age = 31 years) and 154 HCs (59% women, mean age = 30 years) completed the ACE and ETI-SR between June 2010 and April 2015. These surveys measured EALs before age 18 in the domains of physical, sexual, and emotional abuse, and general trauma. IBS and abdominal pain severity was measured by a 20-point scale (0 = none, 20 = worst symptoms). The ACE score increased the odds of having IBS (odds ratio [OR] = 2.05, 95% confidence interval [CI]: 1.21-3.48, p = 0.008). Household mental illness (p < 0.001), emotional abuse (p = 0.004), and incarcerated household member (p = 0.019) were significant predictors of IBS. Adverse childhood experiences and ETI-SR scores were strongly correlated (r = 0.59, p < 0.001). ACE, but not ETI-SR, modestly correlated with IBS severity (r = 0.17, p = 0.036) and abdominal pain (r = 0.20, p = 0.015). The ACE questionnaire is a useful instrument to measure EALs in IBS based on its use in large studies, its ability to measure prevalence across different EAL domains, and its correlation with symptom severity. © 2016 John Wiley & Sons Ltd.

Crystal structures of RIalpha subunit of cyclic adenosine 5'-monophosphate (cAMP)-dependent protein kinase complexed with (Rp)-adenosine 3',5'-cyclic monophosphothioate and (Sp)-adenosine 3',5'-cyclic monophosphothioate, the phosphothioate analogues of cAMP.

PubMed

Wu, Jian; Jones, John M; Nguyen-Huu, Xuong; Ten Eyck, Lynn F; Taylor, Susan S

2004-06-01

Cyclic adenosine 5'-monophosphate (cAMP) is an ancient signaling molecule, and in vertebrates, a primary target for cAMP is cAMP-dependent protein kinase (PKA). (R(p))-adenosine 3',5'-cyclic monophosphothioate ((R(p))-cAMPS) and its analogues are the only known competitive inhibitors and antagonists for cAMP activation of PKA, while (S(p))-adenosine 3',5'-cyclic monophosphothioate ((S(p))-cAMPS) functions as an agonist. The crystal structures of a Delta(1-91) deletion mutant of the RIalpha regulatory subunit of PKA bound to (R(p))-cAMPS and (S(p))-cAMPS were determined at 2.4 and 2.3 A resolution, respectively. While the structures are similar to each other and to the crystal structure of RIalpha bound to cAMP, differences in the dynamical properties of the protein when (R(p))-cAMPS is bound are apparent. The structures highlight the critical importance of the exocyclic oxygen's interaction with the invariant arginine in the phosphate binding cassette (PBC) and the importance of this interaction for the dynamical properties of the interactions that radiate out from the PBC. The conformations of the phosphate binding cassettes containing two invariant arginine residues (Arg209 on domain A, and Arg333 on domain B) are somewhat different due to the sulfur interacting with this arginine. Furthermore, the B-site ligand together with the entire domain B show significant differences in their overall dynamic properties in the crystal structure of Delta(1-91) RIalpha complexed with (R(p))-cAMPS phosphothioate analogue ((R(p))-RIalpha) compared to the cAMP- and (S(p))-cAMPS-bound type I and II regulatory subunits, based on the temperature factors. In all structures, two structural solvent molecules exist within the A-site ligand binding pocket; both mediate water-bridged interactions between the ligand and the protein. No structured waters are in the B-site pocket. Owing to the higher resolution data, the N-terminal segment (109-117) of the RIalpha subunit can also be traced

Hierarchical assembly of branched supramolecular polymers from (cyclic Peptide)-polymer conjugates.

PubMed

Koh, Ming Liang; Jolliffe, Katrina A; Perrier, Sébastien

2014-11-10

We report the synthesis and assembly of (N-methylated cyclic peptide)-polymer conjugates for which the cyclic peptide is attached to either the α- or both α- and ω- end groups of a polymer. A combination of chromatographic, spectroscopic, and scattering techniques reveals that the assembly of the conjugates follows a two-level hierarchy, initially driven by H-bond formation between two N-methylated cyclic peptides, followed by unspecific, noncovalent aggregation of this peptide into small domains that behave as branching points and lead to the formation of branched supramolecular polymers.

Are South African Speech-Language Therapists adequately equipped to assess English Additional Language (EAL) speakers who are from an indigenous linguistic and cultural background? A profile and exploration of the current situation

PubMed Central

Mdlalo, Thandeka; Flack, Penelope

2016-01-01

This article presents the results of a survey conducted on Speech-Language Therapists (SLTs) regarding current practices in the assessment of English Additional Language (EAL) speakers in South Africa. It forms part of the rationale for a broader (PhD) study that critiques the use of assessment instruments on EAL speakers from an indigenous linguistic and cultural background. This article discusses an aspect of the broader research and presents the background, method, findings, discussion and implications of the survey. The results of this survey highlight the challenges of human and material resources to, and the dominance of English in, the profession in South Africa. The findings contribute to understanding critical factors for acquiring reliable and valid assessment results with diverse populations, particularly the implications from a cultural and linguistic perspective. PMID:27247254

RP-1776, a novel cyclic peptide produced by Streptomyces sp., inhibits the binding of PDGF to the extracellular domain of its receptor.

PubMed

Toki, S; Agatsuma, T; Ochiai, K; Saitoh, Y; Ando, K; Nakanishi, S; Lokker, N A; Giese, N A; Matsuda, Y

2001-05-01

RP-1776, a novel cyclic peptide, was isolated from the culture broth of Streptomyces sp. KY11784. RP-1776 selectively inhibited the binding of PDGF BB to the extracellular domain of the PDGF beta-receptor with an IC50 value of 11 +/- 6 microM. Detailed binding experiments suggested that RP-1776 directly interacts with PDGF BB. RP-1776 inhibited the phosphorylation of the PDGF beta-receptor induced by PDGF BB. These results suggested that RP-1776 antagonizes the signaling of PDGF BB probably through the inhibition of PDGF BB binding to the PDGF beta-receptor.

Sequencing Cyclic Peptides by Multistage Mass Spectrometry

PubMed Central

Mohimani, Hosein; Yang, Yu-Liang; Liu, Wei-Ting; Hsieh, Pei-Wen; Dorrestein, Pieter C.; Pevzner, Pavel A.

2012-01-01

Some of the most effective antibiotics (e.g., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of mass spectrometry based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage mass spectrometry, and show its advantages over single stage mass spectrometry. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria. PMID:21751357

Fatigue effect in ferroelectric crystals: Growth of the frozen domains

NASA Astrophysics Data System (ADS)

Shur, V. Ya.; Akhmatkhanov, A. R.; Baturin, I. S.

2012-06-01

The model of the fatigue effect during cyclic switching caused by growth of the frozen domain area with charged domain walls has been proposed. It was claimed on the basis of the previous experimental results that for switching in increasing field the frozen domain area started to grow at the given sub-threshold field value and stopped at the threshold field. The influence of the shape and frequency of the field pulses used for cyclic switching has been considered. The uniaxial ferroelectric stoichiometric lithium tantalate single crystals produced by vapor transport equilibration with record low value of coercive field have been chosen as a model material for experimental verification of the model. The formation of the charged domain walls as a result of cyclic switching has been revealed by analysis of the domain images obtained by optical and Raman confocal microscopy. It has been shown that the fatigue degree is equal to the fraction of the frozen domain area. The experimental dependence of the switched charge on the cycle number has been successfully fitted by modified Kolmogorov-Avrami formula. The experimentally observed frequency independence of fatigue profile for rectangular pulses and frequency dependence for triangular pulses has been explained by proposed model.

Instantaneous angular speed monitoring of gearboxes under non-cyclic stationary load conditions

NASA Astrophysics Data System (ADS)

Stander, C. J.; Heyns, P. S.

2005-07-01

Recent developments in the condition monitoring and asset management market have led to the commercialisation of online vibration-monitoring systems. These systems are primarily utilised to monitor large mineral mining equipment such as draglines, continuous miners and hydraulic shovels. Online monitoring systems make diagnostic information continuously available for asset management, production outsourcing and maintenance alliances with equipment manufacturers. However, most online vibration-monitoring systems are based on conventional vibration-monitoring technologies, which are prone to giving false equipment deterioration warnings on gears that operate under fluctuating load conditions. A simplified mathematical model of a gear system was developed to illustrate the feasibility of monitoring the instantaneous angular speed (IAS) as a means of monitoring the condition of gears that are subjected to fluctuating load conditions. A distinction is made between cyclic stationary load modulation and non-cyclic stationary load modulation. It is shown that rotation domain averaging will suppress the modulation caused by non-cyclic stationary load conditions but will not suppress the modulation caused by cyclic stationary load conditions. An experimental investigation on a test rig indicated that the IAS of a gear shaft could be monitored with a conventional shaft encoder to indicate a deteriorating gear fault condition.

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

PubMed Central

2010-01-01

Background Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. Results In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. Conclusions We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at http

Role of MrkJ, a Phosphodiesterase, in Type 3 Fimbrial Expression and Biofilm Formation in Klebsiella pneumoniae▿

PubMed Central

Johnson, Jeremiah G.; Clegg, Steven

2010-01-01

Klebsiella pneumoniae is an opportunistic pathogen that has been shown to adhere to human extracellular matrices using the type 3 fimbriae. Introduction of plasmids carrying genes known to alter intracellular cyclic-di-GMP pools in Vibrio parahaemolyticus revealed that these genes also altered type 3 fimbrial surface expression in K. pneumoniae. Immediately adjacent to the type 3 fimbrial gene cluster is a gene, mrkJ, that is related to a family of bacterial genes encoding phosphodiesterases. We identify here a role for MrkJ, a functional phosphodiesterase exhibiting homology to EAL domain-containing proteins, in controlling type 3 fimbria production and biofilm formation in K. pneumoniae. Deletion of mrkJ resulted in an increase in type 3 fimbria production and biofilm formation as a result of the accumulation of intracellular cyclic-di-GMP. This gene was shown to encode a functional phosphodiesterase via restoration of motility in a V. parahaemolyticus strain previously shown to accumulate cyclic-di-GMP and in vitro using phosphodiesterase activity assays. The effect of the mrkJ mutation on type 3 fimbrial expression was shown to be at the level of mrkA gene transcription by using quantitative reverse transcription-PCR. These results reveal a previously unknown role for cyclic-di-GMP in type 3 fimbrial production. PMID:20511505

A Cyclic-Plasticity-Based Mechanistic Approach for Fatigue Evaluation of 316 Stainless Steel Under Arbitrary Loading

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

Barua, Bipul; Mohanty, Subhasish; Listwan, Joseph T.

In this paper, a cyclic-plasticity based fully mechanistic fatigue modeling approach is presented. This is based on time-dependent stress-strain evolution of the material over the entire fatigue life rather than just based on the end of live information typically used for empirical S~N curve based fatigue evaluation approaches. Previously we presented constant amplitude fatigue test based related material models for 316 SS base, 508 LAS base and 316 SS- 316 SS weld which are used in nuclear reactor components such as pressure vessels, nozzles, and surge line pipes. However, we found that constant amplitude fatigue data based models have limitationmore » in capturing the stress-strain evolution under arbitrary fatigue loading. To address the above mentioned limitation, in this paper, we present a more advanced approach that can be used for modeling the cyclic stress-strain evolution and fatigue life not only under constant amplitude but also under any arbitrary (random/variable) fatigue loading. The related material model and analytical model results are presented for 316 SS base metal. Two methodologies (either based on time/cycle or based on accumulated plastic strain energy) to track the material parameters at a given time/cycle are discussed and associated analytical model results are presented. From the material model and analytical cyclic plasticity model results, it is found that the proposed cyclic plasticity model can predict all the important stages of material behavior during the entire fatigue life of the specimens with more than 90% accuracy« less

A Cyclic-Plasticity-Based Mechanistic Approach for Fatigue Evaluation of 316 Stainless Steel Under Arbitrary Loading

DOE PAGES

Barua, Bipul; Mohanty, Subhasish; Listwan, Joseph T.; ...

2017-12-05

In this paper, a cyclic-plasticity based fully mechanistic fatigue modeling approach is presented. This is based on time-dependent stress-strain evolution of the material over the entire fatigue life rather than just based on the end of live information typically used for empirical S~N curve based fatigue evaluation approaches. Previously we presented constant amplitude fatigue test based related material models for 316 SS base, 508 LAS base and 316 SS- 316 SS weld which are used in nuclear reactor components such as pressure vessels, nozzles, and surge line pipes. However, we found that constant amplitude fatigue data based models have limitationmore » in capturing the stress-strain evolution under arbitrary fatigue loading. To address the above mentioned limitation, in this paper, we present a more advanced approach that can be used for modeling the cyclic stress-strain evolution and fatigue life not only under constant amplitude but also under any arbitrary (random/variable) fatigue loading. The related material model and analytical model results are presented for 316 SS base metal. Two methodologies (either based on time/cycle or based on accumulated plastic strain energy) to track the material parameters at a given time/cycle are discussed and associated analytical model results are presented. From the material model and analytical cyclic plasticity model results, it is found that the proposed cyclic plasticity model can predict all the important stages of material behavior during the entire fatigue life of the specimens with more than 90% accuracy« less

Advances in targeting cyclic nucleotide phosphodiesterases

PubMed Central

Maurice, Donald H.; Ke, Hengming; Ahmad, Faiyaz; Wang, Yousheng; Chung, Jay; Manganiello, Vincent C.

2014-01-01

Cyclic nucleotide phosphodiesterases (PDEs) catalyse the hydrolysis of cyclic AMP and cyclic GMP, thereby regulating the intracellular concentrations of these cyclic nucleotides, their signalling pathways and, consequently, myriad biological responses in health and disease. Currently, a small number of PDE inhibitors are used clinically for treating the pathophysiological dysregulation of cyclic nucleotide signalling in several disorders, including erectile dysfunction, pulmonary hypertension, acute refractory cardiac failure, intermittent claudication and chronic obstructive pulmonary disease. However, pharmaceutical interest in PDEs has been reignited by the increasing understanding of the roles of individual PDEs in regulating the subcellular compartmentalization of specific cyclic nucleotide signalling pathways, by the structure-based design of novel specific inhibitors and by the development of more sophisticated strategies to target individual PDE variants. PMID:24687066

The cyclic stress-strain behavior of a nickel-base superalloy at 650 C

NASA Technical Reports Server (NTRS)

Gabb, T. P.; Welsch, G. E.

1986-01-01

It is pointed out that examinations of the monotonic tensile and fatigue behaviors of single crystal nickel-base superalloys have disclosed orientation-dependent tension-compression anisotropies and significant differences in the mechanical response of octahedral and cube slip at intermediate temperatures. An examination is conducted of the cyclic hardening response of the single crystal superalloy PWA 1480 at 650 C. In the considered case, tension-compression anisotropy is present, taking into account primarily conditions under which a single slip system is operative. Aspects of a deformation by single slip are considered along with cyclic hardening anisotropy in tension and compression. It is found that specimens deforming by octahedral slip on a single slip system have similar hardening responses in tensile and low cycle fatigue loading. Cyclic strain hardening is very low for specimens displaying single slip.

Structure-based Design of Cyclically Permuted HIV-1 gp120 Trimers That Elicit Neutralizing Antibodies*

PubMed Central

Kesavardhana, Sannula; Das, Raksha; Citron, Michael; Datta, Rohini; Ecto, Linda; Srilatha, Nonavinakere Seetharam; DiStefano, Daniel; Swoyer, Ryan; Joyce, Joseph G.; Dutta, Somnath; LaBranche, Celia C.; Montefiori, David C.; Flynn, Jessica A.; Varadarajan, Raghavan

2017-01-01

A major goal for HIV-1 vaccine development is an ability to elicit strong and durable broadly neutralizing antibody (bNAb) responses. The trimeric envelope glycoprotein (Env) spikes on HIV-1 are known to contain multiple epitopes that are susceptible to bNAbs isolated from infected individuals. Nonetheless, all trimeric and monomeric Env immunogens designed to date have failed to elicit such antibodies. We report the structure-guided design of HIV-1 cyclically permuted gp120 that forms homogeneous, stable trimers, and displays enhanced binding to multiple bNAbs, including VRC01, VRC03, VRC-PG04, PGT128, and the quaternary epitope-specific bNAbs PGT145 and PGDM1400. Constructs that were cyclically permuted in the V1 loop region and contained an N-terminal trimerization domain to stabilize V1V2-mediated quaternary interactions, showed the highest homogeneity and the best antigenic characteristics. In guinea pigs, a DNA prime-protein boost regimen with these new gp120 trimer immunogens elicited potent neutralizing antibody responses against highly sensitive Tier 1A isolates and weaker neutralizing antibody responses with an average titer of about 115 against a panel of heterologous Tier 2 isolates. A modest fraction of the Tier 2 virus neutralizing activity appeared to target the CD4 binding site on gp120. These results suggest that cyclically permuted HIV-1 gp120 trimers represent a viable platform in which further modifications may be made to eventually achieve protective bNAb responses. PMID:27879316

Creep-Fatigue Interaction and Cyclic Strain Analysis in P92 Steel Based on Test

NASA Astrophysics Data System (ADS)

Ji, Dongmei; Zhang, Lai-Chang; Ren, Jianxing; Wang, Dexian

2015-04-01

This work focused on the interaction of creep and fatigue and cyclic strain analysis in high-chromium ferritic P92 steel based on load-controlled creep-fatigue (CF) tests and conventional creep test at 873 K. Mechanical testing shows that the cyclic load inhibits the propagation of creep damage in the P92 steel and CF interaction becomes more severe with the decrease in the holding period duration and stress ratio. These results are also verified by the analysis of cyclic strain. The fatigue lifetime reduces with the increasing of the holding period duration and it does not reduce much with the increasing stress ratio especially under the conditions of long holding period duration. The cyclic strains (i.e., the strain range and creep strain) of CF tests consist of three stages, which is the same as those for the conventional creep behavior. The microscopic fracture surface observations illustrated that two different kinds of voids are observed at the fracture surfaces and Laves phase precipitates at the bottom of the voids.

A statistical analysis of elevated temperature gravimetric cyclic oxidation data of 36 Ni- and Co-base superalloys based on an oxidation attack parameter

NASA Technical Reports Server (NTRS)

Barrett, Charles A.

1992-01-01

A large body of high temperature cyclic oxidation data generated from tests at NASA Lewis Research Center involving gravimetric/time values for 36 Ni- and Co-base superalloys was reduced to a single attack parameter, K(sub a), for each run. This K(sub a) value was used to rank the cyclic oxidation resistance of each alloy at 1000, 1100, and 1150 C. These K(sub a) values were also used to derive an estimating equation using multiple linear regression involving log(sub 10)K(sub a) as a function of alloy chemistry and test temperature. This estimating equation has a high degree of fit and could be used to predict cyclic oxidation behavior for similar alloys and to design an optimum high strength Ni-base superalloy with maximum high temperature cyclic oxidation resistance. The critical alloy elements found to be beneficial were Al, Cr, and Ta.

Crystal structure of cGMP-dependent protein kinase Iβ cyclic nucleotide-binding-B domain : Rp-cGMPS complex reveals an apo-like, inactive conformation

DOE PAGES

Campbell, James C.; VanSchouwen, Bryan; Lorenz, Robin; ...

2016-12-23

The R-diastereomer of phosphorothioate analogs of cGMP, Rp-cGMPS, is one of few known inhibitors of cGMP-dependent protein kinase I (PKG I); however, its mechanism of inhibition is currently not fully understood. We determined the crystal structure of the PKG Iβ cyclic nucleotide-binding domain (PKG Iβ CNB-B), considered a ‘gatekeeper’ for cGMP activation, bound to Rp-cGMPS at 1.3 Å. Our structural and NMR data show that PKG Iβ CNB-B bound to Rp-cGMPS displays an apo-like structure with its helical domain in an open conformation. Comparison with the cAMP-dependent protein kinase regulatory subunit (PKA RIα) showed that this conformation resembles the catalyticmore » subunit-bound inhibited state of PKA RIα more closely than the apo or Rp-cAMPS-bound conformations. Our results suggest that Rp-cGMPS inhibits PKG I by stabilizing the inactive conformation of CNB-B.« less

Damage evolution analysis of coal samples under cyclic loading based on single-link cluster method

NASA Astrophysics Data System (ADS)

Zhang, Zhibo; Wang, Enyuan; Li, Nan; Li, Xuelong; Wang, Xiaoran; Li, Zhonghui

2018-05-01

In this paper, the acoustic emission (AE) response of coal samples under cyclic loading is measured. The results show that there is good positive relation between AE parameters and stress. The AE signal of coal samples under cyclic loading exhibits an obvious Kaiser Effect. The single-link cluster (SLC) method is applied to analyze the spatial evolution characteristics of AE events and the damage evolution process of coal samples. It is found that a subset scale of the SLC structure becomes smaller and smaller when the number of cyclic loading increases, and there is a negative linear relationship between the subset scale and the degree of damage. The spatial correlation length ξ of an SLC structure is calculated. The results show that ξ fluctuates around a certain value from the second cyclic loading process to the fifth cyclic loading process, but spatial correlation length ξ clearly increases in the sixth loading process. Based on the criterion of microcrack density, the coal sample failure process is the transformation from small-scale damage to large-scale damage, which is the reason for changes in the spatial correlation length. Through a systematic analysis, the SLC method is an effective method to research the damage evolution process of coal samples under cyclic loading, and will provide important reference values for studying coal bursts.

Windows(Registered Trademark)-Based Software Models Cyclic Oxidation Behavior

NASA Technical Reports Server (NTRS)

Smialek, J. L.; Auping, J. V.

2004-01-01

Oxidation of high-temperature aerospace materials is a universal issue for combustion-path components in turbine or rocket engines. In addition to the question of the consumption of material due to growth of protective scale at use temperatures, there is also the question of cyclic effects and spallation of scale on cooldown. The spallation results in the removal of part of the protective oxide in a discontinuous step and thereby opens the way for more rapid oxidation upon reheating. In experiments, cyclic oxidation behavior is most commonly characterized by measuring changes in weight during extended time intervals that include hundreds or thousands of heating and cooling cycles. Weight gains occurring during isothermal scale-growth processes have been well characterized as being parabolic or nearly parabolic functions of time because diffusion controls reaction rates. In contrast, the net weight change in cyclic oxidation is the sum of the effects of the growth and spallation of scale. Typically, the net weight gain in cyclic oxidation is determined only empirically (that is, by measurement), with no unique or straightforward mathematical connection to either the rate of growth or the amount of metal consumed. Thus, there is a need for mathematical modeling to infer spallation mechanisms. COSP is a computer program that models the growth and spallation processes of cyclic oxidation on the basis of a few elementary assumptions that were discussed in COSP: A Computer Model of Cyclic Oxidation, Oxidation of Metals, vol. 36, numbers 1 and 2, 1991, pages 81-112. Inputs to the model include the selection of an oxidation-growth law and a spalling geometry, plus oxide-phase, growth-rate, cycle-duration, and spall-constant parameters. (The spalling fraction is often shown to be a constant factor times the existing amount of scale.) The output of COSP includes the net change in weight, the amounts of retained and spalled oxide, the total amounts of oxygen and metal

Assessment of burned coal shale properties based on cyclic load

NASA Astrophysics Data System (ADS)

Grygierek, Marcin; Kalisz, Piotr; Pacześniowski, Krzysztof; Pytlik, Andrzej; Zięba, Magdalena

2018-04-01

Road surfaces that are subjected to cyclic loads generated by vehicle wheels must meet the requirements concerning the durability in the assumed period of use. The durability of the layered pavement construction systems depends on the value and frequency of the load as well as on the mechanical features of its individual layers. Layers of unbound, mechanically stabilized mixtures are a significant aspect of surfaces that are susceptible. Mixtures of this type can be applied both to the subgrade layers as well as to the bottom pavement layers, including the improved course. Considering the cyclic nature of the load on the surface of the entire system, mechanically stabilized layers are subject to continuous, but slow, densification during the period of use, which results in the formation of permanent deformations and so-called structural ruts. Post-mining waste is frequently used in road construction. which is the so-called burned shale that can be used for the bottom layers of the surface and layers of the improved subgrade (soil replacement). This material was the subject of the analysis. The evaluation was based mainly on the results of pilot studies covering cyclic loads of the layer/course made of the so-called red shale. The applied research method was aimed at preliminary assessment of its suitability for the assessment of the behaviour of the disintegrated medium under the conditions of test loads simulating the movement of vehicles.

Visual search of cyclic spatio-temporal events

NASA Astrophysics Data System (ADS)

Gautier, Jacques; Davoine, Paule-Annick; Cunty, Claire

2018-05-01

The analysis of spatio-temporal events, and especially of relationships between their different dimensions (space-time-thematic attributes), can be done with geovisualization interfaces. But few geovisualization tools integrate the cyclic dimension of spatio-temporal event series (natural events or social events). Time Coil and Time Wave diagrams represent both the linear time and the cyclic time. By introducing a cyclic temporal scale, these diagrams may highlight the cyclic characteristics of spatio-temporal events. However, the settable cyclic temporal scales are limited to usual durations like days or months. Because of that, these diagrams cannot be used to visualize cyclic events, which reappear with an unusual period, and don't allow to make a visual search of cyclic events. Also, they don't give the possibility to identify the relationships between the cyclic behavior of the events and their spatial features, and more especially to identify localised cyclic events. The lack of possibilities to represent the cyclic time, outside of the temporal diagram of multi-view geovisualization interfaces, limits the analysis of relationships between the cyclic reappearance of events and their other dimensions. In this paper, we propose a method and a geovisualization tool, based on the extension of Time Coil and Time Wave, to provide a visual search of cyclic events, by allowing to set any possible duration to the diagram's cyclic temporal scale. We also propose a symbology approach to push the representation of the cyclic time into the map, in order to improve the analysis of relationships between space and the cyclic behavior of events.

Image encryption algorithm based on multiple mixed hash functions and cyclic shift

NASA Astrophysics Data System (ADS)

Wang, Xingyuan; Zhu, Xiaoqiang; Wu, Xiangjun; Zhang, Yingqian

2018-08-01

This paper proposes a new one-time pad scheme for chaotic image encryption that is based on the multiple mixed hash functions and the cyclic-shift function. The initial value is generated using both information of the plaintext image and the chaotic sequences, which are calculated from the SHA1 and MD5 hash algorithms. The scrambling sequences are generated by the nonlinear equations and logistic map. This paper aims to improve the deficiencies of traditional Baptista algorithms and its improved algorithms. We employ the cyclic-shift function and piece-wise linear chaotic maps (PWLCM), which give each shift number the characteristics of chaos, to diffuse the image. Experimental results and security analysis show that the new scheme has better security and can resist common attacks.

Direct activation of the olfactory cyclic nucleotide-gated channel through modification of sulfhydryl groups by NO compounds.

PubMed

Broillet, M C; Firestein, S

1996-02-01

The activation of a cyclic nucleotide-gated channel is the final step in sensory transduction in olfaction. Normally, this channel is opened by the intracellular cyclic nucleotide second messenger cAMP or cGMP. However, in single channel recordings we found that donors of nitric oxide, a putative intercellular messenger, could directly activate the native olfactory neuron channel. Its action was independent of the presence of the normal ligand and did not involve the cyclic nucleotide binding site, suggesting an alternate site on the molecule that is critical in channel gating. The biochemical pathway appears to utilize nitric oxide in one of its alternate redox states, the nitrosonium ion, transnitrosylating a free sulfhydryl group belonging to a cysteine residue tentatively identified as being in the region linking the S6 transmembrane domain to the ligand binding domain.

The Cyclic Stress-Strain Behavior of a Single Crystal Nickel-Base Superalloy. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Gabb, Timothy P.

1988-01-01

The cyclic stress-strain response and similar deformation structures of the single crystal nickel based superalloy was described under a specific set of conditions. The isothermal low cycle fatigue response and deformation structures were described at a typical intermediate temperature and at high temperature. Specimens oriented near the (001) and (111) crystallographic orientations were tested at 1050 C, where more moderate orientation effects were expected. This enabled the description of the deformation structures at each of the 2 temperatures and their relationship to the observed cyclic stress-strain behavior. The initial yield strength of all specimens tested at 650 C was controlled by the shearing of the gamma prime precipitates by dislocation pairs. Low cycle fatigue tests at 650 C had cyclic hardening, which was associated with dislocation interactions in the gamma matrix. The initial yield strength of specimens tested at 1050 C was associated with dislocation bypassing of the gamma prime precipitates. Low cycle fatigue tests at 1050 C had cyclic softening, associated with extensive dislocation recovery at the gamma-gamma prime interfaces along with some gamma prime precipitate coarsening.

Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain

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

Suzuki, Nobuhiro; Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602; Yamazaki, Yasuo

2008-10-01

The structures of pseudechetoxin and pseudecin suggest that both proteins bind to cyclic nucleotide-gated ion channels in a manner in which the concave surface occludes the pore entrance. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction by retinal photoreceptors and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins belong to a cysteine-rich secretory protein (CRISP) family containing an N-terminal pathogenesis-related proteins of group 1 (PR-1) domain and a C-terminal cysteine-rich domain (CRD). PsTx and Pdc are highly homologous proteins, but their blocking affinitiesmore » on CNG channels are different: PsTx blocks both the olfactory and retinal channels with ∼15–30-fold higher affinity than Pdc. To gain further insights into their structure and function, the crystal structures of PsTx, Pdc and Zn{sup 2+}-bound Pdc were determined. The structures revealed that most of the amino-acid-residue differences between PsTx and Pdc are located around the concave surface formed between the PR-1 domain and the CRD, suggesting that the concave surface is functionally important for CNG-channel binding and inhibition. A structural comparison in the presence and absence of Zn{sup 2+} ion demonstrated that the concave surface can open and close owing to movement of the CRD upon Zn{sup 2+} binding. The data suggest that PsTx and Pdc occlude the pore entrance and that the dynamic motion of the concave surface facilitates interaction with the CNG channels.« less

High-Temperature Cyclic Oxidation Data, Volume 1

NASA Technical Reports Server (NTRS)

Barrett, C. A.; Garlick, R. G.; Lowell, C. E.

1984-01-01

This first in a series of cyclic oxidation handbooks contains specific-weight-change-versus-time data and X-ray diffraction results derived from high-temperature cyclic tests on high-temperature, high-strength nickel-base gamma/gamma' and cobalt-base turbine alloys. Each page of data summarizes a complete test on a given alloy sample.

Determination of babbit mechanical properties based on tin under static and cyclic loading

NASA Astrophysics Data System (ADS)

Zernin, M. V.

2018-03-01

Based on the results of studies of babbitt on the basis of tin under static loading under three types of stress state, the parameters of the criterion for the equivalence of stressed states were refined and a single diagram of the babbitt deformation was obtained. It is shown that the criterion of equivalence for static loading should contain the first principal stress and stress intensity. With cyclic loading, the first main voltage can be used as a criterion. The stages of development of fatigue cracks are described and it is logical to use a statistical approach to reveal the boundary of the transition from short cracks to macrocracks, based on a significant difference in the characteristics of the dispersion of the crack speeds at these two stages. The results of experimental studies of the cyclic crack resistance of babbitt are presented and the parameters of this boundary are obtained.

Cyclic Peptides Arising by Evolutionary Parallelism via Asparaginyl-Endopeptidase–Mediated Biosynthesis[C][W

PubMed Central

Mylne, Joshua S.; Chan, Lai Yue; Chanson, Aurelie H.; Daly, Norelle L.; Schaefer, Hanno; Bailey, Timothy L.; Nguyencong, Philip; Cascales, Laura; Craik, David J.

2012-01-01

The cyclic miniprotein Momordica cochinchinensis Trypsin Inhibitor II (MCoTI-II) (34 amino acids) is a potent trypsin inhibitor (TI) and a favored scaffold for drug design. We have cloned the corresponding genes and determined that each precursor protein contains a tandem series of cyclic TIs terminating with the more commonly known, and potentially ancestral, acyclic TI. Expression of the precursor protein in Arabidopsis thaliana showed that production of the cyclic TIs, but not the terminal acyclic TI, depends on asparaginyl endopeptidase (AEP) for maturation. The nature of their repetitive sequences and the almost identical structures of emerging TIs suggest these cyclic peptides evolved by internal gene amplification associated with recruitment of AEP for processing between domain repeats. This is the third example of similar AEP-mediated processing of a class of cyclic peptides from unrelated precursor proteins in phylogenetically distant plant families. This suggests that production of cyclic peptides in angiosperms has evolved in parallel using AEP as a constraining evolutionary channel. We believe this is evolutionary evidence that, in addition to its known roles in proteolysis, AEP is especially suited to performing protein cyclization. PMID:22822203

Toward structure prediction of cyclic peptides.

PubMed

Yu, Hongtao; Lin, Yu-Shan

2015-02-14

Cyclic peptides are a promising class of molecules that can be used to target specific protein-protein interactions. A computational method to accurately predict their structures would substantially advance the development of cyclic peptides as modulators of protein-protein interactions. Here, we develop a computational method that integrates bias-exchange metadynamics simulations, a Boltzmann reweighting scheme, dihedral principal component analysis and a modified density peak-based cluster analysis to provide a converged structural description for cyclic peptides. Using this method, we evaluate the performance of a number of popular protein force fields on a model cyclic peptide. All the tested force fields seem to over-stabilize the α-helix and PPII/β regions in the Ramachandran plot, commonly populated by linear peptides and proteins. Our findings suggest that re-parameterization of a force field that well describes the full Ramachandran plot is necessary to accurately model cyclic peptides.

Study of CO2 cyclic absorption stability of CaO-based sorbents derived from lime mud purified by sucrose method.

PubMed

Ma, AiHua; Jia, QingMing; Su, HongYing; Zhi, YunFei; Tian, Na; Wu, Jing; Shan, ShaoYun

2016-02-01

Using lime mud (LM) purified by sucrose method, derived from paper-making industry, as calcium precursor, and using mineral rejects-bauxite-tailings (BTs) from aluminum production as dopant, the CaO-based sorbents for high-temperature CO2 capture were prepared. Effects of BTs content, precalcining time, and temperature on CO2 cyclic absorption stability were illustrated. The cyclic carbonation behavior was investigated in a thermogravimetric analyzer (TGA). Phase composition and morphologies were analyzed by XRD and SEM. The results reflected that the as-synthesized CaO-based sorbent doped with 10 wt% BTs showed a superior CO2 cyclic absorption-desorption conversion during multiple cycles, with conversion being >38 % after 50 cycles. Occurrence of Ca12Al14O33 phase during precalcination was probably responsible for the excellent CO2 cyclic stability.

Color visualization of cyclic magnitudes

NASA Astrophysics Data System (ADS)

Restrepo, Alfredo; Estupiñán, Viviana

2014-02-01

We exploit the perceptual, circular ordering of the hues in a technique for the visualization of cyclic variables. The hue is thus meaningfully used for the indication of variables such as the azimuth and the units of the measurement of time. The cyclic (or circular) variables may be both of the continuous type or the discrete type; among the first there is azimuth and among the last you find the musical notes and the days of the week. A correspondence between the values of a cyclic variable and the chromatic hues, where the natural circular ordering of the variable is respected, is called a color code for the variable. We base such a choice of hues on an assignment of of the unique hues red, yellow, green and blue, or one of the 8 even permutations of this ordered list, to 4 cardinal values of the cyclic variable, suitably ordered; color codes based on only 3 cardinal points are also possible. Color codes, being intuitive, are easy to remember. A possible low accuracy when reading instruments that use this technique is compensated by fast, ludic and intuitive readings; also, the use of a referential frame makes readings precise. An achromatic version of the technique, that can be used by dichromatic people, is proposed.

Cyclic di-GMP-dependent Signaling Pathways in the Pathogenic Firmicute Listeria monocytogenes

PubMed Central

Chen, Li-Hong; Köseoğlu, Volkan K.; Güvener, Zehra T.; Myers-Morales, Tanya; Reed, Joseph M.; D'Orazio, Sarah E. F.; Miller, Kurt W.; Gomelsky, Mark

2014-01-01

We characterized key components and major targets of the c-di-GMP signaling pathways in the foodborne pathogen Listeria monocytogenes, identified a new c-di-GMP-inducible exopolysaccharide responsible for motility inhibition, cell aggregation, and enhanced tolerance to disinfectants and desiccation, and provided first insights into the role of c-di-GMP signaling in listerial virulence. Genome-wide genetic and biochemical analyses of c-di-GMP signaling pathways revealed that L. monocytogenes has three GGDEF domain proteins, DgcA (Lmo1911), DgcB (Lmo1912) and DgcC (Lmo2174), that possess diguanylate cyclase activity, and three EAL domain proteins, PdeB (Lmo0131), PdeC (Lmo1914) and PdeD (Lmo0111), that possess c-di-GMP phosphodiesterase activity. Deletion of all phosphodiesterase genes (ΔpdeB/C/D) or expression of a heterologous diguanylate cyclase stimulated production of a previously unknown exopolysaccharide. The synthesis of this exopolysaccharide was attributed to the pssA-E (lmo0527-0531) gene cluster. The last gene of the cluster encodes the fourth listerial GGDEF domain protein, PssE, that functions as an I-site c-di-GMP receptor essential for exopolysaccharide synthesis. The c-di-GMP-inducible exopolysaccharide causes cell aggregation in minimal medium and impairs bacterial migration in semi-solid agar, however, it does not promote biofilm formation on abiotic surfaces. The exopolysaccharide also greatly enhances bacterial tolerance to commonly used disinfectants as well as desiccation, which may contribute to survival of L. monocytogenes on contaminated food products and in food-processing facilities. The exopolysaccharide and another, as yet unknown c-di-GMP-dependent target, drastically decrease listerial invasiveness in enterocytes in vitro, and lower pathogen load in the liver and gallbladder of mice infected via an oral route, which suggests that elevated c-di-GMP levels play an overall negative role in listerial virulence. PMID:25101646

Proline-Based Cyclic Dipeptides from Korean Fermented Vegetable Kimchi and from Leuconostoc mesenteroides LBP-K06 Have Activities against Multidrug-Resistant Bacteria.

PubMed

Liu, Rui; Kim, Andrew H; Kwak, Min-Kyu; Kang, Sa-Ouk

2017-01-01

Lactobacillus plantarum and Leuconostoc mesenteroides play a prominent role as functional starters and predominant isolates in the production of various types of antimicrobial compound-containing fermented foods, especially including kimchi. In the case of the bioactive cyclic dipeptides, their racemic diastereomers inhibitory to bacteria and fungi have been suggested to come solely from Lactobacillus spp. of these strains. We previously demonstrated the antifungal and antiviral activities of proline-based cyclic dipeptides, which were fractionated from culture filtrates of Lb. plantarum LBP-K10 originated from kimchi. However, cyclic dipeptides have not been identified in the filtrates, either from cultures or fermented subject matter, driven by Ln. mesenteroides , which have been widely used as starter cultures for kimchi fermentation. Most importantly, the experimental verification of cyclic dipeptide-content changes during kimchi fermentation have also not been elucidated. Herein, the antibacterial fractions, including cyclo(Leu-Pro) and cyclo(Phe-Pro), from Ln. mesenteroides LBP-K06 culture filtrates, which exhibited a typical chromatographic retention behavior (t R ), were identified by using semi-preparative high-performance liquid chromatography and gas chromatography-mass spectrometry. Based on this finding, the proline-based cyclic dipeptides, including cyclo(Ser-Pro), cyclo(Tyr-Pro), and cyclo(Leu-Pro), were additionally identified in the filtrates only when fermenting Chinese cabbage produced with Ln. mesenteroides LBP-K06 starter cultures. The detection and isolation of cyclic dipeptides solely in controlled fermented cabbage were conducted under the control of fermentation-process parameters concomitantly with strong CDP selectivity by using a two-consecutive-purification strategy. Interestingly, cyclic dipeptides in the filtrates, when using this strain as a starter, increased with fermentation time. However, no cyclic dipeptides were observed in the

Strain controlled cyclic tests on miniaturized specimens

NASA Astrophysics Data System (ADS)

Procházka, R.; Džugan, J.

2017-02-01

The paper is dealing with strain controlled cyclic tests using a non-contact strain measurement based on digital image correlation techniques on proportional sizes of conventional specimens. The cyclic behaviour of 34CrNiMo6 high-strength steel was investigated on miniaturized round specimens with diameter of 2mm that were compared with specimens in accordance with ASTM E606 standards. The cycle asymmetry coefficient was R= -1. This application is intended to be used for life time assessment of in service components in future work which enables to carried out a group of mechanical tests from a limited amount of the experimental material. The attention was paid to confirm the suitability of the proposed size miniaturization geometry, testing set up and procedure. The test results obtained enabled to construct Manson-Coffin curves and assess fatigue parameters. The purpose of this study is to present differences between cyclic curves and cyclic parameters which have been evaluated based on conventional and miniaturized specimens.

More Cyclic-Oxidation Data For Turbine Alloys

NASA Technical Reports Server (NTRS)

Barrett, Charles A.; Garlick, Ralph G.

1993-01-01

Document presents data on cyclic oxidation of high-temperature, high-strength, nickel-base and cobalt-base alloys for turbines. Completes presentation of data begun in NASA Technical Memorandum 83665 (Revised 1989), "High-Temperature Cyclic Oxidation Data, Turbine Alloys, Part 1." Data consist of plots and tabulations of changes in specific weight as function of time, and lists of surface and spalled material phases identified by x-ray diffraction measurements.

Cyclic softening based on dislocation annihilation at sub-cell boundary for SA333 Grade-6 C-Mn steel

NASA Astrophysics Data System (ADS)

Bhattacharjee, S.; Dhar, S.; Acharyya, S. K.; Gupta, S. K.

2018-01-01

In this work, the response of SA333 Grade-6 C-Mn steel subjected to uniaxial and in-phase biaxial tension-torsion cyclic loading is experimented and an attempt is made to model the material behaviour. Experimentally observed cyclic softening is modelled based on ‘dislocation annihilation at low angle grain boundary’, while Ohno-Wang kinematic hardening rule is used to simulate the stress-strain hysteresis loops. The relevant material parameters are extracted from the appropriate experimental results and metallurgical investigations. The material model is plugged as user material subroutine into ABAQUS FE platform to simulate pre-saturation low cycle fatigue loops with cyclic softening and other cyclic plastic behaviour under prescribed loading. The stress-strain hysteresis loops and peak stress with cycles were compared with the experimental results and good agreements between experimental and simulated results validated the material model.

Statistical damage constitutive model for rocks subjected to cyclic stress and cyclic temperature

NASA Astrophysics Data System (ADS)

Zhou, Shu-Wei; Xia, Cai-Chu; Zhao, Hai-Bin; Mei, Song-Hua; Zhou, Yu

2017-10-01

A constitutive model of rocks subjected to cyclic stress-temperature was proposed. Based on statistical damage theory, the damage constitutive model with Weibull distribution was extended. Influence of model parameters on the stress-strain curve for rock reloading after stress-temperature cycling was then discussed. The proposed model was initially validated by rock tests for cyclic stress-temperature and only cyclic stress. Finally, the total damage evolution induced by stress-temperature cycling and reloading after cycling was explored and discussed. The proposed constitutive model is reasonable and applicable, describing well the stress-strain relationship during stress-temperature cycles and providing a good fit to the test results. Elastic modulus in the reference state and the damage induced by cycling affect the shape of reloading stress-strain curve. Total damage induced by cycling and reloading after cycling exhibits three stages: initial slow increase, mid-term accelerated increase, and final slow increase.

Cyclic plasticity models and application in fatigue analysis

NASA Technical Reports Server (NTRS)

Kalev, I.

1981-01-01

An analytical procedure for prediction of the cyclic plasticity effects on both the structural fatigue life to crack initiation and the rate of crack growth is presented. The crack initiation criterion is based on the Coffin-Manson formulae extended for multiaxial stress state and for inclusion of the mean stress effect. This criterion is also applied for the accumulated damage ahead of the existing crack tip which is assumed to be related to the crack growth rate. Three cyclic plasticity models, based on the concept of combination of several yield surfaces, are employed for computing the crack growth rate of a crack plane stress panel under several cyclic loading conditions.

Cyclic steady state stress-strain behavior of UHMW polyethylene.

PubMed

Krzypow, D J; Rimnac, C M

2000-10-01

To increase the long-term performance of total joint replacements, finite element analyses of ultra high molecular weight polyethylene (UHMWPE) components have been conducted to predict the effect of load on the stress and strain distributions occurring on and within these components. Early models incorporated the monotonic behavior of UHMWPE without considering the unloading and cyclic loading behavior. However, UHMWPE components undergo cyclic loading during use and at least two wear damage modes (pitting and delamination) are thought to be associated with the fatigue fracture properties of UHMWPE. The objective of this study was to examine the fully reversed uniaxial tension/compression cyclic steady state stress-strain behavior of UHMWPE as a first step towards developing a cyclic constitutive relationship for UHMWPE. The hypothesis that cycling results in a permanent change in the stress-strain relationship, that is, that the cyclic steady state represents a new cyclically stabilized state, was examined. It was found that, like other ductile polymers, UHMWPE substantially cyclically softens under fully reversed uniaxial straining. More cyclic softening occurred in tension than in compression. Furthermore, cyclic steady state was attained, but not cyclic stability. It is suggested that it may be more appropriate to base a material constitutive relationship for UHMWPE for finite element analyses of components upon a cyclically modified stress-strain relationship.

Mechanical Behavior and Microcrack Development in Nominally Dry Synthetic Salt-rock During Cyclic Loading

NASA Astrophysics Data System (ADS)

Ding, J.; Chester, F. M.; Chester, J. S.; Zhu, C.; Shen, X.; Arson, C. F.

2016-12-01

Synthetic salt-rock is produced through uniaxial consolidation of sieved granular salt (0.3-0.355 mm grain diam.) at 75-107 MPa pressure and 100-200 0 C for 15 min duration, to produce low porosity (3%-6%) aggregates. Based on microstructural observations, consolidation mechanisms are grain rearrangement, intragranular plastic flow, and minor microfracture and recrystallization. Following consolidation, the salt-rock is deformed by cyclic, triaxial loading at room temperature and 4 MPa confining pressure to investigate microfracture development, closure and healing effects on elastic properties and flow strength. Load cycles are performed within the elastic regime, up to yielding, and during steady ductile flow. The mechanical properties are determined using an internal load cell and strain gages bonded to the samples. Elastic properties vary systematically during deformation reflecting cracking and pore and grain shape changes. Between triaxial load cycles, samples are held at isostatic loads for durations up to one day to determine healing rates and strength recovery; a change in mechanical behavior is observed when significant healing is induced. The microstructures of all samples are characterized before and after cyclic loading using optical microscopy. The consolidation and cyclic triaxial tests, and optical microscopy investigations, are conducted in a controlled low-humidity environment to ensure nominally dry conditions. The microstructures of samples from different stages of cyclic triaxial deformation indicate that intracrystalline plasticity, accompanied by minor recovery by recrystallization, is dominant; but, grain-boundary crack opening also becomes significant. Grain-boundary microcracks have preferred orientations that are sub-parallel to the load axis. The stress-strain behavior correlates with microcrack fabrics and densities during cyclic loading. These experiments are used to both inform and test continuum damage mechanics models of salt

Rational Design of Cyclic Antimicrobial Peptides Based on BPC194 and BPC198.

PubMed

Cirac, Anna D; Torné, Maria; Badosa, Esther; Montesinos, Emilio; Salvador, Pedro; Feliu, Lidia; Planas, Marta

2017-06-24

A strategy for the design of antimicrobial cyclic peptides derived from the lead compounds c(KKLKKFKKLQ) ( BPC194 ) and c(KLKKKFKKLQ) ( BPC198 ) is reported. First, the secondary β-structure of BPC194 and BPC198 was analyzed by carrying out molecular dynamics (MD) simulations. Then, based on the sequence pattern and the β-structure of BPC194 or BPC198 , fifteen analogues were designed and synthesized on solid-phase. The best peptides ( BPC490 , BPC918, and BPC924 ) showed minimum inhibitory concentration (MIC) values <6.2 μM against Pseudomonas syringae pv. syringae and Xanthomonas axonopodis pv. vesicatoria , and an MIC value of 12.5 to 25 μM against Erwinia amylovora , being as active as BPC194 and BPC198 . Interestingly, these three analogues followed the structural pattern defined from the MD simulations of the parent peptides. Thus, BPC490 maintained the parallel alignment of the hydrophilic pairs K¹-K⁸, K²-K⁷, and K⁴-K⁵, whereas BPC918 and BPC924 included the two hydrophilic interactions K³-Q 10 and K⁵-K⁸. In short, MD simulations have proved to be very useful for ascertaining the structural features of cyclic peptides that are crucial for their biological activity. Such approaches could be further employed for the development of new antibacterial cyclic peptides.

Domain Adaptation for Pedestrian Detection Based on Prediction Consistency

PubMed Central

Huan-ling, Tang; Zhi-yong, An

2014-01-01

Pedestrian detection is an active area of research in computer vision. It remains a quite challenging problem in many applications where many factors cause a mismatch between source dataset used to train the pedestrian detector and samples in the target scene. In this paper, we propose a novel domain adaptation model for merging plentiful source domain samples with scared target domain samples to create a scene-specific pedestrian detector that performs as well as rich target domain simples are present. Our approach combines the boosting-based learning algorithm with an entropy-based transferability, which is derived from the prediction consistency with the source classifications, to selectively choose the samples showing positive transferability in source domains to the target domain. Experimental results show that our approach can improve the detection rate, especially with the insufficient labeled data in target scene. PMID:25013850

Observation of Failure and Domain Switching in Lead Zirconate Titanate Ceramics

NASA Astrophysics Data System (ADS)

Okayasu, Mitsuhiro; Sugiyama, Eriko; Sato, Kazuto; Mizuno, Mamoru

The mechanical and electrical properties (electromechanical coupling coefficient, piezoelectric constant and dielectric constant) of lead zirconate titanate (PZT) ceramics are investigated during mechanical static and cyclic loading. There are several failure characteristics which can alter the material properties of PZT ceramics. The elastic constant increases and electrical properties decrease with increasing the applied load. This is due to the internal strain arising from the domain switching. In this case, 90° domain switching occurs anywhere in the samples as the sample is loaded. It is also apparent that electrogenesis occurs several times during cyclic loading to the final fracture. This occurrence is related to the domain switching. The elastic constant and electrical properties can decrease because of crack generation in the PZT ceramics. Moreover, the elastic constant increases with increase of the mechanical load and decreases with decrease of the load. On the contrary, the opposite sense of change of the electrical properties is observed.

Domain similarity based orthology detection.

PubMed

Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

2015-05-13

Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

Cyclic control stick

DOEpatents

Whitaker, Charles N.; Zimmermann, Richard E.

1989-01-01

A cyclic control stick of the type used in helicopters for reducing the safety hazards associated with such a mechanism in the event of a crewman being thrown violently into contact with the cyclic control stick resulting from a crash or the like. The cyclic control stick is configured to break away upon the exertion of an impact force which exceeds a predetermined value and/or is exerted for more than a momentary time duration. The cyclic control stick is also configured to be adjustable so as to locate the grip thereof as far away from the crewman as possible for safety reasons without comprising the comfort of the crewman or the use of the control stick, and a crushable pad is provided on the top of the grip for impact energy absorbing purposes.

Text-based plagiarism in scientific publishing: issues, developments and education.

PubMed

Li, Yongyan

2013-09-01

Text-based plagiarism, or copying language from sources, has recently become an issue of growing concern in scientific publishing. Use of CrossCheck (a computational text-matching tool) by journals has sometimes exposed an unexpected amount of textual similarity between submissions and databases of scholarly literature. In this paper I provide an overview of the relevant literature, to examine how journal gatekeepers perceive textual appropriation, and how automated plagiarism-screening tools have been developed to detect text matching, with the technique now available for self-check of manuscripts before submission; I also discuss issues around English as an additional language (EAL) authors and in particular EAL novices being the typical offenders of textual borrowing. The final section of the paper proposes a few educational directions to take in tackling text-based plagiarism, highlighting the roles of the publishing industry, senior authors and English for academic purposes professionals.

Probing the Interaction between Cyclic ADTC1 Ac-CADTPPVC-NH2) Peptide with EC1-EC2 domain of E-cadherin using Molecular Docking Approach

NASA Astrophysics Data System (ADS)

Siahaan, P.; Wuning, S.; Manna, A.; Prasasty, V. D.; Hudiyanti, D.

2018-04-01

Deeply understanding that intermolecular interaction between molecules on the paracellular pathway has given insight to its microscopic and macroscopic properties. In the paracellular pathway, synthetic cyclic ADTC1 (Ac-CADTPPVC-NH2) peptide has been studied to modulate EC1-EC2 domain, computationally using molecular docking method. The aim of this research is to probe the effect of amino acid alanine (A) of ADTC1 on its interaction properties. The study carried out in two steps: 1. the optimization using GROMACS v4.6.5 program and; 2. Determination of the interaction properties using AutoDock 4.2 program. The interaction was done for A-J box, and the best position of the binding site and binding energy on the OC and CC ADTC1 peptides against the EC1-EC2 domain of E-cadherin was selected. The result showed that the CC of the F box ADTC1 has the best interaction with binding energy of - 26.36 kJ/mol and its energy was lower than ADTC5 without alanine amino acid. ADTC1 interacted with EC1 of EC1-EC2 on Asp1, Trp2, Val3, Ile4, Ile24, Lys25, Ser26, Asn27, and Met92 residues.

