multiple core complexes: Topics by Science.gov

Sample records for multiple core complexes

Multiple domains of fission yeast Cdc19p (MCM2) are required for its association with the core MCM complex.

PubMed

Sherman, D A; Pasion, S G; Forsburg, S L

1998-07-01

The members of the MCM protein family are essential eukaryotic DNA replication factors that form a six-member protein complex. In this study, we use antibodies to four MCM proteins to investigate the structure of and requirements for the formation of fission yeast MCM complexes in vivo, with particular regard to Cdc19p (MCM2). Gel filtration analysis shows that the MCM protein complexes are unstable and can be broken down to subcomplexes. Using coimmunoprecipitation, we find that Mis5p (MCM6) and Cdc21p (MCM4) are tightly associated with one another in a core complex with which Cdc19p loosely associates. Assembly of Cdc19p with the core depends upon Cdc21p. Interestingly, there is no obvious change in Cdc19p-containing MCM complexes through the cell cycle. Using a panel of Cdc19p mutants, we find that multiple domains of Cdc19p are required for MCM binding. These studies indicate that MCM complexes in fission yeast have distinct substructures, which may be relevant for function.
Multiple Domains of Fission Yeast Cdc19p (MCM2) Are Required for Its Association with the Core MCM Complex

PubMed Central

Sherman, Daniel A.; Pasion, Sally G.; Forsburg, Susan L.

1998-01-01

The members of the MCM protein family are essential eukaryotic DNA replication factors that form a six-member protein complex. In this study, we use antibodies to four MCM proteins to investigate the structure of and requirements for the formation of fission yeast MCM complexes in vivo, with particular regard to Cdc19p (MCM2). Gel filtration analysis shows that the MCM protein complexes are unstable and can be broken down to subcomplexes. Using coimmunoprecipitation, we find that Mis5p (MCM6) and Cdc21p (MCM4) are tightly associated with one another in a core complex with which Cdc19p loosely associates. Assembly of Cdc19p with the core depends upon Cdc21p. Interestingly, there is no obvious change in Cdc19p-containing MCM complexes through the cell cycle. Using a panel of Cdc19p mutants, we find that multiple domains of Cdc19p are required for MCM binding. These studies indicate that MCM complexes in fission yeast have distinct substructures, which may be relevant for function. PMID:9658174
Using Multiple Sources of Information in Establishing Text Complexity. Reading Research Report. #11.03

ERIC Educational Resources Information Center

Hiebert, Elfrieda H.

2011-01-01

A focus of the Common Core State Standards/English Language Arts (CCSS/ELA) is that students become increasingly more capable with complex text over their school careers. This focus has redirected attention to the measurement of text complexity. Although CCSS/ELA suggests multiple criteria for this task, the standards offer a single measure of…
Evidence for Multiple Mediator Complexes in Yeast Independently Recruited by Activated Heat Shock Factor

PubMed Central

Anandhakumar, Jayamani; Moustafa, Yara W.; Chowdhary, Surabhi; Kainth, Amoldeep S.

2016-01-01

Mediator is an evolutionarily conserved coactivator complex essential for RNA polymerase II transcription. Although it has been generally assumed that in Saccharomyces cerevisiae, Mediator is a stable trimodular complex, its structural state in vivo remains unclear. Using the “anchor away” (AA) technique to conditionally deplete select subunits within Mediator and its reversibly associated Cdk8 kinase module (CKM), we provide evidence that Mediator's tail module is highly dynamic and that a subcomplex consisting of Med2, Med3, and Med15 can be independently recruited to the regulatory regions of heat shock factor 1 (Hsf1)-activated genes. Fluorescence microscopy of a scaffold subunit (Med14)-anchored strain confirmed parallel cytoplasmic sequestration of core subunits located outside the tail triad. In addition, and contrary to current models, we provide evidence that Hsf1 can recruit the CKM independently of core Mediator and that core Mediator has a role in regulating postinitiation events. Collectively, our results suggest that yeast Mediator is not monolithic but potentially has a dynamic complexity heretofore unappreciated. Multiple species, including CKM-Mediator, the 21-subunit core complex, the Med2-Med3-Med15 tail triad, and the four-subunit CKM, can be independently recruited by activated Hsf1 to its target genes in AA strains. PMID:27185874
Evidence for Multiple Mediator Complexes in Yeast Independently Recruited by Activated Heat Shock Factor.

PubMed

Anandhakumar, Jayamani; Moustafa, Yara W; Chowdhary, Surabhi; Kainth, Amoldeep S; Gross, David S

2016-07-15

Mediator is an evolutionarily conserved coactivator complex essential for RNA polymerase II transcription. Although it has been generally assumed that in Saccharomyces cerevisiae, Mediator is a stable trimodular complex, its structural state in vivo remains unclear. Using the "anchor away" (AA) technique to conditionally deplete select subunits within Mediator and its reversibly associated Cdk8 kinase module (CKM), we provide evidence that Mediator's tail module is highly dynamic and that a subcomplex consisting of Med2, Med3, and Med15 can be independently recruited to the regulatory regions of heat shock factor 1 (Hsf1)-activated genes. Fluorescence microscopy of a scaffold subunit (Med14)-anchored strain confirmed parallel cytoplasmic sequestration of core subunits located outside the tail triad. In addition, and contrary to current models, we provide evidence that Hsf1 can recruit the CKM independently of core Mediator and that core Mediator has a role in regulating postinitiation events. Collectively, our results suggest that yeast Mediator is not monolithic but potentially has a dynamic complexity heretofore unappreciated. Multiple species, including CKM-Mediator, the 21-subunit core complex, the Med2-Med3-Med15 tail triad, and the four-subunit CKM, can be independently recruited by activated Hsf1 to its target genes in AA strains. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
Spectral and kinetic effects accompanying the assembly of core complexes of Rhodobacter sphaeroides.