Life prediction modeling based on cyclic damage accumulation

NASA Technical Reports Server (NTRS)

Nelson, Richard S.

1988-01-01

A high temperature, low cycle fatigue life prediction method was developed. This method, Cyclic Damage Accumulation (CDA), was developed for use in predicting the crack initiation lifetime of gas turbine engine materials, where initiation was defined as a 0.030 inch surface length crack. A principal engineering feature of the CDA method is the minimum data base required for implementation. Model constants can be evaluated through a few simple specimen tests such as monotonic loading and rapic cycle fatigue. The method was expanded to account for the effects on creep-fatigue life of complex loadings such as thermomechanical fatigue, hold periods, waveshapes, mean stresses, multiaxiality, cumulative damage, coatings, and environmental attack. A significant data base was generated on the behavior of the cast nickel-base superalloy B1900+Hf, including hundreds of specimen tests under such loading conditions. This information is being used to refine and extend the CDA life prediction model, which is now nearing completion. The model is also being verified using additional specimen tests on wrought INCO 718, and the final version of the model is expected to be adaptable to most any high-temperature alloy. The model is currently available in the form of equations and related constants. A proposed contract addition will make the model available in the near future in the form of a computer code to potential users.

EAL Teacher Agency: Implications for Participation in Professional Development

ERIC Educational Resources Information Center

Gurney, Laura; Liyanage, Indika

2016-01-01

Teachers construct their practice, education and professional development within two domains of professionalism: sponsored and independent. The association between these two domains, however, is complex; it is overlapping, inseparable and sometimes uneasy. The complexity is further exacerbated by the codependent nature of association between the…

Comparison of cyclic and impact-based reference point indentation measurements in human cadaveric tibia.

PubMed

Karim, Lamya; Van Vliet, Miranda; Bouxsein, Mary L

2018-01-01

Although low bone mineral density (BMD) is strongly associated with increased fracture risk, up to 50% of those who suffer fractures are not detected as high-risk patients by BMD testing. Thus, new approaches may improve identification of those at increased risk for fracture by in vivo assessment of altered bone tissue properties, which may contribute to skeletal fragility. Recently developed reference point indentation (RPI) allows for assessment of cortical bone indentation properties in vivo using devices that apply cyclic loading or impact loading, but there is little information available to assist with interpretation of RPI measurements. Our goals were to use human cadaveric tibia to determine: 1) the associations between RPI variables, cortical bone density, and morphology; 2) the association between variables obtained from RPI systems using cyclic, slow loading versus a single impact load; and 3) age-related differences in RPI variables. We obtained 20 human tibia and femur pairs from female donors (53-97years), measured total hip BMD using dual-energy X-ray absorptiometry, assessed tibial cortical microarchitecture using high-resolution peripheral quantitative computed tomography (HR-pQCT), and assessed cortical bone indentation properties at the mid-tibial diaphysis using both the cyclic and impact-based RPI systems (Biodent and Osteoprobe, respectively, Active Life Scientific, Santa Barbara, CA). We found a few weak associations between RPI variables, BMD, and cortical geometry; a few weak associations between measurements obtained by the two RPI systems; and no age-related differences in RPI variables. Our findings indicate that in cadaveric tibia from older women RPI measurements are largely independent of age, femoral BMD, and cortical geometry. Furthermore, measurements from the cyclic and impact loading RPI devices are weakly related to each other, indicating that each device reflects different aspects of cortical bone indentation properties

A fictitious domain method for lithosphere-asthenosphere interaction: Application to periodic slab folding in the upper mantle

NASA Astrophysics Data System (ADS)

Cerpa, Nestor G.; Hassani, Riad; Gerbault, Muriel; Prévost, Jean-Herve

2014-05-01

We present a new approach for the lithosphere-asthenosphere interaction in subduction zones. The lithosphere is modeled as a Maxwell viscoelastic body sinking in the viscous asthenosphere. Both domains are discretized by the finite element method, and we use a staggered coupling method. The interaction is provided by a nonmatching interface method called the fictitious domain method. We describe a simplified formulation of this numerical technique and present 2-D examples and benchmarks. We aim at studying the effect of mantle viscosity on the cyclicity of slab folding at the 660 km depth transition zone. Such cyclicity has previously been shown to occur depending on the kinematics of both the overriding and subducting plates, in analog and numerical models that approximate the 660 km depth transition zone as an impenetrable barrier. Here we applied far-field plate velocities corresponding to those of the South-American and Nazca plates at present. Our models show that the viscosity of the asthenosphere impacts on folding cyclicity and consequently on the slab's dip as well as the stress regime of the overriding plate. Values of the mantle viscosity between 3 and 5 × 1020 Pa s are found to produce cycles similar to those reported for the Andes, which are of the order of 30-40 Myr (based on magmatism and sedimentological records). Moreover, we discuss the episodic development of horizontal subduction induced by cyclic folding and, hence, propose a new explanation for episodes of flat subduction under the South-American plate.

Mother and child characteristics at birth and early age leukemia: a case-cohort population-based study.

PubMed

Reis, Rejane de Souza; Silva, Neimar de Paula; Santos, Marceli de Oliveira; Oliveira, Julio Fernando Pinto; Thuler, Luiz Claudio Santos; de Camargo, Beatriz; Pombo-de-Oliveira, Maria S

The population-based cancer registries (PBCR) and the Information System on Live Births in Brazil (Sistema de Informações sobre Nascidos Vivos [SINASC]) have information that enables the test for risk factors associated with leukemia at an early age. The aim of this study was to identify maternal and birth characteristics associated with early-age acute leukemia (EAL) in Brazil. A case-cohort study was performed using secondary dataset information of PBCR and SINASC. The risk association variables were grouped into (i) characteristics of the child at birth and (ii) characteristics of maternal exposure during pregnancy. The case-control ratio was 1:4. Linkage was performed using R software; odds ratio (OR) and 95% confidence interval (CI) were calculated by logistic regression models. EAL was associated with maternal occupational exposure to chemicals (agricultural, chemical, and petrochemical industry; adjOR: 2.18, 95% CI: 1.16-4.10) and with birth defects (adjOR: 3.62, 95% CI: 1.19-11.00). The results of this study, with the identification of EAL risk factors in population-based case-cohort study, strengthen the knowledge and improve databases, contributing to investigations on risk factors associated with childhood leukemia worldwide. Copyright © 2017 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Cyclic variation of ultrasonic backscattering from porcine whole blood under pulsatile flow

NASA Astrophysics Data System (ADS)

Lin, Yu-Hong

1997-10-01

The cyclic variation of ultrasonic backscattering from blood under pulsatile flow is believed to be related to the change of aggregation state of red cells and is only observed in whole blood. This study was to investigate the phenomenon by an invasive approach which was performed by inserting a 10 MHz catheter mounted transducer into a vessel. For ultrasonic measurement from blood, the most fundamental scheme is the hematocrit dependence. The backscatter maximum location was changed as the blood was stirred or stationary, as well as under steady laminar or turbulent flows. The same trend was also observed under pulsatile flow with 10% to 50% hematocrits in this study, as the backscattering to hematocrit curves were plotted at different times during a flow cycle. When the cyclic variation at 20 beats per minute (BPM) was interpreted in time domain, the enhanced aggregation at the beginning of shearing was observed. At 20 BPM with 40% hematocrit, the amplitude of cyclic variation was reduced when the shear rate was increased and the threshold of 150 s-1 was estimated. The results showed that there was no cyclic variation at 60 BPM. The backscattering was also plotted against the mean flow velocity, which demonstrated the hysteresis loops. The ultrasonic measurements showed that the relationship between the forward and backward paths of the loops were altered as beat rate, hematocrit, and shear rate were varied. Since the pulsatile flow was very complicated, a computational fluid dynamics package, FIDAPTM, was used to compute the shear rate based on the Power Law Model for non-Newtonian fluid viscosity. The non- Newtonian index and consistency in the model were computed from the viscosity to shear rate curves at 10% to 50% hematocrits measured by a cone-plate viscometer. For in vivo measurements, small pigs were used as models. Ultrasonic backscattering measurements were performed in the arteries and veins. The effect of stenosis was also investigated at the site

The mycotoxin definition reconsidered towards fungal cyclic depsipeptides.

PubMed

Taevernier, Lien; Wynendaele, Evelien; De Vreese, Leen; Burvenich, Christian; De Spiegeleer, Bart

2016-04-02

Currently, next to the major classes, cyclic depsipeptides beauvericin and enniatins are also positioned as mycotoxins. However, as there are hundreds more fungal cyclic depsipeptides already identified, should these not be considered as mycotoxins as well? The current status of the mycotoxin definition revealed a lack of consistency, leading to confusion about what compounds should be called mycotoxins. Because this is of pivotal importance in risk assessment prioritization, a clear and quantitatively expressed mycotoxin definition is proposed, based on data of widely accepted mycotoxins. Finally, this definition is applied to a set of fungal cyclic depsipeptides, revealing that some of these should indeed be considered as mycotoxins.

Genetics Home Reference: cyclic neutropenia

MedlinePlus

... Facebook Twitter Home Health Conditions Cyclic neutropenia Cyclic neutropenia Printable PDF Open All Close All Enable Javascript to view the expand/collapse boxes. Description Cyclic neutropenia is a disorder that causes frequent infections and ...

Involvement of oxidative and nitrosative stress in promoting retinal vasculitis in patients with Eales' disease.

PubMed

Rajesh, Mohanraj; Sulochana, Konerirajapuram N; Punitham, Ranganathan; Biswas, Jyotirmay; Lakshmi, Soundarajan; Ramakrishnan, Sivaramakrishnan

2003-07-01

Eales' disease (ED) is an idiopathic retinal vasculitis condition, which affects retina of young adult males. The histopathological hallmark in ED is the adhesion of leukocytes to the endothelium and the infiltration of these cells into the retinal parenchyma. Phagocyte generated free radicals have been implicated in mediating tissue damage associated with various inflammatory vasculopathies. In the present study, we have investigated the possible role of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in causing retinal tissue damage in ED. 35 patients with ED and 20 healthy control subjects were included in the study. Monocytes (MC) were separated from peripheral blood of the respective study participants. Inducible nitric oxide synthase (iNOS) protein expression was assessed using Western blot and 3 nitrotyrosine (3NTYR) by reversed phase high performance liquid chromatography (RP HPLC). Thiobarbituric acid reactive substances (TBARS) were determined by measuring malondialdehyde (MDA) formed. Superoxide dismutase (SOD) activity was assayed based on the ability of SOD to inhibit auto-oxidation of epinephrine. Iron, copper and zinc content were determined using Atomic Absorption Spectrophotometer. Immunolocalization of iNOS and 3NTYR was performed on the surgically excised epiretinal membranes (ERM) from patients with ED. There was a significant increase in the expression of iNOS, as well as 3NTYR accumulation, diminished SOD activity, elevated lipid peroxides, iron, copper and decreased zinc content in the MC of patients with ED when compared with healthy control subjects. The elevated levels of ROS and RNS products correlated with diminished antioxidant status in patients with ED. Strong immunoreactivity for iNOS and 3NTYR was observed in inflammatory cells and endothelial cells in ERM obtained from patients with ED. Our findings from this study clearly reveal the involvement of RNS and ROS in the development of retinal vasculitis in ED. Based

XML Based Markup Languages for Specific Domains

NASA Astrophysics Data System (ADS)

Varde, Aparna; Rundensteiner, Elke; Fahrenholz, Sally

A challenging area in web based support systems is the study of human activities in connection with the web, especially with reference to certain domains. This includes capturing human reasoning in information retrieval, facilitating the exchange of domain-specific knowledge through a common platform and developing tools for the analysis of data on the web from a domain expert's angle. Among the techniques and standards related to such work, we have XML, the eXtensible Markup Language. This serves as a medium of communication for storing and publishing textual, numeric and other forms of data seamlessly. XML tag sets are such that they preserve semantics and simplify the understanding of stored information by users. Often domain-specific markup languages are designed using XML, with a user-centric perspective. Standardization bodies and research communities may extend these to include additional semantics of areas within and related to the domain. This chapter outlines the issues to be considered in developing domain-specific markup languages: the motivation for development, the semantic considerations, the syntactic constraints and other relevant aspects, especially taking into account human factors. Illustrating examples are provided from domains such as Medicine, Finance and Materials Science. Particular emphasis in these examples is on the Materials Markup Language MatML and the semantics of one of its areas, namely, the Heat Treating of Materials. The focus of this chapter, however, is not the design of one particular language but rather the generic issues concerning the development of domain-specific markup languages.

Ultra-broadband THz time-domain spectroscopy of common polymers using THz air photonics.

PubMed

D'Angelo, Francesco; Mics, Zoltán; Bonn, Mischa; Turchinovich, Dmitry

2014-05-19

Terahertz-range dielectric properties of the common polymers low-density polyethylene (LDPE), cyclic olefin/ethylene copolymer (TOPAS®), polyamide-6 (PA6), and polytetrafluoroethylene (PTFE or Teflon®) are characterized in the ultra-broadband frequency window 2-15 THz, using a THz time-domain spectrometer employing air-photonics for the generation and detection of single-cycle sub-50 fs THz transients. The time domain measurements provide direct access to both the absorption and refractive index spectra. The polymers LDPE and TOPAS® demonstrate negligible absorption and spectrally-flat refractive index across the entire spectroscopy window, revealing the high potential of these polymers for applications in THz photonics such as ultra-broadband polymer-based dielectric mirrors, waveguides, and fibers. Resonant high-frequency polar vibrational modes are observed and assigned in polymers PA6 and PTFE, and their dielectric functions in the complete frequency window 2-15 THz are theoretically reproduced. Our results demonstrate the potential of ultra-broadband air-photonics-based THz time domain spectroscopy as a valuable analytic tool for materials science.

A Fast, Efficient Domain Adaptation Technique for Cross-Domain Electroencephalography(EEG)-Based Emotion Recognition.

PubMed

Chai, Xin; Wang, Qisong; Zhao, Yongping; Li, Yongqiang; Liu, Dan; Liu, Xin; Bai, Ou

2017-05-03

Electroencephalography (EEG)-based emotion recognition is an important element in psychiatric health diagnosis for patients. However, the underlying EEG sensor signals are always non-stationary if they are sampled from different experimental sessions or subjects. This results in the deterioration of the classification performance. Domain adaptation methods offer an effective way to reduce the discrepancy of marginal distribution. However, for EEG sensor signals, both marginal and conditional distributions may be mismatched. In addition, the existing domain adaptation strategies always require a high level of additional computation. To address this problem, a novel strategy named adaptive subspace feature matching (ASFM) is proposed in this paper in order to integrate both the marginal and conditional distributions within a unified framework (without any labeled samples from target subjects). Specifically, we develop a linear transformation function which matches the marginal distributions of the source and target subspaces without a regularization term. This significantly decreases the time complexity of our domain adaptation procedure. As a result, both marginal and conditional distribution discrepancies between the source domain and unlabeled target domain can be reduced, and logistic regression (LR) can be applied to the new source domain in order to train a classifier for use in the target domain, since the aligned source domain follows a distribution which is similar to that of the target domain. We compare our ASFM method with six typical approaches using a public EEG dataset with three affective states: positive, neutral, and negative. Both offline and online evaluations were performed. The subject-to-subject offline experimental results demonstrate that our component achieves a mean accuracy and standard deviation of 80.46% and 6.84%, respectively, as compared with a state-of-the-art method, the subspace alignment auto-encoder (SAAE), which achieves values

An Exemplar-Based Multi-View Domain Generalization Framework for Visual Recognition.

PubMed

Niu, Li; Li, Wen; Xu, Dong; Cai, Jianfei

2018-02-01

In this paper, we propose a new exemplar-based multi-view domain generalization (EMVDG) framework for visual recognition by learning robust classifier that are able to generalize well to arbitrary target domain based on the training samples with multiple types of features (i.e., multi-view features). In this framework, we aim to address two issues simultaneously. First, the distribution of training samples (i.e., the source domain) is often considerably different from that of testing samples (i.e., the target domain), so the performance of the classifiers learnt on the source domain may drop significantly on the target domain. Moreover, the testing data are often unseen during the training procedure. Second, when the training data are associated with multi-view features, the recognition performance can be further improved by exploiting the relation among multiple types of features. To address the first issue, considering that it has been shown that fusing multiple SVM classifiers can enhance the domain generalization ability, we build our EMVDG framework upon exemplar SVMs (ESVMs), in which a set of ESVM classifiers are learnt with each one trained based on one positive training sample and all the negative training samples. When the source domain contains multiple latent domains, the learnt ESVM classifiers are expected to be grouped into multiple clusters. To address the second issue, we propose two approaches under the EMVDG framework based on the consensus principle and the complementary principle, respectively. Specifically, we propose an EMVDG_CO method by adding a co-regularizer to enforce the cluster structures of ESVM classifiers on different views to be consistent based on the consensus principle. Inspired by multiple kernel learning, we also propose another EMVDG_MK method by fusing the ESVM classifiers from different views based on the complementary principle. In addition, we further extend our EMVDG framework to exemplar-based multi-view domain

Affordable Cyclic Voltammetry

ERIC Educational Resources Information Center

Stewart, Greg; Kuntzleman, Thomas S.; Amend, John R.; Collins, Michael J.

2009-01-01

Cyclic voltammetry is an important component of the undergraduate chemical curriculum. Unfortunately, undergraduate students rarely have the opportunity to conduct experiments in cyclic voltammetry owing to the high cost of potentiostats, which are required to control these experiments. By using MicroLab data acquisition interfaces in conjunction…

Solution structure of the catalytic domain of RICH protein from goldfish.

PubMed

Kozlov, Guennadi; Denisov, Alexey Y; Pomerantseva, Ekaterina; Gravel, Michel; Braun, Peter E; Gehring, Kalle

2007-03-01

Regeneration-induced CNPase homolog (RICH) is an axonal growth-associated protein, which is induced in teleost fish upon optical nerve injury. RICH consists of a highly acidic N-terminal domain, a catalytic domain with 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) activity and a C-terminal isoprenylation site. In vitro RICH and mammalian brain CNPase specifically catalyze the hydrolysis of 2',3'-cyclic nucleotides to produce 2'-nucleotides, but the physiologically relevant in vivo substrate remains unknown. Here, we report the NMR structure of the catalytic domain of goldfish RICH and describe its binding to CNPase inhibitors. The structure consists of a twisted nine-stranded antiparallel beta-sheet surrounded by alpha-helices on both sides. Despite significant local differences mostly arising from a seven-residue insert in the RICH sequence, the active site region is highly similar to that of human CNPase. Likewise, refinement of the catalytic domain of rat CNPase using residual dipolar couplings gave improved agreement with the published crystal structure. NMR titrations of RICH with inhibitors point to a similar catalytic mechanism for RICH and CNPase. The results suggest a functional importance for the evolutionarily conserved phosphodiesterase activity and hint of a link with pre-tRNA splicing.

A cyclic peptide derived from alpha-fetoprotein inhibits the proliferative effects of the epidermal growth factor and estradiol in MCF7 cells.

PubMed

Torres, Cristian; Antileo, Elmer; Epuñán, Maráa José; Pino, Ana María; Valladares, Luis Emilio; Sierralta, Walter Daniel

2008-06-01

A cyclic peptide derived from the active domain of alpha-fetoprotein (AFP) significantly inhibited the proliferation of MCF7 cells stimulated with the epidermal growth factor (EGF) or estradiol (E2). The action of these three agents on cell growth was independent of the presence of calf serum in the culture medium. Our results demonstrated that the cyclic peptide interfered markedly with the regulation of MAPK by activated c-erbB2. The cyclic peptide showed no effect on the E2-stimulated release of matrix metalloproteinases 2 and 9 nor on the shedding of heparin-binding EGF into the culture medium. We propose that the AFP-derived cyclic peptide represents a valuable novel antiproliferative agent for treating breast cancer.

A micromechanical constitutive model for anisotropic cyclic deformation of super-elastic NiTi shape memory alloy single crystals

NASA Astrophysics Data System (ADS)

Yu, Chao; Kang, Guozheng; Kan, Qianhua

2015-09-01

Based on the experimental observations on the anisotropic cyclic deformation of super-elastic NiTi shape memory alloy single crystals done by Gall and Maier (2002), a crystal plasticity based micromechanical constitutive model is constructed to describe such anisotropic cyclic deformation. To model the internal stress caused by the unmatched inelastic deformation between the austenite and martensite phases on the plastic deformation of austenite phase, 24 induced martensite variants are assumed to be ellipsoidal inclusions with anisotropic elasticity and embedded in the austenite matrix. The homogeneous stress fields in the austenite matrix and each induced martensite variant are obtained by using the Mori-Tanaka homogenization method. Two different inelastic mechanisms, i.e., martensite transformation and transformation-induced plasticity, and their interactions are considered in the proposed model. Following the assumption of instantaneous domain growth (Cherkaoui et al., 1998), the Helmholtz free energy of a representative volume element of a NiTi shape memory single crystal is established and the thermodynamic driving forces of the internal variables are obtained from the dissipative inequalities. The capability of the proposed model to describe the anisotropic cyclic deformation of super-elastic NiTi single crystals is first verified by comparing the predicted results with the experimental ones. It is concluded that the proposed model can capture the main quantitative features observed in the experiments. And then, the proposed model is further used to predict the uniaxial and multiaxial transformation ratchetting of a NiTi single crystal.

Cyclic Nucleotide Monophosphates in Plants and Plant Signaling.

PubMed

Marondedze, Claudius; Wong, Aloysius; Thomas, Ludivine; Irving, Helen; Gehring, Chris

2017-01-01

Cyclic nucleotide monophosphates (cNMPs) and the enzymes that can generate them are of increasing interest in the plant sciences. Arguably, the major recent advance came with the release of the complete Arabidopsis thaliana genome that has enabled the systematic search for adenylate (ACs) or guanylate cyclases (GCs) and did eventually lead to the discovery of a number of GCs in higher plants. Many of these proteins have complex domain architectures with AC or GC centers moonlighting within cytosolic kinase domains. Recent reports indicated the presence of not just the canonical cNMPs (i.e., cAMP and cGMP), but also the noncanonical cCMP, cUMP, cIMP, and cdTMP in plant tissues, and this raises several questions. Firstly, what are the functions of these cNMPs, and, secondly, which enzymes can convert the substrate triphosphates into the respective noncanonical cNMPs? The first question is addressed here by comparing the reactive oxygen species (ROS) response of cAMP and cGMP to that elicited by the noncanonical cCMP or cIMP. The results show that particularly cIMP can induce significant ROS production. To answer, at least in part, the second question, we have evaluated homology models of experimentally confirmed plant GCs probing the substrate specificity by molecular docking simulations to determine if they can conceivably catalytically convert substrates other than ATP or GTP. In summary, molecular modeling and substrate docking simulations can contribute to the evaluation of cyclases for noncanonical cyclic mononucleotides and thereby further our understanding of the molecular mechanism that underlie cNMP-dependent signaling in planta.

Poly(ethylene glycol)-grafted cyclic acetals based polymer networks with non-water-swellable, biodegradable and surface hydrophilic properties.

PubMed

Yin, Ruixue; Zhang, Nan; Wu, Wentao; Wang, Kemin

2016-05-01

Cyclic acetals based biomaterial without acidic products during hydrolytic degradation is a promising candidate for tissue engineering applications; however, low hydrophilicity is still one limitation for its biomedical application. In this work, we aim to achieve non-water-swellable cyclic acetal networks with improved hydrophilicity and surface wettability by copolymerization of cyclic acetal units based monomer, 5-ethyl-5-(hydroxymethyl)-β,β-dimethyl-1, 3-dioxane-2-ethanol diacrylate (EHD) and methoxy poly(ethylene glycol) monoacrylate (mPEGA) under UV irradiation, to avoid swelling of conventional hydrogels which could limit their applicability in particular of the mechanical properties and geometry integrity. Various EHD/mPEGA networks were fabricated with different concentrations of mPEGA from 0 to 30%, and the results showed photopolymerization behavior, mechanical property and thermal stability could not be significantly affected by addition of mPEGA, while the surface hydrophilicity was dramatically improved with the increase of mPEGA and could achieve a water contact angle of 37° with 30% mPEGA concentration. The obtained EHD/mPEGA network had comparative degradation rate to the PECA hydrogels reported previously, and MTT assay indicated it was biocompatible to L929 cells. Copyright © 2016 Elsevier B.V. All rights reserved.

PETO Interacts with Other Effectors of Cyclic Electron Flow in Chlamydomonas.

PubMed

Takahashi, Hiroko; Schmollinger, Stefan; Lee, Jae-Hyeok; Schroda, Michael; Rappaport, Fabrice; Wollman, Francis-André; Vallon, Olivier

2016-04-04

While photosynthetic linear electron flow produces both ATP and NADPH, cyclic electron flow (CEF) around photosystem I (PSI) and cytochrome b6f generates only ATP. CEF is thus essential to balance the supply of ATP and NADPH for carbon fixation; however, it remains unclear how the system tunes the relative levels of linear and cyclic flow. Here, we show that PETO, a transmembrane thylakoid phosphoprotein specific of green algae, contributes to the stimulation of CEF when cells are placed in anoxia. In oxic conditions, PETO co-fractionates with other thylakoid proteins involved in CEF (ANR1, PGRL1, FNR). In PETO-knockdown strains, interactions between these CEF proteins are affected. Anoxia triggers a reorganization of the membrane, so that a subpopulation of PSI and cytochrome b6f now co-fractionates with the CEF effectors in sucrose gradients. The absence of PETO impairs this reorganization. Affinity purification identifies ANR1 as a major interactant of PETO. ANR1 contains two ANR domains, which are also found in the N-terminal region of NdhS, the ferredoxin-binding subunit of the plant ferredoxin-plastoquinone oxidoreductase (NDH). We propose that the ANR domain was co-opted by two unrelated CEF systems (PGR and NDH), possibly as a sensor of the redox state of the membrane. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

A Fast, Efficient Domain Adaptation Technique for Cross-Domain Electroencephalography(EEG)-Based Emotion Recognition

PubMed Central

Chai, Xin; Wang, Qisong; Zhao, Yongping; Li, Yongqiang; Liu, Dan; Liu, Xin; Bai, Ou

2017-01-01

Electroencephalography (EEG)-based emotion recognition is an important element in psychiatric health diagnosis for patients. However, the underlying EEG sensor signals are always non-stationary if they are sampled from different experimental sessions or subjects. This results in the deterioration of the classification performance. Domain adaptation methods offer an effective way to reduce the discrepancy of marginal distribution. However, for EEG sensor signals, both marginal and conditional distributions may be mismatched. In addition, the existing domain adaptation strategies always require a high level of additional computation. To address this problem, a novel strategy named adaptive subspace feature matching (ASFM) is proposed in this paper in order to integrate both the marginal and conditional distributions within a unified framework (without any labeled samples from target subjects). Specifically, we develop a linear transformation function which matches the marginal distributions of the source and target subspaces without a regularization term. This significantly decreases the time complexity of our domain adaptation procedure. As a result, both marginal and conditional distribution discrepancies between the source domain and unlabeled target domain can be reduced, and logistic regression (LR) can be applied to the new source domain in order to train a classifier for use in the target domain, since the aligned source domain follows a distribution which is similar to that of the target domain. We compare our ASFM method with six typical approaches using a public EEG dataset with three affective states: positive, neutral, and negative. Both offline and online evaluations were performed. The subject-to-subject offline experimental results demonstrate that our component achieves a mean accuracy and standard deviation of 80.46% and 6.84%, respectively, as compared with a state-of-the-art method, the subspace alignment auto-encoder (SAAE), which achieves values

Wavelet-based 3-D inversion for frequency-domain airborne EM data

NASA Astrophysics Data System (ADS)

Liu, Yunhe; Farquharson, Colin G.; Yin, Changchun; Baranwal, Vikas C.

2018-04-01

In this paper, we propose a new wavelet-based 3-D inversion method for frequency-domain airborne electromagnetic (FDAEM) data. Instead of inverting the model in the space domain using a smoothing constraint, this new method recovers the model in the wavelet domain based on a sparsity constraint. In the wavelet domain, the model is represented by two types of coefficients, which contain both large- and fine-scale informations of the model, meaning the wavelet-domain inversion has inherent multiresolution. In order to accomplish a sparsity constraint, we minimize an L1-norm measure in the wavelet domain that mostly gives a sparse solution. The final inversion system is solved by an iteratively reweighted least-squares method. We investigate different orders of Daubechies wavelets to accomplish our inversion algorithm, and test them on synthetic frequency-domain AEM data set. The results show that higher order wavelets having larger vanishing moments and regularity can deliver a more stable inversion process and give better local resolution, while the lower order wavelets are simpler and less smooth, and thus capable of recovering sharp discontinuities if the model is simple. At last, we test this new inversion algorithm on a frequency-domain helicopter EM (HEM) field data set acquired in Byneset, Norway. Wavelet-based 3-D inversion of HEM data is compared to L2-norm-based 3-D inversion's result to further investigate the features of the new method.

Spatial games with cyclic interactions: the response of empty sites

NASA Astrophysics Data System (ADS)

Brown, Bart; Pleimling, Michel

2015-03-01

Predator-prey models of the May-Leonard family employ empty sites in a spatial setting as an intermediate step in the reproduction process. This requirement makes the number and arrangement of empty sites important to the formation of space-time patterns. We study the density of empty sites in a stochastic predator-prey model in which the species compete in a cyclic way in two dimensions. In some cases systems of this type quickly form domains of neutral species after which all predation, and therefore, reproduction occur near the interface of competing domains. Using Monte Carlo simulations we investigate the relationship of this density of empty sites to the time-dependent domain length. We further explore the dynamics by introducing perturbations to the interaction rates of the system after which we measure the perturbed density, i.e. the response of empty sites, as the system relaxes. A dynamical scaling behavior is observed in the response of empty sites. This work is supported by the US National Science Foundation through Grant DMR-1205309.

Cyclic nucleotide content of tobacco BY-2 cells.

PubMed

Richards, Helen; Das, Swadipa; Smith, Christopher J; Pereira, Louisa; Geisbrecht, Alan; Devitt, Nicola J; Games, David E; van Geyschem, Jan; Gareth Brenton, A; Newton, Russell P

2002-11-01

The cyclic nucleotide content of cultured tobacco bright yellow-2 (BY-2) cells was determined, after freeze-killing, perchlorate extraction and sequential chromatography, by radioimmunoassay. The identities of the putative cyclic nucleotides, adenosine 3',5'-cyclic monophosphate (cyclic AMP), guanosine 3',5'-cyclic monophosphate (cyclic GMP) and cytidine 3',5'-cyclic monophosphate (cyclic CMP) were unambiguously confirmed by tandem mass spectrometry. The potential of BY-2 cell cultures as a model system for future investigations of cyclic nucleotide function in higher plants is discussed.

Study on stress-strain response of multi-phase TRIP steel under cyclic loading

NASA Astrophysics Data System (ADS)

Dan, W. J.; Hu, Z. G.; Zhang, W. G.; Li, S. H.; Lin, Z. Q.

2013-12-01

The stress-strain response of multi-phase TRIP590 sheet steel is studied in cyclic loading condition at room temperature based on a cyclic phase transformation model and a multi-phase mixed kinematic hardening model. The cyclic martensite transformation model is proposed based on the shear-band intersection, where the repeat number, strain amplitude and cyclic frequency are used to control the phase transformation process. The multi-phase mixed kinematic hardening model is developed based on the non-linear kinematic hardening rule of per-phase. The parameters of transformation model are identified with the relationship between the austenite volume fraction and the repeat number. The parameters in Kinematic hardening model are confirmed by the experimental hysteresis loops in different strain amplitude conditions. The responses of hysteresis loop and stress amplitude are evaluated by tension-compression data.

3D DDD modelling of dislocation-precipitate interaction in a nickel-based single crystal superalloy under cyclic deformation

NASA Astrophysics Data System (ADS)

Lin, Bing; Huang, Minsheng; Zhao, Liguo; Roy, Anish; Silberschmidt, Vadim; Barnard, Nick; Whittaker, Mark; McColvin, Gordon

2018-06-01

Strain-controlled cyclic deformation of a nickel-based single crystal superalloy has been modelled using three-dimensional (3D) discrete dislocation dynamics (DDD) for both [0 0 1] and [1 1 1] orientations. The work focused on the interaction between dislocations and precipitates during cyclic plastic deformation at elevated temperature, which has not been well studied yet. A representative volume element with cubic γ‧-precipitates was chosen to represent the material, with enforced periodical boundary conditions. In particular, cutting of superdislocations into precipitates was simulated by a back-force method. The global cyclic stress-strain responses were captured well by the DDD model when compared to experimental data, particularly the effects of crystallographic orientation. Dislocation evolution showed that considerably high density of dislocations was produced for [1 1 1] orientation when compared to [0 0 1] orientation. Cutting of dislocations into the precipitates had a significant effect on the plastic deformation, leading to material softening. Contour plots of in-plane shear strain proved the development of heterogeneous strain field, resulting in the formation of shear-band embryos.

Conformational rearrangements in the transmembrane domain of CNGA1 channels revealed by single-molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Maity, Sourav; Mazzolini, Monica; Arcangeletti, Manuel; Valbuena, Alejandro; Fabris, Paolo; Lazzarino, Marco; Torre, Vincent

2015-05-01

Cyclic nucleotide-gated (CNG) channels are activated by binding of cyclic nucleotides. Although structural studies have identified the channel pore and selectivity filter, conformation changes associated with gating remain poorly understood. Here we combine single-molecule force spectroscopy (SMFS) with mutagenesis, bioinformatics and electrophysiology to study conformational changes associated with gating. By expressing functional channels with SMFS fingerprints in Xenopus laevis oocytes, we were able to investigate gating of CNGA1 in a physiological-like membrane. Force spectra determined that the S4 transmembrane domain is mechanically coupled to S5 in the closed state, but S3 in the open state. We also show there are multiple pathways for the unfolding of the transmembrane domains, probably caused by a different degree of α-helix folding. This approach demonstrates that CNG transmembrane domains have dynamic structure and establishes SMFS as a tool for probing conformational change in ion channels.

Up-regulation of Hyperpolarization-activated Cyclic Nucleotide-gated Channel 3 (HCN3) by Specific Interaction with K+ Channel Tetramerization Domain-containing Protein 3 (KCTD3)*

PubMed Central

Cao-Ehlker, Xiaochun; Zong, Xiangang; Hammelmann, Verena; Gruner, Christian; Fenske, Stefanie; Michalakis, Stylianos; Wahl-Schott, Christian; Biel, Martin

2013-01-01

Most ion channels consist of the principal ion-permeating core subunit(s) and accessory proteins that are assembled with the channel core. The biological functions of the latter proteins are diverse and include the regulation of the biophysical properties of the ion channel, its connection to signaling pathways and the control of its cell surface expression. There is recent evidence that native hyperpolarization-activated cyclic nucleotide-gated channel complexes (HCN1–4) also contain accessory subunits, among which TRIP8b (tetratricopeptide repeat-containing Rab8b-interacting protein) has been most extensively studied. Here, we identify KCTD3, a so far uncharacterized member of the potassium channel tetramerization-domain containing (KCTD) protein family as an HCN3-interacting protein. KCTD3 is widely expressed in brain and some non-neuronal tissues and colocalizes with HCN3 in specific regions of the brain including hypothalamus. Within the HCN channel family, KCTD3 specifically binds to HCN3 and leads to a profound up-regulation of cell surface expression and current density of this channel. HCN3 can also functionally interact with TRIP8b; however, we found no evidence for channel complexes containing both TRIP8b and KCTD3. The C terminus of HCN3 is crucially required for functional interaction with KCTD3. Replacement of the cytosolic C terminus of HCN2 by the corresponding domain of HCN3 renders HCN2 sensitive to regulation by KCTD3. The C-terminal-half of KCTD3 is sufficient for binding to HCN3. However, the complete protein including the N-terminal tetramerization domain is needed for HCN3 current up-regulation. Together, our experiments indicate that KCTD3 is an accessory subunit of native HCN3 complexes. PMID:23382386

Smart-aggregate-based damage detection of fiber-reinforced-polymer-strengthened columns under reversed cyclic loading

NASA Astrophysics Data System (ADS)

Howser, Rachel; Moslehy, Yashar; Gu, Haichang; Dhonde, Hemant; Mo, Y. L.; Ayoub, Ashraf; Song, Gangbing

2011-07-01

Structural health monitoring is an important aspect of the maintenance of large civil infrastructures, especially for bridge columns in areas of high seismic activity. In this project, recently developed innovative piezoceramic-based sensors were utilized to perform the health monitoring of a shear-critical reinforced concrete (RC) bridge column subjected to reversed cyclic loading. After the column failed, it was wrapped with fiber reinforced polymer (FRP) sheets, commonly used to retrofit seismically damaged structures. The FRP-strengthened column was retested under the same reversed cyclic loading pattern. Innovative piezoceramic-based sensors, called 'smart aggregates', were utilized as transducers for health monitoring purposes. On the basis of the smart aggregates developed, an active-sensing approach and an impact-hammer-based approach were used to evaluate the health status of the RC column during the loading procedure. Wave transmission energy is attenuated by the existence of cracks during the loading procedure, and this attenuation phenomenon alters the curve of the transfer function between the actuator and sensor. To detect the damage occurrence and evaluate the damage severity, transfer function curves were compared with those obtained during the period of healthy status. A transfer-function-based damage index matrix was developed to demonstrate the damage severity at different locations. Experimental results verified the effectiveness of the smart aggregates in health monitoring of the FRP-strengthened column as well as the unstrengthened column. The experimental results show that the proposed smart-aggregate-based approach can successfully detect damage occurrence and evaluate its severity.

Three is much more than two in coarsening dynamics of cyclic competitions

NASA Astrophysics Data System (ADS)

Mitarai, Namiko; Gunnarson, Ivar; Pedersen, Buster Niels; Rosiek, Christian Anker; Sneppen, Kim

2016-04-01

The classical game of rock-paper-scissors has inspired experiments and spatial model systems that address the robustness of biological diversity. In particular, the game nicely illustrates that cyclic interactions allow multiple strategies to coexist for long-time intervals. When formulated in terms of a one-dimensional cellular automata, the spatial distribution of strategies exhibits coarsening with algebraically growing domain size over time, while the two-dimensional version allows domains to break and thereby opens the possibility for long-time coexistence. We consider a quasi-one-dimensional implementation of the cyclic competition, and study the long-term dynamics as a function of rare invasions between parallel linear ecosystems. We find that increasing the complexity from two to three parallel subsystems allows a transition from complete coarsening to an active steady state where the domain size stays finite. We further find that this transition happens irrespective of whether the update is done in parallel for all sites simultaneously or done randomly in sequential order. In both cases, the active state is characterized by localized bursts of dislocations, followed by longer periods of coarsening. In the case of the parallel dynamics, we find that there is another phase transition between the active steady state and the coarsening state within the three-line system when the invasion rate between the subsystems is varied. We identify the critical parameter for this transition and show that the density of active boundaries has critical exponents that are consistent with the directed percolation universality class. On the other hand, numerical simulations with the random sequential dynamics suggest that the system may exhibit an active steady state as long as the invasion rate is finite.

Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems

PubMed Central

Makarova, Kira S.; Wolf, Yuri I.

2017-01-01

ABSTRACT The two-component signal transduction (TCS) machinery is a key mechanism of sensing environmental changes in the prokaryotic world. TCS systems have been characterized thoroughly in bacteria but to a much lesser extent in archaea. Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data. We describe the domain architectures of the archaeal TCS components, including several novel output domains, and discuss the evolution of the archaeal TCS machinery. The distribution of TCS systems in archaea is strongly biased, with high levels of abundance in haloarchaea and thaumarchaea but none detected in the sequenced genomes from the phyla Crenarchaeota, Nanoarchaeota, and Korarchaeota. The archaeal sensor histidine kinases are generally similar to their well-studied bacterial counterparts but are often located in the cytoplasm and carry multiple PAS and/or GAF domains. In contrast, archaeal response regulators differ dramatically from the bacterial ones. Most archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. Instead, archaea encode multiple copies of response regulators containing either the stand-alone receiver (REC) domain or combinations of REC with PAS and/or GAF domains. Therefore, the prevailing mechanism of archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation. IMPORTANCE Although the Archaea represent a separate domain of life, their signaling systems have been assumed to be closely similar to the bacterial ones. A study of the domain architectures of the archaeal two-component signal transduction (TCS) machinery

Light-induced conformational changes of LOV1 (light oxygen voltage-sensing domain 1) and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin.

PubMed

Okajima, Koji; Aihara, Yusuke; Takayama, Yuki; Nakajima, Mihoko; Kashojiya, Sachiko; Hikima, Takaaki; Oroguchi, Tomotaka; Kobayashi, Amane; Sekiguchi, Yuki; Yamamoto, Masaki; Suzuki, Tomomi; Nagatani, Akira; Nakasako, Masayoshi; Tokutomi, Satoru

2014-01-03

Phototropin (phot), a blue light (BL) receptor in plants, has two photoreceptive domains named LOV1 and LOV2 as well as a Ser/Thr kinase domain (KD) and acts as a BL-regulated protein kinase. A LOV domain harbors a flavin mononucleotide that undergoes a cyclic photoreaction upon BL excitation via a signaling state in which the inhibition of the kinase activity by LOV2 is negated. To understand the molecular mechanism underlying the BL-dependent activation of the kinase, the photochemistry, kinase activity, and molecular structure were studied with the phot of Chlamydomonas reinhardtii. Full-length and LOV2-KD samples of C. reinhardtii phot showed cyclic photoreaction characteristics with the activation of LOV- and BL-dependent kinase. Truncation of LOV1 decreased the photosensitivity of the kinase activation, which was well explained by the fact that the signaling state lasted for a shorter period of time compared with that of the phot. Small angle x-ray scattering revealed monomeric forms of the proteins in solution and detected BL-dependent conformational changes, suggesting an extension of the global molecular shapes of both samples. Constructed molecular model of full-length phot based on the small angle x-ray scattering data proved the arrangement of LOV1, LOV2, and KD for the first time that showed a tandem arrangement both in the dark and under BL irradiation. The models suggest that LOV1 alters its position relative to LOV2-KD under BL irradiation. This finding demonstrates that LOV1 may interact with LOV2 and modify the photosensitivity of the kinase activation through alteration of the duration of the signaling state in LOV2.

Evaluation of the base/subgrade soil under repeated loading : phase II, in-box and ALF cyclic plate load tests.

DOT National Transportation Integrated Search

2012-03-01

This research study aims at evaluating the performance of base and subgrade soil in flexible pavements under repeated loading test conditions. For this purpose, an indoor cyclic plate load testing equipment was developed and used to conduct a series ...

Adjoint-based optimization of PDEs in moving domains

NASA Astrophysics Data System (ADS)

Protas, Bartosz; Liao, Wenyuan

2008-02-01

In this investigation we address the problem of adjoint-based optimization of PDE systems in moving domains. As an example we consider the one-dimensional heat equation with prescribed boundary temperatures and heat fluxes. We discuss two methods of deriving an adjoint system necessary to obtain a gradient of a cost functional. In the first approach we derive the adjoint system after mapping the problem to a fixed domain, whereas in the second approach we derive the adjoint directly in the moving domain by employing methods of the noncylindrical calculus. We show that the operations of transforming the system from a variable to a fixed domain and deriving the adjoint do not commute and that, while the gradient information contained in both systems is the same, the second approach results in an adjoint problem with a simpler structure which is therefore easier to implement numerically. This approach is then used to solve a moving boundary optimization problem for our model system.

A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP.

PubMed

Vigil, Dominico; Lin, Jung-Hsin; Sotriffer, Christoph A; Pennypacker, Juniper K; McCammon, J Andrew; Taylor, Susan S

2006-01-01

Cyclic AMP activates protein kinase A by binding to an inhibitory regulatory (R) subunit and releasing inhibition of the catalytic (C) subunit. Even though crystal structures of regulatory and catalytic subunits have been solved, the precise molecular mechanism by which cyclic AMP activates the kinase remains unknown. The dynamic properties of the cAMP binding domain in the absence of cAMP or C-subunit are also unknown. Here we report molecular-dynamics simulations and mutational studies of the RIalpha R-subunit that identify the C-helix as a highly dynamic switch which relays cAMP binding to the helical C-subunit binding regions. Furthermore, we identify an important salt bridge which links cAMP binding directly to the C-helix that is necessary for normal activation. Additional mutations show that a hydrophobic "hinge" region is not as critical for the cross-talk in PKA as it is in the homologous EPAC protein, illustrating how cAMP can control diverse functions using the evolutionarily conserved cAMP-binding domains.

Design, synthesis and biological evaluation of (S)-valine thiazole-derived cyclic and non-cyclic peptidomimetic oligomers as modulators of human P-glycoprotein (ABCB1)

PubMed Central

Singh, Satyakam; Prasad, Nagarajan Rajendra; Kapoor, Khyati; Chufan, Eduardo E.; Patel, Bhargav A.; Ambudkar, Suresh V.; Talele, Tanaji T.

2014-01-01

Multidrug resistance (MDR) caused by ATP-binding cassette (ABC) transporter P-glycoprotein (P-gp) through extrusion of anticancer drugs from the cells is a major cause of failure to cancer chemotherapy. Previously, selenazole containing cyclic peptides were reported as P-gp inhibitors and these were also used for co-crystallization with mouse P-gp, which has 87% homology to human P-gp. It has been reported that human P-gp, can simultaneously accommodate 2-3 moderate size molecules at the drug binding pocket. Our in-silico analysis based on the homology model of human P-gp spurred our efforts to investigate the optimal size of (S)-valine-derived thiazole units that can be accommodated at drug-binding pocket. Towards this goal, we synthesized varying lengths of linear and cyclic derivatives of (S)-valine-derived thiazole units to investigate the optimal size, lipophilicity and the structural form (linear and cyclic) of valine-derived thiazole peptides that can accommodate well in the P-gp binding pocket and affects its activity, previously an unexplored concept. Among these oligomers, lipophilic linear- (13) and cyclic-trimer (17) derivatives of QZ59S-SSS were found to be the most and equally potent inhibitors of human P-gp (IC50 = 1.5 μM). Cyclic trimer and linear trimer being equipotent, future studies can be focused on non-cyclic counterparts of cyclic peptides maintaining linear trimer length. Binding model of the linear trimer (13) within the drug-binding site on the homology model of human P-gp represents an opportunity for future optimization, specifically replacing valine and thiazole groups in the non-cyclic form. PMID:24288265

Cyclic Bis-porphyrin-Based Flexible Molecular Containers: Controlling Guest Arrangements and Supramolecular Catalysis by Tuning Cavity Size.

PubMed

Mondal, Pritam; Sarkar, Sabyasachi; Rath, Sankar Prasad

2017-05-23

Three cyclic zinc(II) bis-porphyrins (CB) with highly flexible linkers are employed as artificial molecular containers that efficiently encapsulate/coordinate various aromatic aldehydes within their cavities. Interestingly, the arrangements of guests and their reactivity inside the molecular clefts are significantly influenced by the cavity size of the cyclic containers. In the presence of polycyclic aromatic aldehydes, such as 3-formylperylene, as a guest, the cyclic bis-porphyrin host with a smaller cavity (CB1) forms a 1:1 sandwich complex. Upon slightly increasing the spacer length and thereby the cavity size, the cyclic host (CB2) encapsulates two molecules of 3-formylperylene that are also stacked together due to strong π-π interactions between them and CH-π interactions with the porphyrin rings. However, in the cyclic host (CB3) with an even larger cavity, two metal centers of the bis-porphyrin axially coordinate two molecules of 3-formylperylene within its cavity. Different arrangements of guest inside the cyclic bis-porphyrin hosts are investigated by using UV/Vis, ESI-MS, and 1 H NMR spectroscopy, along with X-ray structure determination of the host-guest complexes. Moreover, strong binding of guests within the cyclic bis-porphyrin hosts support the robust nature of the host-guest assemblies in solution. Such preferential binding of the bis-porphyrinic cavity towards aromatic aldehydes through encapsulation/coordination has been employed successfully to catalyze the Knoevenagel condensation of a series of polycyclic aldehydes with active methylene compounds (such as Meldrum's acid and 1, 3-dimethylbarbituric acid) under ambient conditions. Interestingly, the yields of the condensed products significantly increase upon increasing spacer lengths of the cyclic bis-porphyrins because more substrates can then be encapsulated within the cavity. Such controllable cavity size of the cyclic containers has profound implications for constructing highly

Mechanism of RNA 2′,3′-cyclic phosphate end healing by T4 polynucleotide kinase–phosphatase

PubMed Central

Das, Ushati; Shuman, Stewart

2013-01-01

T4 polynucleotide kinase–phosphatase (Pnkp) exemplifies a family of enzymes with 5′-kinase and 3′-phosphatase activities that function in nucleic acid repair. The polynucleotide 3′-phosphatase reaction is executed by the Pnkp C-terminal domain, which belongs to the DxDxT acylphosphatase superfamily. The 3′-phosphatase reaction entails formation and hydrolysis of a covalent enzyme-(Asp165)-phosphate intermediate, driven by general acid–base catalyst Asp167. We report that Pnkp also has RNA 2′-phosphatase activity that requires Asp165 and Asp167. The physiological substrate for Pnkp phosphatase is an RNA 2′,3′-cyclic phosphate end (RNA > p), but the pathway of cyclic phosphate removal and its enzymic requirements are undefined. Here we find that Pnkp reactivity with RNA > p requires Asp165, but not Asp167. Whereas wild-type Pnkp transforms RNA > p to RNAOH, mutant D167N converts RNA > p to RNA 3′-phosphate, which it sequesters in the phosphatase active site. In support of the intermediacy of an RNA phosphomonoester, the reaction of mutant S211A with RNA > p results in transient accumulation of RNAp en route to RNAOH. Our results suggest that healing of 2′,3′-cyclic phosphate ends is a four-step processive reaction: RNA > p + Pnkp → RNA-(3′-phosphoaspartyl)-Pnkp → RNA3′p + Pnkp → RNAOH + phosphoaspartyl-Pnkp → Pi + Pnkp. PMID:23118482

Biometric identification based on novel frequency domain facial asymmetry measures

NASA Astrophysics Data System (ADS)

Mitra, Sinjini; Savvides, Marios; Vijaya Kumar, B. V. K.

2005-03-01

In the modern world, the ever-growing need to ensure a system's security has spurred the growth of the newly emerging technology of biometric identification. The present paper introduces a novel set of facial biometrics based on quantified facial asymmetry measures in the frequency domain. In particular, we show that these biometrics work well for face images showing expression variations and have the potential to do so in presence of illumination variations as well. A comparison of the recognition rates with those obtained from spatial domain asymmetry measures based on raw intensity values suggests that the frequency domain representation is more robust to intra-personal distortions and is a novel approach for performing biometric identification. In addition, some feature analysis based on statistical methods comparing the asymmetry measures across different individuals and across different expressions is presented.

Pharmacological evaluation of a novel cyclic phosphatidic acid derivative 3-S-cyclic phosphatidic acid (3-S-cPA).

PubMed

Nozaki, Emi; Gotoh, Mari; Tanaka, Ryo; Kato, Masaru; Suzuki, Takahiro; Nakazaki, Atsuo; Hotta, Harumi; Kobayashi, Susumu; Murakami-Murofushi, Kimiko

2012-05-15

Cyclic phosphatidic acid (cPA) is a naturally occurring phospholipid mediator possessing cyclic phosphate ring, which is necessary for its specific biological activities. To stabilize cyclic phosphate ring of cPA, we synthesized a series of cPA derivatives. We have shown that racemic 3-S-cPA, with a phosphate oxygen atom replaced with a sulfur atom at the sn-3, was a more effective autotaxin (ATX) inhibitor than cPA. In this study, we showed that racemic 3-S-cPA also had potent biological activities such as inhibition of cancer cell migration, suppression of the nociceptive reflex, and attenuation of ischemia-induced delayed neuronal cell death in the hippocampal CA1. Moreover, we synthesized both enantiomers of palmitoleoyl derivative of 3-S-cPA, and found that the chirality of 3-S-cPA is not involved in ATX inhibition. Based on these findings, racemic 3-S-cPA is suggested as an effective therapeutic compound like cPA. Copyright © 2012 Elsevier Ltd. All rights reserved.

endodermal-amyloplast less 1 is a novel allele of SHORT-ROOT

NASA Astrophysics Data System (ADS)

Morita, Miyo T.; Saito, Chieko; Nakano, Akihiko; Tasaka, Masao

Plants can sense the direction of gravity and change the growth orientation of their organs. Arabidopsis mutants have been isolated and characterized in order to elucidate the molecular mechanisms of gravitropism. endodermal-amyloplast less 1 ( eal1) is a unique mutant that completely lacks gravitropism in inflorescence stems and exhibits reduced gravitropism in hypocotyls, whereas its roots showed normal gravitropism. Previously, it was suggested that differentiation or development of amyloplasts in shoot statocytes (endodermal cells) is affected by the eal1 mutation. Here, we have identified EAL1 as a SHORT-ROOT ( SHR) allele based on map position. Three nucleotides in the SHR coding region were deleted in the eal1 mutant, resulting in the deletion of just one amino acid. The protein encoded by the novel allele of SHR appears to have retained its function as a transcription factor since the endodermal cell layer was formed both in roots and in shoots of eal1. SCARECROW (SCR) promoter activity monitored by reporter protein expression was significantly decreased in eal1, suggesting that the activity of SHR lacking one amino acid is reduced. In addition, transcription levels of SHOOT GRAVITROPISM 5 (SGR5), which is mainly expressed in the endodermis of inflorescence stems, was markedly decreased. Together with the presence of abnormal endodermal amyloplasts in eal1, these results strongly suggest that the endodermis observed in eal1 is not sufficiently differentiated to execute shoot gravitropism.