PubMed

Freiberg, Arvi; Chenchiliyan, Manoop; Rätsep, Margus; Timpmann, Kõu

2016-11-01

In the present work, spectral and kinetic changes accompanying the assembly of the light-harvesting 1 (LH1) complex with the reaction center (RC) complex into monomeric RC-LH1 and dimeric RC-LH1-PufX core complexes of the photosynthetic purple bacterium Rhodobacter sphaeroides are systematically studied over the temperature range of 4.5-300K. The samples were interrogated with a combination of optical absorption, hole burning, fluorescence excitation, steady state and picosecond time resolved fluorescence spectroscopy. Fair additivity of the LH1 and RC absorption spectra suggests rather weak electronic coupling between them. A low-energy tail revealed at cryogenic temperatures in the absorption spectra of both monomeric and dimeric core complexes is proved to be due to the special pair of the RC. At selected excitation intensity and temperature, the fluorescence decay time of core complexes is shown to be a function of multiple factors, most importantly of the presence/absence of RCs, the supramolecular architecture (monomeric or dimeric) of the complexes, and whether the complexes were studied in a native membrane environment or in a detergent - purified state. Copyright © 2016 Elsevier B.V. All rights reserved.
Data Acquisition System for Multi-Frequency Radar Flight Operations Preparation

NASA Technical Reports Server (NTRS)

Leachman, Jonathan

2010-01-01

A three-channel data acquisition system was developed for the NASA Multi-Frequency Radar (MFR) system. The system is based on a commercial-off-the-shelf (COTS) industrial PC (personal computer) and two dual-channel 14-bit digital receiver cards. The decimated complex envelope representations of the three radar signals are passed to the host PC via the PCI bus, and then processed in parallel by multiple cores of the PC CPU (central processing unit). The innovation is this parallelization of the radar data processing using multiple cores of a standard COTS multi-core CPU. The data processing portion of the data acquisition software was built using autonomous program modules or threads, which can run simultaneously on different cores. A master program module calculates the optimal number of processing threads, launches them, and continually supplies each with data. The benefit of this new parallel software architecture is that COTS PCs can be used to implement increasingly complex processing algorithms on an increasing number of radar range gates and data rates. As new PCs become available with higher numbers of CPU cores, the software will automatically utilize the additional computational capacity.
The Structure of Cognition: Attentional Episodes in Mind and Brain

PubMed Central

Duncan, John

2013-01-01

Cognition is organized in a structured series of attentional episodes, allowing complex problems to be addressed through solution of simpler subproblems. A “multiple-demand” (MD) system of frontal and parietal cortex is active in many different kinds of tasks, and using data from neuroimaging, electrophysiology, neuropsychology, and cognitive studies of intelligence, I propose a core role for MD regions in assembly of the attentional episode. Monkey and human data show dynamic neural coding of attended information across multiple MD regions, with rapid communication within and between regions. Neuropsychological and imaging data link MD function to fluid intelligence, explaining some but not all “executive” deficits after frontal lobe lesions. Cognitive studies link fluid intelligence to goal neglect, and the problem of dividing complex task requirements into focused parts. Like the innate releasing mechanism of ethology, I suggest that construction of the attentional episode provides a core organizational principle for complex, adaptive cognition. PMID:24094101
Navigating Complex Trade-Offs in Conservation and Development: An Integrative Framework

ERIC Educational Resources Information Center

Hirsch, Paul D.; Brosius, J. Peter

2013-01-01

We present a framework that makes space for multiple perspectives and ways of thinking about complex trade-off problems in conservation and development. At the core of the framework are three "integrative lenses" designed to facilitate lines of inquiry according to three unique ways of perceiving complexity. The aim of the framework is…
Oligomerization of the E. coli Core RNA Polymerase: Formation of (α2ββ'ω)2–DNA Complexes and Regulation of the Oligomerization by Auxiliary Subunits

PubMed Central

Kansara, Seema G.; Sukhodolets, Maxim V.

2011-01-01

In this work, using multiple, dissimilar physico-chemical techniques, we demonstrate that the Escherichia coli RNA polymerase core enzyme obtained through a classic purification procedure forms stable (α2ββ'ω)2 complexes in the presence or absence of short DNA probes. Multiple control experiments indicate that this self-association is unlikely to be mediated by RNA polymerase-associated non-protein molecules. We show that the formation of (α2ββ'ω)2 complexes is subject to regulation by known RNA polymerase interactors, such as the auxiliary SWI/SNF subunit of RNA polymerase RapA, as well as NusA and σ70. We also demonstrate that the separation of the core RNA polymerase and RNA polymerase holoenzyme species during Mono Q chromatography is likely due to oligomerization of the core enzyme. We have analyzed the oligomeric state of the polymerase in the presence or absence of DNA, an aspect that was missing from previous studies. Importantly, our work demonstrates that RNA polymerase oligomerization is compatible with DNA binding. Through in vitro transcription and in vivo experiments (utilizing a RapAR599/Q602 mutant lacking transcription-stimulatory function), we demonstrate that the formation of tandem (α2ββ'ω)2–DNA complexes is likely functionally significant and beneficial for the transcriptional activity of the polymerase. Taken together, our findings suggest a novel structural aspect of the E. coli elongation complex. We hypothesize that transcription by tandem RNA polymerase complexes initiated at hypothetical bidirectional “origins of transcription” may explain recurring switches of the direction of transcription in bacterial genomes. PMID:21533049
Multiple Core Galaxies

NASA Technical Reports Server (NTRS)

Miller, R.H.; Morrison, David (Technical Monitor)

1994-01-01

Nuclei of galaxies often show complicated density structures and perplexing kinematic signatures. In the past we have reported numerical experiments indicating a natural tendency for galaxies to show nuclei offset with respect to nearby isophotes and for the nucleus to have a radial velocity different from the galaxy's systemic velocity. Other experiments show normal mode oscillations in galaxies with large amplitudes. These oscillations do not damp appreciably over a Hubble time. The common thread running through all these is that galaxies often show evidence of ringing, bouncing, or sloshing around in unexpected ways, even though they have not been disturbed by any external event. Recent observational evidence shows yet another phenomenon indicating the dynamical complexity of central regions of galaxies: multiple cores (M31, Markarian 315 and 463 for example). These systems can hardly be static. We noted long-lived multiple core systems in galaxies in numerical experiments some years ago, and we have more recently followed up with a series of experiments on multiple core galaxies, starting with two cores. The relevant parameters are the energy in the orbiting clumps, their relative.masses, the (local) strength of the potential well representing the parent galaxy, and the number of cores. We have studied the dependence of the merger rates and the nature of the final merger product on these parameters. Individual cores survive much longer in stronger background potentials. Cores can survive for a substantial fraction of a Hubble time if they travel on reasonable orbits.
Symmetrical group theory for mathematical complexity reduction of digital holograms

NASA Astrophysics Data System (ADS)

Perez-Ramirez, A.; Guerrero-Juk, J.; Sanchez-Lara, R.; Perez-Ramirez, M.; Rodriguez-Blanco, M. A.; May-Alarcon, M.

2017-10-01

This work presents the use of mathematical group theory through an algorithm to reduce the multiplicative computational complexity in the process of creating digital holograms. An object is considered as a set of point sources using mathematical symmetry properties of both the core in the Fresnel integral and the image, where the image is modeled using group theory. This algorithm has multiplicative complexity equal to zero and an additive complexity ( k - 1) × N for the case of sparse matrices and binary images, where k is the number of pixels other than zero and N is the total points in the image.
Perispeckles are major assembly sites for the exon junction core complex

PubMed Central

Daguenet, Elisabeth; Baguet, Aurélie; Degot, Sébastien; Schmidt, Ute; Alpy, Fabien; Wendling, Corinne; Spiegelhalter, Coralie; Kessler, Pascal; Rio, Marie-Christine; Le Hir, Hervé; Bertrand, Edouard; Tomasetto, Catherine

2012-01-01

The exon junction complex (EJC) is loaded onto mRNAs as a consequence of splicing and regulates multiple posttranscriptional events. MLN51, Magoh, Y14, and eIF4A3 form a highly stable EJC core, but where this tetrameric complex is assembled in the cell remains unclear. Here we show that EJC factors are enriched in domains that we term perispeckles and are visible as doughnuts around nuclear speckles. Fluorescence resonance energy transfer analyses and EJC assembly mutants show that perispeckles do not store free subunits, but instead are enriched for assembled cores. At the ultrastructural level, perispeckles are distinct from interchromatin granule clusters that may function as storage sites for splicing factors and intermingle with perichromatin fibrils, where nascent RNAs and active RNA Pol II are present. These results support a model in which perispeckles are major assembly sites for the tetrameric EJC core. This subnuclear territory thus represents an intermediate region important for mRNA maturation, between transcription sites and splicing factor reservoirs and assembly sites. PMID:22419818
Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit.

PubMed

Cevher, Murat A; Shi, Yi; Li, Dan; Chait, Brian T; Malik, Sohail; Roeder, Robert G

2014-12-01

The evolutionarily conserved Mediator complex is a critical coactivator for RNA polymerase II (Pol II)-mediated transcription. Here we report the reconstitution of a functional 15-subunit human core Mediator complex and its characterization by functional assays and chemical cross-linking coupled to MS (CX-MS). Whereas the reconstituted head and middle modules can stably associate, basal and coactivator functions are acquired only after incorporation of MED14 into the bimodular complex. This results from a dramatically enhanced ability of MED14-containing complexes to associate with Pol II. Altogether, our analyses identify MED14 as both an architectural and a functional backbone of the Mediator complex. We further establish a conditional requirement for metazoan-specific MED26 that becomes evident in the presence of heterologous nuclear factors. This general approach paves the way for systematic dissection of the multiple layers of functionality associated with the Mediator complex.
Characterization of Trinuclear Oxo Bridged Cobalt Complexes in Isolation

NASA Astrophysics Data System (ADS)

Lang, Johannes; Fries, Daniela V.; Niedner-Schatteburg, Gereon

2018-05-01

This study elucidates molecular structures, fragmentation pathways and relative stabilities of isolated trinuclear oxo bridged cobalt complexes of the structural type [Co3O(OAc)6(Py)n]+ (OAc=acetate, Py=pyridine, n=0, 1, 2, 3). We present infrared multiple photon dissociation (IR-MPD) spectra in combination with quantum chemical calculations. They indicate that the coordination of axial pyridine ligands to the [Co3O(OAc)6]+ subunit disturbs the triangular geometry of the Co3O core. [Co3O(OAc)6]+ exhibits a nearly equilateral triangular Co3O core geometry. The coordination of one or two pyridine ligands disturbs this arrangement resulting in isosceles triangular Co3O core geometries (in the cases of n=1 and 2). Coordination of three pyridine ligands (n=3) results in an equilateral triangular Co3O core geometry as in the case of n=0. Collision induced dissociation (CID) studies reveal that the complexes undergo a consecutive elimination of pyridine and acetate ligands with increasing excitation energy. Relative stabilities of the complexes decrease with the number of coordinated pyridine ligands. The presented results help to gain a fundamental insight into the molecular structure of trinuclear oxo bridged cobalt complexes void of any external effects such as crystal packing or solvation.
Recruitment of Fanconi Anemia and Breast Cancer Proteins to DNA Damage Sites is differentially Governed by Replication

PubMed Central

Shen, Xi; Do, Huong; Li, Yongjian; Chung, Woo-Hyun; Tomasz, Maria; de Winter, Johan P.; Xia, Bing; Elledge, Stephen J.; Wang, Weidong; Li, Lei