Synthesis and screening of one-bead-one-compound cyclic peptide libraries.

PubMed

Qian, Ziqing; Upadhyaya, Punit; Pei, Dehua

2015-01-01

Cyclic peptides have been a rich source of biologically active molecules. Herein we present a method for the combinatorial synthesis and screening of large one-bead-one-compound (OBOC) libraries of cyclic peptides against biological targets such as proteins. Up to ten million different cyclic peptides are rapidly synthesized on TentaGel microbeads by the split-and-pool synthesis method and subjected to a multistage screening protocol which includes magnetic sorting, on-bead enzyme-linked and fluorescence-based assays, and in-solution binding analysis of cyclic peptides selectively released from single beads by fluorescence anisotropy. Finally, the most active hit(s) is identified by the partial Edman degradation-mass spectrometry (PED-MS) method. This method allows a single researcher to synthesize and screen up to ten million cyclic peptides and identify the most active ligand(s) in ~1 month, without the time-consuming and expensive hit resynthesis or the use of any special equipment.

A Constitutive Model for the Inelastic Multiaxial Cyclic Response of a Nickel Base Superalloy Rene 80. Ph.D. Thesis. Final Report

NASA Technical Reports Server (NTRS)

Ramaswamy, V. G.

1986-01-01

The objective was to develop unified constitutive equations which can model a variety of nonlinear material phenomena observed in Rene 80 at elevated temperatures. A constitutive model was developed based on back stress and drag stress. The tensorial back stress was used to model directional effects; whereas, the scalar drag stress was used to model isotropic effects and cyclic hardening or softening. A flow equation and evolution equations for the state variables were developed in multiaxial form. Procedures were developed to generate the material parameters. The model predicted very well the monotonic tensile, cyclic, creep, and stress relaxation behavior of Rene 80 at 982 C. The model was then extended to 871, 760, and 538 C. It was shown that strain rate dependent behavior at high temperatures and strain rate independent behavior at the lower temperatures could be predicted very well. A large number of monotonic tensile, creep, stress relation, and cyclic experiments were predicted. The multiaxial capabilities of the model were verified extensively for combined tension/torsion experiments. The prediction of the model agreed very well for proportional, nonproportional, and pure shear cyclic loading conditions at 982 and 871 C.

Si/Ti2O3/Reduced Graphene Oxide Nanocomposite Anodes for Lithium-Ion Batteries with Highly Enhanced Cyclic Stability.

PubMed

Park, A Reum; Son, Dae-Yong; Kim, Jung Sub; Lee, Jun Young; Park, Nam-Gyu; Park, Juhyun; Lee, Joong Kee; Yoo, Pil J

2015-08-26

Silicon (Si) has attracted tremendous attention as a high-capacity anode material for next generation Li-ion batteries (LIBs); unfortunately, it suffers from poor cyclic stability due to excessive volume expansion and reduced electrical conductivity after repeated cycles. To circumvent these issues, we propose that Si can be complexed with electrically conductive Ti2O3 to significantly enhance the reversible capacity and cyclic stability of Si-based anodes. We prepared a ternary nanocomposite of Si/Ti2O3/reduced graphene oxide (rGO) using mechanical blending and subsequent thermal reduction of the Si, TiO2 nanoparticles, and rGO nanosheets. As a result, the obtained ternary nanocomposite exhibited a specific capacity of 985 mAh/g and a Coulombic efficiency of 98.4% after 100 cycles at a current density of 100 mA/g. Furthermore, these ternary nanocomposite anodes exhibited outstanding rate capability characteristics, even with an increased current density of 10 A/g. This excellent electrochemical performance can be ascribed to the improved electron and ion transport provided by the Ti2O3 phase within the Si domains and the structurally reinforced conductive framework comprised of the rGO nanosheets. Therefore, it is expected that our approach can also be applied to other anode materials to enable large reversible capacity, excellent cyclic stability, and good rate capability for high-performance LIBs.

Probabilistic Simulation of Combined Thermo-Mechanical Cyclic Fatigue in Composites

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

2011-01-01

A methodology to compute probabilistically-combined thermo-mechanical fatigue life of polymer matrix laminated composites has been developed and is demonstrated. Matrix degradation effects caused by long-term environmental exposure and mechanical/thermal cyclic loads are accounted for in the simulation process. A unified time-temperature-stress-dependent multifactor-interaction relationship developed at NASA Glenn Research Center has been used to model the degradation/aging of material properties due to cyclic loads. The fast probability-integration method is used to compute probabilistic distribution of response. Sensitivities of fatigue life reliability to uncertainties in the primitive random variables (e.g., constituent properties, fiber volume ratio, void volume ratio, ply thickness, etc.) computed and their significance in the reliability-based design for maximum life is discussed. The effect of variation in the thermal cyclic loads on the fatigue reliability for a (0/+/-45/90)s graphite/epoxy laminate with a ply thickness of 0.127 mm, with respect to impending failure modes has been studied. The results show that, at low mechanical-cyclic loads and low thermal-cyclic amplitudes, fatigue life for 0.999 reliability is most sensitive to matrix compressive strength, matrix modulus, thermal expansion coefficient, and ply thickness. Whereas at high mechanical-cyclic loads and high thermal-cyclic amplitudes, fatigue life at 0.999 reliability is more sensitive to the shear strength of matrix, longitudinal fiber modulus, matrix modulus, and ply thickness.

Probabilistic Simulation of Combined Thermo-Mechanical Cyclic Fatigue in Composites

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

2010-01-01

A methodology to compute probabilistically-combined thermo-mechanical fatigue life of polymer matrix laminated composites has been developed and is demonstrated. Matrix degradation effects caused by long-term environmental exposure and mechanical/thermal cyclic loads are accounted for in the simulation process. A unified time-temperature-stress-dependent multifactor-interaction relationship developed at NASA Glenn Research Center has been used to model the degradation/aging of material properties due to cyclic loads. The fast probability-integration method is used to compute probabilistic distribution of response. Sensitivities of fatigue life reliability to uncertainties in the primitive random variables (e.g., constituent properties, fiber volume ratio, void volume ratio, ply thickness, etc.) computed and their significance in the reliability-based design for maximum life is discussed. The effect of variation in the thermal cyclic loads on the fatigue reliability for a (0/+/-45/90)s graphite/epoxy laminate with a ply thickness of 0.127 mm, with respect to impending failure modes has been studied. The results show that, at low mechanical-cyclic loads and low thermal-cyclic amplitudes, fatigue life for 0.999 reliability is most sensitive to matrix compressive strength, matrix modulus, thermal expansion coefficient, and ply thickness. Whereas at high mechanical-cyclic loads and high thermal-cyclic amplitudes, fatigue life at 0.999 reliability is more sensitive to the shear strength of matrix, longitudinal fiber modulus, matrix modulus, and ply thickness.

Furnace Cyclic Oxidation Behavior of Multicomponent Low Conductivity Thermal Barrier Coatings

NASA Astrophysics Data System (ADS)

Zhu, Dongming; Nesbitt, James A.; Barrett, Charles A.; McCue, Terry R.; Miller, Robert A.

2004-03-01

Ceramic thermal barrier coatings (TBCs) will play an increasingly important role in advanced gas turbine engines due to their ability to further increase engine operating temperatures and reduce cooling, thus helping achieve future engine low emission, high efficiency, and improved reliability goals. Advanced multicomponent zirconia (ZrO2)-based TBCs are being developed using an oxide defect clustering design approach to achieve the required coating low thermal conductivity and high-temperature stability. Although the new composition coatings were not yet optimized for cyclic durability, an initial durability screening of the candidate coating materials was conducted using conventional furnace cyclic oxidation tests. In this paper, furnace cyclic oxidation behavior of plasma-sprayed ZrO2-based defect cluster TBCs was investigated at 1163°C using 45 min hot-time cycles. The ceramic coating failure mechanisms were studied using scanning electron microscopy (SEM) combined with x-ray diffraction (XRD) phase analysis after the furnace tests. The coating cyclic lifetime is also discussed in relation to coating processing, phase structures, dopant concentration, and other thermo-physical properties.

Are Math Grades Cyclical?

ERIC Educational Resources Information Center

Adams, Gerald J.; Dial, Micah

1998-01-01

The cyclical nature of mathematics grades was studied for a cohort of elementary school students from a large metropolitan school district in Texas over six years (average cohort size of 8495). The study used an autoregressive integrated moving average (ARIMA) model. Results indicate that grades do exhibit a significant cyclical pattern. (SLD)

Cyclic Deformation and Fatigue of Monocrystalline Ni-Base Superalloys.

DTIC Science & Technology

1983-12-16

understanding crack nucleation (Laird et al at Pennsylvania, Fine et al at Northwestern, Neumann et al at Dusseldorf and Mughrabi et al at Stuttgart...hardened alloy in a project supported by the army. This work concentrated on the stability of precipitates under cyclic deformation ( Al -Ag, Al -Cu systems...and the strain-localization behavior of alloys containing shearable precipitates ( Al -Cu, e") and non-shearable precipitates ( Al -Cu, e’). Furthermore

Degradation forecast for PEMFC cathode-catalysts under cyclic loads

NASA Astrophysics Data System (ADS)

Moein-Jahromi, M.; Kermani, M. J.; Movahed, S.

2017-08-01

Degradation of Fuel Cell (FC) components under cyclic loads is one of the biggest bottlenecks in FC commercialization. In this paper, a novel experimental based algorithm is presented to predict the Catalyst Layer (CL) performance loss during cyclic load. The algorithm consists of two models namely Models 1 and 2. The Model 1 calculates the Electro-Chemical Surface Area (ECSA) and agglomerate size (e.g. agglomerate radius, rt,agg) for the catalyst layer under cyclic load. The Model 2 is the already-existing model from our earlier studies that computes catalyst performance with fixed structural parameters. Combinations of these two Models predict the CL performance under an arbitrary cyclic load. A set of parametric/sensitivity studies is performed to investigate the effects of operating parameters on the percentage of Voltage Degradation Rate (VDR%) with rank 1 for the most influential one. Amongst the considered parameters (such as: temperature, relative humidity, pressure, minimum and maximum voltage of the cyclic load), the results show that temperature and pressure have the most and the least influences on the VDR%, respectively. So that, increase of temperature from 60 °C to 80 °C leads to over 20% VDR intensification, the VDR will also reduce 1.41% by increasing pressure from 2 atm to 4 atm.

Epilepsy in cerebrovascular diseases: Review of experimental and clinical data with meta-analysis of risk factors.

PubMed

Ferlazzo, Edoardo; Gasparini, Sara; Beghi, Ettore; Sueri, Chiara; Russo, Emilio; Leo, Antonio; Labate, Angelo; Gambardella, Antonio; Belcastro, Vincenzo; Striano, Pasquale; Paciaroni, Maurizio; Pisani, Laura Rosa; Aguglia, Umberto

2016-08-01

Seizures may occur in close temporal association with a stroke or after a variable interval. Moreover, epilepsy is often encountered in patients with leukoaraiosis. Although early post-stroke seizures have been studied extensively, less attention has been paid to post-stroke epilepsy (PSE) and to epilepsy associated with leukoaraiosis (EAL). The aim of this paper is to review data concerning pathophysiology, prognosis, and treatment of PSE and EAL. We performed an extensive literature search to identify experimental and clinical articles on PSE and EAL. We also conducted a systematic review of risk factors for PSE and EAL among eligible studies. PSE is caused by enhanced neuronal excitability within and near the scar. The role played by white matter changes in EAL remains to be elucidated. Meta-analysis showed that cortical involvement (odds ratio [OR] 3.71, 95% confidence interval [CI] 2.34-5.90, p < 0.001), cerebral hemorrhage (OR 2.41, 95% CI 1.57-3.70, p < 0.001), and early seizures (OR 4.43, 95% CI 2.36-8.32, p < 0.001) are associated with an increased risk of PSE. As regards EAL, no prospective, population-based studies evaluated the role of different variables on seizure risk. Studies about the management of PSE are limited. PSE is generally well controlled by drugs. Data about risk factors, prognosis, and treatment of EAL are lacking. Pathophysiology and risk factors are well defined for PSE but need to be elucidated for EAL. Management of PSE and EAL relies on the clinician's judgment and should be tailored on an individual basis. Wiley Periodicals, Inc. © 2016 International League Against Epilepsy.

40 CFR 721.2120 - Cyclic amide.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Cyclic amide. 721.2120 Section 721... Cyclic amide. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as a cyclic amide (PMN P-92-131) is subject to reporting under this section for the...

Time-domain multiplexed high resolution fiber optics strain sensor system based on temporal response of fiber Fabry-Perot interferometers.

PubMed

Chen, Jiageng; Liu, Qingwen; He, Zuyuan

2017-09-04

We developed a multiplexed strain sensor system with high resolution using fiber Fabry-Perot interferometers (FFPI) as sensing elements. The temporal responses of the FFPIs excited by rectangular laser pulses are used to obtain the strain applied on each FFPI. The FFPIs are connected by cascaded couplers and delay fiber rolls for the time-domain multiplexing. A compact optoelectronic system performing closed-loop cyclic interrogation is employed to improve the sensing resolution and the frequency response. In the demonstration experiment, 3-channel strain sensing with resolutions better than 0.1 nε and frequency response higher than 100 Hz is realized.

Characterization of Runella slithyformis HD-Pnk, a bifunctional DNA/RNA end-healing enzyme composed of an N-terminal 2',3' -phosphoesterase HD domain and a C-terminal 5' -OH polynucleotide kinase domain.

PubMed

Munir, Annum; Shuman, Stewart

2016-11-28

5' and 3' end healing are key steps in nucleic acid break repair in which 5' -OH ends are phosphorylated by a polynucleotide kinase and 3' -PO 4 or 2',3' -cyclic-PO 4 ends are hydrolyzed by a phosphoesterase to generate the 5' -PO 4 and 3' -OH termini required for sealing by classic polynucleotide ligases. End healing and sealing enzymes are present in diverse bacterial taxa, often organized as modular units within a single multifunctional polypeptide or as subunits of a repair complex. Here we identify and characterize Runella slithyformis HD-Pnk as a novel bifunctional end-healing enzyme composed of an N-terminal 2',3' -phosphoesterase HD domain and a C-terminal 5' -OH polynucleotide kinase P-loop domain. HD-Pnk phosphorylates 5' -OH polynucleotides (9-mers or longer) in the presence of magnesium and any NTP donor. HD-Pnk dephosphorylates RNA 2',3' -cyclic phosphate, RNA 3' -phosphate, RNA 2' -phosphate, and DNA 3' -phosphate ends in the presence of a transition metal cofactor, which can be nickel, copper or cobalt. HD-Pnkp homologs are present in genera from eleven bacterial phyla and are often encoded in an operon with a putative ATP-dependent polynucleotide ligase. The present study provides insights to the diversity of nucleic acid repair strategies via the characterization of Runella slithyformis HD-Pnkp as the exemplar of a novel clade of dual 5' and 3' end-healing enzymes that phosphorylate 5' -OH termini and dephosphorylate 2',3' -cyclic-PO 4 , 3' -PO 4 , and 2' -PO 4 ends. The distinctive feature of HD-Pnk is its domain composition: a fusion of an N-terminal HD phosphohydrolase module to a C-terminal P-loop polynucleotide kinase module. Homologs of Runella HD-Pnk with the same domain composition, domain order, and similar polypeptide size are distributed widely among genera from eleven bacterial phyla. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Reevaluation of Performance of Electric Double-layer Capacitors from Constant-current Charge/Discharge and Cyclic Voltammetry

PubMed Central

Allagui, Anis; Freeborn, Todd J.; Elwakil, Ahmed S.; Maundy, Brent J.

2016-01-01

The electric characteristics of electric-double layer capacitors (EDLCs) are determined by their capacitance which is usually measured in the time domain from constant-current charging/discharging and cyclic voltammetry tests, and from the frequency domain using nonlinear least-squares fitting of spectral impedance. The time-voltage and current-voltage profiles from the first two techniques are commonly treated by assuming ideal SsC behavior in spite of the nonlinear response of the device, which in turn provides inaccurate values for its characteristic metrics. In this paper we revisit the calculation of capacitance, power and energy of EDLCs from the time domain constant-current step response and linear voltage waveform, under the assumption that the device behaves as an equivalent fractional-order circuit consisting of a resistance Rs in series with a constant phase element (CPE(Q, α), with Q being a pseudocapacitance and α a dispersion coefficient). In particular, we show with the derived (Rs, Q, α)-based expressions, that the corresponding nonlinear effects in voltage-time and current-voltage can be encompassed through nonlinear terms function of the coefficient α, which is not possible with the classical RsC model. We validate our formulae with the experimental measurements of different EDLCs. PMID:27934904

Reevaluation of Performance of Electric Double-layer Capacitors from Constant-current Charge/Discharge and Cyclic Voltammetry

NASA Astrophysics Data System (ADS)

Allagui, Anis; Freeborn, Todd J.; Elwakil, Ahmed S.; Maundy, Brent J.

2016-12-01

The electric characteristics of electric-double layer capacitors (EDLCs) are determined by their capacitance which is usually measured in the time domain from constant-current charging/discharging and cyclic voltammetry tests, and from the frequency domain using nonlinear least-squares fitting of spectral impedance. The time-voltage and current-voltage profiles from the first two techniques are commonly treated by assuming ideal SsC behavior in spite of the nonlinear response of the device, which in turn provides inaccurate values for its characteristic metrics. In this paper we revisit the calculation of capacitance, power and energy of EDLCs from the time domain constant-current step response and linear voltage waveform, under the assumption that the device behaves as an equivalent fractional-order circuit consisting of a resistance Rs in series with a constant phase element (CPE(Q, α), with Q being a pseudocapacitance and α a dispersion coefficient). In particular, we show with the derived (Rs, Q, α)-based expressions, that the corresponding nonlinear effects in voltage-time and current-voltage can be encompassed through nonlinear terms function of the coefficient α, which is not possible with the classical RsC model. We validate our formulae with the experimental measurements of different EDLCs.

Reevaluation of Performance of Electric Double-layer Capacitors from Constant-current Charge/Discharge and Cyclic Voltammetry.

PubMed

Allagui, Anis; Freeborn, Todd J; Elwakil, Ahmed S; Maundy, Brent J

2016-12-09

The electric characteristics of electric-double layer capacitors (EDLCs) are determined by their capacitance which is usually measured in the time domain from constant-current charging/discharging and cyclic voltammetry tests, and from the frequency domain using nonlinear least-squares fitting of spectral impedance. The time-voltage and current-voltage profiles from the first two techniques are commonly treated by assuming ideal R s C behavior in spite of the nonlinear response of the device, which in turn provides inaccurate values for its characteristic metrics [corrected]. In this paper we revisit the calculation of capacitance, power and energy of EDLCs from the time domain constant-current step response and linear voltage waveform, under the assumption that the device behaves as an equivalent fractional-order circuit consisting of a resistance R s in series with a constant phase element (CPE(Q, α), with Q being a pseudocapacitance and α a dispersion coefficient). In particular, we show with the derived (R s , Q, α)-based expressions, that the corresponding nonlinear effects in voltage-time and current-voltage can be encompassed through nonlinear terms function of the coefficient α, which is not possible with the classical R s C model. We validate our formulae with the experimental measurements of different EDLCs.

Cyclic completion of the anamorphic universe

NASA Astrophysics Data System (ADS)

Ijjas, Anna

2018-04-01

Cyclic models of the universe have the advantage of avoiding initial conditions problems related to postulating any sort of beginning in time. To date, the best known viable examples of cyclic models have been ekpyrotic. In this paper, we show that the recently proposed anamorphic scenario can also be made cyclic. The key to the cyclic completion is a classically stable, non-singular bounce. Remarkably, even though the bounce construction was originally developed to connect a period of contraction with a period of expansion both described by Einstein gravity, we show here that it can naturally be modified to connect an ordinary contracting phase described by Einstein gravity with a phase of anamorphic smoothing. The paper will present the basic principles and steps in constructing cyclic anamorphic models.

IOMIDAZOLIUM-BASED INDIUM(III) TETRAHIDES: RECYCLABLE CATALYSTS FOR EFFICIENT COUPLING OF CARBON DIOXIDE WITH EXPOXIDES TO FORM CYCLIC CARBONATES

EPA Science Inventory

The transformation of CO2 an abundant greenhouse gas, into cyclic carbonates by coupling reaction with epoxides is receiving well-deserved attention. A series of imidazolium-based indium tetrahalides, prepared efficiently via microwave assisted reaction of InX3 with [1-R-3-metht...

Natural-Annotation-based Unsupervised Construction of Korean-Chinese Domain Dictionary

NASA Astrophysics Data System (ADS)

Liu, Wuying; Wang, Lin

2018-03-01

The large-scale bilingual parallel resource is significant to statistical learning and deep learning in natural language processing. This paper addresses the automatic construction issue of the Korean-Chinese domain dictionary, and presents a novel unsupervised construction method based on the natural annotation in the raw corpus. We firstly extract all Korean-Chinese word pairs from Korean texts according to natural annotations, secondly transform the traditional Chinese characters into the simplified ones, and finally distill out a bilingual domain dictionary after retrieving the simplified Chinese words in an extra Chinese domain dictionary. The experimental results show that our method can automatically build multiple Korean-Chinese domain dictionaries efficiently.

A lead (II) 3D coordination polymer based on a marine cyclic peptide motif.

PubMed

Chakraborty, Subrata; Tyagi, Pooja; Tai, Dar-Fu; Lee, Gene-Hsiang; Peng, Shie-Ming

2013-04-26

The crystal structure of a naturally occurring cyclic tetrapeptide cyclo(Gly-L-Ser-L-Pro-L-Glu) [cyclo(GSPE)] was obtained. The conformation of synthesized cyclo(GSPE) fixes the coordination to lead ion in a 1:1 ratio. This cyclo(GSPE)-Pb complex was constructed as an asymmetric 3D network in the crystalline state. The polymerization of a heavy metal ion with a rigid asymmetric cyclic tetrapeptide represents the first example of a new class of macrocyclic complexes.

History-independent cyclic response of nanotwinned metals

NASA Astrophysics Data System (ADS)

Pan, Qingsong; Zhou, Haofei; Lu, Qiuhong; Gao, Huajian; Lu, Lei

2017-11-01

Nearly 90 per cent of service failures of metallic components and structures are caused by fatigue at cyclic stress amplitudes much lower than the tensile strength of the materials involved. Metals typically suffer from large amounts of cumulative, irreversible damage to microstructure during cyclic deformation, leading to cyclic responses that are unstable (hardening or softening) and history-dependent. Existing rules for fatigue life prediction, such as the linear cumulative damage rule, cannot account for the effect of loading history, and engineering components are often loaded by complex cyclic stresses with variable amplitudes, mean values and frequencies, such as aircraft wings in turbulent air. It is therefore usually extremely challenging to predict cyclic behaviour and fatigue life under a realistic load spectrum. Here, through both atomistic simulations and variable-strain-amplitude cyclic loading experiments at stress amplitudes lower than the tensile strength of the metal, we report a history-independent and stable cyclic response in bulk copper samples that contain highly oriented nanoscale twins. We demonstrate that this unusual cyclic behaviour is governed by a type of correlated ‘necklace’ dislocation consisting of multiple short component dislocations in adjacent twins, connected like the links of a necklace. Such dislocations are formed in the highly oriented nanotwinned structure under cyclic loading and help to maintain the stability of twin boundaries and the reversible damage, provided that the nanotwins are tilted within about 15 degrees of the loading axis. This cyclic deformation mechanism is distinct from the conventional strain localizing mechanisms associated with irreversible microstructural damage in single-crystal, coarse-grained, ultrafine-grained and nanograined metals.

Gearsketch: An Adaptive Drawing-Based Learning Environment for the Gears Domain

ERIC Educational Resources Information Center

Leenaars, Frank A.; Joolingen, Wouter R.; Gijlers, Hannie; Bollen, Lars

2014-01-01

GearSketch is a learning environment for the gears domain, aimed at students in the final years of primary school. It is designed for use with a touchscreen device and is based on ideas from drawing-based learning and research on cognitive tutors. At the heart of GearSketch is a domain model that is used to transform learners' strokes into…

A Protein Domain and Family Based Approach to Rare Variant Association Analysis.

PubMed

Richardson, Tom G; Shihab, Hashem A; Rivas, Manuel A; McCarthy, Mark I; Campbell, Colin; Timpson, Nicholas J; Gaunt, Tom R

2016-01-01

It has become common practice to analyse large scale sequencing data with statistical approaches based around the aggregation of rare variants within the same gene. We applied a novel approach to rare variant analysis by collapsing variants together using protein domain and family coordinates, regarded to be a more discrete definition of a biologically functional unit. Using Pfam definitions, we collapsed rare variants (Minor Allele Frequency ≤ 1%) together in three different ways 1) variants within single genomic regions which map to individual protein domains 2) variants within two individual protein domain regions which are predicted to be responsible for a protein-protein interaction 3) all variants within combined regions from multiple genes responsible for coding the same protein domain (i.e. protein families). A conventional collapsing analysis using gene coordinates was also undertaken for comparison. We used UK10K sequence data and investigated associations between regions of variants and lipid traits using the sequence kernel association test (SKAT). We observed no strong evidence of association between regions of variants based on Pfam domain definitions and lipid traits. Quantile-Quantile plots illustrated that the overall distributions of p-values from the protein domain analyses were comparable to that of a conventional gene-based approach. Deviations from this distribution suggested that collapsing by either protein domain or gene definitions may be favourable depending on the trait analysed. We have collapsed rare variants together using protein domain and family coordinates to present an alternative approach over collapsing across conventionally used gene-based regions. Although no strong evidence of association was detected in these analyses, future studies may still find value in adopting these approaches to detect previously unidentified association signals.

A cup product structure for cyclic cohomology

NASA Astrophysics Data System (ADS)

Espinosa Tintos, Jose Eduardo

In this work we construct a cup product structure for cyclic cohomology of a cyclic set X. introduced by Comics. We make use of a categorical construction of cyclic homology by Fiedorowicz and Loday to define our cup product structure by using a large resolution of the cyclic category. We also provide a way to construct a chain map from a smaller resolution where the action of the finite groups is clear. and in the process of constructing this map we learn the large complex can be viewed as all factorizations in the category DeltaC using the cyclic structure of X.

Electrochromatography on acrylate-based monolith in cyclic olefin copolymer microchip: an attractive technology.

PubMed

Ladner, Y; Cretier, G; Faure, K

2015-01-01

Electrochromatography (EC) on a porous monolithic stationary phase prepared within the channels of a microsystem is an attractive alternative for on-chip separation. It combines the separation mechanisms of electrophoresis and liquid chromatography. Moreover, the porous polymer monolithic materials have become popular as stationary phase due to the ease and rapidity of fabrication via free radical photopolymerization. Here, we describe a hexyl acrylate (HA)-based porous monolith which is simultaneously in situ synthesized and anchored to the inner walls of the channel of a cyclic olefin copolymer (COC) device in only 2 min. The baseline separation of a mixture of neurotransmitters including six amino acids and two catecholamines is realized.

On the energy efficiency of cyclic mechanisms

NASA Astrophysics Data System (ADS)

Briskin, E. S.; Kalinin, Ya. V.; Maloletov, A. V.; Chernyshev, V. V.

2014-01-01

We consider cyclic mechanisms with one degree of freedom driven by engines of various types such as alternating and direct current motors, internal combustion engines, etc. We pose the problem of modifying the mechanism structure by joining additional links or by varying the parameters or operation mode of the original mechanism so as to minimize the thermal losses in the driving motor. The solution is based on the minimization of the functional determining the irreversible power losses. We show that, for the engines considered, all cyclic mechanisms with one degree of freedom should satisfy a fundamental condition ensuring the minimum of losses. We consider two examples, one of which corresponds to actually existing mechanisms.

Cyclic AMP-induced Chromatin Changes Support the NFATc-mediated Recruitment of GATA-3 to the Interleukin 5 Promoter*

PubMed Central

Klein-Hessling, Stefan; Bopp, Tobias; Jha, Mithilesh K.; Schmidt, Arthur; Miyatake, Shoichiro; Schmitt, Edgar; Serfling, Edgar

2008-01-01

Elevated intracellular cyclic AMP levels, which suppress the proliferation of naive T cells and type 1 T helper (Th1) cells are a property of T helper 2 (Th2) cells and regulatory T cells. While cyclic AMP signals interfere with the IL-2 promoter induction, they support the induction of Th2-type genes, in particular of il-5 gene. We show here that cyclic AMP signals support the generation of three inducible DNase I hypersensitive chromatin sites over the il-5 locus, including its promoter region. In addition, cyclic AMP signals enhance histone H3 acetylation at the IL-5 promoter and the concerted binding of GATA-3 and NFATc to the promoter. This is facilitated by direct protein-protein interactions involving the C-terminal Zn2+-finger of GATA-3 and the C-terminal region of the NFATc1 DNA binding domain. Because inhibition of NFATc binding to the IL-5 promoter in vivo also affects the binding of GATA-3, one may conclude that upon induction of Th2 effector cells NFATc recruits GATA-3 to Th2-type genes. These data demonstrate the functional importance of cyclic AMP signals for the interplay between GATA-3 and NFATc factors in the transcriptional control of lymphokine expression in Th2 effector cells. PMID:18772129

Topological chaos, braiding and bifurcation of almost-cyclic sets.

PubMed

Grover, Piyush; Ross, Shane D; Stremler, Mark A; Kumar, Pankaj

2012-12-01

In certain two-dimensional time-dependent flows, the braiding of periodic orbits provides a way to analyze chaos in the system through application of the Thurston-Nielsen classification theorem (TNCT). We expand upon earlier work that introduced the application of the TNCT to braiding of almost-cyclic sets, which are individual components of almost-invariant sets [Stremler et al., "Topological chaos and periodic braiding of almost-cyclic sets," Phys. Rev. Lett. 106, 114101 (2011)]. In this context, almost-cyclic sets are periodic regions in the flow with high local residence time that act as stirrers or "ghost rods" around which the surrounding fluid appears to be stretched and folded. In the present work, we discuss the bifurcation of the almost-cyclic sets as a system parameter is varied, which results in a sequence of topologically distinct braids. We show that, for Stokes' flow in a lid-driven cavity, these various braids give good lower bounds on the topological entropy over the respective parameter regimes in which they exist. We make the case that a topological analysis based on spatiotemporal braiding of almost-cyclic sets can be used for analyzing chaos in fluid flows. Hence, we further develop a connection between set-oriented statistical methods and topological methods, which promises to be an important analysis tool in the study of complex systems.

Biodegradation of the cyclic nitramine explosives RDX, HMX, and CL-20.

PubMed

Crocker, Fiona H; Indest, Karl J; Fredrickson, Herbert L

2006-11-01

Cyclic nitramine explosives are synthesized globally mainly as military munitions, and their use has resulted in environmental contamination. Several biodegradation pathways have been proposed, and these are based mainly on end-product characterization because many of the metabolic intermediates are hypothetical and unstable in water. Biodegradation mechanisms for cyclic nitramines include (a) formation of a nitramine free radical and loss of nitro functional groups, (b) reduction of nitro functional groups, (c) direct enzymatic cleavage, (d) alpha-hydroxylation, or (e) hydride ion transfer. Pathway intermediates spontaneously decompose in water producing nitrite, nitrous oxide, formaldehyde, or formic acid as common end-products. In vitro enzyme and functional gene expression studies have implicated a limited number of enzymes/genes involved in cyclic nitramine catabolism. Advances in molecular biology methods such as high-throughput DNA sequencing, microarray analysis, and nucleic acid sample preparation are providing access to biochemical and genetic information on cultivable and uncultivable microorganisms. This information can provide the knowledge base for rational engineering of bioremediation strategies, biosensor development, environmental monitoring, and green biosynthesis of explosives. This paper reviews recent developments on the biodegradation of cyclic nitramines and the potential of genomics to identify novel functional genes of explosive metabolism.

Cyclic degassing of Erebus volcano, Antarctica

NASA Astrophysics Data System (ADS)

Ilanko, Tehnuka; Oppenheimer, Clive; Burgisser, Alain; Kyle, Philip

2015-06-01

Field observations have previously identified rapid cyclic changes in the behaviour of the lava lake of Erebus volcano. In order to understand more fully the nature and origins of these cycles, we present here a wavelet-based frequency analysis of time series measurements of gas emissions from the lava lake, obtained by open-path Fourier transform infrared spectroscopy. This reveals (i) a cyclic change in total gas column amount, a likely proxy for gas flux, with a period of about 10 min, and (ii) a similarly phased cyclic change in proportions of volcanic gases, which can be explained in terms of chemical equilibria and pressure-dependent solubilities. Notably, the wavelet analysis shows a persistent periodicity in the CO2/CO ratio and strong periodicity in H2O and SO2 degassing. The `peaks' of the cycles, defined by maxima in H2O and SO2 column amounts, coincide with high CO2/CO ratios and proportionally smaller increases in column amounts of CO2, CO, and OCS. We interpret the cycles to arise from recharge of the lake by intermittent pulses of magma from shallow depths, which degas H2O at low pressure, combined with a background gas flux that is decoupled from this very shallow magma degassing.

Region and Domain Dependent Action of Nomifensine

PubMed Central

Shu, Zhan; Taylor, I. Mitch; Walters, Seth H.; Michael, Adrian C.

2014-01-01

The dopamine (DA) terminal fields in the rat dorsal striatum (DS) and nucleus accumbens core (NAcc) are organized as patchworks of domains that exhibit distinct kinetics of DA release and clearance. The present study used fast-scan cyclic voltammetry recordings of electrically evoked DA overflow to test the hypothesis that nomifensine might exhibit domain-dependent actions within the NAcc, as we previously found to be the case within the DS. Within the NAcc, nomifensine preferentially enhanced evoked dopamine overflow in the slow compared to the fast domains. To seek a kinetic explanation for nomifensine’s selective actions, we quantified the apparent KM of DA clearance by numerically evaluating the derivative of the descending phase of the DA signal after the end of the stimulus. For comparison, we likewise quantified apparent KM in the domains of the DS. As expected because it is a competitive inhibitor, nomifensine significantly increased the apparent KM in both the fast and slow domains of both the NAcc and DS. However, our analysis also leads to the novel finding that nomifensine preferentially increases the apparent KM in the NAcc compared to the DS: apparent KM increased by ~500% in the NAcc and ~200% in the DS. PMID:24766210

Furnace Cyclic Oxidation Behavior of Multi-Component Low Conductivity Thermal Barrier Coatings

NASA Technical Reports Server (NTRS)

Zhu, Dong-Ming; Nesbitt, James A.; Barrett, Charles A.; McCue, Terry R.; Miller, Robert A.

2004-01-01

Ceramic thermal barrier coatings will play an increasingly important role in advanced gas turbine engines because of their ability to further increase engine operating temperatures and reduce cooling, thus helping achieve future engine low emission, high efficiency and improved reliability goals. Advanced multi-component zirconia-based thermal barrier coatings are being developed using an oxide defect clustering design approach to achieve the required coating low thermal conductivity and high temperature stability. Although the new composition coatings were not yet optimized for cyclic durability, an initial durability screening of the candidate coating materials was conducted using conventional furnace cyclic oxidation tests. In this paper, furnace cyclic oxidation behavior of plasma-sprayed zirconia-based defect cluster thermal barrier coatings was investigated at 1163 C using 45 min hot cycles. The ceramic coating failure mechanisms were studied using scanning electron microscopy (SEM) combined with X-ray diffraction (XRD) phase analysis after the furnace tests. The coating cyclic lifetime is also discussed in relation to coating processing, phase structures, dopant concentration, and other thermo-physical properties.

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

Liu, Shengqiang; Li, Jie; Yu, Junsheng, E-mail: jsyu@uestc.edu.cn

A color tuning index (I{sub CT}) parameter for evaluating the color change capability of color-tunable organic light-emitting diodes (CT-OLEDs) was proposed and formulated. And a series of CT-OLEDs, consisting of five different carrier/exciton adjusting interlayers (C/EALs) inserted between two complementary emitting layers, were fabricated and applied to disclose the relationship between I{sub CT} and C/EALs. The result showed that the trend of electroluminescence spectra behavior in CT-OLEDs has good accordance with I{sub CT} values, indicating that the I{sub CT} parameter is feasible for the evaluation of color variation. Meanwhile, by changing energy level and C/EAL thickness, the optimized device withmore » the widest color tuning range was based on N,N′-dicarbazolyl-3,5-benzene C/EAL, exhibiting the highest I{sub CT} value of 41.2%. Based on carrier quadratic hopping theory and exciton transfer model, two fitting I{sub CT} formulas derived from the highest occupied molecular orbital (HOMO) energy level and triplet energy level were simulated. Finally, a color tuning prediction (CTP) model was developed to deduce the I{sub CT} via C/EAL HOMO and triplet energy levels, and verified by the fabricated OLEDs with five different C/EALs. We believe that the CTP model assisted with I{sub CT} parameter will be helpful for fabricating high performance CT-OLEDs with a broad range of color tuning.« less

Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.

PubMed

Galperin, Michael Y; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2018-04-01

The two-component signal transduction (TCS) machinery is a key mechanism of sensing environmental changes in the prokaryotic world. TCS systems have been characterized thoroughly in bacteria but to a much lesser extent in archaea. Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data. We describe the domain architectures of the archaeal TCS components, including several novel output domains, and discuss the evolution of the archaeal TCS machinery. The distribution of TCS systems in archaea is strongly biased, with high levels of abundance in haloarchaea and thaumarchaea but none detected in the sequenced genomes from the phyla Crenarchaeota , Nanoarchaeota , and Korarchaeota The archaeal sensor histidine kinases are generally similar to their well-studied bacterial counterparts but are often located in the cytoplasm and carry multiple PAS and/or GAF domains. In contrast, archaeal response regulators differ dramatically from the bacterial ones. Most archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. Instead, archaea encode multiple copies of response regulators containing either the stand-alone receiver (REC) domain or combinations of REC with PAS and/or GAF domains. Therefore, the prevailing mechanism of archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation. IMPORTANCE Although the Archaea represent a separate domain of life, their signaling systems have been assumed to be closely similar to the bacterial ones. A study of the domain architectures of the archaeal two-component signal transduction (TCS) machinery revealed an

Virtual screening using combinatorial cyclic peptide libraries reveals protein interfaces readily targetable by cyclic peptides.

PubMed

Duffy, Fergal J; O'Donovan, Darragh; Devocelle, Marc; Moran, Niamh; O'Connell, David J; Shields, Denis C

2015-03-23

Protein-protein and protein-peptide interactions are responsible for the vast majority of biological functions in vivo, but targeting these interactions with small molecules has historically been difficult. What is required are efficient combined computational and experimental screening methods to choose among a number of potential protein interfaces worthy of targeting lead macrocyclic compounds for further investigation. To achieve this, we have generated combinatorial 3D virtual libraries of short disulfide-bonded peptides and compared them to pharmacophore models of important protein-protein and protein-peptide structures, including short linear motifs (SLiMs), protein-binding peptides, and turn structures at protein-protein interfaces, built from 3D models available in the Protein Data Bank. We prepared a total of 372 reference pharmacophores, which were matched against 108,659 multiconformer cyclic peptides. After normalization to exclude nonspecific cyclic peptides, the top hits notably are enriched for mimetics of turn structures, including a turn at the interaction surface of human α thrombin, and also feature several protein-binding peptides. The top cyclic peptide hits also cover the critical "hot spot" interaction sites predicted from the interaction crystal structure. We have validated our method by testing cyclic peptides predicted to inhibit thrombin, a key protein in the blood coagulation pathway of important therapeutic interest, identifying a cyclic peptide inhibitor with lead-like activity. We conclude that protein interfaces most readily targetable by cyclic peptides and related macrocyclic drugs may be identified computationally among a set of candidate interfaces, accelerating the choice of interfaces against which lead compounds may be screened.

Characterization of Runella slithyformis HD-Pnk, a Bifunctional DNA/RNA End-Healing Enzyme Composed of an N-Terminal 2′,3′-Phosphoesterase HD Domain and a C-Terminal 5′-OH Polynucleotide Kinase Domain

PubMed Central

Munir, Annum

2016-01-01

ABSTRACT 5′- and 3′-end-healing reactions are key steps in nucleic acid break repair in which 5′-OH ends are phosphorylated by a polynucleotide kinase (Pnk) and 3′-PO4 or 2′,3′-cyclic-PO4 ends are hydrolyzed by a phosphoesterase to generate the 5′-PO4 and 3′-OH termini required for sealing by classic polynucleotide ligases. End-healing and sealing enzymes are present in diverse bacterial taxa, often organized as modular units within a single multifunctional polypeptide or as subunits of a repair complex. Here we identify and characterize Runella slithyformis HD-Pnk as a novel bifunctional end-healing enzyme composed of an N-terminal 2′,3′-phosphoesterase HD domain and a C-terminal 5′-OH polynucleotide kinase P-loop domain. HD-Pnk phosphorylates 5′-OH polynucleotides (9-mers or longer) in the presence of magnesium and any nucleoside triphosphate donor. HD-Pnk dephosphorylates RNA 2′,3′-cyclic phosphate, RNA 3′-phosphate, RNA 2′-phosphate, and DNA 3′-phosphate ends in the presence of a transition metal cofactor, which can be nickel, copper, or cobalt. HD-Pnk homologs are present in genera from 11 bacterial phyla and are often encoded in an operon with a putative ATP-dependent polynucleotide ligase. IMPORTANCE The present study provides insights regarding the diversity of nucleic acid repair strategies via the characterization of Runella slithyformis HD-Pnk as the exemplar of a novel clade of dual 5′- and 3′-end-healing enzymes that phosphorylate 5′-OH termini and dephosphorylate 2′,3′-cyclic-PO4, 3′-PO4, and 2′-PO4 ends. The distinctive feature of HD-Pnk is its domain composition, i.e., a fusion of an N-terminal HD phosphohydrolase module and a C-terminal P-loop polynucleotide kinase module. Homologs of Runella HD-Pnk with the same domain composition, same domain order, and similar polypeptide sizes are distributed widely among genera from 11 bacterial phyla. PMID:27895092

The roles of RIIbeta linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of Type IIbeta Protein Kinase A. A small angle X-ray and neutron scattering study

DOE PAGES

Blumenthal, Donald K.; Copps, Jeffrey; Smith-Nguyen, Eric V.; ...

2014-08-11

Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. Moreover, the PKA holoenzyme is a tetramer (R 2:C 2), with a regulatory subunit homodimer (R 2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the typemore » IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1–280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. These results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA.« less

Comparison of Example-Based Learning and Problem-Based Learning in Engineering Domain

ERIC Educational Resources Information Center

Sern, Lai Chee; Salleh, Kahirol Mohd; Sulaiman, Nor lisa; Mohamad, Mimi Mohaffyza; Yunos, Jailani Md

2015-01-01

The research was conducted to compare the impacts of problem-based learning (PBL) and example-based learning (EBL) on the learning performance in an engineering domain. The research was implemented by means of experimental design. Specifically, a two-group experiment with a pre- and post-test design was used in this research. A total of 37…

The Domain Five Observation Instrument: A Competency-Based Coach Evaluation Tool

ERIC Educational Resources Information Center

Shangraw, Rebecca

2017-01-01

The Domain Five Observation Instrument (DFOI) is a competency-based observation instrument recommended for sport leaders or researchers who wish to evaluate coaches' instructional behaviors. The DFOI includes 10 behavior categories and four timed categories that encompass 34 observable instructional benchmarks outlined in domain five of the…

Directed evolution of the TALE N-terminal domain for recognition of all 5' bases.

PubMed

Lamb, Brian M; Mercer, Andrew C; Barbas, Carlos F

2013-11-01

Transcription activator-like effector (TALE) proteins can be designed to bind virtually any DNA sequence. General guidelines for design of TALE DNA-binding domains suggest that the 5'-most base of the DNA sequence bound by the TALE (the N0 base) should be a thymine. We quantified the N0 requirement by analysis of the activities of TALE transcription factors (TALE-TF), TALE recombinases (TALE-R) and TALE nucleases (TALENs) with each DNA base at this position. In the absence of a 5' T, we observed decreases in TALE activity up to >1000-fold in TALE-TF activity, up to 100-fold in TALE-R activity and up to 10-fold reduction in TALEN activity compared with target sequences containing a 5' T. To develop TALE architectures that recognize all possible N0 bases, we used structure-guided library design coupled with TALE-R activity selections to evolve novel TALE N-terminal domains to accommodate any N0 base. A G-selective domain and broadly reactive domains were isolated and characterized. The engineered TALE domains selected in the TALE-R format demonstrated modularity and were active in TALE-TF and TALEN architectures. Evolved N-terminal domains provide effective and unconstrained TALE-based targeting of any DNA sequence as TALE binding proteins and designer enzymes.

Calculus domains modelled using an original bool algebra based on polygons

NASA Astrophysics Data System (ADS)

Oanta, E.; Panait, C.; Raicu, A.; Barhalescu, M.; Axinte, T.

2016-08-01

Analytical and numerical computer based models require analytical definitions of the calculus domains. The paper presents a method to model a calculus domain based on a bool algebra which uses solid and hollow polygons. The general calculus relations of the geometrical characteristics that are widely used in mechanical engineering are tested using several shapes of the calculus domain in order to draw conclusions regarding the most effective methods to discretize the domain. The paper also tests the results of several CAD commercial software applications which are able to compute the geometrical characteristics, being drawn interesting conclusions. The tests were also targeting the accuracy of the results vs. the number of nodes on the curved boundary of the cross section. The study required the development of an original software consisting of more than 1700 computer code lines. In comparison with other calculus methods, the discretization using convex polygons is a simpler approach. Moreover, this method doesn't lead to large numbers as the spline approximation did, in that case being required special software packages in order to offer multiple, arbitrary precision. The knowledge resulted from this study may be used to develop complex computer based models in engineering.

Movement of gating machinery during the activation of rod cyclic nucleotide-gated channels.

PubMed Central

Brown, R L; Snow, S D; Haley, T L

1998-01-01

In the visual and olfactory systems, cyclic nucleotide-gated (CNG) ion channels convert stimulus-induced changes in the internal concentrations of cGMP and cAMP into changes in membrane potential. Although it is known that significant activation of these channels requires the binding of three or more molecules of ligand, the detailed molecular mechanism remains obscure. We have probed the structural changes that occur during channel activation by using sulfhydryl-reactive methanethiosulfonate (MTS) reagents and N-ethylmaleimide (NEM). When expressed in Xenopus oocytes, the alpha-subunit of the bovine retinal channel forms homomultimeric channels that are activated by cGMP with a K1/2 of approximately 100 microM. Cyclic AMP, on the other hand, is a very poor activator; a saturating concentration elicits only 1% of the maximum current produced by cGMP. Treatment of excised patches with MTS-ethyltrimethylamine (MTSET) or NEM dramatically potentiated the channel's response to both cyclic nucleotides. After MTSET treatment, the dose-response relation for cGMP was shifted by over two orders of magnitude to lower concentrations. The effect on channel activation by cAMP was even more striking. After modification, the channels were fully activated by cAMP with a K1/2 of approximately 60 microM. This potentiation was abolished by conversion of Cys481 to a nonreactive alanine residue. Potentiation occurred more rapidly in the presence of saturating cGMP, indicating that this region of the channel is more accessible when the channel is open. Cys481 is located in a linker region between the transmembrane and cGMP-binding domains of the channel. These results suggest that this region of the channel undergoes significant movement during the activation process and is critical for coupling ligand binding to pore opening. Potentiation, however, is not mediated by the recently reported interaction between the amino- and carboxy-terminal regions of the alpha-subunit. Deletion of the

Cyclic Load Effects on Long Term Behavior of Polymer Matrix Composites

NASA Technical Reports Server (NTRS)

Shah, A. R.; Chamis, C. C.

1996-01-01

A methodology to compute the fatigue life for different ratios, r, of applied stress to the laminate strength based on first ply failure criteria combined with thermal cyclic loads has been developed and demonstrated. Degradation effects resulting from long term environmental exposure and thermo-mechanical cyclic loads are considered in the simulation process. A unified time-stress dependent multi-factor interaction equation model developed at NASA Lewis Research Center has been used to account for the degradation of material properties caused by cyclic and aging loads. Effect of variation in the thermal cyclic load amplitude on a quasi-symmetric graphite/epoxy laminate has been studied with respect to the impending failure modes. The results show that, for the laminate under consideration, the fatigue life under combined mechanical and low thermal amplitude cyclic loads is higher than that due to mechanical loads only. However, as the thermal amplitude increases, the life also decreases. The failure mode changes from tensile under mechanical loads only to the compressive and shear at high mechanical and thermal loads. Also, implementation of the developed methodology in the design process has been discussed.

Cyclic Boronates Inhibit All Classes of β-Lactamases

PubMed Central

Cain, Ricky; Wang, David Y.; Lohans, Christopher T.; Wareham, David W.; Oswin, Henry P.; Mohammed, Jabril; Spencer, James; Fishwick, Colin W. G.; McDonough, Michael A.

2017-01-01

ABSTRACT β-Lactamase-mediated resistance is a growing threat to the continued use of β-lactam antibiotics. The use of the β-lactam-based serine-β-lactamase (SBL) inhibitors clavulanic acid, sulbactam, and tazobactam and, more recently, the non-β-lactam inhibitor avibactam has extended the utility of β-lactams against bacterial infections demonstrating resistance via these enzymes. These molecules are, however, ineffective against the metallo-β-lactamases (MBLs), which catalyze their hydrolysis. To date, there are no clinically available metallo-β-lactamase inhibitors. Coproduction of MBLs and SBLs in resistant infections is thus of major clinical concern. The development of “dual-action” inhibitors, targeting both SBLs and MBLs, is of interest, but this is considered difficult to achieve due to the structural and mechanistic differences between the two enzyme classes. We recently reported evidence that cyclic boronates can inhibit both serine- and metallo-β-lactamases. Here we report that cyclic boronates are able to inhibit all four classes of β-lactamase, including the class A extended spectrum β-lactamase CTX-M-15, the class C enzyme AmpC from Pseudomonas aeruginosa, and class D OXA enzymes with carbapenem-hydrolyzing capabilities. We demonstrate that cyclic boronates can potentiate the use of β-lactams against Gram-negative clinical isolates expressing a variety of β-lactamases. Comparison of a crystal structure of a CTX-M-15:cyclic boronate complex with structures of cyclic boronates complexed with other β-lactamases reveals remarkable conservation of the small-molecule binding mode, supporting our proposal that these molecules work by mimicking the common tetrahedral anionic intermediate present in both serine- and metallo-β-lactamase catalysis. PMID:28115348

High temperature cyclic oxidation data. Part 1: Turbine alloys

NASA Technical Reports Server (NTRS)

Barrett, Charles A.; Garlick, Ralph G.; Lowell, Carl E.

1989-01-01

Specific-weight-change-versus-time data and x ray diffraction results are presented derived from high temperature cyclic tests on high temperature, high strength nickel-base gamma/gamma prime and cobalt-base turbine alloys. Each page of data summarizes a complete test on a given alloy sample.