2009-01-01

Summary Fanconi anemia (FA) is characterized by cellular hypersensivity to DNA crosslinking agents, but how the Fanconi pathway protects cells from DNA crosslinks and whether FA proteins act directly on crosslinks remains unclear. We developed a chromatin-IP-based strategy termed eChIP and detected association of multiple FA proteins with DNA crosslinks in vivo. Inter-dependence analyses revealed that crosslink-specific enrichment of various FA proteins is controlled by distinct mechanisms. BRCA-related FA proteins (BRCA2, FANCJ/BACH1, and FANCN/PALB2), but not FA core and I/D2 complexes, require replication for their crosslink association. FANCD2, but not FANCJ and FANCN, requires the FA core complex for its recruitment. FA core complex requires nucleotide excision repair proteins XPA and XPC for its association. Consistent with the distinct recruitment mechanism, recombination-independent crosslink repair was inversely affected in cells deficient of FANC-core versus BRCA-related FA proteins. Thus, FA proteins participate in distinct DNA damage response mechanisms governed by DNA replication status. PMID:19748364
Multiple Analogies for Complex Concepts: Antidotes for Analogy-Induced Misconception in Advanced Knowledge Acquisition. Technical Report No. 439.

ERIC Educational Resources Information Center

Spiro, Rand J.; And Others

This report argues that there exists a pervasive tendency for analogies to contribute to the development of entrenched misconceptions in the form of reducing complex new knowledge to the core of a source analogy. The report presents a taxonomy of ways that simple analogy induces conceptual error and an alternative approach involving integrated…
Reconstitution of active human core Mediator complex reveals a pivotal role of the MED14 subunit

PubMed Central

Cevher, Murat A.; Shi, Yi; Li, Dan; Chait, Brian T.; Malik, Sohail; Roeder, Robert G.

2014-01-01

The evolutionarily conserved Mediator complex is a critical coactivator for RNA polymerase II (Pol II)-mediated transcription. Here, we report the reconstitution of a functional 15-subunit human core Mediator complex and its characterization by functional assays and chemical cross-linking coupled to mass spectrometry (CX-MS). Whereas the reconstituted head and middle modules can stably associate, only with incorporation of MED14 into the bi-modular complex does it acquire basal and coactivator functions. This results from a dramatically enhanced ability of MED14-containing complexes to associate with Pol II. Altogether, our analyses identify MED14 as both an architectural and a functional backbone of the Mediator complex. We further establish a conditional requirement for metazoan-specific MED26 that becomes evident in the presence of heterologous nuclear factors. This general approach paves the way for systematically dissecting the multiple layers of functionalities associated with the Mediator complex. PMID:25383669
CMS Readiness for Multi-Core Workload Scheduling

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

Perez-Calero Yzquierdo, A.; Balcas, J.; Hernandez, J.

In the present run of the LHC, CMS data reconstruction and simulation algorithms benefit greatly from being executed as multiple threads running on several processor cores. The complexity of the Run 2 events requires parallelization of the code to reduce the memory-per- core footprint constraining serial execution programs, thus optimizing the exploitation of present multi-core processor architectures. The allocation of computing resources for multi-core tasks, however, becomes a complex problem in itself. The CMS workload submission infrastructure employs multi-slot partitionable pilots, built on HTCondor and GlideinWMS native features, to enable scheduling of single and multi-core jobs simultaneously. This provides amore » solution for the scheduling problem in a uniform way across grid sites running a diversity of gateways to compute resources and batch system technologies. This paper presents this strategy and the tools on which it has been implemented. The experience of managing multi-core resources at the Tier-0 and Tier-1 sites during 2015, along with the deployment phase to Tier-2 sites during early 2016 is reported. The process of performance monitoring and optimization to achieve efficient and flexible use of the resources is also described.« less
CMS readiness for multi-core workload scheduling

NASA Astrophysics Data System (ADS)

Perez-Calero Yzquierdo, A.; Balcas, J.; Hernandez, J.; Aftab Khan, F.; Letts, J.; Mason, D.; Verguilov, V.

2017-10-01

In the present run of the LHC, CMS data reconstruction and simulation algorithms benefit greatly from being executed as multiple threads running on several processor cores. The complexity of the Run 2 events requires parallelization of the code to reduce the memory-per- core footprint constraining serial execution programs, thus optimizing the exploitation of present multi-core processor architectures. The allocation of computing resources for multi-core tasks, however, becomes a complex problem in itself. The CMS workload submission infrastructure employs multi-slot partitionable pilots, built on HTCondor and GlideinWMS native features, to enable scheduling of single and multi-core jobs simultaneously. This provides a solution for the scheduling problem in a uniform way across grid sites running a diversity of gateways to compute resources and batch system technologies. This paper presents this strategy and the tools on which it has been implemented. The experience of managing multi-core resources at the Tier-0 and Tier-1 sites during 2015, along with the deployment phase to Tier-2 sites during early 2016 is reported. The process of performance monitoring and optimization to achieve efficient and flexible use of the resources is also described.

Application of simplified Complexity Theory concepts for healthcare social systems to explain the implementation of evidence into practice.

PubMed

Chandler, Jacqueline; Rycroft-Malone, Jo; Hawkes, Claire; Noyes, Jane

2016-02-01

To examine the application of core concepts from Complexity Theory to explain the findings from a process evaluation undertaken in a trial evaluating implementation strategies for recommendations about reducing surgical fasting times. The proliferation of evidence-based guidance requires a greater focus on its implementation. Theory is required to explain the complex processes across the multiple healthcare organizational levels. This social healthcare context involves the interaction between professionals, patients and the organizational systems in care delivery. Complexity Theory may provide an explanatory framework to explain the complexities inherent in implementation in social healthcare contexts. A secondary thematic analysis of qualitative process evaluation data informed by Complexity Theory. Seminal texts applying Complexity Theory to the social context were annotated, key concepts extracted and core Complexity Theory concepts identified. These core concepts were applied as a theoretical lens to provide an explanation of themes from a process evaluation of a trial evaluating the implementation of strategies to reduce surgical fasting times. Sampled substantive texts provided a representative spread of theoretical development and application of Complexity Theory from late 1990's-2013 in social science, healthcare, management and philosophy. Five Complexity Theory core concepts extracted were 'self-organization', 'interaction', 'emergence', 'system history' and 'temporality'. Application of these concepts suggests routine surgical fasting practice is habituated in the social healthcare system and therefore it cannot easily be reversed. A reduction to fasting times requires an incentivised new approach to emerge in the surgical system's priority of completing the operating list. The application of Complexity Theory provides a useful explanation for resistance to change fasting practice. Its utility in implementation research warrants further attention and evaluation. © 2015 John Wiley & Sons Ltd.
Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes.