Effect of material inhomogeneity on the cyclic plastic deformation behavior at the microstructural level: micromechanics-based modeling of dual-phase steel

NASA Astrophysics Data System (ADS)

Paul, Surajit Kumar

2013-07-01

The microstructure of dual-phase (DP) steels typically consists of a soft ferrite matrix with dispersed islands of hard martensite phase. Due to the composite effect of ferrite and martensite, DP steels exhibit a unique combination of strain hardening, strength and ductility. A microstructure-based micromechanical modeling approach is adopted in this work to capture the tensile and cyclic plastic deformation behavior of DP steel. During tensile straining, strain incompatibility between the softer ferrite matrix and the harder martensite phase arises due to a difference in the flow characteristics of these two phases. Microstructural-level inhomogeneity serves as the initial imperfection, triggering strain incompatibility, strain partitioning and finally shear band localization during tensile straining. The local deformation in the ferrite phase is constrained by adjacent martensite islands, which locally results in stress triaxiality development in the ferrite phase. As the martensite distribution varies within the microstructure, the stress triaxiality also varies in a band within the microstructure. Inhomogeneous stress and strain distribution within the softer ferrite phase arises even during small tensile straining because of material inhomogeneity. The magnitude of cyclic plastic deformation within the softer ferrite phase also varies according to the stress distribution in the first-quarter cycle tensile loading. Accumulation of tensile/compressive plastic strain with number of cycles is noted in different locations within the ferrite phase during both symmetric stress and strain controlled cycling. The basic mode of cyclic plastic deformation in an inhomogeneous material is cyclic strain accumulation, i.e. ratcheting. Microstructural inhomogeneity results in cyclic strain accumulation in the aggregate DP material even in symmetric stress cycling.

Numerical time-domain electromagnetics based on finite-difference and convolution

NASA Astrophysics Data System (ADS)

Lin, Yuanqu

Time-domain methods posses a number of advantages over their frequency-domain counterparts for the solution of wideband, nonlinear, and time varying electromagnetic scattering and radiation phenomenon. Time domain integral equation (TDIE)-based methods, which incorporate the beneficial properties of integral equation method, are thus well suited for solving broadband scattering problems for homogeneous scatterers. Widespread adoption of TDIE solvers has been retarded relative to other techniques by their inefficiency, inaccuracy and instability. Moreover, two-dimensional (2D) problems are especially problematic, because 2D Green's functions have infinite temporal support, exacerbating these difficulties. This thesis proposes a finite difference delay modeling (FDDM) scheme for the solution of the integral equations of 2D transient electromagnetic scattering problems. The method discretizes the integral equations temporally using first- and second-order finite differences to map Laplace-domain equations into the Z domain before transforming to the discrete time domain. The resulting procedure is unconditionally stable because of the nature of the Laplace- to Z-domain mapping. The first FDDM method developed in this thesis uses second-order Lagrange basis functions with Galerkin's method for spatial discretization. The second application of the FDDM method discretizes the space using a locally-corrected Nystrom method, which accelerates the precomputation phase and achieves high order accuracy. The Fast Fourier Transform (FFT) is applied to accelerate the marching-on-time process in both methods. While FDDM methods demonstrate impressive accuracy and stability in solving wideband scattering problems for homogeneous scatterers, they still have limitations in analyzing interactions between several inhomogenous scatterers. Therefore, this thesis devises a multi-region finite-difference time-domain (MR-FDTD) scheme based on domain-optimal Green's functions for solving

SSME structural dynamic model development, phase 2

NASA Technical Reports Server (NTRS)

Foley, M. J.; Wilson, V. L.

1985-01-01

A set of test correlated mathematical models of the SSME High Pressure Oxygen Turbopump (HPOTP) housing and rotor assembly was produced. New analysis methods within the EISI/EAL and SPAR systems were investigated and runstreams for future use were developed. The LOX pump models have undergone extensive modification since the first phase of this effort was completed. The rotor assembly from the original model was abandoned and a new, more detailed model constructed. A description of the new rotor math model is presented. Also, the pump housing model was continually modified as additional test data have become available. This model is documented along with measured test results. Many of the more advanced features of the EAL/SPAR finite element analysis system were exercised. These included the cyclic symmetry option, the macro-element procedures, and the fluid analysis capability. In addition, a new tool was developed that allows an automated analysis of a disjoint structure in terms of its component modes. A complete description of the implementation of the Craig-Bampton method is given along with two worked examples.

CoMoDo: identifying dynamic protein domains based on covariances of motion.

PubMed

Wieninger, Silke A; Ullmann, G Matthias

2015-06-09

Most large proteins are built of several domains, compact units which enable functional protein motions. Different domain assignment approaches exist, which mostly rely on concepts of stability, folding, and evolution. We describe the automatic assignment method CoMoDo, which identifies domains based on protein dynamics. Covariances of atomic fluctuations, here calculated by an Elastic Network Model, are used to group residues into domains of different hierarchical levels. The so-called dynamic domains facilitate the study of functional protein motions involved in biological processes like ligand binding and signal transduction. By applying CoMoDo to a large number of proteins, we demonstrate that dynamic domains exhibit features absent in the commonly assigned structural domains, which can deliver insight into the interactions between domains and between subunits of multimeric proteins. CoMoDo is distributed as free open source software at www.bisb.uni-bayreuth.de/CoMoDo.html .

Nonlinear behavior of shells of revolution under cyclic loading.

NASA Technical Reports Server (NTRS)

Levine, H. S.; Armen, H., Jr.; Winter, R.; Pifko, A.

1973-01-01

A large deflection elastic-plastic analysis is presented applicable to orthotropic axisymmetric plates and shells of revolution subjected to monotonic and cyclic loading conditions. The analysis is based on the finite-element method. It employs a new higher order, fully compatible, doubly curved orthotropic shell-of-revolution element using cubic Hermitian expansions for both meridional and normal displacements. Both perfectly plastic and strain hardening behavior are considered. Strain hardening is incorporated through use of the Prager-Ziegler kinematic hardening theory, which predicts an ideal Bauschinger effect. Numerous sample problems involving monotonic and cyclic loading conditions are analyzed.

Temperature-responsive in situ nanoparticle hydrogels based on hydrophilic pendant cyclic ether modified PEG-PCL-PEG.

PubMed

Feng, Zujian; Zhao, Junqiang; Li, Yin; Xu, Shuxin; Zhou, Junhui; Zhang, Jianhua; Deng, Liandong; Dong, Anjie

2016-10-20

Thermo-sensitive injectable hydrogels based on poly(ε-caprolactone)/poly(ethylene glycol) (PCL/PEG) block copolymers have attracted considerable attention for sustained drug release and tissue engineering applications. Previously, we have reported a thermo-sensitive hydrogel of P(CL-co-TOSUO)-PEG-P(CL-co-TOSUO) (PECT) triblock copolymers modified by hydrophilic cyclic ether pendant groups 1,4,8-trioxa-[4.6]spiro-9-undecanone (TOSUO). Unfortunately, the low gel modulus of PECT (only 50-70 Pa) may limit its applications. Herein, another kind of thermogelling triblock copolymer of a pendant cyclic ether-modified caprolactonic poloxamer analog, PEG-P(CL-co-TOSUO)-PEG (PECTE), was successfully prepared by control of the hydrophilicity/hydrophobicity balance and chemical compositions of the copolymers. PECTE powder could directly disperse in water to form a stable nanoparticle (NP) aqueous dispersion and underwent sol-gel-sol transition behavior at a higher concentration with the temperature increasing from ambient or lower temperatures. Significantly, the microstructure parameters (e.g., different chemical compositions of the hydrophobic block and topology) played a critical role in the phase transition behavior. Furthermore, comparison studies on PECTE and PEG-PCL-PEG (PECE) showed that the introduction of pendant cyclic ether groups into PCL blocks could avoid unexpected ahead-of-time gelling of the PECE aqueous solution. In addition, the rheological analysis of PECTE and PECT indicated that the storage modulus of the PECTE hydrogel could be 100 times greater than that of the PECT hydrogel under the same mole ratios of TOSUO/CL and lower molecular weight. Consequently, PECTE thermal hydrogel systems are believed to be promising as in situ gel-forming biomaterials for drug delivery and tissue engineering.

How many molecules are required to measure a cyclic voltammogram?

NASA Astrophysics Data System (ADS)

Cutress, Ian J.; Compton, Richard G.

2011-05-01

The stochastic limit at which fully-reversible cyclic voltammetry can accurately be measured is investigated. Specifically, Monte Carlo GPU simulation is used to study low concentration cyclic voltammetry at a microdisk electrode over a range of scan rates and concentrations, and the results compared to the statistical limit as predicted by finite difference simulation based on Fick's Laws of Diffusion. Both Butler-Volmer and Marcus-Hush electrode kinetics are considered, simulated via random-walk methods, and shown to give identical results in the fast kinetic limit.

Optimal Couple Projections for Domain Adaptive Sparse Representation-based Classification.

PubMed

Zhang, Guoqing; Sun, Huaijiang; Porikli, Fatih; Liu, Yazhou; Sun, Quansen

2017-08-29

In recent years, sparse representation based classification (SRC) is one of the most successful methods and has been shown impressive performance in various classification tasks. However, when the training data has a different distribution than the testing data, the learned sparse representation may not be optimal, and the performance of SRC will be degraded significantly. To address this problem, in this paper, we propose an optimal couple projections for domain-adaptive sparse representation-based classification (OCPD-SRC) method, in which the discriminative features of data in the two domains are simultaneously learned with the dictionary that can succinctly represent the training and testing data in the projected space. OCPD-SRC is designed based on the decision rule of SRC, with the objective to learn coupled projection matrices and a common discriminative dictionary such that the between-class sparse reconstruction residuals of data from both domains are maximized, and the within-class sparse reconstruction residuals of data are minimized in the projected low-dimensional space. Thus, the resulting representations can well fit SRC and simultaneously have a better discriminant ability. In addition, our method can be easily extended to multiple domains and can be kernelized to deal with the nonlinear structure of data. The optimal solution for the proposed method can be efficiently obtained following the alternative optimization method. Extensive experimental results on a series of benchmark databases show that our method is better or comparable to many state-of-the-art methods.

Effective domain-dependent reuse in medical knowledge bases.

PubMed

Dojat, M; Pachet, F

1995-12-01

Knowledge reuse is now a critical issue for most developers of medical knowledge-based systems. As a rule, reuse is addressed from an ambitious, knowledge-engineering perspective that focuses on reusable general purpose knowledge modules, concepts, and methods. However, such a general goal fails to take into account the specific aspects of medical practice. From the point of view of the knowledge engineer, whose goal is to capture the specific features and intricacies of a given domain, this approach addresses the wrong level of generality. In this paper, we adopt a more pragmatic viewpoint, introducing the less ambitious goal of "domain-dependent limited reuse" and suggesting effective means of achieving it in practice. In a knowledge representation framework combining objects and production rules, we propose three mechanisms emerging from the combination of object-oriented programming and rule-based programming. We show these mechanisms contribute to achieve limited reuse and to introduce useful limited variations in medical expertise.

MARS-MD: rejection based image domain material decomposition

NASA Astrophysics Data System (ADS)

Bateman, C. J.; Knight, D.; Brandwacht, B.; McMahon, J.; Healy, J.; Panta, R.; Aamir, R.; Rajendran, K.; Moghiseh, M.; Ramyar, M.; Rundle, D.; Bennett, J.; de Ruiter, N.; Smithies, D.; Bell, S. T.; Doesburg, R.; Chernoglazov, A.; Mandalika, V. B. H.; Walsh, M.; Shamshad, M.; Anjomrouz, M.; Atharifard, A.; Vanden Broeke, L.; Bheesette, S.; Kirkbride, T.; Anderson, N. G.; Gieseg, S. P.; Woodfield, T.; Renaud, P. F.; Butler, A. P. H.; Butler, P. H.

2018-05-01

This paper outlines image domain material decomposition algorithms that have been routinely used in MARS spectral CT systems. These algorithms (known collectively as MARS-MD) are based on a pragmatic heuristic for solving the under-determined problem where there are more materials than energy bins. This heuristic contains three parts: (1) splitting the problem into a number of possible sub-problems, each containing fewer materials; (2) solving each sub-problem; and (3) applying rejection criteria to eliminate all but one sub-problem's solution. An advantage of this process is that different constraints can be applied to each sub-problem if necessary. In addition, the result of this process is that solutions will be sparse in the material domain, which reduces crossover of signal between material images. Two algorithms based on this process are presented: the Segmentation variant, which uses segmented material classes to define each sub-problem; and the Angular Rejection variant, which defines the rejection criteria using the angle between reconstructed attenuation vectors.

Knowledge-based approach for generating target system specifications from a domain model

NASA Technical Reports Server (NTRS)

Gomaa, Hassan; Kerschberg, Larry; Sugumaran, Vijayan

1992-01-01

Several institutions in industry and academia are pursuing research efforts in domain modeling to address unresolved issues in software reuse. To demonstrate the concepts of domain modeling and software reuse, a prototype software engineering environment is being developed at George Mason University to support the creation of domain models and the generation of target system specifications. This prototype environment, which is application domain independent, consists of an integrated set of commercial off-the-shelf software tools and custom-developed software tools. This paper describes the knowledge-based tool that was developed as part of the environment to generate target system specifications from a domain model.

Characterization of the 2′,3′ cyclic phosphodiesterase activities of Clostridium thermocellum polynucleotide kinase-phosphatase and bacteriophage λ phosphatase

PubMed Central

Keppetipola, Niroshika; Shuman, Stewart

2007-01-01

Clostridium thermocellum polynucleotide kinase-phosphatase (CthPnkp) catalyzes 5′ and 3′ end-healing reactions that prepare broken RNA termini for sealing by RNA ligase. The central phosphatase domain of CthPnkp belongs to the dinuclear metallophosphoesterase superfamily exemplified by bacteriophage λ phosphatase (λ-Pase). CthPnkp is a Ni2+/Mn2+-dependent phosphodiesterase-monoesterase, active on nucleotide and non-nucleotide substrates, that can be transformed toward narrower metal and substrate specificities via mutations of the active site. Here we characterize the Mn2+-dependent 2′,3′ cyclic nucleotide phosphodiesterase activity of CthPnkp, the reaction most relevant to RNA repair pathways. We find that CthPnkp prefers a 2′,3′ cyclic phosphate to a 3′,5′ cyclic phosphate. A single H189D mutation imposes strict specificity for a 2′,3′ cyclic phosphate, which is cleaved to form a single 2′-NMP product. Analysis of the cyclic phosphodiesterase activities of mutated CthPnkp enzymes illuminates the active site and the structural features that affect substrate affinity and kcat. We also characterize a previously unrecognized phosphodiesterase activity of λ-Pase, which catalyzes hydrolysis of bis-p-nitrophenyl phosphate. λ-Pase also has cyclic phosphodiesterase activity with nucleoside 2′,3′ cyclic phosphates, which it hydrolyzes to yield a mixture of 2′-NMP and 3′-NMP products. We discuss our results in light of available structural and functional data for other phosphodiesterase members of the binuclear metallophosphoesterase family and draw inferences about how differences in active site composition influence catalytic repertoire. PMID:17986465

Cyclic tensile strain and cyclic hydrostatic pressure differentially regulate expression of hypertrophic markers in primary chondrocytes.

PubMed

Wong, Marcy; Siegrist, Mark; Goodwin, Kelly

2003-10-01

Endochondral ossification is regulated by many factors, including mechanical stimuli, which can suppress or accelerate chondrocyte maturation. Mathematical models of endochondral ossification have suggested that tension (or shear stress) can accelerate the formation of endochondral bone, while hydrostatic stress preserves the cartilage phenotype. The goal of this study was to test this hypothesis by examining the expression of hypertrophic chondrocyte markers (transcription factor Cbfa1, MMP-13, type X collagen, VEGF, CTGF) and cartilage matrix proteins under cyclic tension and cyclic hydrostatic pressure. Chondrocyte-seeded alginate constructs were exposed to one of the two loading modes for a period of 3 h per day for 3 days. Gene expression was analyzed using real-time RT-PCR. Cyclic tension upregulated the expression of Cbfa1, MMP-13, CTGF, type X collagen and VEGF and downregulated the expression of TIMP-1. Cyclic tension also upregulated the expression of type 2 collagen, COMP and lubricin, but did not change the expression of SOX9 and aggrecan. Cyclic hydrostatic pressure downregulated the expression of MMP-13 and type I collagen and upregulated expression of TIMP-1 compared to the unloaded controls. Hydrostatic pressure may slow chondrocyte differentiation and have a chondroprotective, anti-angiogenic influence on cartilage tissue. Our results suggest that cyclic tension activates the Cbfa1/MMP-13 pathway and increases the expression of terminal differentiation hypertrophic markers. Mammalian chondrocytes appear to have evolved complex mechanoresponsive mechanisms, the effects of which can be observed in the histomorphologic establishment of the cartilaginous skeleton during development and maturation.

Revisiting the formation of cyclic clusters in liquid ethanol

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

Balanay, Mannix P.; Fan, Haiyan, E-mail: haiyan.fan@nu.edu.kz; Kim, Dong Hee

2016-04-21

The liquid phase of ethanol in pure and in non-polar solvents was studied at room temperature using Fourier transform infrared (FT-IR) and {sup 1}H nuclear magnetic resonance (NMR) spectroscopies together with theoretical approach. The FT-IR spectra for pure ethanol and solution in cyclohexane at different dilution stages are consistent with {sup 1}H NMR results. The results from both methods were best explained by the results of the density functional theory based on a multimeric model. It is suggested that cyclic trimers and tetramers are dominated in the solution of cyclohexane/hexane with the concentration greater than 0.5M at room temperature. Inmore » liquid ethanol, while the primary components at room temperature are cyclic trimers and tetramers, there is a certain amount (∼14%) of open hydroxide group representing the existence of chain like structures in the equilibria. The cyclic cluster model in the liquid and concentrated solution phase (>0.5M) can be used to explain the anomalously lower freezing point of ethanol (159 K) than that of water (273 K) at ambient conditions. In addition, {sup 1}H NMR at various dilution stages reveals the dynamics for the formation of cyclic clusters.« less

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures

PubMed Central

2012-01-01

Background The NCBI Conserved Domain Database (CDD) consists of a collection of multiple sequence alignments of protein domains that are at various stages of being manually curated into evolutionary hierarchies based on conserved and divergent sequence and structural features. These domain models are annotated to provide insights into the relationships between sequence, structure and function via web-based BLAST searches. Results Here we automate the generation of conserved domain (CD) hierarchies using a combination of heuristic and Markov chain Monte Carlo (MCMC) sampling procedures and starting from a (typically very large) multiple sequence alignment. This procedure relies on statistical criteria to define each hierarchy based on the conserved and divergent sequence patterns associated with protein functional-specialization. At the same time this facilitates the sequence and structural annotation of residues that are functionally important. These statistical criteria also provide a means to objectively assess the quality of CD hierarchies, a non-trivial task considering that the protein subgroups are often very distantly related—a situation in which standard phylogenetic methods can be unreliable. Our aim here is to automatically generate (typically sub-optimal) hierarchies that, based on statistical criteria and visual comparisons, are comparable to manually curated hierarchies; this serves as the first step toward the ultimate goal of obtaining optimal hierarchical classifications. A plot of runtimes for the most time-intensive (non-parallelizable) part of the algorithm indicates a nearly linear time complexity so that, even for the extremely large Rossmann fold protein class, results were obtained in about a day. Conclusions This approach automates the rapid creation of protein domain hierarchies and thus will eliminate one of the most time consuming aspects of conserved domain database curation. At the same time, it also facilitates protein domain

Domain-Generality of Timing-Based Serial Order Processes in Short-Term Memory: New Insights from Musical and Verbal Domains

PubMed Central

Kowialiewski, Benjamin; Majerus, Steve

2016-01-01

Several models in the verbal domain of short-term memory (STM) consider a dissociation between item and order processing. This view is supported by data demonstrating that different types of time-based interference have a greater effect on memory for the order of to-be-remembered items than on memory for the items themselves. The present study investigated the domain-generality of the item versus serial order dissociation by comparing the differential effects of time-based interfering tasks, such as rhythmic interference and articulatory suppression, on item and order processing in verbal and musical STM domains. In Experiment 1, participants had to maintain sequences of verbal or musical information in STM, followed by a probe sequence, this under different conditions of interference (no-interference, rhythmic interference, articulatory suppression). They were required to decide whether all items of the probe list matched those of the memory list (item condition) or whether the order of the items in the probe sequence matched the order in the memory list (order condition). In Experiment 2, participants performed a serial order probe recognition task for verbal and musical sequences ensuring sequential maintenance processes, under no-interference or rhythmic interference conditions. For Experiment 1, serial order recognition was not significantly more impacted by interfering tasks than was item recognition, this for both verbal and musical domains. For Experiment 2, we observed selective interference of the rhythmic interference condition on both musical and verbal order STM tasks. Overall, the results suggest a similar and selective sensitivity to time-based interference for serial order STM in verbal and musical domains, but only when the STM tasks ensure sequential maintenance processes. PMID:27992565

Domain-Generality of Timing-Based Serial Order Processes in Short-Term Memory: New Insights from Musical and Verbal Domains.

PubMed

Gorin, Simon; Kowialiewski, Benjamin; Majerus, Steve

2016-01-01

Several models in the verbal domain of short-term memory (STM) consider a dissociation between item and order processing. This view is supported by data demonstrating that different types of time-based interference have a greater effect on memory for the order of to-be-remembered items than on memory for the items themselves. The present study investigated the domain-generality of the item versus serial order dissociation by comparing the differential effects of time-based interfering tasks, such as rhythmic interference and articulatory suppression, on item and order processing in verbal and musical STM domains. In Experiment 1, participants had to maintain sequences of verbal or musical information in STM, followed by a probe sequence, this under different conditions of interference (no-interference, rhythmic interference, articulatory suppression). They were required to decide whether all items of the probe list matched those of the memory list (item condition) or whether the order of the items in the probe sequence matched the order in the memory list (order condition). In Experiment 2, participants performed a serial order probe recognition task for verbal and musical sequences ensuring sequential maintenance processes, under no-interference or rhythmic interference conditions. For Experiment 1, serial order recognition was not significantly more impacted by interfering tasks than was item recognition, this for both verbal and musical domains. For Experiment 2, we observed selective interference of the rhythmic interference condition on both musical and verbal order STM tasks. Overall, the results suggest a similar and selective sensitivity to time-based interference for serial order STM in verbal and musical domains, but only when the STM tasks ensure sequential maintenance processes.

Video repairing under variable illumination using cyclic motions.

PubMed

Jia, Jiaya; Tai, Yu-Wing; Wu, Tai-Pang; Tang, Chi-Keung

2006-05-01

This paper presents a complete system capable of synthesizing a large number of pixels that are missing due to occlusion or damage in an uncalibrated input video. These missing pixels may correspond to the static background or cyclic motions of the captured scene. Our system employs user-assisted video layer segmentation, while the main processing in video repair is fully automatic. The input video is first decomposed into the color and illumination videos. The necessary temporal consistency is maintained by tensor voting in the spatio-temporal domain. Missing colors and illumination of the background are synthesized by applying image repairing. Finally, the occluded motions are inferred by spatio-temporal alignment of collected samples at multiple scales. We experimented on our system with some difficult examples with variable illumination, where the capturing camera can be stationary or in motion.

A web-based system architecture for ontology-based data integration in the domain of IT benchmarking

NASA Astrophysics Data System (ADS)

Pfaff, Matthias; Krcmar, Helmut

2018-03-01

In the domain of IT benchmarking (ITBM), a variety of data and information are collected. Although these data serve as the basis for business analyses, no unified semantic representation of such data yet exists. Consequently, data analysis across different distributed data sets and different benchmarks is almost impossible. This paper presents a system architecture and prototypical implementation for an integrated data management of distributed databases based on a domain-specific ontology. To preserve the semantic meaning of the data, the ITBM ontology is linked to data sources and functions as the central concept for database access. Thus, additional databases can be integrated by linking them to this domain-specific ontology and are directly available for further business analyses. Moreover, the web-based system supports the process of mapping ontology concepts to external databases by introducing a semi-automatic mapping recommender and by visualizing possible mapping candidates. The system also provides a natural language interface to easily query linked databases. The expected result of this ontology-based approach of knowledge representation and data access is an increase in knowledge and data sharing in this domain, which will enhance existing business analysis methods.

A protein domain-based interactome network for C. elegans early embryogenesis

PubMed Central

Boxem, Mike; Maliga, Zoltan; Klitgord, Niels; Li, Na; Lemmens, Irma; Mana, Miyeko; de Lichtervelde, Lorenzo; Mul, Joram D.; van de Peut, Diederik; Devos, Maxime; Simonis, Nicolas; Yildirim, Muhammed A.; Cokol, Murat; Kao, Huey-Ling; de Smet, Anne-Sophie; Wang, Haidong; Schlaitz, Anne-Lore; Hao, Tong; Milstein, Stuart; Fan, Changyu; Tipsword, Mike; Drew, Kevin; Galli, Matilde; Rhrissorrakrai, Kahn; Drechsel, David; Koller, Daphne; Roth, Frederick P.; Iakoucheva, Lilia M.; Dunker, A. Keith; Bonneau, Richard; Gunsalus, Kristin C.; Hill, David E.; Piano, Fabio; Tavernier, Jan; van den Heuvel, Sander; Hyman, Anthony A.; Vidal, Marc

2008-01-01

Summary Many protein-protein interactions are mediated through independently folding modular domains. Proteome-wide efforts to model protein-protein interaction or “interactome” networks have largely ignored this modular organization of proteins. We developed an experimental strategy to efficiently identify interaction domains and generated a domain-based interactome network for proteins involved in C. elegans early embryonic cell divisions. Minimal interacting regions were identified for over 200 proteins, providing important information on their domain organization. Furthermore, our approach increased the sensitivity of the two-hybrid system, resulting in a more complete interactome network. This interactome modeling strategy revealed new insights into C. elegans centrosome function and is applicable to other biological processes in this and other organisms. PMID:18692475

Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP

PubMed Central

Wang, Xin C.; Wilson, Stephen C.; Hammond, Ming C.

2016-01-01

Bacteria occupy a diverse set of environmental niches with differing oxygen availability. Anaerobic environments such as mammalian digestive tracts and industrial reactors harbor an abundance of both obligate and facultative anaerobes, many of which play significant roles in human health and biomanufacturing. Studying bacterial function under partial or fully anaerobic conditions, however, is challenging given the paucity of suitable live-cell imaging tools. Here, we introduce a series of RNA-based fluorescent biosensors that respond selectively to cyclic di-GMP, an intracellular bacterial second messenger that controls cellular motility and biofilm formation. We demonstrate the utility of these biosensors in vivo under both aerobic and anaerobic conditions, and we show that biosensor expression does not interfere with the native motility phenotype. Together, our results attest to the effectiveness and versatility of RNA-based fluorescent biosensors, priming further development and application of these and other analogous sensors to study host–microbial and microbial–microbial interactions through small molecule signals. PMID:27382070

Design of Cyclic Peptide Based Glucose Receptors and Their Application in Glucose Sensing.

PubMed

Li, Chao; Chen, Xin; Zhang, Fuyuan; He, Xingxing; Fang, Guozhen; Liu, Jifeng; Wang, Shuo

2017-10-03

Glucose assay is of great scientific significance in clinical diagnostics and bioprocess monitoring, and to design a new glucose receptor is necessary for the development of more sensitive, selective, and robust glucose detection techniques. Herein, a series of cyclic peptide (CP) glucose receptors were designed to mimic the binding sites of glucose binding protein (GBP), and CPs' sequence contained amino acid sites Asp, Asn, His, Asp, and Arg, which constituted the first layer interactions of GBP. The properties of these CPs used as a glucose receptor or substitute for the GBP were studied by using a quartz crystal microbalance (QCM) technique. It was found that CPs can form a self-assembled monolayer at the Au quartz electrode surface, and the monolayer's properties were characterized by using cyclic voltammetry, electrochemical impedance spectroscopy, and atomic force microscopy. The CPs' binding affinity to saccharide (i.e., galactose, fructose, lactose, sucrose, and maltose) was investigated, and the CPs' sensitivity and selectivity toward glucose were found to be dependent upon the configuration,i.e., the amino acids sequence of the CPs. The cyclic unit with a cyclo[-CNDNHCRDNDC-] sequence gave the highest selectivity and sensitivity for glucose sensing. This work suggests that a synthetic peptide bearing a particular functional sequence could be applied for developing a new generation of glucose receptors and would find huge application in biological, life science, and clinical diagnostics fields.

Solid-phase receptor-based assay for the detection of cyclic imines by chemiluminescence, fluorescence, or colorimetry.

PubMed

Rodríguez, Laura P; Vilariño, Natalia; Molgó, Jordi; Aráoz, Rómulo; Antelo, Alvaro; Vieytes, Mercedes R; Botana, Luis M

2011-08-01

The spirolides and gymnodimines are marine phycotoxins included in the group of cyclic imines. The toxicity of these compounds to humans is still unknown, although their toxicity by intraperitoneal injection in rodents is very high. A receptor-based method was developed using the competition of the 13-desmethyl spirolide C with biotin-labeled α-bungarotoxin for binding to nicotinic acetylcholine receptors and the immobilization of the α-bungarotoxin-receptor complex on streptavidin-coated surfaces. The quantification of the immobilized receptor can be achieved using a specific antibody. Finally, after the addition of a secondary antibody labeled with horseradish peroxidase, three alternative substrates of this enzyme generate a chemiluminescent, fluorescent, or colorimetric signal. The assay performs well in shellfish extracts and the detection range is 5-150 nM of 13-desmethyl spirolide C in shellfish extracts, which is at least 5 times more sensitive than the existing fluorescence polarization assay. This assay can also detect gymnodimine, although with 10 times lower sensitivity than the spirolide. The detection of cyclic imines with microplate assays would be useful for screening purposes in order to reduce the number of samples to be processed by bioassays or analytical methods.

DOGMA: domain-based transcriptome and proteome quality assessment.

PubMed

Dohmen, Elias; Kremer, Lukas P M; Bornberg-Bauer, Erich; Kemena, Carsten

2016-09-01

Genome studies have become cheaper and easier than ever before, due to the decreased costs of high-throughput sequencing and the free availability of analysis software. However, the quality of genome or transcriptome assemblies can vary a lot. Therefore, quality assessment of assemblies and annotations are crucial aspects of genome analysis pipelines. We developed DOGMA, a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds. DOGMA is implemented in Python and published under GNU GPL v.3 license. The source code is available on https://ebbgit.uni-muenster.de/domainWorld/DOGMA/ CONTACTS: e.dohmen@wwu.de or c.kemena@wwu.de Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

[Erythromycin in therapy of cyclic vomiting syndrome].

PubMed

Pavlović, Momcilo; Radlović, Nedeljko; Leković, Zoran; Berenji, Karolina

2007-01-01

Cyclic vomiting syndrome is an insufficiently understood disorder which manifests itself in stereotypical episodes of vomiting with no detectable organic cause. Considering its unknown aetiology, drugs borrowed from various medication classes are applied in the therapy of this disorder, with variable success. Among other medicaments, erythromycin is also used in treatment of cyclic vomiting syndrome. This is a case study in which the application of erythromycin led to the prevention of attacks of cyclic vomiting syndrome. Our case report presents how periodical erythromycin therapy in two-week intervals at expected attack periods in a girl led to disappearance of cyclic vomiting. Adverse effects of erythromycin did not show up.

[Cyclic Cushing's Syndrome - rare or rarely recognized].

PubMed

Kiałka, Marta; Doroszewska, Katarzyna; Mrozińska, Sandra; Milewicz, Tomasz; Stochmal, Ewa

2015-01-01

Cyclic Cushing's syndrome is a type of Cushing's disease which is characterized by alternating periods of increasing and decreasing levels of cortisol in the blood. The diagnostic criteria for cyclic Cushing's syndrome are at least three periods of hypercortisolism alternating with at least two episodes of normal levels of serum cortisol concentration. The epidemiology, signs, symptoms, pathogenesis and treatment of cyclic Cushing's syndrome have been discussed.

Elevated Aerosol Layers and Their Radiative Impact over Kanpur During Monsoon Onset Period

NASA Technical Reports Server (NTRS)

Sarangi, Chandan; Tripathi, S. N.; Mishra, A. K.; Welton, E. J.

2016-01-01

Accurate information about aerosol vertical distribution is needed to reduce uncertainties in aerosol radiative forcing and its effect on atmospheric dynamics. The present study deals with synergistic analyses of aerosol vertical distribution and aerosol optical depth (AOD) with meteorological variables using multisatellite and ground-based remote sensors over Kanpur in central Indo-Gangetic Plain (IGP). Micro-Pulse Lidar Network-derived aerosol vertical extinction (sigma) profiles are analyzed to quantify the interannual and daytime variations during monsoon onset period (May-June) for 2009-2011. The mean aerosol profile is broadly categorized into two layers viz., a surface layer (SL) extending up to 1.5 km (where sigma decreased exponentially with height) and an elevated aerosol layer (EAL) extending between 1.5 and 5.5 km. The increase in total columnar aerosol loading is associated with relatively higher increase in contribution from EAL loading than that from SL. The mean contributions of EALs are about 60%, 51%, and 50% to total columnar AOD during 2009, 2010, and 2011, respectively. We observe distinct parabolic EALs during early morning and late evening but uniformly mixed EALs during midday. The interannual and daytime variations of EALs are mainly influenced by long-range transport and convective capacity of the local emissions, respectively. Radiative flux analysis shows that clear-sky incoming solar radiation at surface is reduced with increase in AOD, which indicates significant cooling at surface. Collocated analysis of atmospheric temperature and aerosol loading reveals that increase in AOD not only resulted in surface dimming but also reduced the temperature (approximately 2-3 C) of lower troposphere (below 3 km altitude). Radiative transfer simulations indicate that the reduction of incoming solar radiation at surface is mainly due to increased absorption by EALs (with increase in total AOD). The observed cooling in lower troposphere in high

The role of peel stresses in cyclic debonding

NASA Technical Reports Server (NTRS)

Everett, R. A., Jr.

1982-01-01

When an adhesively bonded joint is undergoing cyclic loading, one of the possible damage modes that occurs is called cyclic debonding - progressive separation of the adherends by failure of the adhesive bond under cyclic loading. In most practical structures, both peel and shear stresses exist in the adhesive bonding during cyclic loading. The results of an experimental and analytical study to determine the role of peel stresses on cyclic debonding in a mixed mode specimen are presented. Experimentally, this was done by controlling the forces that create the peel stresses by applying a clamping force to oppose the peel stresses. Cracked lap shear joints were chosen for this study. A finite element analysis was developed to assess the effect of the clamping force on the strain energy release rates due to shear and peel stresses. The results imply that the peel stress is the principal stress causing cyclic debonding.

Effect of Cyclic Thermo-Mechanical Loads on Fatigue Reliability in Polymer Matrix Composites

NASA Technical Reports Server (NTRS)

Shah, A. R.; Murthy, P. L. N.; Chamis, C. C.

1996-01-01

A methodology to compute probabilistic fatigue life of polymer matrix laminated composites has been developed and demonstrated. Matrix degradation effects caused by long term environmental exposure and mechanical/thermal cyclic loads are accounted for in the simulation process. A unified time-temperature-stress dependent multi-factor interaction relationship developed at NASA Lewis Research Center has been used to model the degradation/aging of material properties due to cyclic loads. The fast probability integration method is used to compute probabilistic distribution of response. Sensitivities of fatigue life reliability to uncertainties in the primitive random variables (e.g., constituent properties, fiber volume ratio, void volume ratio, ply thickness, etc.) computed and their significance in the reliability- based design for maximum life is discussed. The effect of variation in the thermal cyclic loads on the fatigue reliability for a (0/+/- 45/90)(sub s) graphite/epoxy laminate with a ply thickness of 0.127 mm, with respect to impending failure modes has been studied. The results show that, at low mechanical cyclic loads and low thermal cyclic amplitudes, fatigue life for 0.999 reliability is most sensitive to matrix compressive strength, matrix modulus, thermal expansion coefficient, and ply thickness. Whereas at high mechanical cyclic loads and high thermal cyclic amplitudes, fatigue life at 0.999 reliability is more sensitive to the shear strength of matrix, longitudinal fiber modulus, matrix modulus, and ply thickness.

Hybrid protection algorithms based on game theory in multi-domain optical networks

NASA Astrophysics Data System (ADS)

Guo, Lei; Wu, Jingjing; Hou, Weigang; Liu, Yejun; Zhang, Lincong; Li, Hongming

2011-12-01

With the network size increasing, the optical backbone is divided into multiple domains and each domain has its own network operator and management policy. At the same time, the failures in optical network may lead to a huge data loss since each wavelength carries a lot of traffic. Therefore, the survivability in multi-domain optical network is very important. However, existing survivable algorithms can achieve only the unilateral optimization for profit of either users or network operators. Then, they cannot well find the double-win optimal solution with considering economic factors for both users and network operators. Thus, in this paper we develop the multi-domain network model with involving multiple Quality of Service (QoS) parameters. After presenting the link evaluation approach based on fuzzy mathematics, we propose the game model to find the optimal solution to maximize the user's utility, the network operator's utility, and the joint utility of user and network operator. Since the problem of finding double-win optimal solution is NP-complete, we propose two new hybrid protection algorithms, Intra-domain Sub-path Protection (ISP) algorithm and Inter-domain End-to-end Protection (IEP) algorithm. In ISP and IEP, the hybrid protection means that the intelligent algorithm based on Bacterial Colony Optimization (BCO) and the heuristic algorithm are used to solve the survivability in intra-domain routing and inter-domain routing, respectively. Simulation results show that ISP and IEP have the similar comprehensive utility. In addition, ISP has better resource utilization efficiency, lower blocking probability, and higher network operator's utility, while IEP has better user's utility.

Structure-based multiscale approach for identification of interaction partners of PDZ domains.

PubMed

Tiwari, Garima; Mohanty, Debasisa

2014-04-28

PDZ domains are peptide recognition modules which mediate specific protein-protein interactions and are known to have a complex specificity landscape. We have developed a novel structure-based multiscale approach which identifies crucial specificity determining residues (SDRs) of PDZ domains from explicit solvent molecular dynamics (MD) simulations on PDZ-peptide complexes and uses these SDRs in combination with knowledge-based scoring functions for proteomewide identification of their interaction partners. Multiple explicit solvent simulations ranging from 5 to 50 ns duration have been carried out on 28 PDZ-peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these simulations show a correlation coefficient of 0.755 with the experimental binding affinities. On the basis of the SDRs of PDZ domains identified by MD simulations, we have developed a simple scoring scheme for evaluating binding energies for PDZ-peptide complexes using residue based statistical pair potentials. This multiscale approach has been benchmarked on a mouse PDZ proteome array data set by calculating the binding energies for 217 different substrate peptides in binding pockets of 64 different mouse PDZ domains. Receiver operating characteristic (ROC) curve analysis indicates that, the area under curve (AUC) values for binder vs nonbinder classification by our structure based method is 0.780. Our structure based method does not require experimental PDZ-peptide binding data for training.

Nonlinear behavior of shells of revolution under cyclic loading

NASA Technical Reports Server (NTRS)

Levine, H. S.; Armen, H., Jr.; Winter, R.; Pifko, A.

1972-01-01

A large deflection elastic-plastic analysis is presented, applicable to orthotropic axisymmetric plates and shells of revolution subjected to monotonic and cyclic loading conditions. The analysis is based on the finite-element method. It employs a new higher order, fully compatible, doubly curved orthotropic shell-of-revolution element using cubic Hermitian expansions for both meridional and normal displacements. Both perfectly plastic and strain hardening behavior are considered. Strain hardening is incorporated through use of the Prager-Ziegler kinematic hardening theory, which predicts an ideal Bauschinger effect. Numerous sample problems involving monotonic and cyclic loading conditions are analyzed. The monotonic results are compared with other theoretical solutions.

A constitutive model for AS4/PEEK thermoplastic composites under cyclic loading

NASA Technical Reports Server (NTRS)

Rui, Yuting; Sun, C. T.

1990-01-01

Based on the basic and essential features of the elastic-plastic response of the AS4/PEEK thermoplastic composite subjected to off-axis cyclic loadings, a simple rate-independent constitutive model is proposed to describe the orthotropic material behavior for cyclic loadings. A one-parameter memory surface is introduced to distinguish the virgin deformation and the subsequent deformation process and to characterize the loading range effect. Cyclic softening is characterized by the change of generalized plastic modulus. By the vanishing yield surface assumption, a yield criterion is not needed and it is not necessary to consider loading and unloading separately. The model is compared with experimental results and good agreement is obtained.

Quantifying effects of cyclic stretch on cell-collagen substrate adhesiveness of vascular endothelial cells.

PubMed

Omidvar, Ramin; Tafazzoli-Shadpour, Mohammad; Mahmoodi-Nobar, Farbod; Azadi, Shohreh; Khani, Mohammad-Mehdi

2018-05-01

Vascular endothelium is continuously subjected to mechanical stimulation in the form of shear forces due to blood flow as well as tensile forces as a consequence of blood pressure. Such stimuli influence endothelial behavior and regulate cell-tissue interaction for an optimized functionality. This study aimed to quantify influence of cyclic stretch on the adhesive property and stiffness of endothelial cells. The 10% cyclic stretch with frequency of 1 Hz was applied to a layer of endothelial cells cultured on a polydimethylsiloxane substrate. Cell-substrate adhesion of endothelial cells was examined by the novel approach of atomic force microscope-based single-cell force spectroscopy and cell stiffness was measured by atomic force microscopy. Furthermore, the adhesive molecular bonds were evaluated using modified Hertz contact theory. Our results show that overall adhesion of endothelial cells with substrate decreased after cyclic stretch while they became stiffer. Based on the experimental results and theoretical modeling, the decrease in the number of molecular bonds after cyclic stretch was quantified. In conclusion, in vitro cyclic stretch caused alterations in both adhesive capacity and elastic modulus of endothelial cells through mechanotransductive pathways as two major determinants of the function of these cells within the cardiovascular system.

A new putative cyclic nucleotide-gated channel gene, cng-3, is critical for thermotolerance in Caenorhabditis elegans.

PubMed

Cho, Suk-Woo; Choi, Kyu Yeong; Park, Chul-Seung

2004-12-10

Cyclic nucleotide-gated (CNG) channels encoded by tax-4 and tax-2 genes are required for chemo- and thermo-sensation in Caenorhabditis elegans. Here we report the identification and the characterization of cng-3, a new CNG channel gene, found in C. elegans. CNG-3 contains six putative transmembrane regions and a cyclic nucleotide-binding domain that show high homology with CNG channels of higher animals as well as TAX-4. The expression of cng-3 is detected from early stages in worm development and restricted in five sensory neurons of amphid including AFD neuron. While a cng-3 null mutant displays normal chemotaxis to volatile odorants, the mutant worms exhibit impaired thermal tolerance. These results indicate that CNG-3, a new member of CNG channel subunits, may play a critical role in sensation or response of thermal stress in C. elegans.

Cyclic membrane separation process

DOEpatents

Bowser, John

2004-04-13

A cyclic process for controlling environmental emissions of volatile organic compounds (VOC) from vapor recovery in storage and dispensing operations of liquids maintains a vacuum in the storage tank ullage. In one of a two-part cyclic process ullage vapor is discharged through a vapor recovery system in which VOC are stripped from vented gas with a selectively gas permeable membrane. In the other part, the membrane is inoperative while gas pressure rises in the ullage. Ambient air is charged to the membrane separation unit during the latter part of the cycle.

Segregation process and phase transition in cyclic predator-prey models with an even number of species.

PubMed

Szabó, György; Szolnoki, Attila; Sznaider, Gustavo Ariel

2007-11-01

We study a spatial cyclic predator-prey model with an even number of species (for n=4, 6, and 8) that allows the formation of two defensive alliances consisting of the even and odd label species. The species are distributed on the sites of a square lattice. The evolution of spatial distribution is governed by iteration of two elementary processes on neighboring sites chosen randomly: if the sites are occupied by a predator-prey pair then the predator invades the prey's site; otherwise the species exchange their sites with a probability X . For low X values, a self-organizing pattern is maintained by cyclic invasions. If X exceeds a threshold value, then two types of domain grow up that are formed by the odd and even label species, respectively. Monte Carlo simulations indicate the blocking of this segregation process within a range of X for n=8.

Silver Nanoparticle Oligonucleotide Conjugates Based on DNA with Triple Cyclic Disulfide Moieties

PubMed Central

Lee, Jae-Seung; Lytton-Jean, Abigail K. R.; Hurst, Sarah J.; Mirkin, Chad A.

2011-01-01

We report a new strategy for preparing silver nanoparticle oligonucleotide conjugates that are based upon DNA with cyclic disulfide-anchoring groups. These particles are extremely stable and can withstand NaCl concentrations up to 1.0 M. When silver nanoparticles functionalized with complementary sequences are combined, they assemble to form DNA-linked nanoparticle networks. This assembly process is reversible with heating and is associated with a red-shifting of the particle surface plasmon resonance and a concomitant color change from yellow to pale red. Analogous to the oligonucleotide-functionalized gold nanoparticles, these particles also exhibit highly cooperative binding properties with extremely sharp melting transitions. This work is an important step towards being able to use silver nanoparticle oligonucleotide conjugates for a variety of purposes, including molecular diagnostic labels, synthons in programmable materials synthesis approaches, and functional components for nanoelectronic and plasmonic devices. PMID:17571909

A population based twin study of DSM-5 maladaptive personality domains.

PubMed

South, Susan C; Krueger, Robert F; Knudsen, Gun Peggy; Ystrom, Eivind; Czajkowski, Nikolai; Aggen, Steven H; Neale, Michael C; Gillespie, Nathan A; Kendler, Kenneth S; Reichborn-Kjennerud, Ted

2017-10-01

Personality disorders (PDs) can be partly captured by dimensional traits, a viewpoint reflected in the most recent Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (DSM-5) Alternative (Section III) Model for PD classification. The current study adds to the literature on the Alternative Model by examining the magnitude of genetic and environmental influences on 6 domains of maladaptive personality: negative emotionality, detachment, antagonism, disinhibition, compulsivity, and psychoticism. In a large, population-based sample (N = 2,293) of Norwegian male and female twin pairs, we investigated (a) if the domains demonstrated measurement invariance across gender at the phenotypic level, meaning that the relationships between the items and the latent factor were equivalent in men and women; and (b) if genetic and environmental influences on variation in these domains were equivalent across gender. Multiple group confirmatory factor modeling provided evidence that all 6 domain scale measurement models were gender-invariant. The best fitting biometric model for 4 of the 6 domains (negative emotionality, detachment, disinhibition, and compulsivity) was one in which genetic and environmental influences could be set invariant across gender. Evidence for sex differences in psychoticism was mixed, but the only clear evidence for quantitative sex differences was for the antagonism scale, with greater genetic influences found for men than women. Genetic influences across domains were moderate overall (19-37%), in line with previous research using symptom-based measures of PDs. This study adds to the very limited knowledge currently existing on the etiology of maladaptive personality traits. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Multigene Family Encoding 3′,5′-Cyclic-GMP-Dependent Protein Kinases in Paramecium tetraurelia Cells

PubMed Central

Kissmehl, Roland; Krüger, Tim P.; Treptau, Tilman; Froissard, Marine; Plattner, Helmut

2006-01-01

In the ciliate Paramecium tetraurelia, 3′,5′-cyclic GMP (cGMP) is one of the second messengers involved in several signal transduction pathways. The enzymes for its production and degradation are well established for these cells, whereas less is known about the potential effector proteins. On the basis of a current Paramecium genome project, we have identified a multigene family with at least 35 members, all of which encode cGMP-dependent protein kinases (PKGs). They can be classified into 16 subfamilies with several members each. Two of the genes, PKG1-1 and PKG2-1, were analyzed in more detail after molecular cloning. They encode monomeric enzymes of 770 and 819 amino acids, respectively, whose overall domain organization resembles that in higher eukaryotes. The enzymes contain a regulatory domain of two tandem cyclic nucleotide-binding sites flanked by an amino-terminal region for intracellular localization and a catalytic domain with highly conserved regions for ATP binding and catalysis. However, some Paramecium PKGs show a different structure. In Western blots, PKGs are detected both as cytosolic and as structure-bound forms. Immunofluorescence labeling shows enrichment in the cell cortex, notably around the dense-core secretory vesicles (trichocysts), as well as in cilia. Immunogold electron microscopy analysis reveals consistent labeling of ciliary membranes, of the membrane complex composed of cell membrane and cortical Ca2+ stores, and of regions adjacent to ciliary basal bodies, trichocysts, and trafficking vesicles. Since PKGs (re)phosphorylate the exocytosis-sensitive phosphoprotein pp63/pf upon stimulation, the role of PKGs during stimulated exocytosis is discussed, in addition to a role in ciliary beat regulation. PMID:16400170

Electric-field domain boundary instability in weakly coupled semiconductor superlattices

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

Rasulova, G. K., E-mail: rasulova@sci.lebedev.ru; Pentin, I. V.; Brunkov, P. N.

2016-05-28

Damped oscillations of the current were observed in the transient current pulse characteristics of a 30-period weakly coupled GaAs/AlGaAs superlattice (SL). The switching time of the current is exponentially decreased as the voltage is verged towards the current discontinuity region indicating that the space charge necessary for the domain boundary formation is gradually accumulated in a certain SL period in a timescale of several hundreds ns. The spectral features in the electroluminescence spectra of two connected in parallel SL mesas correspond to the energy of the intersubband transitions and the resonance detuning of subbands caused by charge trapping in themore » quantum wells (QWs) residing in a region of the expanded domain boundary. The obtained results support our understanding of the origin of self-oscillations as a cyclic dynamics of the subband structure in the QWs forming the expanded domain boundary.« less

NASTRAN forced vibration analysis of rotating cyclic structures

NASA Technical Reports Server (NTRS)

Elchuri, V.; Smith, G. C. C.; Gallo, A. M.

1983-01-01

Theoretical aspects of a new capability developed and implemented in NASTRAN level 17.7 to analyze forced vibration of a cyclic structure rotating about its axis of symmetry are presented. Fans, propellers, and bladed shrouded discs of turbomachines are some examples of such structures. The capability includes the effects of Coriolis and centripetal accelerations on the rotating structure which can be loaded with: (1) directly applied loads moving with the structure and (2) inertial loas due to the translational acceleration of the axis of rotation (''base' acceleration). Steady-state sinusoidal or general periodic loads are specified to represent: (1) the physical loads on various segments of the complete structure, or (2) the circumferential harmonic components of the loads in (1). The cyclic symmetry feature of the rotating structure is used in deriving and solving the equations of forced motion. Consequently, only one of the cyclic sectors is modelled and analyzed using finite elements, yielding substantial savings in the analysis cost. Results, however, are obtained for the entire structure. A tuned twelve bladed disc example is used to demonstrate the various features of the capability.

The roles of the RIIβ linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of the type IIβ protein kinase A: a small angle x-ray and neutron scattering study.

PubMed

Blumenthal, Donald K; Copps, Jeffrey; Smith-Nguyen, Eric V; Zhang, Ping; Heller, William T; Taylor, Susan S

2014-10-10

Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. The PKA holoenzyme is a tetramer (R2:C2), with a regulatory subunit homodimer (R2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the type IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1-280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. Our results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Real-Time GNSS-Based Attitude Determination in the Measurement Domain

PubMed Central

Zhao, Lin; Li, Na; Li, Liang; Zhang, Yi; Cheng, Chun

2017-01-01

A multi-antenna-based GNSS receiver is capable of providing high-precision and drift-free attitude solution. Carrier phase measurements need be utilized to achieve high-precision attitude. The traditional attitude determination methods in the measurement domain and the position domain resolve the attitude and the ambiguity sequentially. The redundant measurements from multiple baselines have not been fully utilized to enhance the reliability of attitude determination. A multi-baseline-based attitude determination method in the measurement domain is proposed to estimate the attitude parameters and the ambiguity simultaneously. Meanwhile, the redundancy of attitude resolution has also been increased so that the reliability of ambiguity resolution and attitude determination can be enhanced. Moreover, in order to further improve the reliability of attitude determination, we propose a partial ambiguity resolution method based on the proposed attitude determination model. The static and kinematic experiments were conducted to verify the performance of the proposed method. When compared with the traditional attitude determination methods, the static experimental results show that the proposed method can improve the accuracy by at least 0.03° and enhance the continuity by 18%, at most. The kinematic result has shown that the proposed method can obtain an optimal balance between accuracy and reliability performance. PMID:28165434

Real-Time GNSS-Based Attitude Determination in the Measurement Domain.

PubMed

Zhao, Lin; Li, Na; Li, Liang; Zhang, Yi; Cheng, Chun

2017-02-05

A multi-antenna-based GNSS receiver is capable of providing high-precision and drift-free attitude solution. Carrier phase measurements need be utilized to achieve high-precision attitude. The traditional attitude determination methods in the measurement domain and the position domain resolve the attitude and the ambiguity sequentially. The redundant measurements from multiple baselines have not been fully utilized to enhance the reliability of attitude determination. A multi-baseline-based attitude determination method in the measurement domain is proposed to estimate the attitude parameters and the ambiguity simultaneously. Meanwhile, the redundancy of attitude resolution has also been increased so that the reliability of ambiguity resolution and attitude determination can be enhanced. Moreover, in order to further improve the reliability of attitude determination, we propose a partial ambiguity resolution method based on the proposed attitude determination model. The static and kinematic experiments were conducted to verify the performance of the proposed method. When compared with the traditional attitude determination methods, the static experimental results show that the proposed method can improve the accuracy by at least 0.03° and enhance the continuity by 18%, at most. The kinematic result has shown that the proposed method can obtain an optimal balance between accuracy and reliability performance.

Arctium lappa ameliorates endothelial dysfunction in rats fed with high fat/cholesterol diets.

PubMed

Lee, Yun Jung; Choi, Deok Ho; Cho, Guk Hyun; Kim, Jin Sook; Kang, Dae Gill; Lee, Ho Sub

2012-08-06

Arctium lappa L. (Asteraceae), burdock, is a medicinal plant that is popularly used for treating hypertension, gout, hepatitis, and other inflammatory disorders. This study was performed to test the effect of ethanol extract of Arctium lappa L. (EAL) seeds on vascular reactivity and inflammatory factors in rats fed a high fat/cholesterol diet (HFCD). EAL-I (100 mg·kg-1/day), EAL-II (200 mg·kg-1/day), and fluvastatin (3 mg·kg-1/day) groups initially received HFCD alone for 8 weeks, with EAL supplementation provided during the final 6 weeks. Treatment with low or high doses of EAL markedly attenuated plasma levels of triglycerides and augmented plasma levels of high-density lipoprotein (HDL) in HFCD-fed rats. Chronic treatment with EAL markedly reduced impairments of acetylcholine (ACh)-induced relaxation of aortic rings. Furthermore, chronic treatment with EAL significantly lowered systolic blood pressure (SBP) and maintained smooth and flexible intimal endothelial layers in HFCD-fed rats. Chronic treatment with EAL suppressed upregulation of intercellular adhesion molecule (ICAM)-1, vascular cell adhesion molecule (VCAM)-1, and E-selectin in the aorta. Chronic treatment with EAL also suppressed increases in matrix metalloproteinase (MMP)-2 expression. These results suggested that EAL can inhibit HFCD-induced vascular inflammation in the rat model. The present study provides evidence that EAL ameliorates HFCD-induced vascular dysfunction through protection of vascular relaxation and suppression of vascular inflammation.

Arctium lappa ameliorates endothelial dysfunction in rats fed with high fat/cholesterol diets

PubMed Central

2012-01-01

Background Arctium lappa L. (Asteraceae), burdock, is a medicinal plant that is popularly used for treating hypertension, gout, hepatitis, and other inflammatory disorders. This study was performed to test the effect of ethanol extract of Arctium lappa L. (EAL) seeds on vascular reactivity and inflammatory factors in rats fed a high fat/cholesterol diet (HFCD). Method EAL-I (100 mg·kg−1/day), EAL-II (200 mg·kg−1/day), and fluvastatin (3 mg·kg−1/day) groups initially received HFCD alone for 8 weeks, with EAL supplementation provided during the final 6 weeks. Results Treatment with low or high doses of EAL markedly attenuated plasma levels of triglycerides and augmented plasma levels of high-density lipoprotein (HDL) in HFCD-fed rats. Chronic treatment with EAL markedly reduced impairments of acetylcholine (ACh)-induced relaxation of aortic rings. Furthermore, chronic treatment with EAL significantly lowered systolic blood pressure (SBP) and maintained smooth and flexible intimal endothelial layers in HFCD-fed rats. Chronic treatment with EAL suppressed upregulation of intercellular adhesion molecule (ICAM)-1, vascular cell adhesion molecule (VCAM)-1, and E-selectin in the aorta. Chronic treatment with EAL also suppressed increases in matrix metalloproteinase (MMP)-2 expression. These results suggested that EAL can inhibit HFCD-induced vascular inflammation in the rat model. Conclusion The present study provides evidence that EAL ameliorates HFCD-induced vascular dysfunction through protection of vascular relaxation and suppression of vascular inflammation. PMID:22866890

Clinic expert information extraction based on domain model and block importance model.

PubMed

Zhang, Yuanpeng; Wang, Li; Qian, Danmin; Geng, Xingyun; Yao, Dengfu; Dong, Jiancheng

2015-11-01

To extract expert clinic information from the Deep Web, there are two challenges to face. The first one is to make a judgment on forms. A novel method based on a domain model, which is a tree structure constructed by the attributes of query interfaces is proposed. With this model, query interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from response Web pages indexed by query interfaces. To filter the noisy information on a Web page, a block importance model is proposed, both content and spatial features are taken into account in this model. The experimental results indicate that the domain model yields a precision 4.89% higher than that of the rule-based method, whereas the block importance model yields an F1 measure 10.5% higher than that of the XPath method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mechanism-Based Condition Screening for Sustainable Catalysis in Single-Electron Steps by Cyclic Voltammetry.

PubMed

Liedtke, Theresa; Spannring, Peter; Riccardi, Ludovico; Gansäuer, Andreas

2018-04-23

A cyclic-voltammetry-based screening method for Cp 2 TiX-catalyzed reactions is introduced. Our mechanism-based approach enables the study of the influence of various additives on the electrochemically generated active catalyst Cp 2 TiX, which is in equilibrium with catalytically inactive [Cp 2 TiX 2 ] - . Thioureas and ureas are most efficient in the generation of Cp 2 TiX in THF. Knowing the precise position of the equilibrium between Cp 2 TiX and [Cp 2 TiX 2 ] - allowed us to identify reaction conditions for the bulk electrolysis of Cp 2 TiX 2 complexes and for Cp 2 TiX-catayzed radical arylations without having to carry out the reactions. Our time- and resource-efficient approach is of general interest for the design of catalytic reactions that proceed in single-electron steps. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cyclic Voltammetry.

ERIC Educational Resources Information Center

Evans, Dennis H.; And Others

1983-01-01

Cyclic voltammetry is a simple experiment that has become popular in chemical research because it can provide useful information about redox reactions in a form which is easily obtained and interpreted. Discusses principles of the method and illustrates its use in the study of four electrode reactions. (Author/JN)

Theoretical Studies of Some HEDM Species: Cyclic O4, Cyclic O3 and Cubane

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Langhoff, Steve R. (Technical Monitor)

1996-01-01

Calculations have been carried out for the HEDM species (cyclic O4, cyclic O3, and cubane) using CASSCF/derivative and CASSCF/ICCI methods. Cyclic O4 is of interest both as a potential HEDM species and because of its possible role in the ozone deficit problem in atmospheric chemistry. We have studied the pathway for decomposition from the D(2d) minimum and also have found the approximate location of the singlet triplet crossing. The barrier to decomposition is found to be about 9 kcal/mol and is not limited by the singlet triplet crossing. For cyclic O3 we have focused on the crossings between the lowest five surfaces (X(1)A(1), s(1)A(1), (1)A(2), (1)B(1), and (1)B(2)) to provide some insight into ways to form cyclic O3 photochemically. The crossing region between the X(1)A(1) and 2(1)A(1) surfaces is in agreement with the work of Xantheas et al. The calculations show that vertical excitation from the ground state to the (1)A(2) state leads to a crossing with the (1)A(1) manifold near the crossing region of the X(1)A(1) and 2(1)A(1) surfaces. We have studied the decomposition pathways for cubane to benzene plus acetylene and to cyclooctatetraene. We have also studied the ground and excited states for the photochemical ring closure step. The state which closes to cubane can be described as a double triplet pi to pi* excitation with respect to the ground state. Thus, this state has only a small oscillator strength with respect to the ground state. However, there is a singlet pi to pi* state at nearly the same energy and excitation to this state followed by intersystem crossing could lead to the triplet pi to pi* state.

Functionalized linear and cyclic polyolefins

DOEpatents

Tuba, Robert; Grubbs, Robert H.

2018-02-13

This invention relates to methods and compositions for preparing linear and cyclic polyolefins. More particularly, the invention relates to methods and compositions for preparing functionalized linear and cyclic polyolefins via olefin metathesis reactions. Polymer products produced via the olefin metathesis reactions of the invention may be utilized for a wide range of materials applications. The invention has utility in the fields of polymer and materials chemistry and manufacture.

Computer Simulation Of Cyclic Oxidation

NASA Technical Reports Server (NTRS)

Probst, H. B.; Lowell, C. E.

1990-01-01

Computer model developed to simulate cyclic oxidation of metals. With relatively few input parameters, kinetics of cyclic oxidation simulated for wide variety of temperatures, durations of cycles, and total numbers of cycles. Program written in BASICA and run on any IBM-compatible microcomputer. Used in variety of ways to aid experimental research. In minutes, effects of duration of cycle and/or number of cycles on oxidation kinetics of material surveyed.

Specific Features of the Domain Structure of BaTiO3 Crystals during Thermal Heating and Cooling

NASA Astrophysics Data System (ADS)

Kiselev, D. A.; Ilina, T. S.; Malinkovich, M. D.; Sergeeva, O. N.; Bolshakova, N. N.; Semenova, E. M.; Kuznetsova, Yu. V.

2018-04-01

This paper presents the results of the study of the domain structure of barium titanate crystals in a wide temperature range including the Curie point ( T C) using the polarization-optical method in the reflected light and the force microscopy of the piezoelectric response. It is shown that a new a-c domain structure forms during cyclic heating of the crystal above T C and subsequent cooling to the ferroelectric phase. The role of uncompensated charges appeared on the crystal surface during the phase transition and their influence on the formation of the domain structure during cooling are discussed.

Holographic imaging based on time-domain data of natural-fiber-containing materials

DOEpatents

Bunch, Kyle J.; McMakin, Douglas L.

2012-09-04

Methods and apparatuses for imaging material properties in natural-fiber-containing materials can utilize time-domain data. In particular, images can be constructed that provide quantified measures of localized moisture content. For example, one or more antennas and at least one transceiver can be configured to collect time-domain data from radiation interacting with the natural-fiber-containing materials. The antennas and the transceivers are configured to transmit and receive electromagnetic radiation at one or more frequencies, which are between 50 MHz and 1 THz, according to a time-domain impulse function. A computing device is configured to transform the time-domain data to frequency-domain data, to apply a synthetic imaging algorithm for constructing a three-dimensional image of the natural-fiber-containing materials, and to provide a quantified measure of localized moisture content based on a pre-determined correlation of moisture content to frequency-domain data.

Bifunctional homodimeric triokinase/FMN cyclase: contribution of protein domains to the activities of the human enzyme and molecular dynamics simulation of domain movements.

PubMed

Rodrigues, Joaquim Rui; Couto, Ana; Cabezas, Alicia; Pinto, Rosa María; Ribeiro, João Meireles; Canales, José; Costas, María Jesús; Cameselle, José Carlos

2014-04-11

Mammalian triokinase, which phosphorylates exogenous dihydroxyacetone and fructose-derived glyceraldehyde, is neither molecularly identified nor firmly associated to an encoding gene. Human FMN cyclase, which splits FAD and other ribonucleoside diphosphate-X compounds to ribonucleoside monophosphate and cyclic X-phosphodiester, is identical to a DAK-encoded dihydroxyacetone kinase. This bifunctional protein was identified as triokinase. It was modeled as a homodimer of two-domain (K and L) subunits. Active centers lie between K1 and L2 or K2 and L1: dihydroxyacetone binds K and ATP binds L in different subunits too distant (≈ 14 Å) for phosphoryl transfer. FAD docked to the ATP site with ribityl 4'-OH in a possible near-attack conformation for cyclase activity. Reciprocal inhibition between kinase and cyclase reactants confirmed substrate site locations. The differential roles of protein domains were supported by their individual expression: K was inactive, and L displayed cyclase but not kinase activity. The importance of domain mobility for the kinase activity of dimeric triokinase was highlighted by molecular dynamics simulations: ATP approached dihydroxyacetone at distances below 5 Å in near-attack conformation. Based upon structure, docking, and molecular dynamics simulations, relevant residues were mutated to alanine, and kcat and Km were assayed whenever kinase and/or cyclase activity was conserved. The results supported the roles of Thr(112) (hydrogen bonding of ATP adenine to K in the closed active center), His(221) (covalent anchoring of dihydroxyacetone to K), Asp(401) and Asp(403) (metal coordination to L), and Asp(556) (hydrogen bonding of ATP or FAD ribose to L domain). Interestingly, the His(221) point mutant acted specifically as a cyclase without kinase activity.

In silico molecular docking analysis of the human Argonaute 2 PAZ domain reveals insights into RNA interference.

PubMed

Kandeel, Mahmoud; Kitade, Yukio

2013-07-01

RNA interference (RNAi) is a critical cellular pathway activated by double stranded RNA and regulates the gene expression of target mRNA. During RNAi, the 3' end of siRNA binds with the PAZ domain, followed by release and rebinding in a cyclic manner, which deemed essential for proper gene silencing. Recently, we provided the forces underlying the recognition of small interfering RNA by PAZ in a computational study based on the structure of Drosophila Argonaute 2 (Ago2) PAZ domain. We have now reanalyzed these data within the view of the new available structures from human Argonauts. While the parameters of weak binding are correlated with higher (RNAi) in the Drosophila model, a different profile is predicted with the human Ago2 PAZ domain. On the basis of the human Ago2 PAZ models, the indicators of stronger binding as the total binding energy and the free energy were associated with better RNAi efficacy. This discrepancy might be attributable to differences in the binding site topology and the difference in the conformation of the bound nucleotides.

Directed evolution of the TALE N-terminal domain for recognition of all 5′ bases

PubMed Central

Lamb, Brian M.; Mercer, Andrew C.; Barbas, Carlos F.

2013-01-01

Transcription activator-like effector (TALE) proteins can be designed to bind virtually any DNA sequence. General guidelines for design of TALE DNA-binding domains suggest that the 5′-most base of the DNA sequence bound by the TALE (the N0 base) should be a thymine. We quantified the N0 requirement by analysis of the activities of TALE transcription factors (TALE-TF), TALE recombinases (TALE-R) and TALE nucleases (TALENs) with each DNA base at this position. In the absence of a 5′ T, we observed decreases in TALE activity up to >1000-fold in TALE-TF activity, up to 100-fold in TALE-R activity and up to 10-fold reduction in TALEN activity compared with target sequences containing a 5′ T. To develop TALE architectures that recognize all possible N0 bases, we used structure-guided library design coupled with TALE-R activity selections to evolve novel TALE N-terminal domains to accommodate any N0 base. A G-selective domain and broadly reactive domains were isolated and characterized. The engineered TALE domains selected in the TALE-R format demonstrated modularity and were active in TALE-TF and TALEN architectures. Evolved N-terminal domains provide effective and unconstrained TALE-based targeting of any DNA sequence as TALE binding proteins and designer enzymes. PMID:23980031

Nitric oxide cycle in mammals and the cyclicity principle.

PubMed

Reutov, V P

2002-03-01

This paper continues a series of reports considering nitric oxide (NO) and its cyclic conversions in mammals. Numerous facts are summarized with the goal of developing a general concept that would allow the statement of the multiple effects of NO on various systems of living organisms in the form of a short and comprehensive law. The current state of biological aspects of NO research is analyzed in term of elucidation of possible role of these studies in the system of biological sciences. The general concept is based on a notion on cyclic conversions of NO and its metabolites. NO cycles in living organisms and nitrogen turnover in the biosphere and also the Bethe nitrogen-carbon cycle in star matter are considered. A hypothesis that the cyclic organization of processes in living organisms and the biosphere reflects the evolution of life is proposed: the development of physiological functions and metabolism are suggested to be closely related to space and evolution of the Earth as a planet of the Solar System.

Microfluidic platform for neurotransmitter sensing based on cyclic voltammetry and dielectrophoresis for in vitro experiments.

PubMed

Mathault, Jessy; Zamprogno, Pauline; Greener, Jesse; Miled, Amine

2015-08-01

This paper presents a new microfluidic platform that can simultaneously measure and locally modulate neurotransmitter concentration in a neuron network. This work focuses on the development of a first prototype including a potentiostat and electrode functionalization to detect several neurotransmitter's simultaneously. We tested dopamine as proof of concept to validate functionality. The system is based on 320 bidirectional electrode array for dielectrophoretic manipulation and cyclic voltammetry. Each electrode is connected to a mechanical multiplexer in order to reduce noise interference and fully isolate the electrode. The multiplexing rate is 476 kHz and each electrode can drive a signal with an amplitude of 60 V pp for dielectrophoretic manipulation.

PDE and cognitive processing: beyond the memory domain.

PubMed

Heckman, P R A; Blokland, A; Ramaekers, J; Prickaerts, J

2015-03-01

Phosphodiesterase inhibitors (PDE-Is) enhance cAMP and/or cGMP signaling via reducing the degradation of these cyclic nucleotides. Both cAMP and cGMP signaling are essential for a variety of cellular functions and exert their effects both pre- and post-synaptically. Either of these second messengers relays and amplifies incoming signals at receptors on the cell surface making them important elements in signal transduction cascades and essential in cellular signaling in a variety of cell functions including neurotransmitter release and neuroprotection. Consequently, these processes can be influenced by PDE-Is as they increase cAMP and/or cGMP concentrations. PDE-Is have been considered as possible therapeutic agents to treat impaired memory function linked to several brain disorders, including depression, schizophrenia and Alzheimer's disease (AD). This review will, however, focus on the possible role of phosphodiesterases (PDEs) in cognitive decline beyond the memory domain. Here we will discuss the involvement of PDEs on three related domains: attention, information filtering (sensory- and sensorimotor gating) and response inhibition (drug-induced hyperlocomotion). Currently, these are emerging cognitive domains in the field of PDE research. Here we discuss experimental studies and the potential beneficial effects of PDE-I drugs on these cognitive domains, as effects of PDE-Is on these domains could potentially influence effects on memory performance. Overall, PDE4 seems to be the most promising target for all domains discussed in this review. Copyright © 2014 Elsevier Inc. All rights reserved.

Cyclic membrane separation process

DOEpatents

Nemser, Stuart M.

2005-05-03

A cyclic process for controlling environmental emissions of volatile organic compounds (VOC) from vapor recovery in storage and dispensing operations of liquids maintains a vacuum in the storage tank ullage. In the first part of a two-part cyclic process ullage vapor is discharged through a vapor recovery system in which VOC are stripped from vented gas with a selectively gas permeable membrane. In the second part, the membrane is inoperative while gas pressure rises in the ullage. In one aspect of this invention, a vacuum is drawn in the membrane separation unit thus reducing overall VOC emissions.

Measuring Cyclic Error in Laser Heterodyne Interferometers

NASA Technical Reports Server (NTRS)

Ryan, Daniel; Abramovici, Alexander; Zhao, Feng; Dekens, Frank; An, Xin; Azizi, Alireza; Chapsky, Jacob; Halverson, Peter

2010-01-01

An improved method and apparatus have been devised for measuring cyclic errors in the readouts of laser heterodyne interferometers that are configured and operated as displacement gauges. The cyclic errors arise as a consequence of mixing of spurious optical and electrical signals in beam launchers that are subsystems of such interferometers. The conventional approach to measurement of cyclic error involves phase measurements and yields values precise to within about 10 pm over air optical paths at laser wavelengths in the visible and near infrared. The present approach, which involves amplitude measurements instead of phase measurements, yields values precise to about .0.1 microns . about 100 times the precision of the conventional approach. In a displacement gauge of the type of interest here, the laser heterodyne interferometer is used to measure any change in distance along an optical axis between two corner-cube retroreflectors. One of the corner-cube retroreflectors is mounted on a piezoelectric transducer (see figure), which is used to introduce a low-frequency periodic displacement that can be measured by the gauges. The transducer is excited at a frequency of 9 Hz by a triangular waveform to generate a 9-Hz triangular-wave displacement having an amplitude of 25 microns. The displacement gives rise to both amplitude and phase modulation of the heterodyne signals in the gauges. The modulation includes cyclic error components, and the magnitude of the cyclic-error component of the phase modulation is what one needs to measure in order to determine the magnitude of the cyclic displacement error. The precision attainable in the conventional (phase measurement) approach to measuring cyclic error is limited because the phase measurements are af-

Construction of type-II QC-LDPC codes with fast encoding based on perfect cyclic difference sets

NASA Astrophysics Data System (ADS)

Li, Ling-xiang; Li, Hai-bing; Li, Ji-bi; Jiang, Hua

2017-09-01

In view of the problems that the encoding complexity of quasi-cyclic low-density parity-check (QC-LDPC) codes is high and the minimum distance is not large enough which leads to the degradation of the error-correction performance, the new irregular type-II QC-LDPC codes based on perfect cyclic difference sets (CDSs) are constructed. The parity check matrices of these type-II QC-LDPC codes consist of the zero matrices with weight of 0, the circulant permutation matrices (CPMs) with weight of 1 and the circulant matrices with weight of 2 (W2CMs). The introduction of W2CMs in parity check matrices makes it possible to achieve the larger minimum distance which can improve the error- correction performance of the codes. The Tanner graphs of these codes have no girth-4, thus they have the excellent decoding convergence characteristics. In addition, because the parity check matrices have the quasi-dual diagonal structure, the fast encoding algorithm can reduce the encoding complexity effectively. Simulation results show that the new type-II QC-LDPC codes can achieve a more excellent error-correction performance and have no error floor phenomenon over the additive white Gaussian noise (AWGN) channel with sum-product algorithm (SPA) iterative decoding.

Modulating Charge Transfer Through Cyclic D,L α-Peptide Self-Assembly

PubMed Central

Horne, W. Seth; Ashkenasy, Nurit; Ghadiri, M. Reza

2007-01-01

We describe a concise solid support-based synthetic method for the preparation of cyclic D,L α-peptides bearing 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) side chains. Studies of the structural and photoluminescence properties of these molecules in solution show that the hydrogen bond directed self-assembly of the cyclic D,L α-peptide backbone promotes intermolecular NDI excimer formation. The efficiency of NDI charge transfer in the resulting supramolecular assemblies is shown to depend on the length of the linker between the NDI and the peptide backbone, the distal NDI substituent, and the number of NDIs incorporated in a given structure. The design rationale and synthetic strategies described here should provide a basic blueprint for a series of self-assembling cyclic D,L α-peptide nanotubes with interesting optical and electronic properties. PMID:15624124

Stress-based control of magnetic nanowire domain walls in artificial multiferroic systems

NASA Astrophysics Data System (ADS)

Dean, J.; Bryan, M. T.; Schrefl, T.; Allwood, D. A.

2011-01-01

Artificial multiferroic systems, which combine piezoelectric and piezomagnetic materials, offer novel methods of controlling material properties. Here, we use combined structural and magnetic finite element models to show how localized strains in a piezoelectric film coupled to a piezomagnetic nanowire can attract and pin magnetic domain walls. Synchronous switching of addressable contacts enables the controlled movement of pinning sites, and hence domain walls, in the nanowire without applied magnetic field or spin-polarized current, irrespective of domain wall structure. Conversely, domain wall-induced strain in the piezomagnetic material induces a local potential difference in the piezoelectric, providing a mechanism for sensing domain walls. This approach overcomes the problems in magnetic nanowire memories of domain wall structure-dependent behavior and high power consumption. Nonvolatile random access or shift register memories based on these effects can achieve storage densities >1 Gbit/In2, sub-10 ns switching times, and power consumption <100 keV per operation.

Development of Novel Melanocortin Receptor Agonists Based on the Cyclic Peptide Framework of Sunflower Trypsin Inhibitor-1.

PubMed

Durek, Thomas; Cromm, Philipp M; White, Andrew M; Schroeder, Christina I; Kaas, Quentin; Weidmann, Joachim; Ahmad Fuaad, Abdullah; Cheneval, Olivier; Harvey, Peta J; Daly, Norelle L; Zhou, Yang; Dellsén, Anita; Österlund, Torben; Larsson, Niklas; Knerr, Laurent; Bauer, Udo; Kessler, Horst; Cai, Minying; Hruby, Victor J; Plowright, Alleyn T; Craik, David J

2018-04-26

Ultrastable cyclic peptide frameworks offer great potential for drug design due to their improved bioavailability compared to their linear analogues. Using the sunflower trypsin inhibitor-1 (SFTI-1) peptide scaffold in combination with systematic N-methylation of the grafted pharmacophore led to the identification of novel subtype selective melanocortin receptor (MCR) agonists. Multiple bicyclic peptides were synthesized and tested toward their activity at MC1R and MC3-5R. Double N-methylated compound 18 showed a p K i of 8.73 ± 0.08 ( K i = 1.92 ± 0.34 nM) and a pEC 50 of 9.13 ± 0.04 (EC 50 = 0.75 ± 0.08 nM) at the human MC1R and was over 100 times more selective for MC1R. Nuclear magnetic resonance structural analysis of 18 emphasized the role of peptide bond N-methylation in shaping the conformation of the grafted pharmacophore. More broadly, this study highlights the potential of cyclic peptide scaffolds for epitope grafting in combination with N-methylation to introduce receptor subtype selectivity in the context of peptide-based drug discovery.

Creep crack growth by grain boundary cavitation under monotonic and cyclic loading

NASA Astrophysics Data System (ADS)

Wen, Jian-Feng; Srivastava, Ankit; Benzerga, Amine; Tu, Shan-Tung; Needleman, Alan

2017-11-01

Plane strain finite deformation finite element calculations of mode I crack growth under small scale creep conditions are carried out. Attention is confined to isothermal conditions and two time histories of the applied stress intensity factor: (i) a monononic increase to a plateau value subsequently held fixed; and (ii) a cyclic time variation. The crack growth calculations are based on a micromechanics constitutive relation that couples creep deformation and damage due to grain boundary cavitation. Grain boundary cavitation, with cavity growth due to both creep and diffusion, is taken as the sole failure mechanism contributing to crack growth. The influence on the crack growth rate of loading history parameters, such as the magnitude of the applied stress intensity factor, the ratio of the applied minimum to maximum stress intensity factors, the loading rate, the hold time and the cyclic loading frequency, are explored. The crack growth rate under cyclic loading conditions is found to be greater than under monotonic creep loading with the plateau applied stress intensity factor equal to its maximum value under cyclic loading conditions. Several features of the crack growth behavior observed in creep-fatigue tests naturally emerge, for example, a Paris law type relation is obtained for cyclic loading.

Goal-Based Domain Modeling as a Basis for Cross-Disciplinary Systems Engineering

NASA Astrophysics Data System (ADS)

Jarke, Matthias; Nissen, Hans W.; Rose, Thomas; Schmitz, Dominik

Small and medium-sized enterprises (SMEs) are important drivers for innovation. In particular, project-driven SMEs that closely cooperate with their customers have specific needs in regard to information engineering of their development process. They need a fast requirements capture since this is most often included in the (unpaid) offer development phase. At the same time, they need to maintain and reuse the knowledge and experiences they have gathered in previous projects extensively as it is their core asset. The situation is complicated further if the application field crosses disciplinary boundaries. To bridge the gaps and perspectives, we focus on shared goals and dependencies captured in models at a conceptual level. Such a model-based approach also offers a smarter connection to subsequent development stages, including a high share of automated code generation. In the approach presented here, the agent- and goal-oriented formalism i * is therefore extended by domain models to facilitate information organization. This extension permits a domain model-based similarity search, and a model-based transformation towards subsequent development stages. Our approach also addresses the evolution of domain models reflecting the experiences from completed projects. The approach is illustrated with a case study on software-intensive control systems in an SME of the automotive domain.

A Secondary Structural Transition in the C-helix Promotes Gating of Cyclic Nucleotide-regulated Ion Channels*

PubMed Central

Puljung, Michael C.; Zagotta, William N.

2013-01-01

Cyclic nucleotide-regulated ion channels bind second messengers like cAMP to a C-terminal domain, consisting of a β-roll, followed by two α-helices (B- and C-helices). We monitored the cAMP-dependent changes in the structure of the C-helix of a C-terminal fragment of HCN2 channels using transition metal ion FRET between fluorophores on the C-helix and metal ions bound between histidine pairs on the same helix. cAMP induced a change in the dimensions of the C-helix and an increase in the metal binding affinity of the histidine pair. cAMP also caused an increase in the distance between a fluorophore on the C-helix and metal ions bound to the B-helix. Stabilizing the C-helix of intact CNGA1 channels by metal binding to a pair of histidines promoted channel opening. These data suggest that ordering of the C-helix is part of the gating conformational change in cyclic nucleotide-regulated channels. PMID:23525108

Concomitant prediction of function and fold at the domain level with GO-based profiles.

PubMed

Lopez, Daniel; Pazos, Florencio

2013-01-01

Predicting the function of newly sequenced proteins is crucial due to the pace at which these raw sequences are being obtained. Almost all resources for predicting protein function assign functional terms to whole chains, and do not distinguish which particular domain is responsible for the allocated function. This is not a limitation of the methodologies themselves but it is due to the fact that in the databases of functional annotations these methods use for transferring functional terms to new proteins, these annotations are done on a whole-chain basis. Nevertheless, domains are the basic evolutionary and often functional units of proteins. In many cases, the domains of a protein chain have distinct molecular functions, independent from each other. For that reason resources with functional annotations at the domain level, as well as methodologies for predicting function for individual domains adapted to these resources are required.We present a methodology for predicting the molecular function of individual domains, based on a previously developed database of functional annotations at the domain level. The approach, which we show outperforms a standard method based on sequence searches in assigning function, concomitantly predicts the structural fold of the domains and can give hints on the functionally important residues associated to the predicted function.

Rhodium-Catalyzed Dehydrogenative Borylation of Cyclic Alkenes

PubMed Central

Kondoh, Azusa; Jamison, Timothy F.

2010-01-01

A rhodium-catalyzed dehydrogenative borylation of cyclic alkenes is described. This reaction provides direct access to cyclic 1-alkenylboronic acid pinacol esters, useful intermediates in organic synthesis. Suzuki-Miyaura cross-coupling applications are also presented. PMID:20107646

Stable Cyclic Carbenes and Related Species beyond Diaminocarbenes

PubMed Central

Melaimi, Mohand; Soleilhavoup, Michèle

2011-01-01

The success of homogeneous catalysis can be attributed largely to the development of a diverse range of ligand frameworks that have been used to tune the behavior of various systems. Spectacular results in this area have been achieved using cyclic diaminocarbenes (NHCs) as a result of their strong σ-donor properties. Although it is possible to cursorily tune the structure of NHCs, any diversity is still far from matching their phosphorus-based counterparts, which is one of the great strengths of the latter. A variety of stable acyclic carbenes are known, but they are either reluctant to bind metals or they give rise to fragile metal complexes. During the last five years, new types of stable cyclic carbenes, as well as related carbon-based ligands (which are not NHCs), and which feature even stronger σ-donor properties have been developed. Their synthesis and characterization as well as the stability, electronic properties, coordination behavior, and catalytic activity of the ensuing complexes are discussed, and comparisons with their NHC cousins are made. PMID:20836099

Cyclically optimized electrochemical processes

NASA Astrophysics Data System (ADS)

Ruedisueli, Robert Louis

It has been frequently observed in experiment and industry practice that electrochemical processes (deposition, dissolution, fuel cells) operated in an intermittent or cyclic (AC) mode show improvements in efficiency and/or quality and yield over their steady (DC) mode of operation. Whether rationally invoked by design or empirically tuned-in, the optimal operating frequency and duty cycle is dependent upon the dominant relaxation time constant for the process in question. The electrochemical relaxation time constant is a function of: double-layer and reaction intermediary pseudo-capacitances, ion (charge) transport via electrical migration (mobility), and diffusion across a concentration gradient to electrode surface reaction sites where charge transfer and species incorporation or elimination occurs. The rate determining step dominates the time constant for the reaction or process. Electrochemical impedance spectroscopy (EIS) and piezoelectric crystal electrode (PCE) response analysis have proven to be useful tools in the study and identification of reaction mechanisms. This work explains and demonstrates with the electro-deposition of copper the application of EIS and PCE measurement and analysis to the selection of an optimum cyclic operating schedule, an optimum driving frequency for efficient, sustained cyclic (pulsed) operation.

Dual-Level Security based Cyclic18 Steganographic Method and its Application for Secure Transmission of Keyframes during Wireless Capsule Endoscopy.

PubMed

Muhammad, Khan; Sajjad, Muhammad; Baik, Sung Wook

2016-05-01

In this paper, the problem of secure transmission of sensitive contents over the public network Internet is addressed by proposing a novel data hiding method in encrypted images with dual-level security. The secret information is divided into three blocks using a specific pattern, followed by an encryption mechanism based on the three-level encryption algorithm (TLEA). The input image is scrambled using a secret key, and the encrypted sub-message blocks are then embedded in the scrambled image by cyclic18 least significant bit (LSB) substitution method, utilizing LSBs and intermediate LSB planes. Furthermore, the cover image and its planes are rotated at different angles using a secret key prior to embedding, deceiving the attacker during data extraction. The usage of message blocks division, TLEA, image scrambling, and the cyclic18 LSB method results in an advanced security system, maintaining the visual transparency of resultant images and increasing the security of embedded data. In addition, employing various secret keys for image scrambling, data encryption, and data hiding using the cyclic18 LSB method makes the data recovery comparatively more challenging for attackers. Experimental results not only validate the effectiveness of the proposed framework in terms of visual quality and security compared to other state-of-the-art methods, but also suggest its feasibility for secure transmission of diagnostically important keyframes to healthcare centers and gastroenterologists during wireless capsule endoscopy.

Mutation of domain III and domain VI in L gene conserved domain of Nipah virus

NASA Astrophysics Data System (ADS)

Jalani, Siti Aishah; Ibrahim, Nazlina

2016-11-01

Nipah virus (NiV) is the etiologic agent responsible for the respiratory illness and causes fatal encephalitis in human. NiV L protein subunit is thought to be responsible for the majority of enzymatic activities involved in viral transcription and replication. The L protein which is the viral RNA dependent RNA polymerase has high sequence homology among negative sense RNA viruses. In negative stranded RNA viruses, based on sequence alignment six conserved domain (domain I-IV) have been determined. Each domain is separated on variable regions that suggest the structure to consist concatenated functional domain. To directly address the roles of domains III and VI, site-directed mutations were constructed by the substitution of bases at sequences 2497, 2500, 5528 and 5532. Each mutated L gene can be used in future studies to test the ability for expression on in vitro translation.

Role of ELA region in auto-activation of mutant KIT receptor: a molecular dynamics simulation insight.

PubMed

Purohit, Rituraj

2014-01-01

KIT receptor is the prime target in gastrointestinal stromal tumor (GISTs) therapy. Second generation inhibitor, Sunitinib, binds to an inactivated conformation of KIT receptor and stabilizes it in order to prevent tumor formation. Here, we investigated the dynamic behavior of wild type and mutant D816H KIT receptor, and emphasized the extended A-loop (EAL) region (805-850) by conducting molecular dynamics simulation (∼100 ns). We analyzed different properties such as root mean square cutoff or deviation, root mean square fluctuation, radius of gyration, solvent-accessible surface area, hydrogen bonding network analysis, and essential dynamics. Apart from this, clustering and cross-correlation matrix approach was used to explore the conformational space of the wild type and mutant EAL region of KIT receptor. Molecular dynamics analysis indicated that mutation (D816H) was able to alter intramolecular hydrogen bonding pattern and affected the structural flexibility of EAL region. Moreover, flexible secondary elements, specially, coil and turns were dominated in EAL region of mutant KIT receptor during simulation. This phenomenon increased the movement of EAL region which in turn helped in shifting the equilibrium towards the active kinase conformation. Our atomic investigation of mutant KIT receptor which emphasized on EAL region provided a better insight into the understanding of Sunitinib resistance mechanism of KIT receptor and would help to discover new therapeutics for KIT-based resistant tumor cells in GIST therapy.

Multiple Interactions between Cytoplasmic Domains Regulate Slow Deactivation of Kv11.1 Channels*

PubMed Central

Ng, Chai Ann; Phan, Kevin; Hill, Adam P.; Vandenberg, Jamie I.; Perry, Matthew D.

2014-01-01

The intracellular domains of many ion channels are important for fine-tuning their gating kinetics. In Kv11.1 channels, the slow kinetics of channel deactivation, which are critical for their function in the heart, are largely regulated by the N-terminal N-Cap and Per-Arnt-Sim (PAS) domains, as well as the C-terminal cyclic nucleotide-binding homology (cNBH) domain. Here, we use mutant cycle analysis to probe for functional interactions between the N-Cap/PAS domains and the cNBH domain. We identified a specific and stable charge-charge interaction between Arg56 of the PAS domain and Asp803 of the cNBH domain, as well an additional interaction between the cNBH domain and the N-Cap, both of which are critical for maintaining slow deactivation kinetics. Furthermore, we found that positively charged arginine residues within the disordered region of the N-Cap interact with negatively charged residues of the C-linker domain. Although this interaction is likely more transient than the PAS-cNBD interaction, it is strong enough to stabilize the open conformation of the channel and thus slow deactivation. These findings provide novel insights into the slow deactivation mechanism of Kv11.1 channels. PMID:25074935

Demultiplexing based on frequency-domain joint decision MMA for MDM system

NASA Astrophysics Data System (ADS)

Caili, Gong; Li, Li; Guijun, Hu

2016-06-01

In this paper, we propose a demultiplexing method based on frequency-domain joint decision multi-modulus algorithm (FD-JDMMA) for mode division multiplexing (MDM) system. The performance of FD-JDMMA is compared with frequency-domain multi-modulus algorithm (FD-MMA) and frequency-domain least mean square (FD-LMS) algorithm. The simulation results show that FD-JDMMA outperforms FD-MMA in terms of BER and convergence speed in the cases of mQAM (m=4, 16 and 64) formats. And it is also demonstrated that FD-JDMMA achieves better BER performance and converges faster than FD-LMS in the cases of 16QAM and 64QAM. Furthermore, FD-JDMMA maintains similar computational complexity as the both equalization algorithms.

New perspectives in cyclic nucleotide-mediated functions in the CNS: the emerging role of cyclic nucleotide-gated (CNG) channels.

PubMed

Podda, Maria Vittoria; Grassi, Claudio

2014-07-01

Cyclic nucleotides play fundamental roles in the central nervous system (CNS) under both physiological and pathological conditions. The impact of cAMP and cGMP signaling on neuronal and glial cell functions has been thoroughly characterized. Most of their effects have been related to cyclic nucleotide-dependent protein kinase activity. However, cyclic nucleotide-gated (CNG) channels, first described as key mediators of sensory transduction in retinal and olfactory receptors, have been receiving increasing attention as possible targets of cyclic nucleotides in the CNS. In the last 15 years, consistent evidence has emerged for their expression in neurons and astrocytes of the rodent brain. Far less is known, however, about the functional role of CNG channels in these cells, although several of their features, such as Ca(2+) permeability and prolonged activation in the presence of cyclic nucleotides, make them ideal candidates for mediators of physiological functions in the CNS. Here, we review literature suggesting the involvement of CNG channels in a number of CNS cellular functions (e.g., regulation of membrane potential, neuronal excitability, and neurotransmitter release) as well as in more complex phenomena, like brain plasticity, adult neurogenesis, and pain sensitivity. The emerging picture is that functional and dysfunctional cyclic nucleotide signaling in the CNS has to be reconsidered including CNG channels among possible targets. However, concerted efforts and multidisciplinary approaches are still needed to get more in-depth knowledge in this field.

A label-free and high-efficient GO-based aptasensor for cancer cells based on cyclic enzymatic signal amplification.

PubMed

Xiao, Kunyi; Liu, Juan; Chen, Hui; Zhang, Song; Kong, Jilie

2017-05-15

A label-free and high-efficient graphene oxide (GO)-based aptasensor was developed for the detection of low quantity cancer cells based on cell-triggered cyclic enzymatic signal amplification (CTCESA). In the absence of target cells, hairpin aptamer probes (HAPs) and dye-labeled linker DNAs stably coexisted in solution, and the fluorescence was quenched by the GO-based FÖrster resonance energy transfer (FRET) process. In the presence of target cells, the specific binding of HAPs with the target cells triggered a conformational alternation, which resulted in linker DNA complementary pairing and cleavage by nicking endonuclease-strand scission cycles. Consequently, more cleaved fragments of linker DNAs with more the terminal labeled dyes could show the enhanced fluorescence because these cleaved DNA fragments hardly combine with GOs and prevent the FRET process. Fluorescence analysis demonstrated that this GO-based aptasensor exhibited selective and sensitive response to the presence of target CCRF-CEM cells in the concentration range from 50 to 10 5 cells. The detection limit of this method was 25 cells, which was approximately 20 times lower than the detection limit of normal fluorescence aptasensors without amplification. With high sensitivity and specificity, it provided a simple and cost-effective approach for early cancer diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Reconstruction of three-dimensional ultrasound images based on cyclic Savitzky-Golay filters

NASA Astrophysics Data System (ADS)

Toonkum, Pollakrit; Suwanwela, Nijasri C.; Chinrungrueng, Chedsada

2011-01-01

We present a new algorithm for reconstructing a three-dimensional (3-D) ultrasound image from a series of two-dimensional B-scan ultrasound slices acquired in the mechanical linear scanning framework. Unlike most existing 3-D ultrasound reconstruction algorithms, which have been developed and evaluated in the freehand scanning framework, the new algorithm has been designed to capitalize the regularity pattern of the mechanical linear scanning, where all the B-scan slices are precisely parallel and evenly spaced. The new reconstruction algorithm, referred to as the cyclic Savitzky-Golay (CSG) reconstruction filter, is an improvement on the original Savitzky-Golay filter in two respects: First, it is extended to accept a 3-D array of data as the filter input instead of a one-dimensional data sequence. Second, it incorporates the cyclic indicator function in its least-squares objective function so that the CSG algorithm can simultaneously perform both smoothing and interpolating tasks. The performance of the CSG reconstruction filter compared to that of most existing reconstruction algorithms in generating a 3-D synthetic test image and a clinical 3-D carotid artery bifurcation in the mechanical linear scanning framework are also reported.

Cyclic Voltammetry Experiment.

ERIC Educational Resources Information Center

Van Benschoten, James J.; And Others

1983-01-01

Describes a three-part experiment designed to introduce cyclic voltammetry to graduate/undergraduate students. Part 1 demonstrates formal reduction potential, redox electron transfer, diffusion coefficient, and electrochemical reversibility. Part 2 investigates electrochemical behavior of acetaminophen. Part 3 examines such experimental variables…

A domains-based taxonomy of supported accommodation for people with severe and persistent mental illness.

PubMed

Siskind, Dan; Harris, Meredith; Pirkis, Jane; Whiteford, Harvey

2013-06-01

A lack of definitional clarity in supported accommodation and the absence of a widely accepted system for classifying supported accommodation models creates barriers to service planning and evaluation. We undertook a systematic review of existing supported accommodation classification systems. Using a structured system for qualitative data analysis, we reviewed the stratification features in these classification systems, identified the key elements of supported accommodation and arranged them into domains and dimensions to create a new taxonomy. The existing classification systems were mapped onto the new taxonomy to verify the domains and dimensions. Existing classification systems used either a service-level characteristic or programmatic approach. We proposed a taxonomy based around four domains: duration of tenure; patient characteristics; housing characteristics; and service characteristics. All of the domains in the taxonomy were drawn from the existing classification structures; however, none of the existing classification structures covered all of the domains in the taxonomy. Existing classification systems are regionally based, limited in scope and lack flexibility. A domains-based taxonomy can allow more accurate description of supported accommodation services, aid in identifying the service elements likely to improve outcomes for specific patient populations, and assist in service planning.

Rock-paper-scissors played within competing domains in predator-prey games

NASA Astrophysics Data System (ADS)

Labavić, Darka; Meyer-Ortmanns, Hildegard

2016-11-01

We consider (N, r) games of prey and predation with N species and r  <  N prey and predators, acting in a cyclic way. Further basic reactions include reproduction, decay and diffusion over a one- or two-dimensional regular grid, without a hard constraint on the occupation number per site, so in a ‘bosonic’ implementation. For special combinations of N and r and appropriate parameter choices we observe games within games, that is different coexisting games, depending on the spatial resolution. As a concrete and simplest example we analyze the (6,3) game. Once the players segregate from a random initial distribution, domains emerge, which effectively play a (2,1)-game on the coarse scale of domain diameters, while agents inside the domains play (3,1) (rock-paper-scissors), leading to spiral formation with species chasing each other. The (2,1)-game has a winner in the end, so that the coexistence of domains is transient, while agents inside the remaining domain coexist, until demographic fluctuations lead to extinction of all but one species in the very end. This means that we observe a dynamical generation of multiple space and time scales with emerging re-organization of players upon segregation, starting from a simple set of rules on the smallest scale (that of the grid) and changed rules from the coarser perspective. These observations are based on Gillespie simulations. We discuss the deterministic limit derived from a van Kampen expansion. In this limit we perform a linear stability analysis and numerically integrate the resulting equations. The linear stability analysis predicts the number of forming domains, their composition in terms of species; it explains the instability of interfaces between domains, which drives their extinction; spiral patterns are identified as motion along heteroclinic cycles. The numerical solutions reproduce the observed patterns of the Gillespie simulations including even extinction events, so that the mean

Expanding the domains of attitudes towards evidence-based practice: the evidence based practice attitude scale-50.

PubMed

Aarons, Gregory A; Cafri, Guy; Lugo, Lindsay; Sawitzky, Angelina

2012-09-01

Mental health and social service provider attitudes toward evidence-based practice have been measured through the development and validation of the Evidence-Based Practice Attitude Scale (EBPAS; Aarons, Ment Health Serv Res 6(2):61-74, 2004). Scores on the EBPAS scales are related to provider demographic characteristics, organizational characteristics, and leadership. However, the EBPAS assesses only four domains of attitudes toward EBP. The current study expands and further identifies additional domains of attitudes towards evidence-based practice. A qualitative and quantitative mixed-methods approach was used to: (1) generate items from multiples sources (researcher, mental health program manager, clinician/therapist), (2) identify potential content domains, and (3) examine the preliminary domains and factor structure through exploratory factor analysis. Participants for item generation included the investigative team, a group of mental health program managers (n = 6), and a group of clinicians/therapists (n = 8). For quantitative analyses a sample of 422 mental health service providers from 65 outpatient programs in San Diego County completed a survey that included the new items. Eight new EBPAS factors comprised of 35 items were identified. Factor loadings were moderate to large and internal consistency reliabilities were fair to excellent. We found that the convergence of these factors with the four previously identified evidence-based practice attitude factors (15 items) was small to moderate suggesting that the newly identified factors represent distinct dimensions of mental health and social service provider attitudes toward adopting EBP. Combining the original 15 items with the 35 new items comprises the EBPAS 50-item version (EBPAS-50) that adds to our understanding of provider attitudes toward adopting EBPs. Directions for future research are discussed.

Cyclic Solvent Vapor Annealing for Rapid, Robust Vertical Orientation of Features in BCP Thin Films

NASA Astrophysics Data System (ADS)

Paradiso, Sean; Delaney, Kris; Fredrickson, Glenn

2015-03-01

Methods for reliably controlling block copolymer self assembly have seen much attention over the past decade as new applications for nanostructured thin films emerge in the fields of nanopatterning and lithography. While solvent assisted annealing techniques are established as flexible and simple methods for achieving long range order, solvent annealing alone exhibits a very weak thermodynamic driving force for vertically orienting domains with respect to the free surface. To address the desire for oriented features, we have investigated a cyclic solvent vapor annealing (CSVA) approach that combines the mobility benefits of solvent annealing with selective stress experienced by structures oriented parallel to the free surface as the film is repeatedly swollen with solvent and dried. Using dynamical self-consistent field theory (DSCFT) calculations, we establish the conditions under which the method significantly outperforms both static and cyclic thermal annealing and implicate the orientation selection as a consequence of the swelling/deswelling process. Our results suggest that CSVA may prove to be a potent method for the rapid formation of highly ordered, vertically oriented features in block copolymer thin films.

Single-pixel imaging based on compressive sensing with spectral-domain optical mixing

NASA Astrophysics Data System (ADS)

Zhu, Zhijing; Chi, Hao; Jin, Tao; Zheng, Shilie; Jin, Xiaofeng; Zhang, Xianmin

2017-11-01

In this letter a single-pixel imaging structure is proposed based on compressive sensing using a spatial light modulator (SLM)-based spectrum shaper. In the approach, an SLM-based spectrum shaper, the pattern of which is a predetermined pseudorandom bit sequence (PRBS), spectrally codes the optical pulse carrying image information. The energy of the spectrally mixed pulse is detected by a single-pixel photodiode and the measurement results are used to reconstruct the image via a sparse recovery algorithm. As the mixing of the image signal and the PRBS is performed in the spectral domain, optical pulse stretching, modulation, compression and synchronization in the time domain are avoided. Experiments are implemented to verify the feasibility of the approach.

Application of perturbation theory to lattice calculations based on method of cyclic characteristics

NASA Astrophysics Data System (ADS)

Assawaroongruengchot, Monchai

Perturbation theory is a technique used for the estimation of changes in performance functionals, such as linear reaction rate ratio and eigenvalue affected by small variations in reactor core compositions. Here the algorithm of perturbation theory is developed for the multigroup integral neutron transport problems in 2D fuel assemblies with isotropic scattering. The integral transport equation is used in the perturbative formulation because it represents the interconnecting neutronic systems of the lattice assemblies via the tracking lines. When the integral neutron transport equation is used in the formulation, one needs to solve the resulting integral transport equations for the flux importance and generalized flux importance functions. The relationship between the generalized flux importance and generalized source importance functions is defined in order to transform the generalized flux importance transport equations into the integro-differential equations for the generalized adjoints. Next we develop the adjoint and generalized adjoint transport solution algorithms based on the method of cyclic characteristics (MOCC) in DRAGON code. In the MOCC method, the adjoint characteristics equations associated with a cyclic tracking line are formulated in such a way that a closed form for the adjoint angular function can be obtained. The MOCC method then requires only one cycle of scanning over the cyclic tracking lines in each spatial iteration. We also show that the source importance function by CP method is mathematically equivalent to the adjoint function by MOCC method. In order to speed up the MOCC solution algorithm, a group-reduction and group-splitting techniques based on the structure of the adjoint scattering matrix are implemented. A combined forward flux/adjoint function iteration scheme, based on the group-splitting technique and the common use of a large number of variables storing tracking-line data and exponential values, is proposed to reduce the

Structural and Functional Studies of a Pyran Synthase Domain from a trans-Acyltransferase Assembly Line.

PubMed

Wagner, Drew T; Zhang, Zhicheng; Meoded, Roy A; Cepeda, Alexis J; Piel, Jörn; Keatinge-Clay, Adrian T

2018-04-20

trans-Acyltransferase assembly lines possess enzymatic domains often not observed in their better characterized cis-acyltransferase counterparts. Within this repertoire of largely unexplored biosynthetic machinery is a class of enzymes called the pyran synthases that catalyze the formation of five- and six-membered cyclic ethers from diverse polyketide chains. The 1.55 Å resolution crystal structure of a pyran synthase domain excised from the ninth module of the sorangicin assembly line highlights the similarity of this enzyme to the ubiquitous dehydratase domain and provides insight into the mechanism of ring formation. Functional assays of point mutants reveal the central importance of the active site histidine that is shared with the dehydratases as well as the supporting role of a neighboring semiconserved asparagine.

Cyclic multiverses

NASA Astrophysics Data System (ADS)

Marosek, Konrad; Dąbrowski, Mariusz P.; Balcerzak, Adam

2016-09-01

Using the idea of regularization of singularities due to the variability of the fundamental constants in cosmology we study the cyclic universe models. We find two models of oscillating and non-singular mass density and pressure (`non-singular' bounce) regularized by varying gravitational constant G despite the scale factor evolution is oscillating and having sharp turning points (`singular' bounce). Both violating (big-bang) and non-violating (phantom) null energy condition models appear. Then, we extend this idea on to the multiverse containing cyclic individual universes with either growing or decreasing entropy though leaving the net entropy constant. In order to get an insight into the key idea, we consider the doubleverse with the same geometrical evolution of the two `parallel' universes with their physical evolution [physical coupling constants c(t) and G(t)] being different. An interesting point is that there is a possibility to exchange the universes at the point of maximum expansion - the fact which was already noticed in quantum cosmology. Similar scenario is also possible within the framework of Brans-Dicke theory where varying G(t) is replaced by the dynamical Brans-Dicke field φ(t) though these theories are slightly different.

Prioritisation of associations between protein domains and complex diseases using domain-domain interaction networks.

PubMed

Wang, W; Zhang, W; Jiang, R; Luan, Y

2010-05-01

It is of vital importance to find genetic variants that underlie human complex diseases and locate genes that are responsible for these diseases. Since proteins are typically composed of several structural domains, it is reasonable to assume that harmful genetic variants may alter structures of protein domains, affect functions of proteins and eventually cause disorders. With this understanding, the authors explore the possibility of recovering associations between protein domains and complex diseases. The authors define associations between protein domains and disease families on the basis of associations between non-synonymous single nucleotide polymorphisms (nsSNPs) and complex diseases, similarities between diseases, and relations between proteins and domains. Based on a domain-domain interaction network, the authors propose a 'guilt-by-proximity' principle to rank candidate domains according to their average distance to a set of seed domains in the domain-domain interaction network. The authors validate the method through large-scale cross-validation experiments on simulated linkage intervals, random controls and the whole genome. Results show that areas under receiver operating characteristic curves (AUC scores) can be as high as 77.90%, and the mean rank ratios can be as low as 21.82%. The authors further offer a freely accessible web interface for a genome-wide landscape of associations between domains and disease families.