PubMed

Izard, T; Aevarsson, A; Allen, M D; Westphal, A H; Perham, R N; de Kok, A; Hol, W G

1999-02-16

The pyruvate dehydrogenase multienzyme complex (Mr of 5-10 million) is assembled around a structural core formed of multiple copies of dihydrolipoyl acetyltransferase (E2p), which exhibits the shape of either a cube or a dodecahedron, depending on the source. The crystal structures of the 60-meric dihydrolipoyl acyltransferase cores of Bacillus stearothermophilus and Enterococcus faecalis pyruvate dehydrogenase complexes were determined and revealed a remarkably hollow dodecahedron with an outer diameter of approximately 237 A, 12 large openings of approximately 52 A diameter across the fivefold axes, and an inner cavity with a diameter of approximately 118 A. Comparison of cubic and dodecahedral E2p assemblies shows that combining the principles of quasi-equivalence formulated by Caspar and Klug [Caspar, D. L. & Klug, A. (1962) Cold Spring Harbor Symp. Quant. Biol. 27, 1-4] with strict Euclidean geometric considerations results in predictions of the major features of the E2p dodecahedron matching the observed features almost exactly.
Design of elliptical-core mode-selective photonic lanterns with six modes for MIMO-free mode division multiplexing systems.

PubMed

Sai, Xiaowei; Li, Yan; Yang, Chen; Li, Wei; Qiu, Jifang; Hong, Xiaobin; Zuo, Yong; Guo, Hongxiang; Tong, Weijun; Wu, Jian

2017-11-01

Elliptical-core few mode fiber (EC-FMF) is used in a mode division multiplexing (MDM) transmission system to release multiple-input-multiple-output (MIMO) digital-signal-processing, which reduces the cost and the complexity of the receiver. However, EC-FMF does not match with conventional multiplexers/de-multiplexers (MUXs/DeMUXs) such as a photonic lantern, leading to extra mode coupling loss and crosstalk. We design elliptical-core mode-selective photonic lanterns (EC-MSPLs) with six modes, which can match well with EC-FMF in MIMO-free MDM systems. Simulation of the EC-MSPL using the beam propagation method was demonstrated employing a combination of either step-index or graded-index fibers with six different sizes of cores, and the taper transition length of 8 cm or 4 cm. Through numerical simulations and optimizations, both types of photonic lanterns can realize low loss transmission and low crosstalk of below -20.0 dB for all modes.
Germline-specific H1 variants: the "sexy" linker histones.

PubMed

Pérez-Montero, Salvador; Carbonell, Albert; Azorín, Fernando

2016-03-01

The eukaryotic genome is packed into chromatin, a nucleoprotein complex mainly formed by the interaction of DNA with the abundant basic histone proteins. The fundamental structural and functional subunit of chromatin is the nucleosome core particle, which is composed by 146 bp of DNA wrapped around an octameric protein complex formed by two copies of each core histone H2A, H2B, H3, and H4. In addition, although not an intrinsic component of the nucleosome core particle, linker histone H1 directly interacts with it in a monomeric form. Histone H1 binds nucleosomes near the exit/entry sites of linker DNA, determines nucleosome repeat length and stabilizes higher-order organization of nucleosomes into the ∼30 nm chromatin fiber. In comparison to core histones, histone H1 is less well conserved through evolution. Furthermore, histone H1 composition in metazoans is generally complex with most species containing multiple variants that play redundant as well as specific functions. In this regard, a characteristic feature is the presence of specific H1 variants that replace somatic H1s in the germline and during early embryogenesis. In this review, we summarize our current knowledge about their structural and functional properties.
An enhanceosome containing the Jun B/Fra-2 heterodimer and the HMG-I(Y) architectural protein controls HPV 18 transcription.

PubMed

Bouallaga, I; Massicard, S; Yaniv, M; Thierry, F

2000-11-01

Recent studies have reported new mechanisms that mediate the transcriptional synergy of strong tissue-specific enhancers, involving the cooperative assembly of higher-order nucleoprotein complexes called enhanceosomes. Here we show that the HPV18 enhancer, which controls the epithelial-specific transcription of the E6 and E7 transforming genes, exhibits characteristic features of these structures. We used deletion experiments to show that a core enhancer element cooperates, in a specific helical phasing, with distant essential factors binding to the ends of the enhancer. This core sequence, binding a Jun B/Fra-2 heterodimer, cooperatively recruits the architectural protein HMG-I(Y) in a nucleoprotein complex, where they interact with each other. Therefore, in HeLa cells, HPV18 transcription seems to depend upon the assembly of an enhanceosome containing multiple cellular factors recruited by a core sequence interacting with AP1 and HMG-I(Y).
[Towards computer-aided catalyst design: Three effective core potential studies of C-H activation]. Final report

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

NONE

1998-12-31

Research in the initial grant period focused on computational studies relevant to the selective activation of methane, the prime component of natural gas. Reaction coordinates for methane activation by experimental models were delineated, as well as the bonding and structure of complexes that effect this important reaction. This research, highlighted in the following sections, also provided the impetus for further development, and application of methods for modeling metal-containing catalysts. Sections of the report describe the following: methane activation by multiple-bonded transition metal complexes; computational lanthanide chemistry; and methane activation by non-imido, multiple-bonded ligands.
Segregation and Protectionism: Institutionalised Views of Aboriginal Rurality

ERIC Educational Resources Information Center

Carter, J.; Hollinsworth, D.