Susceptibility of Redundant Versus Singular Clock Domains Implemented in SRAM-Based FPGA TMR Designs

NASA Technical Reports Server (NTRS)

Berg, Melanie D.; LaBel, Kenneth A.; Pellish, Jonathan

2016-01-01

We present the challenges that arise when using redundant clock domains due to their clock-skew. Radiation data show that a singular clock domain (DTMR) provides an improved TMR methodology for SRAM-based FPGAs over redundant clocks.

A developmental screening tool for toddlers with multiple domains based on Rasch analysis.

PubMed

Hwang, Ai-Wen; Chou, Yeh-Tai; Hsieh, Ching-Lin; Hsieh, Wu-Shiun; Liao, Hua-Fang; Wong, Alice May-Kuen

2015-01-01

Using multidomain developmental screening tools is a feasible method for pediatric health care professionals to identify children at risk of developmental problems in multiple domains simultaneously. The purpose of this study was to develop a Rasch-based tool for Multidimensional Screening in Child Development (MuSiC) for children aged 0-3 years. The MuSic was developed by constructing items bank based on three commonly used screening tools, validating with developmental status (at risk for delay or not) on five developmental domains. Parents of a convenient sample of 632 children (aged 3-35.5 months) with and without developmental delays responded to items from the three screening tools funded by health authorities in Taiwan. Item bank was determined by item fit of Rasch analysis for each of the five developmental domains (cognitive skills, language skills, gross motor skills, fine motor skills, and socioadaptive skills). Children's performance scores in logits derived in Rasch analysis were validated with developmental status for each domain using the area under receiver operating characteristic curves. MuSiC, a 75-item developmental screening tool for five domains, was derived. The diagnostic validity of all five domains was acceptable for all stages of development, except for the infant stage (≤11 months and 15 days). MuSiC can be applied simultaneously to well-child care visits as a universal screening tool for children aged 1-3 years on multiple domains. Items with sound validity for infants need to be further developed. Copyright © 2014. Published by Elsevier B.V.

Using CLIPS in the domain of knowledge-based massively parallel programming

NASA Technical Reports Server (NTRS)

Dvorak, Jiri J.

1994-01-01

The Program Development Environment (PDE) is a tool for massively parallel programming of distributed-memory architectures. Adopting a knowledge-based approach, the PDE eliminates the complexity introduced by parallel hardware with distributed memory and offers complete transparency in respect of parallelism exploitation. The knowledge-based part of the PDE is realized in CLIPS. Its principal task is to find an efficient parallel realization of the application specified by the user in a comfortable, abstract, domain-oriented formalism. A large collection of fine-grain parallel algorithmic skeletons, represented as COOL objects in a tree hierarchy, contains the algorithmic knowledge. A hybrid knowledge base with rule modules and procedural parts, encoding expertise about application domain, parallel programming, software engineering, and parallel hardware, enables a high degree of automation in the software development process. In this paper, important aspects of the implementation of the PDE using CLIPS and COOL are shown, including the embedding of CLIPS with C++-based parts of the PDE. The appropriateness of the chosen approach and of the CLIPS language for knowledge-based software engineering are discussed.

Cyclic behavior at quasi-parallel collisionless shocks

NASA Technical Reports Server (NTRS)

Burgess, D.

1989-01-01

Large scale one-dimensional hybrid simulations with resistive electrons have been carried out of a quasi-parallel high-Mach-number collisionless shock. The shock initially appears stable, but then exhibits cyclic behavior. For the magnetic field, the cycle consists of a period when the transition from upstream to downstream is steep and well defined, followed by a period when the shock transition is extended and perturbed. This cyclic shock solution results from upstream perturbations caused by backstreaming gyrating ions convecting into the shock. The cyclic reformation of a sharp shock transition can allow ions, at one time upstream because of reflection or leakage, to contribute to the shock thermalization.

Cyclic joint remote state preparation in noisy environment

NASA Astrophysics Data System (ADS)

Zhang, Chang-yue; Bai, Ming-qiang; Zhou, Si-qi

2018-06-01

We propose a scheme of cyclic joint remote state preparation for three sides, which takes advantage of three GHZ states to compose product state as quantum channel. Suppose there are six legitimate participants, says Alice, Bob, Charlie, David, Emma and Fred in the scheme. It can be shown that Alice and David can remotely prepare a single-qubit state on Bob's side; meanwhile, Bob and Emma can remotely prepare a desired quantum state on Charlie's side, and Charlie and Fred can also remotely prepare a single-qubit state on Alice's side at the same time. Further, it can be achieved in the opposite direction of the cycle by changing the quantum channel. Based on it, we generalize this protocol to N (N≥3) sides utilizing three multi-qubit GHZ-type states as quantum channel. Therefore, the scheme can achieve cyclic joint remote state preparation, which remotely prepares N states in quantum network with N-party, simultaneously. In addition, we consider that the effect of amplitude-damping noise of the initial states is prepared in four different laboratory. Clearly, we use fidelity to describe how much information has been lost in the cyclic process. Our investigation about the effect of noise shows that the preparing of the initial state in different laboratories will affect the loss of information.

A feature dictionary supporting a multi-domain medical knowledge base.

PubMed

Naeymi-Rad, F

1989-01-01

Because different terminology is used by physicians of different specialties in different locations to refer to the same feature (signs, symptoms, test results), it is essential that our knowledge development tools provide a means to access a common pool of terms. This paper discusses the design of an online medical dictionary that provides a solution to this problem for developers of multi-domain knowledge bases for MEDAS (Medical Emergency Decision Assistance System). Our Feature Dictionary supports phrase equivalents for features, feature interactions, feature classifications, and translations to the binary features generated by the expert during knowledge creation. It is also used in the conversion of a domain knowledge to the database used by the MEDAS inference diagnostic sessions. The Feature Dictionary also provides capabilities for complex queries across multiple domains using the supported relations. The Feature Dictionary supports three methods for feature representation: (1) for binary features, (2) for continuous valued features, and (3) for derived features.

Efficient synthesis of cysteine-rich cyclic peptides through intramolecular native chemical ligation of N-Hnb-Cys peptide crypto-thioesters.

PubMed

Terrier, Victor P; Delmas, Agnès F; Aucagne, Vincent

2017-01-04

We herein introduce a straightforward synthetic route to cysteine-containing cyclic peptides based on the intramolecular native chemical ligation of in situ generated thioesters. Key precursors are N-Hnb-Cys crypto-thioesters, easily synthesized by Fmoc-based SPPS. The strategy is applied to a representative range of naturally occurring cyclic disulfide-rich peptide sequences.

Pairwise domain adaptation module for CNN-based 2-D/3-D registration.

PubMed

Zheng, Jiannan; Miao, Shun; Jane Wang, Z; Liao, Rui

2018-04-01

Accurate two-dimensional to three-dimensional (2-D/3-D) registration of preoperative 3-D data and intraoperative 2-D x-ray images is a key enabler for image-guided therapy. Recent advances in 2-D/3-D registration formulate the problem as a learning-based approach and exploit the modeling power of convolutional neural networks (CNN) to significantly improve the accuracy and efficiency of 2-D/3-D registration. However, for surgery-related applications, collecting a large clinical dataset with accurate annotations for training can be very challenging or impractical. Therefore, deep learning-based 2-D/3-D registration methods are often trained with synthetically generated data, and a performance gap is often observed when testing the trained model on clinical data. We propose a pairwise domain adaptation (PDA) module to adapt the model trained on source domain (i.e., synthetic data) to target domain (i.e., clinical data) by learning domain invariant features with only a few paired real and synthetic data. The PDA module is designed to be flexible for different deep learning-based 2-D/3-D registration frameworks, and it can be plugged into any pretrained CNN model such as a simple Batch-Norm layer. The proposed PDA module has been quantitatively evaluated on two clinical applications using different frameworks of deep networks, demonstrating its significant advantages of generalizability and flexibility for 2-D/3-D medical image registration when a small number of paired real-synthetic data can be obtained.

A micro-mechanical model to determine changes of collagen fibrils under cyclic loading

NASA Astrophysics Data System (ADS)

Chen, Michelle L.; Susilo, Monica E.; Ruberti, Jeffrey A.; Nguyen, Thao D.

Dynamic mechanical loading induces growth and remodeling in biological tissues. It can alter the degradation rate and intrinsic mechanical properties of collagen through cellular activity. Experiments showed that repeated cyclic loading of a dense collagen fibril substrate increased collagen stiffness and strength, lengthened the substrate, but did not significantly change the fibril areal fraction or fibril anisotropy (Susilo, et al. ``Collagen Network Hardening Following Cyclic Tensile Loading'', Interface Focus, submitted). We developed a model for the collagen fibril substrate (Tonge, et al. ``A micromechanical modeling study of the mechanical stabilization of enzymatic degradation of collagen tissues'', Biophys J, in press.) to probe whether changes in the fibril morphology and mechanical properties can explain the tissue-level properties observed during cyclic loading. The fibrils were modeled as a continuous distribution of wavy elastica, based on experimental measurements of fibril density and collagen anisotropy, and can experience damage after a critical stress threshold. Other mechanical properties in the model were fit to the stress response measured before and after the extended cyclic loading to determine changes in the strength and stiffness of collagen fibrils.

Cyclic strain rate effects in fatigued face-centred and body-centred cubic metals

NASA Astrophysics Data System (ADS)

Mughrabi, Haël

2013-09-01

The present work deals mainly with the effect and the use of strain rate and temperature changes during cyclic deformation as a means to obtain valuable information on the thermally activated dislocation glide processes, based on the assessment of reversible changes of the thermal effective stress and of transient changes of the athermal stress. The importance of closed-loop testing in true plastic strain control with constant cyclic plastic strain rate throughout the cycle is explained and emphasized, especially with respect to the case of strain rate sensitive materials. Stress responses of face-centred cubic and body-centred cubic (bcc) metals to cyclic strain rate changes are presented to illustrate that the deformation modes of these two classes of materials differ characteristically at temperatures below that the so-called knee temperature of bcc metals. When such tests are performed in cyclic saturation, the temperature and strain rate dependence of bcc metals can be measured very accurately on one and the same specimen, permitting a thorough analysis of thermal activation.

Endogenous and exogenous cyclicity and temperament in bipolar disorder: review, new data and hypotheses.

PubMed

Koukopoulos, Athanasios; Sani, Gabriele; Koukopoulos, Alexia E; Albert, Matthew J; Girardi, Paolo; Tatarelli, Roberto

2006-12-01

In this special issue dedicated to Falret and the French contributions to the concept of cyclicity in manic depressive illness, we begin with a historical overview of the development of the concept of cyclicity and its fundamental significance in manic-depressive illness and we underscore how the concept fell into neglect only to reemerge in recent years. We then look at the intimate relationship between mania and depression. The hypothesis of the primacy of mania is discussed. The thesis is presented, supported by the examination of 100 consecutive index manias, that in most cases mania is triggered by external factors acting upon hyperthymic patients, determining an exogenous cyclicity. On the other hand, in BPII patients the temperamental mood instability (cyclothymia) is an inherent and decisive factor in determining the cyclic autonomous course of the disorder. Finally, a new distinction of Bipolar Disorders, based on premorbid temperament and course of the illness, is considered.

Domain Specific vs Domain General: Implications for Dynamic Assessment

ERIC Educational Resources Information Center

Kaniel, Shlomo

2010-01-01

The article responds to the need for evidence-based dynamic assessment. The article is divided into two sections: In Part 1 we examine the scientific answer to the question of how far human mental activities and capabilities are domain general (DG) / domain specific (DS). A highly complex answer emerges from the literature review of domains such…

A Cross-Domain Collaborative Filtering Algorithm Based on Feature Construction and Locally Weighted Linear Regression.

PubMed

Yu, Xu; Lin, Jun-Yu; Jiang, Feng; Du, Jun-Wei; Han, Ji-Zhong

2018-01-01

Cross-domain collaborative filtering (CDCF) solves the sparsity problem by transferring rating knowledge from auxiliary domains. Obviously, different auxiliary domains have different importance to the target domain. However, previous works cannot evaluate effectively the significance of different auxiliary domains. To overcome this drawback, we propose a cross-domain collaborative filtering algorithm based on Feature Construction and Locally Weighted Linear Regression (FCLWLR). We first construct features in different domains and use these features to represent different auxiliary domains. Thus the weight computation across different domains can be converted as the weight computation across different features. Then we combine the features in the target domain and in the auxiliary domains together and convert the cross-domain recommendation problem into a regression problem. Finally, we employ a Locally Weighted Linear Regression (LWLR) model to solve the regression problem. As LWLR is a nonparametric regression method, it can effectively avoid underfitting or overfitting problem occurring in parametric regression methods. We conduct extensive experiments to show that the proposed FCLWLR algorithm is effective in addressing the data sparsity problem by transferring the useful knowledge from the auxiliary domains, as compared to many state-of-the-art single-domain or cross-domain CF methods.

Towards optimal intraoperative conditions in esophageal surgery: A review of literature for the prevention of esophageal anastomotic leakage.

PubMed

Bootsma, Boukje Titia; Huisman, Daitlin Esmee; Plat, Victor Dirk; Schoonmade, Linda Jeanne; Stens, Jurre; Hubens, Guy; van der Peet, Donald Leonard; Daams, Freek

2018-04-30

Esophageal anastomotic leakage (EAL) is a severe complication following gastric and esophageal surgery for cancer. Several non-modifiable, patient or surgery related risk factors for EAL have been identified, however, the contribution of modifiable intraoperative parameters remains undetermined. This review provides an overview of current literature on potentially modifiable intraoperative risk factors for EAL. The PubMed, EMBASE and Cochrane databases were searched by two researchers independently. Clinical studies published in English between 1970 and January 2017 that evaluated the effect of intraoperative parameters on the development of EAL were included. Levels of evidence as defined by the Centre of Evidence Based Medicine (CEBM) were assigned to the studies. A total of 25 articles were included in the final analysis. These articles show evidence that anemia, increased amount of blood loss, low pH and high pCO2 values, prolonged duration of procedure and lack of surgical experience independently increase the risk of EAL. Supplemental oxygen therapy, epidural analgesia and selective digestive decontamination seem to have a beneficial effect. Potential risk factors include blood pressure, requirement of blood products, vasopressor use and glucocorticoid administration, however the results are ambiguous. Apart from fixed surgical and patient related factors, several intraoperative factors that can be modified in clinical practice can influence the risk of developing EAL. More prospective, observational studies are necessary focusing on modifiable intraoperative parameters to assess more evidence and to elucidate optimal values of these factors. Copyright © 2018 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

Furnace Cyclic Behavior of Plasma-Sprayed Zirconia-Yttria and Multi-Component Rare Earth Oxide Doped Thermal Barrier Coatings

NASA Technical Reports Server (NTRS)

Zhu, Dongming; Nesbitt, James A.; McCue, Terry R.; Barrett, Charles A.; Miller, Robert A.

2002-01-01

Ceramic thermal barrier coatings will play an increasingly important role in advanced gas turbine engines because of their ability to enable further increases in engine temperatures. However, the coating performance and durability become a major concern under the increasingly harsh thermal cycling conditions. Advanced zirconia- and hafnia-based cluster oxide thermal barrier coatings with lower thermal conductivity and improved thermal stability are being developed using a high-heat-flux laser-rig based test approach. Although the new composition coatings were not yet optimized for cyclic durability, an initial durability screening of numerous candidate coating materials was carried out using conventional furnace cyclic tests. In this paper, furnace thermal cyclic behavior of the advanced plasma-sprayed zirconia-yttria-based thermal barrier coatings that were co-doped with multi-component rare earth oxides was investigated at 1163 C using 45 min hot cycles. The ceramic coating failure mechanisms were studied by using scanning electron microscopy combined with X-ray diffraction phase analysis after the furnace tests. The coating cyclic lifetime will be discussed in relation to coating phase structures, total dopant concentrations, and other properties.

Skyrmion domain wall collision and domain wall-gated skyrmion logic

NASA Astrophysics Data System (ADS)

Xing, Xiangjun; Pong, Philip W. T.; Zhou, Yan

2016-08-01

Skyrmions and domain walls are significant spin textures of great technological relevance to magnetic memory and logic applications, where they can be used as carriers of information. The unique topology of skyrmions makes them display emergent dynamical properties as compared with domain walls. Some studies have demonstrated that the two topologically inequivalent magnetic objects could be interconverted by using cleverly designed geometric structures. Here, we numerically address the skyrmion domain wall collision in a magnetic racetrack by introducing relative motion between the two objects based on a specially designed junction. An electric current serves as the driving force that moves a skyrmion toward a trapped domain wall pair. We see different types of collision dynamics depending on the driving parameters. Most importantly, the modulation of skyrmion transport using domain walls is realized in this system, allowing a set of domain wall-gated logical NOT, NAND, and NOR gates to be constructed. This work provides a skyrmion-based spin-logic architecture that is fully compatible with racetrack memories.

Kinetics of Domain Switching by Mechanical and Electrical Stimulation in Relaxor-Based Ferroelectrics

NASA Astrophysics Data System (ADS)

Chen, Zibin; Hong, Liang; Wang, Feifei; An, Xianghai; Wang, Xiaolin; Ringer, Simon; Chen, Long-Qing; Luo, Haosu; Liao, Xiaozhou

2017-12-01

Ferroelectric materials have been extensively explored for applications in high-density nonvolatile memory devices because of their ferroelectric-ferroelastic domain-switching behavior under electric loading or mechanical stress. However, the existence of ferroelectric and ferroelastic backswitching would cause significant data loss, which affects the reliability of data storage. Here, we apply in situ transmission electron microscopy and phase-field modeling to explore the unique ferroelastic domain-switching kinetics and the origin of this in relaxor-based Pb (Mg1 /3Nb2 /3)O3-33 % PbTiO3 single-crystal pillars under electrical and mechanical stimulations. Results showed that the electric-mechanical hysteresis loop shifted for relaxor-based single-crystal pillars because of the low energy levels of domains in the material and the constraint on the pillars, resulting in various mechanically reversible and irreversible domain-switching states. The phenomenon can potentially be used for advanced bit writing and reading in nonvolatile memories, which effectively overcomes the backswitching problem and broadens the types of ferroelectric materials for nonvolatile memory applications.

Experimental Investigation on Deformation Failure Characteristics of Crystalline Marble Under Triaxial Cyclic Loading

NASA Astrophysics Data System (ADS)

Yang, Sheng-Qi; Tian, Wen-Ling; Ranjith, P. G.

2017-11-01

The deformation failure characteristics of marble subjected to triaxial cyclic loading are significant when evaluating the stability and safety of deep excavation damage zones. To date, however, there have been notably few triaxial experimental studies on marble under triaxial cyclic loading. Therefore, in this research, a series of triaxial cyclic tests was conducted to analyze the mechanical damage characteristics of a marble. The post-peak deformation of the marble changed gradually from strain softening to strain hardening as the confining pressure increased from 0 to 10 MPa. Under uniaxial compression, marble specimens showed brittle failure characteristics with a number axial splitting tensile cracks; in the range of σ 3 = 2.5-7.5 MPa, the marble specimens assumed single shear fracture characteristics with larger fracture angles of about 65°. However, at σ 3 = 10 MPa, the marble specimens showed no obvious shear fracture surfaces. The triaxial cyclic experimental results indicate that in the range of the tested confining pressures, the triaxial strengths of the marble specimens under cyclic loading were approximately equal to those under monotonic loading. With the increase in cycle number, the elastic strains of the marble specimens all increased at first and later decreased, achieving maximum values, but the plastic strains of the marble specimens increased nonlinearly. To evaluate quantitatively the damage extent of the marble under triaxial cyclic loading, a damage variable is defined according to the irreversible deformation for each cycle. The evolutions of the elastic modulus for the marble were characterized by four stages: material strengthening, material degradation, material failure and structure slippage. Based on the experimental results of the marble specimens under complex cyclic loading, the cohesion of the marble decreased linearly, but the internal friction angles did not depend on the damage extent. To describe the peak strength

Domain-General and Domain-Specific Strategies for the Assessment of Distress Intolerance

PubMed Central

McHugh, R. Kathryn; Otto, Michael W.

2011-01-01

Recent research has provided evidence that distress intolerance—the perceived inability to tolerate distressing states—varies based on the domain of distress (e.g., pain, anxiety). Although domain-specific assessment strategies may provide information targeted to specific disorders or maladaptive behaviors, domain-general measures have the potential to facilitate comparisons across studies, disorders, and populations. The current study evaluated the utilization of self-report measures of distress intolerance as domain-general measures by examining their association with indices of behavioral avoidance and substance craving. Two groups of participants (N = 55) were recruited including a substance-dependent group and a comparison group equated based on the presence of an affective disorder. Results provided support for the validity of domain-general measures for assessing distress intolerance across varied domains. The importance of both domain-general and domain-specific measurement of distress intolerance is discussed. PMID:21823763

Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration.

PubMed

Sim, Jaehyun; Sim, Jun; Park, Eunsung; Lee, Julian

2015-06-01

Many proteins undergo large-scale motions where relatively rigid domains move against each other. The identification of rigid domains, as well as the hinge residues important for their relative movements, is important for various applications including flexible docking simulations. In this work, we develop a method for protein rigid domain identification based on an exhaustive enumeration of maximal rigid domains, the rigid domains not fully contained within other domains. The computation is performed by mapping the problem to that of finding maximal cliques in a graph. A minimal set of rigid domains are then selected, which cover most of the protein with minimal overlap. In contrast to the results of existing methods that partition a protein into non-overlapping domains using approximate algorithms, the rigid domains obtained from exact enumeration naturally contain overlapping regions, which correspond to the hinges of the inter-domain bending motion. The performance of the algorithm is demonstrated on several proteins. © 2015 Wiley Periodicals, Inc.

Recent progress in synchrotron-based frequency-domain Fourier-transform THz-EPR.

PubMed

Nehrkorn, Joscha; Holldack, Karsten; Bittl, Robert; Schnegg, Alexander

2017-07-01

We describe frequency-domain Fourier-transform THz-EPR as a method to assign spin-coupling parameters of high-spin (S>1/2) systems with very large zero-field splittings. The instrumental foundations of synchrotron-based FD-FT THz-EPR are presented, alongside with a discussion of frequency-domain EPR simulation routines. The capabilities of this approach is demonstrated for selected mono- and multinuclear HS systems. Finally, we discuss remaining challenges and give an outlook on the future prospects of the technique. Copyright © 2017 Elsevier Inc. All rights reserved.

Safety Discrete Event Models for Holonic Cyclic Manufacturing Systems

NASA Astrophysics Data System (ADS)

Ciufudean, Calin; Filote, Constantin

In this paper the expression “holonic cyclic manufacturing systems” refers to complex assembly/disassembly systems or fork/join systems, kanban systems, and in general, to any discrete event system that transforms raw material and/or components into products. Such a system is said to be cyclic if it provides the same sequence of products indefinitely. This paper considers the scheduling of holonic cyclic manufacturing systems and describes a new approach using Petri nets formalism. We propose an approach to frame the optimum schedule of holonic cyclic manufacturing systems in order to maximize the throughput while minimize the work in process. We also propose an algorithm to verify the optimum schedule.

Static and cyclic loading of fiber-reinforced dental resin.

PubMed

Drummond, James L; Bapna, Mahendra S

2003-05-01

The aim of this study was to evaluate the flexure strength of unidirectional fiber-reinforced resins under static and cyclic loading with and without thermal cycling. The fiber-reinforced resin materials chosen for this project were commercially available endodontic posts and commercially procured bar samples. For all materials, controls for flexure strength were tested in air and in water using three-point loading. Specimens were thermal cycled between 7 and 63 degrees C for 6000 cycles. A staircase approach was used to determine the flexure fatigue limit and scanning microscopy was used to examine the microstructure. The carbon/graphite fiber-reinforced resin posts and the glass FiberKor posts were significantly stronger than the ceramic (zirconia) and the other glass-reinforced resin materials. Thermal cycling caused a significant lowering (11-24%) of the flexure strength for each resin based post system. The ceramic post system decreased only by 2%. Further, for standard size glass fiber-reinforced resin bars, no significant differences between testing in air and water was observed, but a significant difference between static and cyclic loading was noted. The decreases in the strength property due to thermal cycling and the cyclic loading of these materials indicates that their utilization in the oral environment enhances their degradation, and potentially shortens their clinical life.

Ferroelectric domain switching dynamics and memristive behaviors in BiFeO3-based magnetoelectric heterojunctions

NASA Astrophysics Data System (ADS)

Huang, Weichuan; Liu, Yukuai; Luo, Zhen; Hou, Chuangming; Zhao, Wenbo; Yin, Yuewei; Li, Xiaoguang

2018-06-01

The ferroelectric domain reversal dynamics and the corresponding resistance switching as well as the memristive behaviors in epitaxial BiFeO3 (BFO, ~150 nm) based multiferroic heterojunctions were systematically investigated. The ferroelectric domain reversal dynamics could be described by the nucleation-limited-switching model with the Lorentzian distribution of logarithmic domain-switching times. By engineering the domain states, multi and even continuously tunable resistances states, i.e. memristive states, could be non-volatilely achieved. The resistance switching speed can be as fast as 30 ns in the BFO-based multiferroic heterojunctions with a write voltage of ~20 V. By reducing the thickness of BFO, the La0.6Sr0.4MnO3/BFO (~5 nm)/La0.6Sr0.4MnO3 multiferroic tunnel junction (MFTJ) shows an even a quicker switching speed (20 ns) with a much lower operation voltage (~4 V). Importantly, the MFTJ exhibits a tunable interfacial magnetoelectric coupling related to the ferroelectric domain switching dynamics. These findings enrich the potential applications of multiferroic BFO based devices in high-speed, low-power, and high-density memories as well as future neuromorphic computational architectures.

Cyclic Disilylated and Digermylated Germylenes

PubMed Central

2013-01-01

The preparation of triethylphosphine adducts of cyclic disilylated or digermylated germylenes was achieved by reaction of 1,4-dipotassio-1,1,4,4-tetrakis(trimethylsilyl)tetramethyltetrasilane with GeBr2·(dioxane) and PEt3. Phosphine abstraction with B(C6F5)3 allowed formation of the base-free germylenes, which undergo 1,2-trimethylsilyl shifts to the germylene atom to form the respective silagermene or digermene, which further dimerize in [2 + 2] cycloadditions to tricyclic compounds. The reasons responsible for the germylenes’ completely different reactivities in comparison to the previously studied analogous stannylenes and plumbylenes were elucidated in a theoretical study. PMID:23874054

Chairside CAD/CAM materials. Part 3: Cyclic fatigue parameters and lifetime predictions.

PubMed

Wendler, Michael; Belli, Renan; Valladares, Diana; Petschelt, Anselm; Lohbauer, Ulrich

2018-06-01

Chemical and mechanical degradation play a key role on the lifetime of dental restorative materials. Therefore, prediction of their long-term performance in the oral environment should base on fatigue, rather than inert strength data, as commonly observed in the dental material's field. The objective of the present study was to provide mechanistic fatigue parameters of current dental CAD/CAM materials under cyclic biaxial flexure and assess their suitability in predicting clinical fracture behaviors. Eight CAD/CAM materials, including polycrystalline zirconia (IPS e.max ZirCAD), reinforced glasses (Vitablocs Mark II, IPS Empress CAD), glass-ceramics (IPS e.max CAD, Suprinity PC, Celtra Duo), as well as hybrid materials (Enamic, Lava Ultimate) were evaluated. Rectangular plates (12×12×1.2mm 3 ) with highly polished surfaces were prepared and tested in biaxial cyclic fatigue in water until fracture using the Ball-on-Three-Balls (B3B) test. Cyclic fatigue parameters n and A* were obtained from the lifetime data for each material and further used to build SPT diagrams. The latter were used to compare in-vitro with in-vivo fracture distributions for IPS e.max CAD and IPS Empress CAD. Susceptibility to subcritical crack growth under cyclic loading was observed for all materials, being more severe (n≤20) in lithium-based glass-ceramics and Vitablocs Mark II. Strength degradations of 40% up to 60% were predicted after only 1 year of service. Threshold stress intensity factors (K th ) representing the onset of subcritical crack growth (SCG), were estimated to lie in the range of 0.37-0.44 of K Ic for the lithium-based glass-ceramics and Vitablocs Mark II and between 0.51-0.59 of K Ic for the other materials. Failure distributions associated with mechanistic estimations of strength degradation in-vitro showed to be useful in interpreting failure behavior in-vivo. The parameter K th stood out as a better predictor of clinical performance in detriment to the SCG n

A Cross-Domain Collaborative Filtering Algorithm Based on Feature Construction and Locally Weighted Linear Regression

PubMed Central

Jiang, Feng; Han, Ji-zhong

2018-01-01

Cross-domain collaborative filtering (CDCF) solves the sparsity problem by transferring rating knowledge from auxiliary domains. Obviously, different auxiliary domains have different importance to the target domain. However, previous works cannot evaluate effectively the significance of different auxiliary domains. To overcome this drawback, we propose a cross-domain collaborative filtering algorithm based on Feature Construction and Locally Weighted Linear Regression (FCLWLR). We first construct features in different domains and use these features to represent different auxiliary domains. Thus the weight computation across different domains can be converted as the weight computation across different features. Then we combine the features in the target domain and in the auxiliary domains together and convert the cross-domain recommendation problem into a regression problem. Finally, we employ a Locally Weighted Linear Regression (LWLR) model to solve the regression problem. As LWLR is a nonparametric regression method, it can effectively avoid underfitting or overfitting problem occurring in parametric regression methods. We conduct extensive experiments to show that the proposed FCLWLR algorithm is effective in addressing the data sparsity problem by transferring the useful knowledge from the auxiliary domains, as compared to many state-of-the-art single-domain or cross-domain CF methods. PMID:29623088

Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape.

PubMed

Yokoyama, Takao; Miura, Fumihito; Araki, Hiromitsu; Okamura, Kohji; Ito, Takashi

2015-08-12

Base-resolution methylome data generated by whole-genome bisulfite sequencing (WGBS) is often used to segment the genome into domains with distinct methylation levels. However, most segmentation methods include many parameters to be carefully tuned and/or fail to exploit the unsurpassed resolution of the data. Furthermore, there is no simple method that displays the composition of the domains to grasp global trends in each methylome. We propose to use changepoint detection for domain demarcation based on base-resolution methylome data. While the proposed method segments the methylome in a largely comparable manner to conventional approaches, it has only a single parameter to be tuned. Furthermore, it fully exploits the base-resolution of the data to enable simultaneous detection of methylation changes in even contrasting size ranges, such as focal hypermethylation and global hypomethylation in cancer methylomes. We also propose a simple plot termed methylated domain landscape (MDL) that globally displays the size, the methylation level and the number of the domains thus defined, thereby enabling one to intuitively grasp trends in each methylome. Since the pattern of MDL often reflects cell lineages and is largely unaffected by data size, it can serve as a novel signature of methylome. Changepoint detection in base-resolution methylome data followed by MDL plotting provides a novel method for methylome characterization and will facilitate global comparison among various WGBS data differing in size and even species origin.

Brazilian adults' sedentary behaviors by life domain: population-based study.

PubMed

Mielke, Grégore I; da Silva, Inácio C M; Owen, Neville; Hallal, Pedro C

2014-01-01

There is rapidly-emerging evidence on the harmful health effects of sedentary behaviors. The aim of this paper was to quantify time in sedentary behaviors and document socio-demographic variations in different life domains among adults. A population-based survey was carried out in 2012 through face-to-face interviews with Brazilian adults aged 20+ years (N = 2,927). Information about time spent sedentary in a typical weekday was collected for five different domains (workplace, commuting, school/university, watching TV, and computer use at home). Descriptive and bivariate analyses examined variations in overall and domain-specific sedentary time by gender, age, educational attainment and socioeconomic position. On average, participants reported spending 5.8 (SD 4.5) hours per day sitting. The median value was 4.5 (interquartile range: 2.5-8) hours. Men, younger adults, those with higher schooling and from the wealthiest socioeconomic groups had higher overall sedentary scores. TV time was higher in women, older adults and among those with low schooling and socioeconomic position. Sedentary time in transport was higher in men, younger adults, and participants with high schooling and high socioeconomic position. Computer use at home was more frequent among young adults and those from high socioeconomic groups. Sitting at work was higher in those with higher schooling and from the wealthiest socioeconomic groups. Sedentary behavior at school was related inversely to age and directly to schooling. Patterns of sedentary behavior are different by life domains. Initiatives to reduce prolonged sitting among Brazilian adults will be required on multiple levels for different life domains.

Matrix cracking in laminated composites under monotonic and cyclic loadings

NASA Technical Reports Server (NTRS)

Allen, David H.; Lee, Jong-Won

1991-01-01

An analytical model based on the internal state variable (ISV) concept and the strain energy method is proposed for characterizing the monotonic and cyclic response of laminated composites containing matrix cracks. A modified constitution is formulated for angle-ply laminates under general in-plane mechanical loading and constant temperature change. A monotonic matrix cracking criterion is developed for predicting the crack density in cross-ply laminates as a function of the applied laminate axial stress. An initial formulation for a cyclic matrix cracking criterion for cross-ply laminates is also discussed. For the monotonic loading case, a number of experimental data and well-known models are compared with the present study for validating the practical applicability of the ISV approach.

Isolation of New Gravitropic Mutants under Hypergravity Conditions.

PubMed

Mori, Akiko; Toyota, Masatsugu; Shimada, Masayoshi; Mekata, Mika; Kurata, Tetsuya; Tasaka, Masao; Morita, Miyo T

2016-01-01

Forward genetics is a powerful approach used to link genotypes and phenotypes, and mutant screening/analysis has provided deep insights into many aspects of plant physiology. Gravitropism is a tropistic response in plants, in which hypocotyls and stems sense the direction of gravity and grow upward. Previous studies of gravitropic mutants have suggested that shoot endodermal cells in Arabidopsis stems and hypocotyls are capable of sensing gravity (i.e., statocytes). In the present study, we report a new screening system using hypergravity conditions to isolate enhancers of gravitropism mutants, and we also describe a rapid and efficient genome mapping method, using next-generation sequencing (NGS) and single nucleotide polymorphism (SNP)-based markers. Using the endodermal-amyloplast less 1 ( eal1 ) mutant, which exhibits defective development of endodermal cells and gravitropism, we found that hypergravity (10 g) restored the reduced gravity responsiveness in eal1 hypocotyls and could, therefore, be used to obtain mutants with further reduction in gravitropism in the eal1 background. Using the new screening system, we successfully isolated six ene ( enhancer of eal1 ) mutants that exhibited little or no gravitropism under hypergravity conditions, and using NGS and map-based cloning with SNP markers, we narrowed down the potential causative genes, which revealed a new genetic network for shoot gravitropism in Arabidopsis .

A Logic for Inclusion of Administrative Domains and Administrators in Multi-domain Authorization

NASA Astrophysics Data System (ADS)

Iranmanesh, Zeinab; Amini, Morteza; Jalili, Rasool

Authorization policies for an administrative domain or a composition of multiple domains in multi-domain environments are determined by either one administrator or multiple administrators' cooperation. Several logic-based models for multi-domain environments' authorization have been proposed; however, they have not considered administrators and administrative domains in policies' representation. In this paper, we propose the syntax, proof theory, and semantics of a logic for multi-domain authorization policies including administrators and administrative domains. Considering administrators in policies provides the possibility of presenting composite administration having applicability in many collaborative applications. Indeed, administrators and administrative domains stated in policies can be used in authorization. The presented logic is based on modal logic and utilizes two calculi named the calculus of administrative domains and the calculus of administrators. It is also proved that the logic is sound. A case study is presented signifying the logic application in practical projects.

Cyclic voltammetric study of Co-Ni-Fe alloys electrodeposition in sulfate medium

NASA Astrophysics Data System (ADS)

Hanafi, I.; Daud, A. R.; Radiman, S.

2013-11-01

Electrochemical technique has been used to study the electrodeposition of cobalt, nickel, iron and Co-Ni-Fe alloy on indium tin oxide (ITO) coated glass substrate. To obtain the nucleation mechanism, cyclic voltammetry is used to characterize the Co-Ni-Fe system. The scanning rate effect on the deposition process was investigated. Deposition of single metal occurs at potential values more positive than that estimated stability potential. Based on the cyclic voltammetry results, the electrodeposition of cobalt, nickel, iron and Co-Ni-Fe alloy clearly show that the process of diffusion occurs is controlled by the typical nucleation mechanism.

Time and frequency domain characteristics of detrending-operation-based scaling analysis: Exact DFA and DMA frequency responses

NASA Astrophysics Data System (ADS)

Kiyono, Ken; Tsujimoto, Yutaka

2016-07-01

We develop a general framework to study the time and frequency domain characteristics of detrending-operation-based scaling analysis methods, such as detrended fluctuation analysis (DFA) and detrending moving average (DMA) analysis. In this framework, using either the time or frequency domain approach, the frequency responses of detrending operations are calculated analytically. Although the frequency domain approach based on conventional linear analysis techniques is only applicable to linear detrending operations, the time domain approach presented here is applicable to both linear and nonlinear detrending operations. Furthermore, using the relationship between the time and frequency domain representations of the frequency responses, the frequency domain characteristics of nonlinear detrending operations can be obtained. Based on the calculated frequency responses, it is possible to establish a direct connection between the root-mean-square deviation of the detrending-operation-based scaling analysis and the power spectrum for linear stochastic processes. Here, by applying our methods to DFA and DMA, including higher-order cases, exact frequency responses are calculated. In addition, we analytically investigate the cutoff frequencies of DFA and DMA detrending operations and show that these frequencies are not optimally adjusted to coincide with the corresponding time scale.

Time and frequency domain characteristics of detrending-operation-based scaling analysis: Exact DFA and DMA frequency responses.

PubMed

Kiyono, Ken; Tsujimoto, Yutaka

2016-07-01

We develop a general framework to study the time and frequency domain characteristics of detrending-operation-based scaling analysis methods, such as detrended fluctuation analysis (DFA) and detrending moving average (DMA) analysis. In this framework, using either the time or frequency domain approach, the frequency responses of detrending operations are calculated analytically. Although the frequency domain approach based on conventional linear analysis techniques is only applicable to linear detrending operations, the time domain approach presented here is applicable to both linear and nonlinear detrending operations. Furthermore, using the relationship between the time and frequency domain representations of the frequency responses, the frequency domain characteristics of nonlinear detrending operations can be obtained. Based on the calculated frequency responses, it is possible to establish a direct connection between the root-mean-square deviation of the detrending-operation-based scaling analysis and the power spectrum for linear stochastic processes. Here, by applying our methods to DFA and DMA, including higher-order cases, exact frequency responses are calculated. In addition, we analytically investigate the cutoff frequencies of DFA and DMA detrending operations and show that these frequencies are not optimally adjusted to coincide with the corresponding time scale.

Mechanical characterization and force-displacement hysteretic curves from in-plane cyclic tests on strong masonry infills.

PubMed

Morandi, Paolo; Hak, Sanja; Magenes, Guido

2018-02-01

This article contains information related to a recent study "Performance-based interpretation of in-plane cyclic tests on RC frames with strong masonry infills" (Morandi et al., 2017 [1]). Motivated by the necessity to improve the knowledge of the in-plane seismic response of rigid strong masonry infills, a wide experimental campaign based on in-plane cyclic tests on full-scale RC infilled frame specimens, supplemented with a complete characterization of the materials, has been conducted at the laboratory of the Department of Civil Engineering and Architecture of the University of Pavia. The masonry is constituted by vertically perforated 35 cm thick clay units with tongue and groove and dry head-joints and general-purpose mortar bed-joints. The paper reports the results of the mechanical characterization and of the force-displacement hysteretic curves from the in-plane cyclic tests.

Gonadotropin level abnormalities in women with cyclic mastalgia.

PubMed

Ecochard, R; Marret, H; Rabilloud, M; Boehringer, H; Mathieu, C; Guerin, J F

2001-01-01

Women with cyclic mastalgia seem to be at risk of fibrocystic breast disease and/or breast cancer. We studied the relationships between mastalgia and hormone levels throughout the menstrual cycle. Ostensibly healthy women were monitored during a sum of 326 cycles. A case-control study compared personal and hormonal variables of 30 women experiencing cyclic mastalgia with those of 77 women without this symptom. Except sleeping times, no significant differences were found in personal variables. Cyclic mastalgia and symptoms of fluid retention were slightly associated. Menses and the luteal phase were significantly longer in cases than in controls. Gonadotropin but not ovarian hormone levels were also significantly higher in cases throughout the cycle. Cyclic mastalgia is less related to symptoms of fluid retention or to ovarian hormone levels than to regularly high gonadotropin levels, specific inhibitors might thus be used to alleviate the symptom.

Using dynamic mode decomposition to extract cyclic behavior in the stock market

NASA Astrophysics Data System (ADS)

Hua, Jia-Chen; Roy, Sukesh; McCauley, Joseph L.; Gunaratne, Gemunu H.

2016-04-01

The presence of cyclic expansions and contractions in the economy has been known for over a century. The work reported here searches for similar cyclic behavior in stock valuations. The variations are subtle and can only be extracted through analysis of price variations of a large number of stocks. Koopman mode analysis is a natural approach to establish such collective oscillatory behavior. The difficulty is that even non-cyclic and stochastic constituents of a finite data set may be interpreted as a sum of periodic motions. However, deconvolution of these irregular dynamical facets may be expected to be non-robust, i.e., to depend on specific data set. We propose an approach to differentiate robust and non-robust features in a time series; it is based on identifying robust features with reproducible Koopman modes, i.e., those that persist between distinct sub-groupings of the data. Our analysis of stock data discovered four reproducible modes, one of which has period close to the number of trading days/year. To the best of our knowledge these cycles were not reported previously. It is particularly interesting that the cyclic behaviors persisted through the great recession even though phase relationships between stocks within the modes evolved in the intervening period.

Elevational gradient in the cyclicity of a forest-defoliating insect

Treesearch

Kyle J. Haynes; Andrew M. Liebhold; Derek M. Johnson

2012-01-01

Observed changes in the cyclicity of herbivore populations along latitudinal gradients and the hypothesis that shifts in the importance of generalist versus specialist predators explain such gradients has long been a matter of intense interest. In contrast, elevational gradients in population cyclicity are largely unexplored. We quantified the cyclicity of gypsy moth...

MICROWAVE-ASSISTED PREPARATION OF CYCLIC UREAS FROM DIAMINES

EPA Science Inventory

Rajender S. Varma* and Yong-Jin Kim
Cyclic ureas are useful intermediates for a variety of pharmaceuticals and pesticides. One of the attractive approaches for the synthesis of cyclic ureas uses condensation of diamines with urea as a carbonyl source under dynamic evacuation. ...

Protective effects of Arctium lappa L. roots against hydrogen peroxide-induced cell injury and potential mechanisms in SH-SY5Y cells.

PubMed

Tian, Xing; Guo, Li-Ping; Hu, Xiao-Long; Huang, Jin; Fan, Yan-Hua; Ren, Tian-Shu; Zhao, Qing-Chun

2015-04-01

Accumulated evidence has shown that excessive reactive oxygen species (ROS) have been implicated in neuronal cell death related with various chronic neurodegenerative disorders. This study was designed to explore neuroprotective effects of ethyl acetate extract of Arctium lappa L. roots (EAL) on hydrogen peroxide (H2O2)-induced cell injury in human SH-SY5Y neuroblastoma cells. The cell viability was significantly decreased after exposure to 200 μM H2O2, whereas pretreatment with different concentrations of EAL attenuated the H2O2-induced cytotoxicity. Hoechst 33342 staining indicated that EAL reversed nuclear condensation in H2O2-treated cells. Meanwhile, TUNEL assay with DAPI staining showed that EAL attenuated apoptosis was induced by H2O2. Pretreatment with EAL also markedly elevated activities of antioxidant enzyme (GSH-Px and SOD), reduced lipid peroxidation (MDA) production, prevented ROS formation, and the decrease of mitochondrial membrane potential. In addition, EAL showed strong radical scavenging ability in 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) assays. Furthermore, EAL inhibited H2O2-induced apoptosis by increases in the Bcl-2/Bax ratio, decreases in cytochrome c release, and attenuation of caspase-3, caspase-9 activities, and expressions. These findings suggest that EAL may be regarded as a potential antioxidant agent and possess potent neuroprotective activity against H2O2-induced injury.

Data encoding based on the shape of the ferroelectric domains produced by a scanning probe microscopy tip

DOE PAGES

Ievlev, Anton; Kalinin, Sergei V.

2015-05-28

Ferroelectric materials are broadly considered for information storage due to extremely high storage and information processing densities they enable. To date, ferroelectric based data storage has invariably relied on formation of cylindrical domains, allowing for binary information encoding. Here we demonstrate and explore the potential of high-density encoding based on domain morphology. We explore the domain morphogenesis during the tip-induced polarization switching by sequences of positive and negative pulses in a lithium niobate single-crystal and demonstrate the principal of information coding by shape and size of the domains. We applied cross-correlation and neural network approaches for recognition of the switchingmore » sequence by the shape of the resulting domains and establish optimal parameters for domain shape recognition. These studies both provide insight into the highly non-trivial mechanism of domain switching and potentially establish a new paradigm for multilevel information storage and content retrieval memories. Furthermore, this approach opens a pathway to exploration of domain switching mechanisms via shape analysis.« less

Bacterial nucleotide-based second messengers.

PubMed

Pesavento, Christina; Hengge, Regine

2009-04-01

In all domains of life nucleotide-based second messengers transduce signals originating from changes in the environment or in intracellular conditions into appropriate cellular responses. In prokaryotes cyclic di-GMP has emerged as an important and ubiquitous second messenger regulating bacterial life-style transitions relevant for biofilm formation, virulence, and many other bacterial functions. This review describes similarities and differences in the architecture of the cAMP, (p)ppGpp, and c-di-GMP signaling systems and their underlying signaling principles. Moreover, recent advances in c-di-GMP-mediated signaling will be presented and the integration of c-di-GMP signaling with other nucleotide-based signaling systems will be discussed.

Transplantation of allogenic bone marrow in canine cyclic neutropenia

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

Dale, D.C.; Graw, R.G. Jr.

Transplantation of normal bone marrow cells to a gray collie dog with cyclic neutropenia resulted in normal granulocytopoiesis. The finding suggests that cyclic neutropenia occurs because the hematopoietic stem cells are defective. Because of the similarity of human and canine cyclic neutropenia, it also suggests that the human disease may be curable by marrow transplantation. One day before transplantation, the recipient received 1000 rads gamma irradiation from opposing /sup 60/Co sources at 9 rad/min. (CH)

The comprehension skills of children learning English as an additional language.

PubMed

Burgoyne, K; Kelly, J M; Whiteley, H E; Spooner, A

2009-12-01

Data from national test results suggests that children who are learning English as an additional language (EAL) experience relatively lower levels of educational attainment in comparison to their monolingual, English-speaking peers. The relative underachievement of children who are learning EAL demands that the literacy needs of this group are identified. To this end, this study aimed to explore the reading- and comprehension-related skills of a group of EAL learners. Data are reported from 92 Year 3 pupils, of whom 46 children are learning EAL. Children completed standardized measures of reading accuracy and comprehension, listening comprehension, and receptive and expressive vocabulary. Results indicate that many EAL learners experience difficulties in understanding written and spoken text. These comprehension difficulties are not related to decoding problems but are related to significantly lower levels of vocabulary knowledge experienced by this group. Many EAL learners experience significantly lower levels of English vocabulary knowledge which has a significant impact on their ability to understand written and spoken text. Greater emphasis on language development is therefore needed in the school curriculum to attempt to address the limited language skills of children learning EAL.

Long-term cyclicities in Phanerozoic sea-level sedimentary record and their potential drivers

NASA Astrophysics Data System (ADS)

Boulila, Slah; Laskar, Jacques; Haq, Bilal U.; Galbrun, Bruno; Hara, Nathan

2018-06-01

Cyclic sedimentation has varied at several timescales and this variability has been geologically well documented at Milankovitch timescales, controlled in part by climatically (insolation) driven sea-level changes. At the longer (tens of Myr) timescales connection between astronomical parameters and sedimentation via cyclic solar-system motions within the Milky Way has also been proposed, but this hypothesis remains controversial because of the lack of long geological records. In addition, the absence of a meaningful physical mechanism that could explain the connection between climate and astronomy at these longer timescales led to the more plausible explanation of plate motions as the main driver of climate and sedimentation through changes in ocean and continent mass distribution on Earth. Here we statistically show a prominent and persistent 36 Myr sedimentary cyclicity superimposed on two megacycles ( 250 Myr) in a relatively well-constrained sea-level (SL) record of the past 542 Myr (Phanerozoic eon). We also show two other significant 9.3 and 91 Myr periodicities, but with lower amplitudes. The 9.3 Myr cyclicity was previously attributed to long-period Milankovitch band based on the Cenozoic record. However, the 91 Myr cyclicity has never been observed before in the geologic record. The 250 Myr cyclicity was attributed to the Wilson tectonic (supercontinent) cycle. The 36 Myr periodicity, also detected for the first time in SL record, has previously been ascribed either to tectonics or to astronomical cyclicity. Given the possible link between amplitudes of the 36 and 250 Myr cyclicities in SL record and the potential that these periodicities fall into the frequency band of solar system motions, we suggest an astronomical origin, and model these periodicities as originating from the path of the solar system in the Milky Way as vertical and radial periods that modulate the flux of cosmic rays on Earth. Our finding of the 36 Myr SL cyclicity lends credibility

Cyclic Dinucleotides in Oral Bacteria and in Oral Biofilms.

PubMed

Gürsoy, Ulvi K; Gürsoy, Mervi; Könönen, Eija; Sintim, Herman O

2017-01-01

Oral cavity acts as a reservoir of bacterial pathogens for systemic infections and several oral microorganisms have been linked to systemic diseases. Quorum sensing and cyclic dinucleotides, two "decision-making" signaling systems, communicate to regulate physiological process in bacteria. Discovery of cyclic dinucleotides has a long history, but the progress in our understanding of how cyclic dinucleotides regulate bacterial lifestyle is relatively new. Oral microorganisms form some of the most intricate biofilms, yet c-di-GMP, and c-di-AMP signaling have been rarely studied in oral biofilms. Recent studies demonstrated that, with the aid of bacterial messenger molecules and their analogs, it is possible to activate host innate and adaptive immune responses and epithelial integrity with a dose that is relevant to inhibit bacterial virulence mechanisms, such as fimbriae and exopolysaccharide production, biofilm formation, and host cell invasion. The aim of this perspective article is to present available information on cyclic dinucleotides in oral bacteria and in oral biofilms. Moreover, technologies that can be used to detect cyclic dinucleotides in oral biofilms are described. Finally, directions for future research are highlighted.

Cyclic and low temperature effects on microcircuits

NASA Technical Reports Server (NTRS)

Weissflug, V. A.; Sisul, E. V.

1977-01-01

Cyclic temperature and low temperature operating life tests, and pre-/post-life device evaluations were used to determine the degrading effects of thermal environments on microcircuit reliability. Low power transistor-transistor-logic gates and linear devices were included in each test group. Device metallization systems included aluminum metallization/aluminum wire, aluminum metallization/gold wire, and gold metallization/gold wire. Fewer than 2% electrical failures were observed during the cyclic and low temperature life tests and the post-life evaluations revealed approximately 2% bond pull failures. Reconstruction of aluminum die metallization was observed in all devices and the severity of the reconstruction appeared to be directly related to the magnitude of the temperature excursion. All types of bonds except the gold/gold bonds were weakened by exposure to repeated cyclic temperature stress.

Genetic reductionist approach for dissecting individual roles of GGDEF proteins within the c-di-GMP signaling network in Salmonella

PubMed Central

Solano, Cristina; García, Begoña; Latasa, Cristina; Toledo-Arana, Alejandro; Zorraquino, Violeta; Valle, Jaione; Casals, Joan; Pedroso, Enrique; Lasa, Iñigo

2009-01-01

Bacteria have developed an exclusive signal transduction system involving multiple diguanylate cyclase and phosphodiesterase domain-containing proteins (GGDEF and EAL/HD-GYP, respectively) that modulate the levels of the same diffusible molecule, 3′-5′-cyclic diguanylic acid (c-di-GMP), to transmit signals and obtain specific cellular responses. Current knowledge about c-di-GMP signaling has been inferred mainly from the analysis of recombinant bacteria that either lack or overproduce individual members of the pathway, without addressing potential compensatory effects or interferences between them. Here, we dissected c-di-GMP signaling by constructing a Salmonella strain lacking all GGDEF-domain proteins and then producing derivatives, each restoring 1 protein. Our analysis showed that most GGDEF proteins are constitutively expressed and that their expression levels are not interdependent. Complete deletion of genes encoding GGDEF-domain proteins abrogated virulence, motility, long-term survival, and cellulose and fimbriae synthesis. Separate restoration revealed that 4 proteins from Salmonella and 1 from Yersinia pestis exclusively restored cellulose synthesis in a c-di-GMP–dependent manner, indicating that c-di-GMP produced by different GGDEF proteins can activate the same target. However, the restored strain containing the STM4551-encoding gene recovered all other phenotypes by means of gene expression modulation independently of c-di-GMP. Specifically, fimbriae synthesis and virulence were recovered through regulation of csgD and the plasmid-encoded spvAB mRNA levels, respectively. This study provides evidence that the regulation of the GGDEF-domain proteins network occurs at 2 levels: a level that strictly requires c-di-GMP to control enzymatic activities directly, restricted to cellulose synthesis in our experimental conditions, and another that involves gene regulation for which c-di-GMP synthesis can be dispensable. PMID:19416883

The Knowledge Base of the Evaluation Domain.