2009-01-01

Rurality is a complex and contested term, with multiple notions and gazes amid calls for theoretical pluralism. In Australia, the spatial categories of "remote", "rural", "regional" and "urban" are applied to places that vary in their distance from an economic and political core and have differing population…
Making Critical Friends

ERIC Educational Resources Information Center

Raven, Sara; Klein, Vanessa; Namdar, Bahadir

2016-01-01

Argumentation has long been promoted as a core scientific practice in which students should engage, yet science classrooms still often omit it. One remedy is to incorporate socioscientific issues (SSIs) in the curricula. SSIs are open-ended and complex, typically subject to multiple perspectives and solutions. These issues, influenced by science…
Impact of Multiple Complex Plaques on Short-and Long-Term Clinical in Patients Presenting with ST-Segment Elevation Myocardial Infarction (From the Harmonizing Outcomes with Revascularization and Stents in Acute Myocardial Infarction [HORIZONS-AMI] Trial)

PubMed Central

Keeley, Ellen C.; Mehran, Roxana; Brener, Sorin J.; Witzenbichler, Bernhard; Guagliumi, Giulio; Dudek, Dariusz; Kornowski, Ran; Dressler, Ovidiu; Fahy, Martin; Xu, Ke; Grines, Cindy L.; Stone, Gregg W.

2014-01-01

It is not known whether the extent and severity of non-culprit coronary lesions correlate with outcomes in patients with STEMI referred for primary PCI. We sought to quantify complex plaques in ST-segment elevation myocardial infarction (STEMI) patients referred for primary percutaneous coronary intervention (PCI) and to determine their effect on short- and long-term clinical outcomes by examining the core laboratory database for plaque analysis from the HORIZONS-AMI study. Baseline demographic, angiographic, and procedural details were compared between patients with single vs. multiple complex plaques undergoing single vessel PCI. Multivariable analysis was performed for predictors of long-term major adverse cardiac events (MACE), a combined end point of death, reinfarction, ischemic target vessel revascularization, or stroke, and for death alone. Single vessel PCI was performed in 3,137 patients (87%): 2,174 (69%) had multiple complex plaques and 963 (31%) had a single complex plaque. Compared to those with a single complex plaque, patients with multiple complex plaques were older (p<0.0001) and had more comorbidities. The presence of multiple complex plaques was an independent predictor of 3-year MACE (hazard ratio [HR]: 1.58; 95% confidence interval [CI]: 1.26–1.98, p<0.0001), and death alone (HR: 1.68; 95% CI: 1.05–2.70, p=0.03). In conclusion, multiple complex plaques are present in the majority of STEMI patients undergoing primary PCI and their presence is an independent predictor of short- and long-term MACE, including death. (Harmonizing Outcomes With Revascularization and Stents in Acute Myocardial Infarction [HORIZONS-AMI]; NCT00433966) PMID:24703369
Device design and signal processing for multiple-input multiple-output multimode fiber links

NASA Astrophysics Data System (ADS)

Appaiah, Kumar; Vishwanath, Sriram; Bank, Seth R.

2012-01-01

Multimode fibers (MMFs) are limited in data rate capabilities owing to modal dispersion. However, their large core diameter simplifies alignment and packaging, and makes them attractive for short and medium length links. Recent research has shown that the use of signal processing and techniques such as multiple-input multiple-output (MIMO) can greatly improve the data rate capabilities of multimode fibers. In this paper, we review recent experimental work using MIMO and signal processing for multimode fibers, and the improvements in data rates achievable with these techniques. We then present models to design as well as simulate the performance benefits obtainable with arrays of lasers and detectors in conjunction with MIMO, using channel capacity as the metric to optimize. We also discuss some aspects related to complexity of the algorithms needed for signal processing and discuss techniques for low complexity implementation.
Recognition of the Xenopus ribosomal core promoter by the transcription factor xUBF involves multiple HMG box domains and leads to an xUBF interdomain interaction.

PubMed

Leblanc, B; Read, C; Moss, T

1993-02-01

The interaction of the ribosomal transcription factor xUBF with the RNA polymerase I core promoter of Xenopus laevis has been studied both at the DNA and protein levels. It is shown that a single xUBF-DNA complex forms over the 40S initiation site (+1) and involves at least the DNA sequences between -20 and +60 bp. DNA sequences upstream of +10 and downstream of +18 are each sufficient to direct complex formation independently. HMG box 1 of xUBF independently recognizes the sequences -20 to -1 and +1 to +22 and the addition of the N-terminal dimerization domain to HMG box 1 stabilizes its interaction with these sequences approximately 10-fold. HMG boxes 2/3 interact with the DNA downstream of +22 and can independently position xUBF across the initiation site. The C-terminal segment of xUBF, HMG boxes 4, 5 or the acidic domain, directly or indirectly interact with HMG box 1, making the core promoter sequences between -11 and -15 hypersensitive to DNase. This interaction also requires the DNA sequences between +17 and +32, i.e. the HMG box 2/3 binding site. The data suggest extensive folding of the core promoter within the xUBF complex.
Multi-dimensional Core-Collapse Supernova Simulations with Neutrino Transport

NASA Astrophysics Data System (ADS)

Pan, Kuo-Chuan; Liebendörfer, Matthias; Hempel, Matthias; Thielemann, Friedrich-Karl

We present multi-dimensional core-collapse supernova simulations using the Isotropic Diffusion Source Approximation (IDSA) for the neutrino transport and a modified potential for general relativity in two different supernova codes: FLASH and ELEPHANT. Due to the complexity of the core-collapse supernova explosion mechanism, simulations require not only high-performance computers and the exploitation of GPUs, but also sophisticated approximations to capture the essential microphysics. We demonstrate that the IDSA is an elegant and efficient neutrino radiation transfer scheme, which is portable to multiple hydrodynamics codes and fast enough to investigate long-term evolutions in two and three dimensions. Simulations with a 40 solar mass progenitor are presented in both FLASH (1D and 2D) and ELEPHANT (3D) as an extreme test condition. It is found that the black hole formation time is delayed in multiple dimensions and we argue that the strong standing accretion shock instability before black hole formation will lead to strong gravitational waves.
Integrated cladding-pumped multicore few-mode erbium-doped fibre amplifier for space-division-multiplexed communications

NASA Astrophysics Data System (ADS)

Chen, H.; Jin, C.; Huang, B.; Fontaine, N. K.; Ryf, R.; Shang, K.; Grégoire, N.; Morency, S.; Essiambre, R.-J.; Li, G.; Messaddeq, Y.; Larochelle, S.

2016-08-01

Space-division multiplexing (SDM), whereby multiple spatial channels in multimode and multicore optical fibres are used to increase the total transmission capacity per fibre, is being investigated to avert a data capacity crunch and reduce the cost per transmitted bit. With the number of channels employed in SDM transmission experiments continuing to rise, there is a requirement for integrated SDM components that are scalable. Here, we demonstrate a cladding-pumped SDM erbium-doped fibre amplifier (EDFA) that consists of six uncoupled multimode erbium-doped cores. Each core supports three spatial modes, which enables the EDFA to amplify a total of 18 spatial channels (six cores × three modes) simultaneously with a single pump diode and a complexity similar to a single-mode EDFA. The amplifier delivers >20 dBm total output power per core and <7 dB noise figure over the C-band. This cladding-pumped EDFA enables combined space-division and wavelength-division multiplexed transmission over multiple multimode fibre spans.
Robust and efficient overset grid assembly for partitioned unstructured meshes

NASA Astrophysics Data System (ADS)

Roget, Beatrice; Sitaraman, Jayanarayanan

2014-03-01

This paper presents a method to perform efficient and automated Overset Grid Assembly (OGA) on a system of overlapping unstructured meshes in a parallel computing environment where all meshes are partitioned into multiple mesh-blocks and processed on multiple cores. The main task of the overset grid assembler is to identify, in parallel, among all points in the overlapping mesh system, at which points the flow solution should be computed (field points), interpolated (receptor points), or ignored (hole points). Point containment search or donor search, an algorithm to efficiently determine the cell that contains a given point, is the core procedure necessary for accomplishing this task. Donor search is particularly challenging for partitioned unstructured meshes because of the complex irregular boundaries that are often created during partitioning.
Interesting and Difficult Mathematical Problems: Changing Teachers' Views by Employing Multiple-Solution Tasks

ERIC Educational Resources Information Center

Guberman, Raisa; Leikin, Roza

2013-01-01

The study considers mathematical problem solving to be at the heart of mathematics teaching and learning, while mathematical challenge is a core element of any educational process. The study design addresses the complexity of teachers' knowledge. It is aimed at exploring the development of teachers' mathematical and pedagogical conceptions…
Modeling Smoke Plume-Rise and Dispersion from Southern United States Prescribed Burns with Daysmoke

Treesearch

G L Achtemeier; S L Goodrick; Y Liu; F Garcia-Menendez; Y Hu; M. Odman

2011-01-01

We present Daysmoke, an empirical-statistical plume rise and dispersion model for simulating smoke from prescribed burns. Prescribed fires are characterized by complex plume structure including multiple-core updrafts which makes modeling with simple plume models difficult. Daysmoke accounts for plume structure in a three-dimensional veering/sheering atmospheric...
Evaluating Multiple Perspectives: Approaching the Synthesis Task through Assessing Credibility

ERIC Educational Resources Information Center

Lafferty, Karen Elizabeth; Summers, Amy; Tanaka, Stephanie; Cavanagh, Jeanne

2016-01-01

Introduction of the Common Core State Standards and assessments like the synthesis performance task pose new challenges for secondary English teachers. As students of all ability levels engage with complex text and in tasks that target higher level cognitive skills, teachers need strategies to support their understanding. This article describes…
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

PubMed Central

2010-01-01

Background The reconstruction of protein complexes from the physical interactome of organisms serves as a building block towards understanding the higher level organization of the cell. Over the past few years, several independent high-throughput experiments have helped to catalogue enormous amount of physical protein interaction data from organisms such as yeast. However, these individual datasets show lack of correlation with each other and also contain substantial number of false positives (noise). Over these years, several affinity scoring schemes have also been devised to improve the qualities of these datasets. Therefore, the challenge now is to detect meaningful as well as novel complexes from protein interaction (PPI) networks derived by combining datasets from multiple sources and by making use of these affinity scoring schemes. In the attempt towards tackling this challenge, the Markov Clustering algorithm (MCL) has proved to be a popular and reasonably successful method, mainly due to its scalability, robustness, and ability to work on scored (weighted) networks. However, MCL produces many noisy clusters, which either do not match known complexes or have additional proteins that reduce the accuracies of correctly predicted complexes. Results Inspired by recent experimental observations by Gavin and colleagues on the modularity structure in yeast complexes and the distinctive properties of "core" and "attachment" proteins, we develop a core-attachment based refinement method coupled to MCL for reconstruction of yeast complexes from scored (weighted) PPI networks. We combine physical interactions from two recent "pull-down" experiments to generate an unscored PPI network. We then score this network using available affinity scoring schemes to generate multiple scored PPI networks. The evaluation of our method (called MCL-CAw) on these networks shows that: (i) MCL-CAw derives larger number of yeast complexes and with better accuracies than MCL, particularly in the presence of natural noise; (ii) Affinity scoring can effectively reduce the impact of noise on MCL-CAw and thereby improve the quality (precision and recall) of its predicted complexes; (iii) MCL-CAw responds well to most available scoring schemes. We discuss several instances where MCL-CAw was successful in deriving meaningful complexes, and where it missed a few proteins or whole complexes due to affinity scoring of the networks. We compare MCL-CAw with several recent complex detection algorithms on unscored and scored networks, and assess the relative performance of the algorithms on these networks. Further, we study the impact of augmenting physical datasets with computationally inferred interactions for complex detection. Finally, we analyse the essentiality of proteins within predicted complexes to understand a possible correlation between protein essentiality and their ability to form complexes. Conclusions We demonstrate that core-attachment based refinement in MCL-CAw improves the predictions of MCL on yeast PPI networks. We show that affinity scoring improves the performance of MCL-CAw. PMID:20939868
An Adaptive Cooperative Strategy for Underlay MIMO Cognitive Radio Networks: An Opportunistic and Low-Complexity Approach

NASA Astrophysics Data System (ADS)

Mazoochi, M.; Pourmina, M. A.; Bakhshi, H.