ERIC Educational Resources Information Center

Seels, Barbara

This paper is concerned with defining evaluation as a domain in instructional technology, and with specifying the sub-areas of the domain. In education, evaluation is the process of determining the adequacy of instruction. It begins with problem analysis, which refers to determining the nature of the solution and the parameters of the problem. A…

Low energy electron attenuation lengths in core–shell nanoparticles

DOE PAGES

Jacobs, Michael I.; Kostko, Oleg; Ahmed, Musahid; ...

2017-05-05

Here, a velocity map imaging spectrometer is used to measure photoemission from free core–shell nanoparticles, where a salt core is coated with a liquid hydrocarbon shell (i.e. squalane). By varying the radial thickness of the hydrocarbon shell, electron attenuation lengths (EALs) are determined by measuring the decay in photoemission intensity from the salt core. In squalane, electrons with kinetic energy (KE) above 2 eV are found to have EALs of 3–5 nm, whereas electrons with smaller KE (<2 eV) have significantly larger EALs of >15 nm. These results (in the context of other energy-resolved EAL measurements) suggest that the energymore » dependent behavior of low energy electrons is similar in dielectrics when KE > 2 eV. At this energy the EALs do not appear to exhibit strong energy dependence. However, at very low KE (<2 eV), the EALs diverge and appear to be extremely material dependent.« less

Cyclic tension promotes fibroblastic differentiation of human MSCs cultured on collagen-fibre scaffolds.

PubMed

Qiu, Yongzhi; Lei, Jennifer; Koob, Thomas J; Temenoff, Johnna S

2016-12-01

Mesenchymal stem cells (MSCs) have been suggested as a potential cell source for tendon/ligament tissue engineering. Extrinsic cues, such as the chemical and physical properties of scaffolds, as well as external forces, play an important role in fibroblastic differentiation of these cells. In this study, we employed a collagen-fibre scaffold that mimics the chemical and fibrous structure and mechanical properties of tendon/ligament, and studied how imparting cyclic tension to these fibrous collagen scaffolds affects tendon/ligament fibroblastic differentiation of MSCs. Human MSCs attached and spread on the surface of the scaffolds, and appeared aligned along the fibres 24 h after seeding. Cyclic tension was then applied to cell-laden scaffolds over a period of 14 days (10% strain, 1 Hz, 3 h on/3 h off). Real time RT-PCR analysis indicated that scleraxis, a transcription factor associated with the tendon fibroblast phenotype, was found to be significantly upregulated only under cyclic tension. Immunohistochemical staining demonstrated that MSCs cultured under cyclic tension after 14 days secreted more extracellular matrix, including collagen I, collagen III and tenascin-C, compared to constructs in static culture, after 14 days in vitro. Our data indicate that cyclic tension can promote fibroblastic differentiation of MSCs in these fibrous collagen-based scaffolds, which may have significant applications in the development of tissue-engineered graft alternatives for tendon and ligament injuries. Copyright © 2014 John Wiley & Sons, Ltd. Copyright © 2014 John Wiley & Sons, Ltd.

Bond–Slip Relationship for CFRP Sheets Externally Bonded to Concrete under Cyclic Loading

PubMed Central

Li, Ke; Cao, Shuangyin; Yang, Yue; Zhu, Juntao

2018-01-01

The objective of this paper was to explore the bond–slip relationship between carbon fiber-reinforced polymer (CFRP) sheets and concrete under cyclic loading through experimental and analytical approaches. Modified beam tests were performed in order to gain insight into the bond–slip relationship under static and cyclic loading. The test variables are the CFRP-to-concrete width ratio, and the bond length of the CFRP sheets. An analysis of the test results in this paper and existing test results indicated that the slope of the ascending segment of the bond–slip curve decreased with an increase in the number of load cycles, but the slip corresponding to the maximum shear stress was almost invariable as the number of load cycles increased. In addition, the rate of reduction in the slope of the ascending range of the bond–slip curve during cyclic loading decreased as the concrete strength increased, and increased as the load level or CFRP-to-concrete width ratio enhanced. However, these were not affected by variations in bond length if the residual bond length was longer than the effective bond length. A bilinear bond–slip model for CFRP sheets that are externally bonded to concrete under cyclic loading, which considered the effects of the cyclic load level, concrete strength, and CFRP-to-concrete ratio, was developed based on the existing static bond–slip model. The accuracy of this proposed model was verified by a comparison between this proposed model and test results. PMID:29495383

Bond-Slip Relationship for CFRP Sheets Externally Bonded to Concrete under Cyclic Loading.

PubMed

Li, Ke; Cao, Shuangyin; Yang, Yue; Zhu, Juntao

2018-02-26

The objective of this paper was to explore the bond-slip relationship between carbon fiber-reinforced polymer (CFRP) sheets and concrete under cyclic loading through experimental and analytical approaches. Modified beam tests were performed in order to gain insight into the bond-slip relationship under static and cyclic loading. The test variables are the CFRP-to-concrete width ratio, and the bond length of the CFRP sheets. An analysis of the test results in this paper and existing test results indicated that the slope of the ascending segment of the bond-slip curve decreased with an increase in the number of load cycles, but the slip corresponding to the maximum shear stress was almost invariable as the number of load cycles increased. In addition, the rate of reduction in the slope of the ascending range of the bond-slip curve during cyclic loading decreased as the concrete strength increased, and increased as the load level or CFRP-to-concrete width ratio enhanced. However, these were not affected by variations in bond length if the residual bond length was longer than the effective bond length. A bilinear bond-slip model for CFRP sheets that are externally bonded to concrete under cyclic loading, which considered the effects of the cyclic load level, concrete strength, and CFRP-to-concrete ratio, was developed based on the existing static bond-slip model. The accuracy of this proposed model was verified by a comparison between this proposed model and test results.

Mechanics Model for Simulating RC Hinges under Reversed Cyclic Loading

PubMed Central

Shukri, Ahmad Azim; Visintin, Phillip; Oehlers, Deric J.; Jumaat, Mohd Zamin

2016-01-01

Describing the moment rotation (M/θ) behavior of reinforced concrete (RC) hinges is essential in predicting the behavior of RC structures under severe loadings, such as under cyclic earthquake motions and blast loading. The behavior of RC hinges is defined by localized slip or partial interaction (PI) behaviors in both the tension and compression region. In the tension region, slip between the reinforcement and the concrete defines crack spacing, crack opening and closing, and tension stiffening. While in the compression region, slip along concrete to concrete interfaces defines the formation and failure of concrete softening wedges. Being strain-based, commonly-applied analysis techniques, such as the moment curvature approach, cannot directly simulate these PI behaviors because they are localized and displacement based. Therefore, strain-based approaches must resort to empirical factors to define behaviors, such as tension stiffening and concrete softening hinge lengths. In this paper, a displacement-based segmental moment rotation approach, which directly simulates the partial interaction behaviors in both compression and tension, is developed for predicting the M/θ response of an RC beam hinge under cyclic loading. Significantly, in order to develop the segmental approach, a partial interaction model to predict the tension stiffening load slip relationship between the reinforcement and the concrete is developed. PMID:28773430

Mechanics Model for Simulating RC Hinges under Reversed Cyclic Loading.

PubMed

Shukri, Ahmad Azim; Visintin, Phillip; Oehlers, Deric J; Jumaat, Mohd Zamin

2016-04-22

Describing the moment rotation (M/θ) behavior of reinforced concrete (RC) hinges is essential in predicting the behavior of RC structures under severe loadings, such as under cyclic earthquake motions and blast loading. The behavior of RC hinges is defined by localized slip or partial interaction (PI) behaviors in both the tension and compression region. In the tension region, slip between the reinforcement and the concrete defines crack spacing, crack opening and closing, and tension stiffening. While in the compression region, slip along concrete to concrete interfaces defines the formation and failure of concrete softening wedges. Being strain-based, commonly-applied analysis techniques, such as the moment curvature approach, cannot directly simulate these PI behaviors because they are localized and displacement based. Therefore, strain-based approaches must resort to empirical factors to define behaviors, such as tension stiffening and concrete softening hinge lengths. In this paper, a displacement-based segmental moment rotation approach, which directly simulates the partial interaction behaviors in both compression and tension, is developed for predicting the M/θ response of an RC beam hinge under cyclic loading. Significantly, in order to develop the segmental approach, a partial interaction model to predict the tension stiffening load slip relationship between the reinforcement and the concrete is developed.

Cyclic Nucleotide Phosphodiesterases: important signaling modulators and therapeutic targets

PubMed Central

Ahmad, Faiyaz; Murata, Taku; Simizu, Kasumi; Degerman, Eva; Maurice, Donald; Manganiello, Vincent

2014-01-01

By catalyzing hydrolysis of cAMP and cGMP, cyclic nucleotide phosphodiesterases are critical regulators of their intracellular concentrations and their biological effects. Since these intracellular second messengers control many cellular homeostatic processes, dysregulation of their signals and signaling pathways initiate or modulate pathophysiological pathways related to various disease states, including erectile dysfunction, pulmonary hypertension, acute refractory cardiac failure, intermittent claudication, chronic obstructive pulmonary disease, and psoriasis. Alterations in expression of PDEs and PDE-gene mutations (especially mutations in PDE6, PDE8B, PDE11A and PDE4) have been implicated in various diseases and cancer pathologies. PDEs also play important role in formation and function of multi-molecular signaling/regulatory complexes called signalosomes. At specific intracellular locations, individual PDEs, together with pathway-specific signaling molecules, regulators, and effectors, are incorporated into specific signalosomes, where they facilitate and regulate compartmentalization of cyclic nucleotide signaling pathways and specific cellular functions. Currently, only a limited number of PDE inhibitors (PDE3, PDE4, PDE5 inhibitors) are used in clinical practice. Future paths to novel drug discovery include the crystal structure-based design approach, which has resulted in generation of more effective family-selective inhibitors, as well as burgeoning development of strategies to alter compartmentalized cyclic nucleotide signaling pathways by selectively targeting individual PDEs and their signalosome partners. PMID:25056711

cGMP and cyclic nucleotide-gated channels participate in mouse sperm capacitation.

PubMed

Cisneros-Mejorado, Abraham; Sánchez Herrera, Daniel P

2012-01-20

During capacitation of mammalian sperm intracellular [Ca(2+)] and cyclic nucleotides increase, suggesting that CNG channels play a role in the physiology of sperm. Here we study the effect of capacitation, 8Br-cAMP (8-bromoadenosine 3',5'-cyclic monophosphate) and 8Br-cGMP (8-bromoguanosine 3',5'-cyclic monophosphate) on the macroscopic ionic currents of mouse sperm, finding the existence of different populations of sperm, in terms of the recorded current and its response to cyclic nucleotides. Our results show that capacitation and cyclic nucleotides increase the ionic current, having a differential sensitivity to cGMP (cyclic guanosine monophosphate) and cAMP (cyclic adenosine monophosphate). Using a specific inhibitor we determine the contribution of CNG channels to macroscopic current and capacitation. Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Domain management OSSs: bridging the gap between legacy and standards-based network management systems

NASA Astrophysics Data System (ADS)

Lemley, Todd A.

1996-11-01

The rapid change in the telecommunications environment is forcing carriers to re-assess not only their service offering, but also their network management philosophy. The competitive carrier environment has taken away the luxury of throwing technology at a problem by using legacy and proprietary systems and architectures. A more flexible management environment is necessary to effectively gain, and maintain operating margins in the new market era. Competitive forces are driving change which gives carriers more choices than those that are available in legacy and standards-based solutions alone. However, creating an operational support system (OSS) with this gap between legacy and standards has become as dynamic as the services which it supports. A philosophy which helps to integrate the legacy and standards systems is domain management. Domain management relates to a specific service or market 'domain,'and its associated operational support requirements. It supports a companies definition of its business model, which drives the definition of each domain. It also attempts to maximize current investment while injecting new technology available in a practical approach. The following paragraphs offer an overview of legacy systems, standards-based philosophy, and the potential of domain management to help bridge the gap between the two types of systems.

Robust Global Image Registration Based on a Hybrid Algorithm Combining Fourier and Spatial Domain Techniques

DTIC Science & Technology

2012-09-01

Robust global image registration based on a hybrid algorithm combining Fourier and spatial domain techniques Peter N. Crabtree, Collin Seanor...00-00-2012 to 00-00-2012 4. TITLE AND SUBTITLE Robust global image registration based on a hybrid algorithm combining Fourier and spatial domain...demonstrate performance of a hybrid algorithm . These results are from analysis of a set of images of an ISO 12233 [12] resolution chart captured in the

Holographic entanglement entropy and cyclic cosmology

NASA Astrophysics Data System (ADS)

Frampton, Paul H.

2018-06-01

We discuss a cyclic cosmology in which the visible universe, or introverse, is all that is accessible to an observer while the extroverse represents the total spacetime originating from the time when the dark energy began to dominate. It is argued that entanglement entropy of the introverse is the more appropriate quantity to render infinitely cyclic, rather than the entropy of the total universe. Since vanishing entanglement entropy implies disconnected spacetimes, at the turnaround when the introverse entropy is zero the disconnected extroverse can be jettisoned with impunity.

Microplate-based method to screen inhibitors of isozymes of cyclic nucleotide phosphodiesterase fused to SUMO.

PubMed

Chen, Chunyan; Liu, Miaomiao; Wu, Jing; Yang, Xiaolan; Hu, Xiaolei; Pu, Jun; Long, Gaobo; Xie, Yanling; Jiang, Hairong; Yuan, Yonghua; Liao, Fei

2014-12-01

The feasibility for microplate-based screening of inhibitors of isozymes of cyclic nucleotide phosphodiesterase (PDE) was tested via the coupled action of a phosphatase on adenosine-5'-monophosphate and an improved malachite green assay of phosphate. Human full-length PDE4B2 and truncated mutant (152-528aa) were expressed in Escherichia coli via fusion to SUMO, which after purification through Ni-NTA column exhibited specific activities >0.017 U mg(-1). In the presence of proteins <30 mg L(-1), absorbance for 10 µΜ phosphate was measurable; a PDE isozyme of specific activity over 0.008 U mg(-1) after reaction for 20 min thus suited for microplate-based screening of inhibitors. By using Biotek ELX 800 microplate reader, affinities of two forms of PEDE4B2 for cAMP, rolipram and papaverine varied over three magnitudes and were consistent with those by routine assay, respectively. Hence, the proposed method was promising for high-throughput-screening of inhibitors of phosphate-releasing enzymes bearing specific activities over 0.008 U mg(-1).

Disulfide exchange in hydrogen-bonded cyclic assemblies: stereochemical self-selection by double dynamic chemistry.

PubMed

ten Cate, A Tessa; Dankers, Patricia Y W; Sijbesma, Rint P; Meijer, E W

2005-07-22

Stereoselective cyclization of cystine-based bifunctional 2-ureido-4[1H]-pyrimidinone derivatives in CDCl(3) solutions was demonstrated by (1)H NMR spectroscopy. Thiolate-catalyzed disulfide exchange in solution led to the equilibration of different diastereomers of 1. At low concentrations, where formation of cyclic assemblies is the dominant mode of association, the molecules act as their own template. At these concentrations the meso diastereomer is formed preferentially, indicating a higher stability of its cyclic assemblies under the applied conditions, in comparison to the other diastereomers.

A Critical Assessment of Cyclic Softening and Hardening Behavior in a Near- α Titanium Alloy During Thermomechanical Fatigue

NASA Astrophysics Data System (ADS)

Prasad, Kartik; Sarkar, Rajdeep; Rao, K. Bhanu Sankara; Sundararaman, M.

2016-10-01

Thermomechanical fatigue behavior of Ti-alloy Timetal 834 has been studied at two temperature intervals viz. 573 K to 723 K (300 °C to 450 °C) and 723 K to 873 K (450 °C to 600 °C) under mechanical strain-controlled cycling. Among the temperatures studied, the alloy exhibited initial cyclic softening followed by cyclic hardening at 723 K (450 °C) in the temperature interval of 573 K to 723 K (300 °C to 450 °C). However, continuous cyclic hardening was observed at 723 K (450 °C) in 723 K to 873 K (450 °C to 600 °C). At 573 K (300 °C) and 873 K (600 °C), cyclic softening was observed in the cyclic stress response curves in both the temperature intervals. The dislocation substructure was observed to be planar in both the modes of TMF loading. Based on TEM microstructures and few unconventional fatigue tests, the observed cyclic hardening is attributed to dynamic strain aging. The reduced fatigue life at 723 K to 873 K (450 °C to 600 °C) under OP-TMF loading was attributed to the combined effect of cyclic hardening (leading to early strain localization and crack initiation), oxidation, and development of tensile mean stresses.

Terahertz Time Domain Spectroscopy of Phonon-Depopulation Based Quantum Cascade Lasers

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

Rungsawang, R.; Dhillon, S. S.; Jukam, N.

2011-12-23

A 3.1 THz phonon depopulation-based quantum-cascade-laser is investigated using terahertz time domain spectroscopy. A gain of 25 cm{sup -1} and absorption features due to the lower laser level being populated from a parasitic electronic channel are highlighted.

Contribution of Cyclic and Pseudo-cyclic Electron Transport to the Formation of Proton Motive Force in Chloroplasts.

PubMed

Shikanai, Toshiharu; Yamamoto, Hiroshi

2017-01-09

Photosynthetic electron transport is coupled to proton translocation across the thylakoid membrane, resulting in the formation of a trans-thylakoid proton gradient (ΔpH) and membrane potential (Δψ). Ion transporters and channels localized to the thylakoid membrane regulate the contribution of each component to the proton motive force (pmf). Although both ΔpH and Δψ contribute to ATP synthesis as pmf, only ΔpH downregulates photosynthetic electron transport via the acidification of the thylakoid lumen by inducing thermal dissipation of excessive absorbed light energy from photosystem II antennae and slowing down of the electron transport through the cytochrome b 6 f complex. To optimize the tradeoff between efficient light energy utilization and protection of both photosystems against photodamage, plants have to regulate the pmf amplitude and its components, ΔpH and Δψ. Cyclic electron transport around photosystem I (PSI) is a major regulator of the pmf amplitude by generating pmf independently of the net production of NADPH by linear electron transport. Chloroplast ATP synthase relaxes pmf for ATP synthesis, and its activity should be finely tuned for maintaining the size of the pmf during steady-state photosynthesis. Pseudo-cyclic electron transport mediated by flavodiiron protein (Flv) forms a large electron sink, which is essential for PSI photoprotection in fluctuating light in cyanobacteria. Flv is conserved from cyanobacteria to gymnosperms but not in angiosperms. The Arabidopsis proton gradient regulation 5 (pgr5) mutant is defective in the main pathway of PSI cyclic electron transport. By introducing Physcomitrella patens genes encoding Flvs, the function of PSI cyclic electron transport was substituted by that of Flv-dependent pseudo-cyclic electron transport. In transgenic plants, the size of the pmf was complemented to the wild-type level but the contribution of ΔpH to the total pmf was lower than that in the wild type. In the pgr5 mutant, the

EnzDP: improved enzyme annotation for metabolic network reconstruction based on domain composition profiles.

PubMed

Nguyen, Nam-Ninh; Srihari, Sriganesh; Leong, Hon Wai; Chong, Ket-Fah

2015-10-01

Determining the entire complement of enzymes and their enzymatic functions is a fundamental step for reconstructing the metabolic network of cells. High quality enzyme annotation helps in enhancing metabolic networks reconstructed from the genome, especially by reducing gaps and increasing the enzyme coverage. Currently, structure-based and network-based approaches can only cover a limited number of enzyme families, and the accuracy of homology-based approaches can be further improved. Bottom-up homology-based approach improves the coverage by rebuilding Hidden Markov Model (HMM) profiles for all known enzymes. However, its clustering procedure relies firmly on BLAST similarity score, ignoring protein domains/patterns, and is sensitive to changes in cut-off thresholds. Here, we use functional domain architecture to score the association between domain families and enzyme families (Domain-Enzyme Association Scoring, DEAS). The DEAS score is used to calculate the similarity between proteins, which is then used in clustering procedure, instead of using sequence similarity score. We improve the enzyme annotation protocol using a stringent classification procedure, and by choosing optimal threshold settings and checking for active sites. Our analysis shows that our stringent protocol EnzDP can cover up to 90% of enzyme families available in Swiss-Prot. It achieves a high accuracy of 94.5% based on five-fold cross-validation. EnzDP outperforms existing methods across several testing scenarios. Thus, EnzDP serves as a reliable automated tool for enzyme annotation and metabolic network reconstruction. Available at: www.comp.nus.edu.sg/~nguyennn/EnzDP .

Probing the interaction between cHAVc3 peptide and the EC1 domain of E-cadherin using NMR and molecular dynamics simulations.

PubMed

Alaofi, Ahmed; Farokhi, Elinaz; Prasasty, Vivitri D; Anbanandam, Asokan; Kuczera, Krzysztof; Siahaan, Teruna J

2017-01-01

The goal of this work is to probe the interaction between cyclic cHAVc3 peptide and the EC1 domain of human E-cadherin protein. Cyclic cHAVc3 peptide (cyclo(1,6)Ac-CSHAVC-NH 2 ) binds to the EC1 domain as shown by chemical shift perturbations in the 2D 1 H,- 15 N-HSQC NMR spectrum. The molecular dynamics (MD) simulations of the EC1 domain showed folding of the C-terminal tail region into the main head region of the EC1 domain. For cHAVc3 peptide, replica exchange molecular dynamics (REMD) simulations generated five structural clusters of cHAVc3 peptide. Representative structures of cHAVc3 and the EC1 structure from MD simulations were used in molecular docking experiments with NMR constraints to determine the binding site of the peptide on EC1. The results suggest that cHAVc3 binds to EC1 around residues Y36, S37, I38, I53, F77, S78, H79, and I94. The dissociation constants (K d values) of cHAVc3 peptide to EC1 were estimated using the NMR chemical shifts data and the estimated K d s are in the range of .5 × 10 -5 -7.0 × 10 -5  M.

Domain atrophy creates rare cases of functional partial protein domains.

PubMed

Prakash, Ananth; Bateman, Alex

2015-04-30

Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain atrophy, where protein domains lose a significant number of core structural elements. Here, we implement a new pipeline to systematically identify new cases of domain atrophy across all known protein sequences. The output of this pipeline was carefully checked by hand, which filtered out partial domain instances that were unlikely to represent true domain atrophy due to misannotations or un-annotated sequence fragments. We identify 75 cases of domain atrophy, of which eight cases are found in a three-dimensional protein structure and 67 cases have been inferred based on mapping to a known homologous structure. Domains with structural variations include ancient folds such as the TIM-barrel and Rossmann folds. Most of these domains are observed to show structural loss that does not affect their functional sites. Our analysis has significantly increased the known cases of domain atrophy. We discuss specific instances of domain atrophy and see that there has often been a compensatory mechanism that helps to maintain the stability of the partial domain. Our study indicates that although domain atrophy is an extremely rare phenomenon, protein domains under certain circumstances can tolerate extreme mutations giving rise to partial, but functional, domains.

Molecular LEGO by domain-imprinting of cytochrome P450 BM3.

PubMed

Jetzschmann, K J; Yarman, A; Rustam, L; Kielb, P; Urlacher, V B; Fischer, A; Weidinger, I M; Wollenberger, U; Scheller, F W

2018-04-01

Electrosynthesis of the MIP nano-film after binding of the separated domains or holo-cytochrome BM3 via an engineered anchor should result in domain-specific cavities in the polymer layer. Both the two domains and the holo P450 BM3 have been bound prior polymer deposition via a N-terminal engineered his6-anchor to the electrode surface. Each step of MIP preparation was characterized by cyclic voltammetry of the redox-marker ferricyanide. Rebinding after template removal was evaluated by quantifying the suppression of the diffusive permeability of the signal for ferricyanide and by the NADH-dependent reduction of cytochrome c by the reductase domain (BMR). The working hypothesis is verified by the discrimination of the two domains by the respective MIPs: The holoenzyme P450 BM3 was ca. 5.5 times more effectively recognized by the film imprinted with the oxidase domain (BMO) as compared to the BMR-MIP or the non-imprinted polymer (NIP). Obviously, a cavity is formed during the imprinting process around the his 6 -tag-anchored BMR which cannot accommodate the broader BMO or the P450 BM3. The affinity of the MIP towards P450 BM3 is comparable with that to the monomer in solution. The his 6 -tagged P450 BM3 binds (30 percent) stronger which shows the additive effect of the interaction with the MIP and the binding to the electrode. Copyright © 2018. Published by Elsevier B.V.

Adsorptive performance of coal-based magnetic activated carbon for cyclic volatile methylsiloxanes from landfill leachate.

PubMed

Zhang, Chunhui; Jiang, Shan; Zhang, Wenwen

2018-02-01

Bituminous coal-based magnetic activated carbon (MAC) was prepared, characterized, and used successfully for removal of cyclic volatile methylsiloxanes (cVMSs) from treated landfill leachate. Batch adsorption studies were performed at different adsorption dosages and contact times. With adsorptive dosage of 0.75 g/L and contact time of 60 min, the removal efficiencies achieved by MAC for octamethylcyclotetrasiloxane (D 4 ), decamethylcyclopentasiloxane (D 5 ), and dodecamethylcyclohexasiloxane (D 6 ) are 100, 82.8, and 71.4%, respectively. The specific magnetization coefficients of MAC before and after adsorption are 4.6 × 10 -7 and 5.2 × 10 -7  m 3 /kg, between 1.26 × 10 -7 and 3.8 × 10 -5  m 3 /kg, which suggests that MAC can be recycled by the high-intensity magnetic separators.

The structure of the cyanobactin domain of unknown function from PatG in the patellamide gene cluster

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

Mann, Greg; Koehnke, Jesko; Bent, Andrew F.

The highly conserved domain of unknown function in the cyanobactin superfamily has a novel fold. The protein does not appear to bind the most plausible substrates, leaving questions as to its role. Patellamides are members of the cyanobactin family of ribosomally synthesized and post-translationally modified cyclic peptide natural products, many of which, including some patellamides, are biologically active. A detailed mechanistic understanding of the biosynthetic pathway would enable the construction of a biotechnological ‘toolkit’ to make novel analogues of patellamides that are not found in nature. All but two of the protein domains involved in patellamide biosynthesis have been characterized.more » The two domains of unknown function (DUFs) are homologous to each other and are found at the C-termini of the multi-domain proteins PatA and PatG. The domain sequence is found in all cyanobactin-biosynthetic pathways characterized to date, implying a functional role in cyanobactin biosynthesis. Here, the crystal structure of the PatG DUF domain is reported and its binding interactions with plausible substrates are investigated.« less

Evaluating cyclic fatigue of sealants during outdoor testing

Treesearch

R. Sam Williams; Steven Lacher; Corey Halpin; Christopher White

2009-01-01

A computer-controlled test apparatus (CCTA) and other instrumentation for subjecting sealant specimens to cyclic fatigue during outdoor exposure was developed. The CCTA enables us to use weather-induced conditions to cyclic fatigue specimens and to conduct controlled tests in-situ during the outdoor exposure. Thermally induced dimensional changes of an aluminum bar...

English as an Additional Language and Initial Teacher Education: Views and Experiences from Northern Ireland

ERIC Educational Resources Information Center

Skinner, Barbara

2010-01-01

This paper addresses training for teaching English as an Additional Language (EAL) at initial teacher education (ITE) level in Northern Ireland. This small-scale qualitative study describes 15 primary and post-primary teachers' perspectives on their preparation for teaching EAL in Northern Ireland. It explores reflections on EAL content in ITE…

Cyclic steaming in heavy oil diatomite

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

Kumar, M.; Beatty, F.D.

1995-12-31

Chevron currently uses cyclic steaming as a recovery method to produce economically its heavy oil diatomite resource in the Cymric field, San Joaquin Valley, California. A highly instrumented, cyclically steaming well from this field was simulated in this study to delineate important production mechanisms, to optimize operations, and to improve reservoir management. The model was constrained, as much as possible, by the available measured data. Results show that fluid flow from the well to the reservoir is primarily through the hydraulic fracture induced by the injected steam. Parameters with unique importance to modeling cyclic steaming in diatomites are: (1) inducedmore » fracture dimension (length and height), (2) matrix permeability, (3) oil/water capillary pressure, (4) grid size perpendicular to fracture face, and (5) producing bottomhole pressures. Additionally, parameters important for conventional steam injection processes, such as relative permeabilities and injected steam volume, quality, and rate, are important for diatomites also. Oil production rates and steam/oil ratios calculated by this model compare reasonably with field data.« less

Sources of Water to Wells for Transient Cyclic Systems

USGS Publications Warehouse

Reilly, T.E.; Pollock, D.W.

1996-01-01

Many state agencies are currently (1995) developing wellhead protection programs. The thrust of some of these programs is to protect water supplies by determining the areas contributing recharge to water-supply wells and by specifying regulations to minimize the opportunity for contamination of the recharge water by activities at the land surface. The area contributing recharge to a discharging well is the surface area at the water table through which the water flowing to the well entered the ground-water system. In the analyses of ground-water flow systems, steady-state average conditions are commonly used to simplify the problem and make a solution tractable. However, recharge is usually cyclic in nature, with seasonal cycles and longer term climatic cycles. The effect of these cyclic stresses on the area contributing recharge to wells is quantitatively analyzed for a hypothetical alluvial valley aquifer system that is representative of a large class of ground-water systems that are extensively developed for water supply. The analysis shows that, in many cases, these cyclic changes in the recharge rates do not significantly affect the location and size of the areas contributing recharge to wells. The ratio of the mean travel time to the length of the cyclic stress period appears to be an indicator of whether the transient effects of the cyclic stress must be explicitly represented in the analysis of contributing areas to wells. For the cases examined, if the ratio of the mean travel time to the period of the cyclic stress was much greater than one, then the transient area contributing recharge to wells was similar to the area calculated using an average steady-state condition. However, cyclic stresses on systems with ratios less than one do have an effect on the location and size of the areas contributing recharge to wells.

A Material Model for the Cyclic Behavior of Nitinol

NASA Astrophysics Data System (ADS)

Rebelo, Nuno; Zipse, Achim; Schlun, Martin; Dreher, Gael

2011-07-01

The uniaxial behavior of Nitinol in different forms and at different temperatures has been well documented in the literature. Mathematical models for the three-dimensional behavior of this class of materials, covering superelasticity, plasticity, and shape memory effects have been previously developed. Phenomenological models embedded in FEA analysis are part of common practice today in the development of devices made out of Nitinol. In vivo loading of medical devices has cyclic characteristics. There have been some indications in the literature that cyclic loading of Nitinol modifies substantially its behavior. A consortium of several stent manufacturers, Safe Technology and Dassault Systèmes Simulia Corp., dedicated to the development of fatigue laws suitable for life prediction of Nitinol devices, has conducted an extensive experimental study of the modifications in uniaxial behavior of both Nitinol wire and tubing due to cyclic loading. The Abaqus Nitinol material model has been extended to capture some of the phenomena observed and is described in this article. Namely, a preload beyond 6% strain alters the transformation plateaus; if the cyclic load amplitude is large enough, permanent deformations (residual martensite) are observed; the lower plateau increases; and the upper plateau changes. The modifications to the upper plateau are very interesting in the sense that it appears broken: its start stress gets lowered creating a new plateau up to the highest level of cyclic strain, followed by resuming the original plateau until full transformation. Since quite often the geometry of a device at the point at which it is subjected to cyclic loading is very much dependent on the manufacturing, deployment, and preloading sequence, it is important that analyses be conducted with the original material behavior up to that point, and then with the cyclic behavior thereafter.

Mechanical annealing under low-amplitude cyclic loading in micropillars

NASA Astrophysics Data System (ADS)

Cui, Yi-nan; Liu, Zhan-li; Wang, Zhang-jie; Zhuang, Zhuo

2016-04-01

Mechanical annealing has been demonstrated to be an effective method for decreasing the overall dislocation density in submicron single crystal. However, simultaneously significant shape change always unexpectedly happens under extremely high monotonic loading to drive the pre-existing dislocations out of the free surfaces. In the present work, through in situ TEM experiments it is found that cyclic loading with low stress amplitude can drive most dislocations out of the submicron sample with virtually little change of the shape. The underlying dislocation mechanism is revealed by carrying out discrete dislocation dynamic (DDD) simulations. The simulation results indicate that the dislocation density decreases within cycles, while the accumulated plastic strain is small. By comparing the evolution of dislocation junction under monotonic, cyclic and relaxation deformation, the cumulative irreversible slip is found to be the key factor of promoting junction destruction and dislocation annihilation at free surface under low-amplitude cyclic loading condition. By introducing this mechanics into dislocation density evolution equations, the critical conditions for mechanical annealing under cyclic and monotonic loadings are discussed. Low-amplitude cyclic loading which strengthens the single crystal without seriously disturbing the structure has the potential applications in the manufacture of defect-free nano-devices.

Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution.

PubMed

Miller, William B; Torday, John S

2018-04-13

Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Virtual network embedding in cross-domain network based on topology and resource attributes

NASA Astrophysics Data System (ADS)

Zhu, Lei; Zhang, Zhizhong; Feng, Linlin; Liu, Lilan

2018-03-01

Aiming at the network architecture ossification and the diversity of access technologies issues, this paper researches the cross-domain virtual network embedding algorithm. By analysing the topological attribute from the local and global perspective of nodes in the virtual network and the physical network, combined with the local network resource property, we rank the embedding priority of the nodes with PCA and TOPSIS methods. Besides, the link load distribution is considered. Above all, We proposed an cross-domain virtual network embedding algorithm based on topology and resource attributes. The simulation results depicts that our algorithm increases the acceptance rate of multi-domain virtual network requests, compared with the existing virtual network embedding algorithm.

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

PubMed Central

Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

2015-01-01

Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

Thermodynamics of Activation Gating in Olfactory-Type Cyclic Nucleotide-Gated (CNGA2) Channels

PubMed Central

Nache, Vasilica; Kusch, Jana; Biskup, Christoph; Schulz, Eckhard; Zimmer, Thomas; Hagen, Volker; Benndorf, Klaus

2008-01-01

Olfactory-type cyclic nucleotide-gated (CNG) ion channels open by the binding of cyclic nucleotides to a binding domain in the C-terminus. Employing the Eyring rate theory, we performed a thermodynamic analysis of the activation gating in homotetrameric CNGA2 channels. Lowering the temperature shifted the concentration-response relationship to lower concentrations, resulting in a decrease of both the enthalpy ΔH and entropy ΔS upon channel opening, suggesting that the order of an open CNGA2 channel plus its environment is higher than that of the closed channel. Activation time courses induced by cGMP concentration jumps were used to study thermodynamics of the transition state. The activation enthalpies ΔH‡ were positive at all cGMP concentrations. In contrast, the activation entropy ΔS‡ was positive at low cGMP concentrations and became then negative at increasing cGMP concentrations. The enthalpic and entropic parts of the activation energies approximately balance each other at all cGMP concentrations, leaving the free enthalpy of activation in the range between 19 and 21 kcal/mol. We conclude that channel activation proceeds through different pathways at different cGMP concentrations. Compared to the unliganded channel, low cGMP concentrations generate a transitional state of lower order whereas high cGMP concentrations generate a transitional state of higher order. PMID:18567637

Fatigue failure of dentin-composite disks subjected to cyclic diametral compression

PubMed Central

Li, Yuping; Carrera, Carola; Chen, Ruoqiong; Li, Jianying; Chen, Yungchung; Lenton, Patricia; Rudney, Joel. D.; Jones, Robert S.; Aparicio, Conrado; Fok, Alex

2015-01-01

Objective Our aim was to establish the relationship between cyclic loading and fatigue life of the dentin-composite interface using the newly developed disk in diametral compression tests. The results were then used to estimate the fatigue life of restored teeth under occlusal loading. Methods Disk specimens (5mm dia. × 2mm thick) were prepared using bovine incisors and restored with either a methacrylate-based composite Z100™ with Adper Single Bond Plus (Z100) or silorane-based composite Filtek ™ LS with LS System adhesive (LS). The dentin-composite disks were tested under cyclic diametral compression to determine the number of cycles to failure (Nf) at three load levels (n = 3 per group). Finite element analysis (FEA) was used to calculate the interfacial stresses (σ) within the specimen, to establish the σ vs. Nf curves, and those within a restored tooth under normal chewing forces (15N maximum). These were then used to estimate the lifetime of the restored tooth for the two restorative systems. Results The disks restored with LS had a higher fatigue resistance than those restored with Z100. The maximum interfacial stress in the restored tooth determined by FEA was ∼0.5MPa. Based on the estimate of 300,000 cycles of chewing per year, the predicted lifetime under occlusal loading for teeth restored with LS and Z100 was 33 and 10 years, respectively. Significance The disk in cyclic diametral compression has been used successfully to provide fatigue data which allows the lifetime of composite-restored teeth under occlusal loading to be predicted using numerical simulation. PMID:25958269

2D photonic crystal complete band gap search using a cyclic cellular automaton refination

NASA Astrophysics Data System (ADS)

González-García, R.; Castañón, G.; Hernández-Figueroa, H. E.

2014-11-01

We present a refination method based on a cyclic cellular automaton (CCA) that simulates a crystallization-like process, aided with a heuristic evolutionary method called differential evolution (DE) used to perform an ordered search of full photonic band gaps (FPBGs) in a 2D photonic crystal (PC). The solution is proposed as a combinatorial optimization of the elements in a binary array. These elements represent the existence or absence of a dielectric material surrounded by air, thus representing a general geometry whose search space is defined by the number of elements in such array. A block-iterative frequency-domain method was used to compute the FPBGs on a PC, when present. DE has proved to be useful in combinatorial problems and we also present an implementation feature that takes advantage of the periodic nature of PCs to enhance the convergence of this algorithm. Finally, we used this methodology to find a PC structure with a 19% bandgap-to-midgap ratio without requiring previous information of suboptimal configurations and we made a statistical study of how it is affected by disorder in the borders of the structure compared with a previous work that uses a genetic algorithm.

Isolation of New Gravitropic Mutants under Hypergravity Conditions

PubMed Central

Mori, Akiko; Toyota, Masatsugu; Shimada, Masayoshi; Mekata, Mika; Kurata, Tetsuya; Tasaka, Masao; Morita, Miyo T.

2016-01-01

Forward genetics is a powerful approach used to link genotypes and phenotypes, and mutant screening/analysis has provided deep insights into many aspects of plant physiology. Gravitropism is a tropistic response in plants, in which hypocotyls and stems sense the direction of gravity and grow upward. Previous studies of gravitropic mutants have suggested that shoot endodermal cells in Arabidopsis stems and hypocotyls are capable of sensing gravity (i.e., statocytes). In the present study, we report a new screening system using hypergravity conditions to isolate enhancers of gravitropism mutants, and we also describe a rapid and efficient genome mapping method, using next-generation sequencing (NGS) and single nucleotide polymorphism (SNP)-based markers. Using the endodermal-amyloplast less 1 (eal1) mutant, which exhibits defective development of endodermal cells and gravitropism, we found that hypergravity (10 g) restored the reduced gravity responsiveness in eal1 hypocotyls and could, therefore, be used to obtain mutants with further reduction in gravitropism in the eal1 background. Using the new screening system, we successfully isolated six ene (enhancer of eal1) mutants that exhibited little or no gravitropism under hypergravity conditions, and using NGS and map-based cloning with SNP markers, we narrowed down the potential causative genes, which revealed a new genetic network for shoot gravitropism in Arabidopsis. PMID:27746791

Flexural creep of structural flakeboards under cyclic humidity

Treesearch

M.C. Yeh; R.C. Tang; Chung-Yun Hse

1990-01-01

Flexural creep behavior of randomly oriented structural flakeboards under cyclic humidity is presented. Specimens fabricated with 5 and 7 percent phenol-formaldehyde resin were subjected to constant concentrated load in bending under slow and fast cyclic relative humidity (RH) between 65 and 95 percent for 100 days. The temperature was set at a constant 75°F through...

Creating and Manipulating a Domain-Specific Formal Object Base to Support a Domain-Oriented Application Composition System

DTIC Science & Technology

1992-12-01

and add new attributes as needed (11:129). 2.2.3.2 Feature Oriented Domain Analysis In their Feature-Oriented Domain Analysis ( FODA ) study, the...dissertation, The University of Texas at Austin, Austin Texas, 1990. 12. Kang, Kyo C. and others. Feature-Oriented Domain Analysis ( FODA ) Feasibil- ity Study...2-1 2.2.2 Requirements Languages ..................... 2-2 2.2.3 Domain Analysis ............................ 2-3 2.2.4

Predicting PDZ domain mediated protein interactions from structure

PubMed Central

2013-01-01

Background PDZ domains are structural protein domains that recognize simple linear amino acid motifs, often at protein C-termini, and mediate protein-protein interactions (PPIs) in important biological processes, such as ion channel regulation, cell polarity and neural development. PDZ domain-peptide interaction predictors have been developed based on domain and peptide sequence information. Since domain structure is known to influence binding specificity, we hypothesized that structural information could be used to predict new interactions compared to sequence-based predictors. Results We developed a novel computational predictor of PDZ domain and C-terminal peptide interactions using a support vector machine trained with PDZ domain structure and peptide sequence information. Performance was estimated using extensive cross validation testing. We used the structure-based predictor to scan the human proteome for ligands of 218 PDZ domains and show that the predictions correspond to known PDZ domain-peptide interactions and PPIs in curated databases. The structure-based predictor is complementary to the sequence-based predictor, finding unique known and novel PPIs, and is less dependent on training–testing domain sequence similarity. We used a functional enrichment analysis of our hits to create a predicted map of PDZ domain biology. This map highlights PDZ domain involvement in diverse biological processes, some only found by the structure-based predictor. Based on this analysis, we predict novel PDZ domain involvement in xenobiotic metabolism and suggest new interactions for other processes including wound healing and Wnt signalling. Conclusions We built a structure-based predictor of PDZ domain-peptide interactions, which can be used to scan C-terminal proteomes for PDZ interactions. We also show that the structure-based predictor finds many known PDZ mediated PPIs in human that were not found by our previous sequence-based predictor and is less dependent on

Recognition of cyclic-di-GMP by a riboswitch conducts translational repression through masking the ribosome-binding site distant from the aptamer domain.

PubMed

Inuzuka, Saki; Kakizawa, Hitoshi; Nishimura, Kei-Ichiro; Naito, Takuto; Miyazaki, Katsushi; Furuta, Hiroyuki; Matsumura, Shigeyoshi; Ikawa, Yoshiya

2018-06-01

The riboswitch is a class of RNA-based gene regulatory machinery that is dependent on recognition of its target ligand by RNA tertiary structures. Ligand recognition is achieved by the aptamer domain, and ligand-dependent structural changes of the expression platform then usually mediate termination of transcription or translational initiation. Ligand-dependent structural changes of the aptamer domain and expression platform have been reported for several riboswitches with short (<40 nucleotides) expression platforms. In this study, we characterized structural changes of the Vc2 c-di-GMP riboswitch that represses translation of downstream open reading frames in a ligand-dependent manner. The Vc2 riboswitch has a long (97 nucleotides) expression platform, but its structure and function are largely unknown. Through mutational analysis and chemical probing, we identified its secondary structures that are possibly responsible for switch-OFF and switch-ON states of translational initiation. © 2018 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Evaluation of homogeneous electrocatalysts by cyclic voltammetry.

PubMed

Rountree, Eric S; McCarthy, Brian D; Eisenhart, Thomas T; Dempsey, Jillian L

2014-10-06

The pursuit of solar fuels has motivated extensive research on molecular electrocatalysts capable of evolving hydrogen from protic solutions, reducing CO2, and oxidizing water. Determining accurate figures of merit for these catalysts requires the careful and appropriate application of electroanalytical techniques. This Viewpoint first briefly presents the fundamentals of cyclic voltammetry and highlights practical experimental considerations before focusing on the application of cyclic voltammetry for the characterization of electrocatalysts. Key metrics for comparing catalysts, including the overpotential (η), potential for catalysis (E(cat)), observed rate constant (k(obs)), and potential-dependent turnover frequency, are discussed. The cyclic voltammetric responses for a general electrocatalytic one-electron reduction of a substrate are presented along with methods to extract figures of merit from these data. The extension of this analysis to more complex electrocatalytic schemes, such as those responsible for H2 evolution and CO2 reduction, is then discussed.

Femtosecond-laser fabrication of cyclic structures in the bulk of transparent dielectrics

NASA Astrophysics Data System (ADS)

Vartapetov, S. K.; Ganin, D. V.; Lapshin, K. E.; Obidin, A. Z.

2015-08-01

We report the results of the experiments on developing precision micromachining technology, obtained under the conditions of focusing the pulses of a femtosecond (FS) laser into the volume of a transparent material, which is important, particularly, in the processing of biomaterials in ophthalmology. The implementation conditions and some characteristic features of the special regime of micromachining are determined, when at a definite relation between the sample scanning velocity and the repetition rate of FS pulses the region, destroyed by the laser radiation, is shifted along the optical axis towards the objective and back, forming cyclic patterns inside the sample. It is supposed that the main causes of the damage region shift are the induced modification of the refractive index and the reduction of the damage threshold due to the change in the material density and structure in the microscopic domain, adjacent to the boundary of the cavity produced by the previous pulse. The results of the performed study with the above regime taken into account were used in the technology of precision cutting of crystals, glasses and polymers. The best quality of the cut surface is achieved under the conditions, eliminating the appearance of the cyclic regime. In the samples of polycarbonate, polymethyl methacrylate and fused silica the cylindrical cavities were obtained with the aspect ratio higher than 200, directed along the laser beam, and microcapillaries with the diameter 1 - 2 μm in the direction, perpendicular to this beam.

Mechanistic Insight into Human ether-à-go-go-related Gene (hERG) K+ Channel Deactivation Gating from the Solution Structure of the EAG Domain

PubMed Central

Muskett, Frederick W.; Thouta, Samrat; Thomson, Steven J.; Bowen, Alexander; Stansfeld, Phillip J.; Mitcheson, John S.

2011-01-01

Human ether-à-go-go-related gene (hERG) K+ channels have a critical role in cardiac repolarization. hERG channels close (deactivate) very slowly, and this is vital for regulating the time course and amplitude of repolarizing current during the cardiac action potential. Accelerated deactivation is one mechanism by which inherited mutations cause long QT syndrome and potentially lethal arrhythmias. hERG deactivation is highly dependent upon an intact EAG domain (the first 135 amino acids of the N terminus). Importantly, deletion of residues 2–26 accelerates deactivation to a similar extent as removing the entire EAG domain. These and other experiments suggest the first 26 residues (NT1–26) contain structural elements required to slow deactivation by stabilizing the open conformation of the pore. Residues 26–135 form a Per-Arnt-Sim domain, but a structure for NT1–26 has not been forthcoming, and little is known about its site of interaction on the channel. In this study, we present an NMR structure for the entire EAG domain, which reveals that NT1–26 is structurally independent from the Per-Arnt-Sim domain and contains a stable amphipathic helix with one face being positively charged. Mutagenesis and electrophysiological studies indicate that neutralizing basic residues and breaking the amphipathic helix dramatically accelerate deactivation. Furthermore, scanning mutagenesis and molecular modeling studies of the cyclic nucleotide binding domain suggest that negatively charged patches on its cytoplasmic surface form an interface with the NT1–26 domain. We propose a model in which NT1–26 obstructs gating motions of the cyclic nucleotide binding domain to allosterically stabilize the open conformation of the pore. PMID:21135103

A short review on structure and role of cyclic-3',5'-adenosine monophosphate-specific phosphodiesterase 4 as a treatment tool.

PubMed

Eskandari, Nahid; Mirmosayyeb, Omid; Bordbari, Gazaleh; Bastan, Reza; Yousefi, Zahra; Andalib, Alireza

2015-01-01

Cyclic nucleotide phosphodiesterases (PDEs) are known as a super-family of enzymes which catalyze the metabolism of the intracellular cyclic nucleotides, cyclic-3',5'-adenosine monophosphate (cAMP), and cyclic-3',5'-guanosine monophosphate that are expressed in a variety of cell types that can exert various functions based on their cells distribution. The PDE4 family has been the focus of vast research efforts over recent years because this family is considered as a prime target for therapeutic intervention in a number of inflammatory diseases such as asthma, chronic obstructive pulmonary disease, and rheumatoid arthritis, and it should be used and researched by pharmacists. This is because the major isoform of PDE that regulates inflammatory cell activity is the cAMP-specific PDE, PDE4. This review discusses the relationship between PDE4 and its inhibitor drugs based on structures, cells distribution, and pharmacological properties of PDE4 which can be informative for all pharmacy specialists.

Emotional textile image classification based on cross-domain convolutional sparse autoencoders with feature selection

NASA Astrophysics Data System (ADS)

Li, Zuhe; Fan, Yangyu; Liu, Weihua; Yu, Zeqi; Wang, Fengqin

2017-01-01

We aim to apply sparse autoencoder-based unsupervised feature learning to emotional semantic analysis for textile images. To tackle the problem of limited training data, we present a cross-domain feature learning scheme for emotional textile image classification using convolutional autoencoders. We further propose a correlation-analysis-based feature selection method for the weights learned by sparse autoencoders to reduce the number of features extracted from large size images. First, we randomly collect image patches on an unlabeled image dataset in the source domain and learn local features with a sparse autoencoder. We then conduct feature selection according to the correlation between different weight vectors corresponding to the autoencoder's hidden units. We finally adopt a convolutional neural network including a pooling layer to obtain global feature activations of textile images in the target domain and send these global feature vectors into logistic regression models for emotional image classification. The cross-domain unsupervised feature learning method achieves 65% to 78% average accuracy in the cross-validation experiments corresponding to eight emotional categories and performs better than conventional methods. Feature selection can reduce the computational cost of global feature extraction by about 50% while improving classification performance.

A High Temperature Cyclic Oxidation Data Base for Selected Materials Tested at NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Barrett, Charles A.

2003-01-01

The cyclic oxidation test results for some 1000 high temperature commercial and experimental alloys have been collected in an EXCEL database. This database represents over thirty years of research at NASA Glenn Research Center in Cleveland, Ohio. The data is in the form of a series of runs of specific weight change versus time values for a set of samples tested at a given temperature, cycle time, and exposure time. Included on each run is a set of embedded plots of the critical data. The nature of the data is discussed along with analysis of the cyclic oxidation process. In addition examples are given as to how a set of results can be analyzed. The data is assembled on a read-only compact disk which is available on request from Materials Durability Branch, NASA Glenn Research Center, Cleveland, Ohio.

English as an Additional Language and Attainment in Primary Schools in England

ERIC Educational Resources Information Center

Demie, Feyisa

2018-01-01

English as an additional language (EAL) and language diversity attract much interest amongst policymakers and educationists; yet little is known about the performance in English schools of EAL pupils who are not fluent in English and speak different languages at home. The findings of the aggregated data confirm that EAL pupils achieved less well…

Properties of Tangential and Cyclic Polygons: An Application of Circulant Matrices

ERIC Educational Resources Information Center

Leung, Allen; Lopez-Real, Francis

2003-01-01

In this paper, the properties of tangential and cyclic polygons proposed by Lopez-Real are proved rigorously using the theory of circulant matrices. In particular, the concepts of slippable tangential polygons and conformable cyclic polygons are defined. It is shown that an n-sided tangential (or cyclic) polygon P[subscript n] with n even is…

Ascorbic Acid Determination in Commercial Fruit Juice Samples by Cyclic Voltammetry

PubMed Central

Pisoschi, Aurelia Magdalena; Danet, Andrei Florin; Kalinowski, Slawomir

2008-01-01

A method was developed for assessing ascorbic acid concentration in commercial fruit juice by cyclic voltammetry. The anodic oxidation peak for ascorbic acid occurs at about 490 mV on a Pt disc working electrode (versus SCE). The influence of the potential sweep speed on the peak height was studied. The obtained calibration graph shows a linear dependence between peak height and ascorbic acid concentration in the domain (0.1–10 mmol·L−1). The equation of the calibration graph was y = 6.391x + 0.1903 (where y represents the value of intensity measured for the anodic peak height, expressed as μA and x the analyte concentration, as mmol·L−1, r2 = 0.9995, r.s.d. = 1.14%, n = 10, Cascorbic acid = 2 mmol·L−1). The developed method was applied to ascorbic acid assessment in fruit juice. The ascorbic acid content determined ranged from 0.83 to 1.67 mmol·L−1 for orange juice, from 0.58 to 1.93 mmol·L−1 for lemon juice, and from 0.46 to 1.84 mmol·L−1 for grapefruit juice. Different ascorbic acid concentrations (from standard solutions) were added to the analysed samples, the degree of recovery being comprised between 94.35% and 104%. Ascorbic acid determination results obtained by cyclic voltammetry were compared with those obtained by the volumetric method with dichlorophenol indophenol. The results obtained by the two methods were in good agreement. PMID:19343183

Graphene Based Surface Plasmon Polariton Modulator Controlled by Ferroelectric Domains in Lithium Niobate

PubMed Central

Wang, Hao; Zhao, Hua; Hu, Guangwei; Li, Siren; Su, Hang; Zhang, Jingwen

2015-01-01

We proposed a ferroelectric domain controlled graphene based surface plasmon polariton modulator. Ferroelectricity-induced electronic and optical property tuning of graphene by domain in lithium niobate was theoretically investigated considering both interband and intraband contributions of surface conductivity. With the corrected Sellmeier equation of lithium niobate, the propagation of transverse magnetic mode surface plasmon polaritons in an air/graphene/lithium niobate structure was studied when monolayer graphene was tuned by down polarization direction ferroelectric domain with different polarization levels. The length of the ferroelectric domain was optimized to be 90 nm for a wavelength of 5.0 μm with signal extinction per unit 14.7 dB/μm, modulation depth 474.1 dB/μm and figure of merit 32.5. This work may promote the study of highly efficient modulators and other ultra-compact nonvolatile electronic and photonic devices in which two-dimensional materials and ferroelectric materials are combined. PMID:26657622

Arrhythmia Classification Based on Multi-Domain Feature Extraction for an ECG Recognition System.

PubMed

Li, Hongqiang; Yuan, Danyang; Wang, Youxi; Cui, Dianyin; Cao, Lu

2016-10-20

Automatic recognition of arrhythmias is particularly important in the diagnosis of heart diseases. This study presents an electrocardiogram (ECG) recognition system based on multi-domain feature extraction to classify ECG beats. An improved wavelet threshold method for ECG signal pre-processing is applied to remove noise interference. A novel multi-domain feature extraction method is proposed; this method employs kernel-independent component analysis in nonlinear feature extraction and uses discrete wavelet transform to extract frequency domain features. The proposed system utilises a support vector machine classifier optimized with a genetic algorithm to recognize different types of heartbeats. An ECG acquisition experimental platform, in which ECG beats are collected as ECG data for classification, is constructed to demonstrate the effectiveness of the system in ECG beat classification. The presented system, when applied to the MIT-BIH arrhythmia database, achieves a high classification accuracy of 98.8%. Experimental results based on the ECG acquisition experimental platform show that the system obtains a satisfactory classification accuracy of 97.3% and is able to classify ECG beats efficiently for the automatic identification of cardiac arrhythmias.

Arrhythmia Classification Based on Multi-Domain Feature Extraction for an ECG Recognition System

PubMed Central

Li, Hongqiang; Yuan, Danyang; Wang, Youxi; Cui, Dianyin; Cao, Lu

2016-01-01

Automatic recognition of arrhythmias is particularly important in the diagnosis of heart diseases. This study presents an electrocardiogram (ECG) recognition system based on multi-domain feature extraction to classify ECG beats. An improved wavelet threshold method for ECG signal pre-processing is applied to remove noise interference. A novel multi-domain feature extraction method is proposed; this method employs kernel-independent component analysis in nonlinear feature extraction and uses discrete wavelet transform to extract frequency domain features. The proposed system utilises a support vector machine classifier optimized with a genetic algorithm to recognize different types of heartbeats. An ECG acquisition experimental platform, in which ECG beats are collected as ECG data for classification, is constructed to demonstrate the effectiveness of the system in ECG beat classification. The presented system, when applied to the MIT-BIH arrhythmia database, achieves a high classification accuracy of 98.8%. Experimental results based on the ECG acquisition experimental platform show that the system obtains a satisfactory classification accuracy of 97.3% and is able to classify ECG beats efficiently for the automatic identification of cardiac arrhythmias. PMID:27775596

Homeopathic potentization based on nanoscale domains.

PubMed

Czerlinski, George; Ypma, Tjalling

2011-12-01

The objectives of this study were to present a simple descriptive and quantitative model of how high potencies in homeopathy arise. The model begins with the mechanochemical production of hydrogen and hydroxyl radicals from water and the electronic stabilization of the resulting nanodomains of water molecules. The life of these domains is initially limited to a few days, but may extend to years when the electromagnetic characteristic of a homeopathic agent is copied onto the domains. This information is transferred between the original agent and the nanodomains, and also between previously imprinted nanodomains and new ones. The differential equations previously used to describe these processes are replaced here by exponential expressions, corresponding to simplified model mechanisms. Magnetic stabilization is also involved, since these long-lived domains apparently require the presence of the geomagnetic field. Our model incorporates this factor in the formation of the long-lived compound. Numerical simulation and graphs show that the potentization mechanism can be described quantitatively by a very simplified mechanism. The omitted factors affect only the fine structure of the kinetics. Measurements of pH changes upon absorption of different electromagnetic frequencies indicate that about 400 nanodomains polymerize to form one cooperating unit. Singlet excited states of some compounds lead to dramatic changes in their hydrogen ion dissociation constant, explaining this pH effect and suggesting that homeopathic information is imprinted as higher singlet excited states. A simple description is provided of the process of potentization in homeopathic dilutions. With the exception of minor details, this simple model replicates the results previously obtained from a more complex model. While excited states are short lived in isolated molecules, they become long lived in nanodomains that form coherent cooperative aggregates controlled by the geomagnetic field. These

Fatigue crack growth under general-yielding cyclic-loading

NASA Technical Reports Server (NTRS)

Minzhong, Z.; Liu, H. W.

1986-01-01

In low cycle fatigue, cracks are initiated and propagated under general yielding cyclic loading. For general yielding cyclic loading, Dowling and Begley have shown that fatigue crack growth rate correlates well with the measured delta J. The correlation of da/dN with delta J was also studied by a number of other investigators. However, none of thse studies have correlated da/dN with delta J calculated specifically for the test specimens. Solomon measured fatigue crack growth in specimens in general yielding cyclic loading. The crack tips fields for Solomon's specimens are calculated using the finite element method and the J values of Solomon's tests are evaluated. The measured crack growth rate in Solomon's specimens correlates very well with the calculated delta J.

Optimal sensor placement for time-domain identification using a wavelet-based genetic algorithm

NASA Astrophysics Data System (ADS)

Mahdavi, Seyed Hossein; Razak, Hashim Abdul

2016-06-01

This paper presents a wavelet-based genetic algorithm strategy for optimal sensor placement (OSP) effective for time-domain structural identification. Initially, the GA-based fitness evaluation is significantly improved by using adaptive wavelet functions. Later, a multi-species decimal GA coding system is modified to be suitable for an efficient search around the local optima. In this regard, a local operation of mutation is introduced in addition with regeneration and reintroduction operators. It is concluded that different characteristics of applied force influence the features of structural responses, and therefore the accuracy of time-domain structural identification is directly affected. Thus, the reliable OSP strategy prior to the time-domain identification will be achieved by those methods dealing with minimizing the distance of simulated responses for the entire system and condensed system considering the force effects. The numerical and experimental verification on the effectiveness of the proposed strategy demonstrates the considerably high computational performance of the proposed OSP strategy, in terms of computational cost and the accuracy of identification. It is deduced that the robustness of the proposed OSP algorithm lies in the precise and fast fitness evaluation at larger sampling rates which result in the optimum evaluation of the GA-based exploration and exploitation phases towards the global optimum solution.

Yang Baxter and anisotropic sigma and lambda models, cyclic RG and exact S-matrices

NASA Astrophysics Data System (ADS)

Appadu, Calan; Hollowood, Timothy J.; Price, Dafydd; Thompson, Daniel C.

2017-09-01

Integrable deformation of SU(2) sigma and lambda models are considered at the classical and quantum levels. These are the Yang-Baxter and XXZ-type anisotropic deformations. The XXZ type deformations are UV safe in one regime, while in another regime, like the Yang-Baxter deformations, they exhibit cyclic RG behaviour. The associ-ated affine quantum group symmetry, realized classically at the Poisson bracket level, has q a complex phase in the UV safe regime and q real in the cyclic RG regime, where q is an RG invariant. Based on the symmetries and RG flow we propose exact factorizable S-matrices to describe the scattering of states in the lambda models, from which the sigma models follow by taking a limit and non-abelian T-duality. In the cyclic RG regimes, the S-matrices are periodic functions of rapidity, at large rapidity, and in the Yang-Baxter case violate parity.

Investigation of using wavelet analysis for classifying pattern of cyclic voltammetry signals

NASA Astrophysics Data System (ADS)

Jityen, Arthit; Juagwon, Teerasak; Jaisuthi, Rawat; Osotchan, Tanakorn

2017-09-01

Wavelet analysis is an excellent technique for data processing analysis based on linear vector algebra since it has an ability to perform local analysis and is able to analyze an unspecific localized area of a large signal. In this work, the wavelet analysis of cyclic waveform was investigated in order to find the distinguishable feature from the cyclic data. The analyzed wavelet coefficients were proposed to be used as selected cyclic feature parameters. The cyclic voltammogram (CV) of different electrodes consisting of carbon nanotube (CNT) and several types of metal phthalocyanine (MPc) including CoPc, FePc, ZnPc and MnPc powders was used as several sets of cyclic data for various types of coffee. The mixture powder was embedded in a hollow Teflon rod and used as working electrodes. Electrochemical response of the fabricated electrodes in Robusta, blend coffee I, blend coffee II, chocolate malt and cocoa at the same concentrations was measured with scanning rate of 0.05V/s from -1.5 to 1.5V respectively to Ag/AgCl electrode for five scanning loops. The CV of blended CNT electrode with some MPc electrodes indicated the ionic interaction which can be the effect of catalytic oxidation of saccharides and/or polyphenol on the sensor surface. The major information of CV response can be extracted by using several mother wavelet families viz. daubechies (dB1 to dB3), coiflets (coiflet1), biorthogonal (Bior1.1) and symlets (sym2) and then the discrimination of these wavelet coefficients of each data group can be separated by principal component analysis (PCA). The PCA results indicated the clearly separate groups with total contribution more than 62.37% representing from PC1 and PC2.

Pixel-based speckle adjustment for noise reduction in Fourier-domain OCT images

PubMed Central

Zhang, Anqi; Xi, Jiefeng; Sun, Jitao; Li, Xingde

2017-01-01

Speckle resides in OCT signals and inevitably effects OCT image quality. In this work, we present a novel method for speckle noise reduction in Fourier-domain OCT images, which utilizes the phase information of complex OCT data. In this method, speckle area is pre-delineated pixelwise based on a phase-domain processing method and then adjusted by the results of wavelet shrinkage of the original image. Coefficient shrinkage method such as wavelet or contourlet is applied afterwards for further suppressing the speckle noise. Compared with conventional methods without speckle adjustment, the proposed method demonstrates significant improvement of image quality. PMID:28663860

Pixel-based speckle adjustment for noise reduction in Fourier-domain OCT images.

PubMed

Zhang, Anqi; Xi, Jiefeng; Sun, Jitao; Li, Xingde

2017-03-01

Speckle resides in OCT signals and inevitably effects OCT image quality. In this work, we present a novel method for speckle noise reduction in Fourier-domain OCT images, which utilizes the phase information of complex OCT data. In this method, speckle area is pre-delineated pixelwise based on a phase-domain processing method and then adjusted by the results of wavelet shrinkage of the original image. Coefficient shrinkage method such as wavelet or contourlet is applied afterwards for further suppressing the speckle noise. Compared with conventional methods without speckle adjustment, the proposed method demonstrates significant improvement of image quality.

Coupling the Torpedo microplate-receptor binding assay with mass spectrometry to detect cyclic imine neurotoxins.

PubMed

Aráoz, Rómulo; Ramos, Suzanne; Pelissier, Franck; Guérineau, Vincent; Benoit, Evelyne; Vilariño, Natalia; Botana, Luis M; Zakarian, Armen; Molgó, Jordi

2012-12-04

Cyclic imine neurotoxins constitute an emergent family of neurotoxins of dinoflagellate origin that are potent antagonists of nicotinic acetylcholine receptors. We developed a target-directed functional method based on the mechanism of action of competitive agonists/antagonists of nicotinic acetylcholine receptors for the detection of marine cyclic imine neurotoxins. The key step for method development was the immobilization of Torpedo electrocyte membranes rich in nicotinic acetylcholine receptors on the surface of microplate wells and the use of biotinylated-α-bungarotoxin as tracer. Cyclic imine neurotoxins competitively inhibit biotinylated-α-bungarotoxin binding to Torpedo-nicotinic acetylcholine receptors in a concentration-dependent manner. The microplate-receptor binding assay allowed rapid detection of nanomolar concentrations of cyclic imine neurotoxins directly in shellfish samples. Although highly sensitive and specific for the detection of neurotoxins targeting nicotinic acetylcholine receptors as a class, the receptor binding assay cannot identify a given analyte. To address the low selectivity of the microplate-receptor binding assay, the cyclic imine neurotoxins tightly bound to the coated Torpedo nicotinic receptor were eluted with methanol, and the chemical nature of the eluted ligands was identified by mass spectrometry. The immobilization of Torpedo electrocyte membranes on the surface of microplate wells proved to be a high-throughput format for the survey of neurotoxins targeting nicotinic acetylcholine receptors directly in shellfish matrixes with high sensitivity and reproducibility.

Coupling the Torpedo Microplate-Receptor Binding Assay with Mass Spectrometry to Detect Cyclic Imine Neurotoxins

PubMed Central

Aráoz, Rómulo; Ramos, Suzanne; Pelissier, Franck; Guérineau, Vincent; Benoit, Evelyne; Vilariño, Natalia; Botana, Luis M.; Zakarian, Armen; Molgó, Jordi

2014-01-01

Cyclic imine neurotoxins constitute an emergent family of neurotoxins of dinoflagellate origin that are potent antagonists of nicotinic acetylcholine receptors. We developed a target-directed functional method based on the mechanism of action of competitive agonists/antagonists of nicotinic acetylcholine receptors for the detection of marine cyclic imine neurotoxins. The key step for method development was the immobilization of Torpedo electrocyte membranes rich in nicotinic acetylcholine receptors on the surface of microplate wells and the use of biotinylated-α-bungarotoxin as tracer. Cyclic imine neurotoxins competitively inhibit biotinylated-α-bungarotoxin binding to Torpedo-nicotinic acetylcholine receptors in a concentration-dependent manner. The microplate-receptor binding assay allowed rapid detection of nanomolar concentrations of cyclic imine neurotoxins directly in shellfish samples. Although highly sensitive and specific for the detection of neurotoxins targeting nicotinic acetylcholine receptors as a class, the receptor binding assay cannot identify a given analyte. To address the low selectivity of the microplate-receptor binding assay, the cyclic imine neurotoxins tightly bound to the coated Torpedo nicotinic receptor were eluted with methanol, and the chemical nature of the eluted ligands was identified by mass spectrometry. The immobilization of Torpedo electrocyte membranes on the surface of microplate wells proved to be a high-throughput format for the survey of neurotoxins targeting nicotinic acetylcholine receptors directly in shellfish matrixes with high sensitivity and reproducibility. PMID:23131021

[Cyclic fatigue of Vita mark II machinable ceramics under Hertzian's contact].

PubMed

Liu, Wei-Cai; Zhang, Zhi-Shen; Huang, Cheng-Min; Chao, Yong-Lie; Wan, Qian-Bing

2006-08-01

To investigate the cyclic fatigue modes of Vita mark II machinable ceramics under Hertzian's contact. Hertzian's contact technique (WC spheres r = 3.18 mm) was used to investigate the cyclic fatigue of Vita mark II machinable ceramic. All specimens were fatigued by cyclic loading in moist environment, furthermore, surviving strength was examined by three point test and morphology damage observation. In homogeneous Vita mark II machinable ceramics, two fatigue damage modes existed after cyclic loading with spheres under moist environment, including conventional tensile-driven cone cracking (brittle mode) and shear-driven microdamage accumulation (quasi-plastic mode). The latter generated radial cracks and deeply penetrating secondary cone crack. Initial strength degradation were caused by the cone cracks, subsequent and much more deleterious loss was caused by radial cracks. Cyclic fatigue modes of Vita mark II machinable ceramics includes brittle and quasi-plastic mode.

Domain wall motion in magnetically frustrated nanorings

NASA Astrophysics Data System (ADS)

Lubarda, M. V.; Escobar, M. A.; Li, S.; Chang, R.; Fullerton, E. E.; Lomakin, V.

2012-06-01

We describe a magnetically frustrated nanoring (MFNR) configuration which is formed by introducing antiferromagnetic coupling across an interface orthogonal to the ring's circumferential direction. Such structures have the unique characteristic that only one itinerant domain wall (DW) can exist in the ring, which does not need to be nucleated or injected into the structure and can never escape making it analogous to a magnetic Möbius strip. Numerical simulations show that the DW in a MFNR can be driven consecutively around the ring with a prescribed cyclicity, and that the frequency of revolutions can be controlled by the applied field. The energy landscapes can be controlled to be flat allowing for low fields of operation or to have a barrier for thermal stability. Potential logic and memory applications of MFNRs are considered and discussed.

Behavior of nonplastic silty soils under cyclic loading.

PubMed

Ural, Nazile; Gunduz, Zeki

2014-01-01

The engineering behavior of nonplastic silts is more difficult to characterize than is the behavior of clay or sand. Especially, behavior of silty soils is important in view of the seismicity of several regions of alluvial deposits in the world, such as the United States, China, and Turkey. In several hazards substantial ground deformation, reduced bearing capacity, and liquefaction of silty soils have been attributed to excess pore pressure generation during dynamic loading. In this paper, an experimental study of the pore water pressure generation of silty soils was conducted by cyclic triaxial tests on samples of reconstituted soils by the slurry deposition method. In all tests silty samples which have different clay percentages were studied under different cyclic stress ratios. The results have showed that in soils having clay content equal to and less than 10%, the excess pore pressure ratio buildup was quicker with an increase in different cyclic stress ratios. When fine and clay content increases, excess pore water pressure decreases constant cyclic stress ratio in nonplastic silty soils. In addition, the applicability of the used criteria for the assessment of liquefaction susceptibility of fine grained soils is examined using laboratory test results.

Behavior of Nonplastic Silty Soils under Cyclic Loading

PubMed Central

Ural, Nazile; Gunduz, Zeki

2014-01-01

The engineering behavior of nonplastic silts is more difficult to characterize than is the behavior of clay or sand. Especially, behavior of silty soils is important in view of the seismicity of several regions of alluvial deposits in the world, such as the United States, China, and Turkey. In several hazards substantial ground deformation, reduced bearing capacity, and liquefaction of silty soils have been attributed to excess pore pressure generation during dynamic loading. In this paper, an experimental study of the pore water pressure generation of silty soils was conducted by cyclic triaxial tests on samples of reconstituted soils by the slurry deposition method. In all tests silty samples which have different clay percentages were studied under different cyclic stress ratios. The results have showed that in soils having clay content equal to and less than 10%, the excess pore pressure ratio buildup was quicker with an increase in different cyclic stress ratios. When fine and clay content increases, excess pore water pressure decreases constant cyclic stress ratio in nonplastic silty soils. In addition, the applicability of the used criteria for the assessment of liquefaction susceptibility of fine grained soils is examined using laboratory test results. PMID:24672343

A Time-Domain CMOS Oscillator-Based Thermostat with Digital Set-Point Programming

PubMed Central

Chen, Chun-Chi; Lin, Shih-Hao

2013-01-01

This paper presents a time-domain CMOS oscillator-based thermostat with digital set-point programming [without a digital-to-analog converter (DAC) or external resistor] to achieve on-chip thermal management of modern VLSI systems. A time-domain delay-line-based thermostat with multiplexers (MUXs) was used to substantially reduce the power consumption and chip size, and can benefit from the performance enhancement due to the scaling down of fabrication processes. For further cost reduction and accuracy enhancement, this paper proposes a thermostat using two oscillators that are suitable for time-domain curvature compensation instead of longer linear delay lines. The final time comparison was achieved using a time comparator with a built-in custom hysteresis to generate the corresponding temperature alarm and control. The chip size of the circuit was reduced to 0.12 mm2 in a 0.35-μm TSMC CMOS process. The thermostat operates from 0 to 90 °C, and achieved a fine resolution better than 0.05 °C and an improved inaccuracy of ± 0.6 °C after two-point calibration for eight packaged chips. The power consumption was 30 μW at a sample rate of 10 samples/s. PMID:23385403

Robust spike classification based on frequency domain neural waveform features.

PubMed

Yang, Chenhui; Yuan, Yuan; Si, Jennie

2013-12-01

We introduce a new spike classification algorithm based on frequency domain features of the spike snippets. The goal for the algorithm is to provide high classification accuracy, low false misclassification, ease of implementation, robustness to signal degradation, and objectivity in classification outcomes. In this paper, we propose a spike classification algorithm based on frequency domain features (CFDF). It makes use of frequency domain contents of the recorded neural waveforms for spike classification. The self-organizing map (SOM) is used as a tool to determine the cluster number intuitively and directly by viewing the SOM output map. After that, spike classification can be easily performed using clustering algorithms such as the k-Means. In conjunction with our previously developed multiscale correlation of wavelet coefficient (MCWC) spike detection algorithm, we show that the MCWC and CFDF detection and classification system is robust when tested on several sets of artificial and real neural waveforms. The CFDF is comparable to or outperforms some popular automatic spike classification algorithms with artificial and real neural data. The detection and classification of neural action potentials or neural spikes is an important step in single-unit-based neuroscientific studies and applications. After the detection of neural snippets potentially containing neural spikes, a robust classification algorithm is applied for the analysis of the snippets to (1) extract similar waveforms into one class for them to be considered coming from one unit, and to (2) remove noise snippets if they do not contain any features of an action potential. Usually, a snippet is a small 2 or 3 ms segment of the recorded waveform, and differences in neural action potentials can be subtle from one unit to another. Therefore, a robust, high performance classification system like the CFDF is necessary. In addition, the proposed algorithm does not require any assumptions on statistical

Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera

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

Pulman, Jane A.; Childs, Kevin L.; Sgambelluri, R. Michael

Here, the cyclic peptide toxins of Amanita mushrooms, such as α-amanitin and phalloidin, are encoded by the “MSDIN” gene family and ribosomally biosynthesized. Based on partial genome sequence and PCR analysis, some members of the MSDIN family were previously identified in Amanita bisporigera, and several other members are known from other species of Amanita. However, the complete complement in any one species, and hence the genetic capacity for these fungi to make cyclic peptides, remains unknown. As a result, draft genome sequences of two cyclic peptide-producing mushrooms, the “Death Cap” A. phalloides and the “Destroying Angel” A. bisporigera, were obtained.more » Each species has ~30 MSDIN genes, most of which are predicted to encode unknown cyclic peptides. Some MSDIN genes were duplicated in one or the other species, but only three were common to both species. A gene encoding cycloamanide B, a previously described nontoxic cyclic heptapeptide, was also present in A. phalloides, but genes for antamanide and cycloamanides A, C, and D were not. In A. bisporigera, RNA expression was observed for 20 of the MSDIN family members. Based on their predicted sequences, novel cyclic peptides were searched for by LC/MS/MS in extracts of A. phalloides. The presence of two cyclic peptides, named cycloamanides E and F with structures cyclo(SFFFPVP) and cyclo(IVGILGLP), was thereby demonstrated. Of the MSDIN genes reported earlier from another specimen of A. bisporigera, 9 of 14 were not found in the current genome assembly. Differences between previous and current results for the complement of MSDIN genes and cyclic peptides in the two fungi probably represents natural variation among geographically dispersed isolates of A. phalloides and among the members of the poorly defined A. bisporigera species complex. Both A. phalloides and A. bisporigera contain two prolyl oligopeptidase genes, one of which (POPB) is probably dedicated to cyclic peptide biosynthesis

Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera

DOE PAGES

Pulman, Jane A.; Childs, Kevin L.; Sgambelluri, R. Michael; ...

2016-12-15

Here, the cyclic peptide toxins of Amanita mushrooms, such as α-amanitin and phalloidin, are encoded by the “MSDIN” gene family and ribosomally biosynthesized. Based on partial genome sequence and PCR analysis, some members of the MSDIN family were previously identified in Amanita bisporigera, and several other members are known from other species of Amanita. However, the complete complement in any one species, and hence the genetic capacity for these fungi to make cyclic peptides, remains unknown. As a result, draft genome sequences of two cyclic peptide-producing mushrooms, the “Death Cap” A. phalloides and the “Destroying Angel” A. bisporigera, were obtained.more » Each species has ~30 MSDIN genes, most of which are predicted to encode unknown cyclic peptides. Some MSDIN genes were duplicated in one or the other species, but only three were common to both species. A gene encoding cycloamanide B, a previously described nontoxic cyclic heptapeptide, was also present in A. phalloides, but genes for antamanide and cycloamanides A, C, and D were not. In A. bisporigera, RNA expression was observed for 20 of the MSDIN family members. Based on their predicted sequences, novel cyclic peptides were searched for by LC/MS/MS in extracts of A. phalloides. The presence of two cyclic peptides, named cycloamanides E and F with structures cyclo(SFFFPVP) and cyclo(IVGILGLP), was thereby demonstrated. Of the MSDIN genes reported earlier from another specimen of A. bisporigera, 9 of 14 were not found in the current genome assembly. Differences between previous and current results for the complement of MSDIN genes and cyclic peptides in the two fungi probably represents natural variation among geographically dispersed isolates of A. phalloides and among the members of the poorly defined A. bisporigera species complex. Both A. phalloides and A. bisporigera contain two prolyl oligopeptidase genes, one of which (POPB) is probably dedicated to cyclic peptide biosynthesis

Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide

PubMed Central

Omura, Hiroki; Oikawa, Daisuke; Nakane, Takanori; Kato, Megumi; Ishii, Ryohei; Ishitani, Ryuichiro; Tokunaga, Fuminori; Nureki, Osamu

2016-01-01

In the innate immune system, pattern recognition receptors (PRRs) specifically recognize ligands derived from bacteria or viruses, to trigger the responsible downstream pathways. DEAD box protein 41 (DDX41) is an intracellular PRR that triggers the downstream pathway involving the adapter STING, the kinase TBK1, and the transcription factor IRF3, to activate the type I interferon response. DDX41 is unique in that it recognizes two different ligands; i.e., double-stranded DNA (dsDNA) and cyclic dinucleotides (CDN), via its DEAD domain. However, the structural basis for the ligand recognition by the DDX41 DEAD domain has remained elusive. Here, we report two crystal structures of the DDX41 DEAD domain in apo forms, at 1.5 and 2.2 Å resolutions. A comparison of the two crystal structures revealed the flexibility in the ATP binding site, suggesting its formation upon ATP binding. Structure-guided functional analyses in vitro and in vivo demonstrated the overlapped binding surface for dsDNA and CDN, which is distinct from the ATP-binding site. We propose that the structural rearrangement of the ATP binding site is crucial for the release of ADP, enabling the fast turnover of DDX41 for the dsDNA/CDN-induced STING activation pathway. PMID:27721487

Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop

PubMed Central

Upert, Gregory; Di Giorgio, Audrey; Upadhyay, Alok; Manvar, Dinesh; Pandey, Nootan; Pandey, Virendra N.; Patino, Nadia

2012-01-01

Human immunodeficiency virus-1 (HIV-1) replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR), to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP) cation-based vectors that efficiently deliver nucleotide analogs (PNAs) into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins. PMID:23029603

Cyclic Oxidation Modeling Program Rewritten for MS Windows

NASA Technical Reports Server (NTRS)

Smialek, James L.; Auping, Judith V.

2002-01-01

Turbine superalloy components are subject to high-temperature oxidation during operation. Protection is often conferred by coatings designed to form slow-growing, adherent oxide scales. Degradation by oxidation is exacerbated by the thermal cycling encountered during normal aircraft operations. Cooling has been identified as the major contributor to stresses in the oxidation scales, and it may often cause some oxide scale spallation with a proportional loss of protective behavior. Overall oxidation resistance is, thus, studied by the weight change behavior of alloy coupons during high-temperature cyclic oxidation in furnace or burner rig tests. The various characteristics of this behavior are crucial in understanding the performance of alloys at high temperatures. This new modeling effort helps in the understanding of the major factors involved in the cyclic oxidation process. Weight change behavior in cyclic oxidation is typified by an initial parabolic weight gain response curve that eventually exhibits a maximum, then transitions into a linear rate of weight loss due to spalling. The overall shape and magnitude of the curve are determined by the parabolic growth rate, kp, the cycle duration, the type of oxide scale, and the regular, repetitive spalling process. This entire process was modeled by a computer program called the Cyclic Oxidation Spalling Program (COSP) previously developed at the NASA Glenn Research Center. Thus, by supplying appropriate oxidation input parameters, one can determine the best fit to the actual data. These parameters describe real behavior and can be used to compare alloys and project cyclic oxidation behavior for longer times or under different cycle frequencies.

Inverted electro-mechanical behaviour induced by the irreversible domain configuration transformation in (K,Na)NbO3-based ceramics

PubMed Central

Huan, Yu; Wang, Xiaohui; Koruza, Jurij; Wang, Ke; Webber, Kyle G.; Hao, Yanan; Li, Longtu

2016-01-01

Miniaturization of domains to the nanometer scale has been previously reported in many piezoelectrics with two-phase coexistence. Despite the observation of nanoscale domain configuration near the polymorphic phase transition (PPT) regionin virgin (K0.5Na0.5)NbO3 (KNN) based ceramics, it remains unclear how this domain state responds to external loads and influences the macroscopic electro-mechanical properties. To this end, the electric-field-induced and stress-induced strain curves of KNN-based ceramics over a wide compositional range across PPT were characterized. It was found that the coercive field of the virgin samples was highest in PPT region, which was related to the inhibited domain wall motion due to the presence of nanodomains. However, the coercive field was found to be the lowest in the PPT region after electrical poling. This was related to the irreversible transformation of the nanodomains into micron-sized domains during the poling process. With the similar micron-sized domain configuration for all poled ceramics, the domains in the PPT region move more easily due to the additional polarization vectors. The results demonstrate that the poling process can give rise to the irreversible domain configuration transformation and then account for the inverted macroscopic piezoelectricity in the PPT region of KNN-based ceramics. PMID:26915972

Collagen insulated from tensile damage by domains that unfold reversibly: in situ X-ray investigation of mechanical yield and damage repair in the mussel byssus

PubMed Central

Harrington, Matthew J.; Gupta, Himadri S.; Fratzl, Peter; Waite, J. Herbert

2009-01-01

The byssal threads of the California mussel, Mytilus californianus, are highly hysteretic, elastomeric fibers that collectively perform a holdfast function in wave-swept rocky seashore habitats. Following cyclic loading past the mechanical yield point, threads exhibit a damage-dependent reduction in mechanical performance. However, the distal portion of the byssal thread is capable of recovering initial material properties through a time-dependent healing process in the absence of active cellular metabolism. Byssal threads are composed almost exclusively of multi-domain hybrid collagens known as preCols, which largely determine the mechanical properties of the thread. Here, the structure-property relationships that govern thread mechanical performance are further probed. The molecular rearrangements that occur during yield and damage repair were investigated using time-resolved in situ wide angle X-ray diffraction (WAXD) coupled with cyclic tensile loading of threads and through thermally enhanced damage-repair studies. Results indicate that the collagen domains in byssal preCols are mechanically protected by the unfolding of sacrificial non-collagenous domains that refold on a slower time-scale. Time-dependent healing is primarily attributed to stochastic recoupling of broken histidine-metal coordination complexes. PMID:19275941

Hybrid time-frequency domain equalization for LED nonlinearity mitigation in OFDM-based VLC systems.

PubMed

Li, Jianfeng; Huang, Zhitong; Liu, Xiaoshuang; Ji, Yuefeng

2015-01-12

A novel hybrid time-frequency domain equalization scheme is proposed and experimentally demonstrated to mitigate the white light emitting diode (LED) nonlinearity in visible light communication (VLC) systems based on orthogonal frequency division multiplexing (OFDM). We handle the linear and nonlinear distortion separately in a nonlinear OFDM system. The linear part is equalized in frequency domain and the nonlinear part is compensated by an adaptive nonlinear time domain equalizer (N-TDE). The experimental results show that with only a small number of parameters the nonlinear equalizer can efficiently mitigate the LED nonlinearity. With the N-TDE the modulation index (MI) and BER performance can be significantly enhanced.

Time Domain and Frequency Domain Deterministic Channel Modeling for Tunnel/Mining Environments.

PubMed

Zhou, Chenming; Jacksha, Ronald; Yan, Lincan; Reyes, Miguel; Kovalchik, Peter

2017-01-01

Understanding wireless channels in complex mining environments is critical for designing optimized wireless systems operated in these environments. In this paper, we propose two physics-based, deterministic ultra-wideband (UWB) channel models for characterizing wireless channels in mining/tunnel environments - one in the time domain and the other in the frequency domain. For the time domain model, a general Channel Impulse Response (CIR) is derived and the result is expressed in the classic UWB tapped delay line model. The derived time domain channel model takes into account major propagation controlling factors including tunnel or entry dimensions, frequency, polarization, electrical properties of the four tunnel walls, and transmitter and receiver locations. For the frequency domain model, a complex channel transfer function is derived analytically. Based on the proposed physics-based deterministic channel models, channel parameters such as delay spread, multipath component number, and angular spread are analyzed. It is found that, despite the presence of heavy multipath, both channel delay spread and angular spread for tunnel environments are relatively smaller compared to that of typical indoor environments. The results and findings in this paper have application in the design and deployment of wireless systems in underground mining environments.

10,000-Hour Cyclic Oxidation Behavior at 982 C (1800 F) of 68 High-Temperature Co-, Fe-, and Ni-Base Alloys

NASA Technical Reports Server (NTRS)

Barrett, Charles A.

1997-01-01

Sixty-eight high temperature Co-, Fe-, and Ni-base alloys were tested for 10-one thousand hour cycles in static air at 982 C (1800 F). The oxidation behavior of the test samples was evaluated by specific weight change/time data, x-ray diffraction of the post-test samples, and their final appearance. The gravimetric and appearance data were combined into a single modified oxidation parameter, KB4 to rank the cyclic oxidation resistance from excellent to catastrophic. The alloys showing the 'best' resistance with no significant oxidation attack were the alumina/aluminate spinel forming Ni-base turbine alloys: U-700, NASA-VIA and B-1900; the Fe-base ferritic alloys with Al: TRW-Valve, HOS-875, NASA-18T, Thermenol and 18SR; and the Ni-base superalloy IN-702.

Amplitude-cyclic frequency decomposition of vibration signals for bearing fault diagnosis based on phase editing

NASA Astrophysics Data System (ADS)

Barbini, L.; Eltabach, M.; Hillis, A. J.; du Bois, J. L.

2018-03-01

In rotating machine diagnosis different spectral tools are used to analyse vibration signals. Despite the good diagnostic performance such tools are usually refined, computationally complex to implement and require oversight of an expert user. This paper introduces an intuitive and easy to implement method for vibration analysis: amplitude cyclic frequency decomposition. This method firstly separates vibration signals accordingly to their spectral amplitudes and secondly uses the squared envelope spectrum to reveal the presence of cyclostationarity in each amplitude level. The intuitive idea is that in a rotating machine different components contribute vibrations at different amplitudes, for instance defective bearings contribute a very weak signal in contrast to gears. This paper also introduces a new quantity, the decomposition squared envelope spectrum, which enables separation between the components of a rotating machine. The amplitude cyclic frequency decomposition and the decomposition squared envelope spectrum are tested on real word signals, both at stationary and varying speeds, using data from a wind turbine gearbox and an aircraft engine. In addition a benchmark comparison to the spectral correlation method is presented.

A Practical Beginner's Guide to Cyclic Voltammetry

ERIC Educational Resources Information Center

Elgrishi, Noémie; Rountree, Kelley J.; McCarthy, Brian D.; Rountree, Eric S.; Eisenhart, Thomas T.; Dempsey, Jillian L.

2018-01-01

Despite the growing popularity of cyclic voltammetry, many students do not receive formalized training in this technique as part of their coursework. Confronted with self-instruction, students can be left wondering where to start. Here, a short introduction to cyclic voltammetry is provided to help the reader with data acquisition and…

Peer Review-Based Scripted Collaboration to Support Domain-Specific and Domain-General Knowledge Acquisition in Computer Science

ERIC Educational Resources Information Center

Demetriadis, Stavros; Egerter, Tina; Hanisch, Frank; Fischer, Frank

2011-01-01

This study investigates the effectiveness of using peer review in the context of scripted collaboration to foster both domain-specific and domain-general knowledge acquisition in the computer science domain. Using a one-factor design with a script and a control condition, students worked in small groups on a series of computer science problems…

Biosynthesis of cyclic 2,3-diphosphoglycerate. Isolation and characterization of 2-phosphoglycerate kinase and cyclic 2,3-diphosphoglycerate synthetase from Methanothermus fervidus.

PubMed

Lehmacher, A; Vogt, A B; Hensel, R

1990-10-15

Starting from 2-phosphoglycerate the biosynthesis of cDPG comprises two steps: (i) the phosphorylation of 2-phosphoglycerate to 2,3-diphosphoglycerate and (ii) the intramolecular cyclization to cyclic 2,3-diphosphoglycerate. The involved enzymes, 2-phosphoglycerate kinase and cyclic 2,3-diphosphoglycerate synthetase, were purified form Methanothermus fervidus. Their molecular and catalytic properties were characterized.

Between-domain relations of students' academic emotions and their judgments of school domain similarity

PubMed Central

Goetz, Thomas; Haag, Ludwig; Lipnevich, Anastasiya A.; Keller, Melanie M.; Frenzel, Anne C.; Collier, Antonie P. M.

2014-01-01

With the aim to deepen our understanding of the between-domain relations of academic emotions, a series of three studies was conducted. We theorized that between-domain relations of trait (i.e., habitual) emotions reflected students' judgments of domain similarities, whereas between-domain relations of state (i.e., momentary) emotions did not. This supposition was based on the accessibility model of emotional self-report, according to which individuals' beliefs tend to strongly impact trait, but not state emotions. The aim of Study 1 (interviews; N = 40; 8th and 11th graders) was to gather salient characteristics of academic domains from students' perspective. In Study 2 (N = 1709; 8th and 11th graders) the 13 characteristics identified in Study 1 were assessed along with academic emotions in four different domains (mathematics, physics, German, and English) using a questionnaire-based trait assessment. With respect to the same domains, state emotions were assessed in Study 3 (N = 121; 8th and 11th graders) by employing an experience sampling approach. In line with our initial assumptions, between-domain relations of trait but not state academic emotions reflected between-domain relations of domain characteristics. Implications for research and practice are discussed. PMID:25374547

Clinical nurse specialist practice domains and evidence-based practice competencies: a matrix of influence.

PubMed

Kring, Daria L

2008-01-01

The purpose of this article is to describe master's-level evidence-based practice (EBP) competencies as determined by a national consensus panel and present an EBP matrix that illustrates the influence that the clinical nurse specialist (CNS) practice can have on driving EBP change. Evidence-based practice is a growing and necessary paradigm for nursing care. The ACE Star Model conceptualizes the knowledge transformation that must occur in an EBP environment as 5 distinct points: discovery, summary, translation, integration, and evaluation. Master's-level EBP competencies based on these 5 steps were established by a national consensus panel. The CNS's practice can be organized around 5 domains: expert practitioner, researcher, consultant, educator, and leader. The master's-level EBP competencies can be transposed on a crosswalk of the ACE Star Model and the 5 CNS practice domains to form a matrix representing the influence that CNSs can have over the EBP process. Each competency falls well within the practice domains of the CNS, making the CNS an ideal person to lead the EBP movement forward, providing tangible outcomes to further demonstrate the need for the CNS role.

Performance Comparison between CDTD and STTD for DS-CDMA/MMSE-FDE with Frequency-Domain ICI Cancellation

NASA Astrophysics Data System (ADS)

Takeda, Kazuaki; Kojima, Yohei; Adachi, Fumiyuki

Frequency-domain equalization (FDE) based on the minimum mean square error (MMSE) criterion can provide a better bit error rate (BER) performance than rake combining. However, the residual inter-chip interference (ICI) is produced after MMSE-FDE and this degrades the BER performance. Recently, we showed that frequency-domain ICI cancellation can bring the BER performance close to the theoretical lower bound. To further improve the BER performance, transmit antenna diversity technique is effective. Cyclic delay transmit diversity (CDTD) can increase the number of equivalent paths and hence achieve a large frequency diversity gain. Space-time transmit diversity (STTD) can obtain antenna diversity gain due to the space-time coding and achieve a better BER performance than CDTD. Objective of this paper is to show that the BER performance degradation of CDTD is mainly due to the residual ICI and that the introduction of ICI cancellation gives almost the same BER performance as STTD. This study provides a very important result that CDTD has a great advantage of providing a higher throughput than STTD. This is confirmed by computer simulation. The computer simulation results show that CDTD can achieve higher throughput than STTD when ICI cancellation is introduced.

Kernel-Based Learning for Domain-Specific Relation Extraction

NASA Astrophysics Data System (ADS)

Basili, Roberto; Giannone, Cristina; Del Vescovo, Chiara; Moschitti, Alessandro; Naggar, Paolo

In a specific process of business intelligence, i.e. investigation on organized crime, empirical language processing technologies can play a crucial role. The analysis of transcriptions on investigative activities, such as police interrogatories, for the recognition and storage of complex relations among people and locations is a very difficult and time consuming task, ultimately based on pools of experts. We discuss here an inductive relation extraction platform that opens the way to much cheaper and consistent workflows. The presented empirical investigation shows that accurate results, comparable to the expert teams, can be achieved, and parametrization allows to fine tune the system behavior for fitting domain-specific requirements.

Micromechanics of soil responses in cyclic simple shear tests

NASA Astrophysics Data System (ADS)

Cui, Liang; Bhattacharya, Subhamoy; Nikitas, George

2017-06-01

Offshore wind turbine (OWT) foundations are subjected to a combination of cyclic and dynamic loading arising from wind, wave, rotor and blade shadowing. Under cyclic loading, most soils change their characteristics including stiffness, which may cause the system natural frequency to approach the loading frequency and lead to unplanned resonance and system damage or even collapse. To investigate such changes and the underlying micromechanics, a series of cyclic simple shear tests were performed on the RedHill 110 sand with different shear strain amplitudes, vertical stresses and initial relative densities of soil. The test results showed that: (a) Vertical accumulated strain is proportional to the shear strain amplitude but inversely proportional to relative density of soil; (b) Shear modulus increases rapidly in the initial loading cycles and then the rate of increase diminishes and the shear modulus remains below an asymptote; (c) Shear modulus increases with increasing vertical stress and relative density, but decreasing with increasing strain amplitude. Coupled DEM simulations were performed using PFC2D to analyse the micromechanics underlying the cyclic behaviour of soils. Micromechanical parameters (e.g. fabric tensor, coordination number) were examined to explore the reasons for the various cyclic responses to different shear strain amplitudes or vertical stresses. Both coordination number and magnitude of fabric anisotropy contribute to the increasing shear modulus.

Inferring protein domains associated with drug side effects based on drug-target interaction network.

PubMed

Iwata, Hiroaki; Mizutani, Sayaka; Tabei, Yasuo; Kotera, Masaaki; Goto, Susumu; Yamanishi, Yoshihiro

2013-01-01

Most phenotypic effects of drugs are involved in the interactions between drugs and their target proteins, however, our knowledge about the molecular mechanism of the drug-target interactions is very limited. One of challenging issues in recent pharmaceutical science is to identify the underlying molecular features which govern drug-target interactions. In this paper, we make a systematic analysis of the correlation between drug side effects and protein domains, which we call "pharmacogenomic features," based on the drug-target interaction network. We detect drug side effects and protein domains that appear jointly in known drug-target interactions, which is made possible by using classifiers with sparse models. It is shown that the inferred pharmacogenomic features can be used for predicting potential drug-target interactions. We also discuss advantages and limitations of the pharmacogenomic features, compared with the chemogenomic features that are the associations between drug chemical substructures and protein domains. The inferred side effect-domain association network is expected to be useful for estimating common drug side effects for different protein families and characteristic drug side effects for specific protein domains.

Angular analysis of the cyclic impacting oscillations in a robotic grinding process

NASA Astrophysics Data System (ADS)

Rafieian, Farzad; Girardin, François; Liu, Zhaoheng; Thomas, Marc; Hazel, Bruce

2014-02-01

In a robotic machining process, a light-weight cutter or grinder is usually held by an articulated robot arm. Material removal is achieved by the rotating cutting tool while the robot end effector ensures that the tool follows a programmed trajectory in order to work on complex curved surfaces or to access hard-to-reach areas. One typical application of such process is maintenance and repair work on hydropower equipment. This paper presents an experimental study of the dynamic characteristics of material removal in robotic grinding, which is unlike conventional grinding due to the lower structural stiffness of the tool-holder robot. The objective of the study is to explore the cyclic nature of this mechanical operation to provide the basis for future development of better process control strategies. Grinding tasks that minimize the number of iterations to converge to the target surface can be better planned based on a good understanding and modeling of the cyclic material removal mechanism. A single degree of freedom dynamic analysis of the process suggests that material removal is performed through high-frequency impacts that mainly last for only a small fraction of the grinding disk rotation period. To detect these discrete cutting events in practice, a grinder is equipped with a rotary encoder. The encoder's signal is acquired through the angular sampling technique. A running cyclic synchronous average is applied to the speed signal to remove its non-cyclic events. The measured instantaneous rotational frequency clearly indicates the impacting nature of the process and captures the transient response excited by these cyclic impacts. The technique also locates the angular positions of cutting impacts in revolution cycles. It is thus possible to draw conclusions about the cyclic nature of dynamic changes in impact-cutting behavior when grinding with a flexible robot. The dynamics of the impacting regime and transient responses to impact-cutting excitations

Cyclic strain increases protease-activated receptor-1 expression in vascular smooth muscle cells

NASA Technical Reports Server (NTRS)

Nguyen, K. T.; Frye, S. R.; Eskin, S. G.; Patterson, C.; Runge, M. S.; McIntire, L. V.

2001-01-01

Cyclic strain regulates many vascular smooth muscle cell (VSMC) functions through changing gene expression. This study investigated the effects of cyclic strain on protease-activated receptor-1 (PAR-1) expression in VSMCs and the possible signaling pathways involved, on the basis of the hypothesis that cyclic strain would enhance PAR-1 expression, reflecting increased thrombin activity. Uniaxial cyclic strain (1 Hz, 20%) of cells cultured on elastic membranes induced a 2-fold increase in both PAR-1 mRNA and protein levels. Functional activity of PAR-1, as assessed by cell proliferation in response to thrombin, was also increased by cyclic strain. In addition, treatment of cells with antioxidants or an NADPH oxidase inhibitor blocked strain-induced PAR-1 expression. Preincubation of cells with protein kinase inhibitors (staurosporine or Ro 31-8220) enhanced strain-increased PAR-1 expression, whereas inhibitors of NO synthase, tyrosine kinase, and mitogen-activated protein kinases had no effect. Cyclic strain in the presence of basic fibroblast growth factor induced PAR-1 mRNA levels beyond the effect of cyclic strain alone, whereas no additive effect was observed between cyclic strain and platelet-derived growth factor-AB. Our findings that cyclic strain upregulates PAR-1 mRNA expression but that shear stress downregulates this gene in VSMCs provide an opportunity to elucidate signaling differences by which VSMCs respond to different mechanical forces.

Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels*♦

PubMed Central

VanSchouwen, Bryan; Akimoto, Madoka; Sayadi, Maryam; Fogolari, Federico; Melacini, Giuseppe

2015-01-01

The hyperpolarization-activated cyclic nucleotide-modulated (HCN) ion channels control rhythmicity in neurons and cardiomyocytes. Cyclic AMP allosterically modulates HCN through the cAMP-dependent formation of a tetrameric gating ring spanning the intracellular region (IR) of HCN, to which cAMP binds. Although the apo versus holo conformational changes of the cAMP-binding domain (CBD) have been previously mapped, only limited information is currently available on the HCN IR dynamics, which have been hypothesized to play a critical role in the cAMP-dependent gating of HCN. Here, using molecular dynamics simulations validated and complemented by experimental NMR and CD data, we comparatively analyze HCN IR dynamics in the four states of the thermodynamic cycle arising from the coupling between cAMP binding and tetramerization equilibria. This extensive set of molecular dynamics trajectories captures the active-to-inactive transition that had remained elusive for other CBDs, and it provides unprecedented insight on the role of IR dynamics in HCN autoinhibition and its release by cAMP. Specifically, the IR tetramerization domain becomes more flexible in the monomeric states, removing steric clashes that the apo-CDB structure would otherwise impose. Furthermore, the simulations reveal that the active/inactive structural transition for the apo-monomeric CBD occurs through a manifold of pathways that are more divergent than previously anticipated. Upon cAMP binding, these pathways become disallowed, pre-confining the CBD conformational ensemble to a tetramer-compatible state. This conformational confinement primes the IR for tetramerization and thus provides a model of how cAMP controls HCN channel gating. PMID:25944904

Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB

NASA Astrophysics Data System (ADS)

Liu, Hao; Guo, Xiang; Han, Jingcheng; Luo, Ray; Chen, Hai-Feng

2018-06-01

Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved. In this study, molecular dynamics (MD) simulations were used to study the order-to-disorder transition kinetics of KID based on the good agreement with the experiment on its disordered-state properties. Specifically, we tested four force fields, ff99SBildn, ff99IDPs, ff14IDPSFF, and ff14IDPs in the simulations of KID and found that ff14IDPSFF can generate more diversified disordered conformers and also reproduce more accurate experimental secondary chemical shifts. Kinetics analysis of MD simulations demonstrates that the order-disorder transition of KID obeys the first-order kinetics, and the transition nucleus is I127/L128/L141. The possible transition pathways from the nucleus to the last folded residues were identified as I127-R125-L138-L141-S143-A145 and L128-R125-L138-L141-S143-A145 based on a residue-level dynamical network analysis. These computational studies not only provide testable prediction/hypothesis on the order-disorder transition of KID but also confirm that the ff14IDPSFF force field can be used to explore the correlation between the structure and function of IDPs.

Domain shape instabilities and dendrite domain growth in uniaxial ferroelectrics

NASA Astrophysics Data System (ADS)

Shur, Vladimir Ya.; Akhmatkhanov, Andrey R.

2018-01-01

The effects of domain wall shape instabilities and the formation of nanodomains in front of moving walls obtained in various uniaxial ferroelectrics are discussed. Special attention is paid to the formation of self-assembled nanoscale and dendrite domain structures under highly non-equilibrium switching conditions. All obtained results are considered in the framework of the unified kinetic approach to domain structure evolution based on the analogy with first-order phase transformation. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

Cyclicity in Silurian island-arc carbonates, Alexander terrane, Alaska

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

Kittredge, L.E.; Soja, C.M.

1993-03-01

Silurian carbonates from Alaska (Alexander terrane) record the evolution of a submarine platform during waning volcanism in an island arc. A detailed stratigraphic analysis of a 47 meter-thick sequence revealed the existence of cyclically repeated limestones: coral-stromatoporoid wackestones alternate with oncoid packstones and bioturbated, silty lime mudstones. The coral-stromatoporoid deposits are characterized by a low-diversity assemblage of dendroid corals, massive stromatoporoids, Atrypoidea brachiopods, and rare occurrences of biostromes associated with Solenopora, high-spired gastropods, and crinoids. Oncoids typically are 2-6 mm in diameter and form massive, meter-thick units. Coated grains are symmetrically developed, have a shell or algal nucleus, and aremore » also a minor component of coral-stromatoporoid beds. These lithologic units form seven, shallowing-upwards cycles (parasequences) that range in thickness from 3-9 meters. Coral-stomatoporoid wackestones form the base of each cycle and grade upwards into oncoid packstones with silty, lime mudstones at the top. This succession of lithofacies within each cycle reflects an increase in energy levels from relatively deeper water environments to relatively shallower ones. The lack of abrasion in the corals and stromatoporoids suggests predominantly quiet-water conditions in shallow subtidal areas affected by periodic turbulence. Comparison with correlative sections in Alaska and lack of correspondence with global sea level curves suggest that the primary cause of cyclicity was tectonic perturbations with secondary eustatic effects. Cyclic deposition in peri/subtidal sites was terminated by rapid drowning of the carbonate platform during late Silurian orogenesis.« less