2015-03-01

The core aim of this work is the maximization of the achievable data rate of the secondary user pairs (SU pairs), while ensuring the QoS of primary users (PUs). All users are assumed to be equipped with multiple antennas. It is assumed that when PUs are present, the direct communications between SU pairs introduces intolerable interference to PUs and thereby SUs transmit signal using the cooperation of other SUs and avoid transmitting in the direct channel. In brief, an adaptive cooperative strategy for multiple-input/multiple-output (MIMO) cognitive radio networks is proposed. At the presence of PUs, the issue of joint relay selection and power allocation in Underlay MIMO Cooperative Cognitive Radio Networks (U-MIMO-CCRN) is addressed. The optimal approach for determining the power allocation and the cooperating SU is proposed. Besides, the outage probability of the proposed communication protocol is further derived. Due to high complexity of the optimal approach, a low-complexity approach is further proposed and its performance is evaluated using simulations. The simulation results reveal that the performance loss due to the low-complexity approach is only about 14%, while the complexity is greatly reduced.
Characterization of Transcription from TATA-Less Promoters: Identification of a New Core Promoter Element XCPE2 and Analysis of Factor Requirements

PubMed Central

Anish, Ramakrishnan; Hossain, Mohammad B.; Jacobson, Raymond H.; Takada, Shinako

2009-01-01

Background More than 80% of mammalian protein-coding genes are driven by TATA-less promoters which often show multiple transcriptional start sites (TSSs). However, little is known about the core promoter DNA sequences or mechanisms of transcriptional initiation for this class of promoters. Methodology/Principal Findings Here we identify a new core promoter element XCPE2 (X core promoter element 2) (consensus sequence: A/C/G-C-C/T-C-G/A-T-T-G/A-C-C/A+1-C/T) that can direct specific transcription from the second TSS of hepatitis B virus X gene mRNA. XCPE2 sequences can also be found in human promoter regions and typically appear to drive one of the start sites within multiple TSS-containing TATA-less promoters. To gain insight into mechanisms of transcriptional initiation from this class of promoters, we examined requirements of several general transcription factors by in vitro transcription experiments using immunodepleted nuclear extracts and purified factors. Our results show that XCPE2-driven transcription uses at least TFIIB, either TFIID or free TBP, RNA polymerase II (RNA pol II) and the MED26-containing mediator complex but not Gcn5. Therefore, XCPE2-driven transcription can be carried out by a mechanism which differs from previously described TAF-dependent mechanisms for initiator (Inr)- or downstream promoter element (DPE)-containing promoters, the TBP- and SAGA (Spt-Ada-Gcn5-acetyltransferase)-dependent mechanism for yeast TATA-containing promoters, or the TFTC (TBP-free-TAF-containing complex)-dependent mechanism for certain Inr-containing TATA-less promoters. EMSA assays using XCPE2 promoter and purified factors further suggest that XCPE2 promoter recognition requires a set of factors different from those for TATA box, Inr, or DPE promoter recognition. Conclusions/Significance We identified a new core promoter element XCPE2 that are found in multiple TSS-containing TATA-less promoters. Mechanisms of promoter recognition and transcriptional initiation for XCPE2-driven promoters appear different from previously shown mechanisms for classical promoters that show single “focused” TSSs. Our studies provide insight into novel mechanisms of RNA Pol II transcription from multiple TSS-containing TATA-less promoters. PMID:19337366

Tier-2 Optimisation for Computational Density/Diversity and Big Data

NASA Astrophysics Data System (ADS)

Fay, R. B.; Bland, J.

2014-06-01

As the number of cores on chip continues to trend upwards and new CPU architectures emerge, increasing CPU density and diversity presents multiple challenges to site administrators. These include scheduling for massively multi-core systems (potentially including Graphical Processing Units (GPU), integrated and dedicated) and Many Integrated Core (MIC)) to ensure a balanced throughput of jobs while preserving overall cluster throughput, as well as the increasing complexity of developing for these heterogeneous platforms, and the challenge in managing this more complex mix of resources. In addition, meeting data demands as both dataset sizes increase and as the rate of demand scales with increased computational power requires additional performance from the associated storage elements. In this report, we evaluate one emerging technology, Solid State Drive (SSD) caching for RAID controllers, with consideration to its potential to assist in meeting evolving demand. We also briefly consider the broader developing trends outlined above in order to identify issues that may develop and assess what actions should be taken in the immediate term to address those.
Architecture of human translation initiation factor 3

PubMed Central

Querol-Audi, Jordi; Sun, Chaomin; Vogan, Jacob M.; Smith, Duane; Gu, Yu; Cate, Jamie; Nogales, Eva

2013-01-01

SUMMARY Eukaryotic translation initiation factor 3 (eIF3) plays a central role in protein synthesis by organizing the formation of the 43S preinitiation complex. Using genetic tag visualization by electron microscopy, we reveal the molecular organization of ten human eIF3 subunits, including an octameric core. The structure of eIF3 bears a close resemblance to that of the proteasome lid, with a conserved spatial organization of eight core subunits containing PCI and MPN domains that coordinate functional interactions in both complexes. We further show that eIF3 subunits a and c interact with initiation factors eIF1 and eIF1A, which control the stringency of start codon selection. Finally, we find that subunit j, which modulates messenger RNA interactions with the small ribosomal subunit, makes multiple independent interactions with the eIF3 octameric core. These results highlight the conserved architecture of eIF3 and how it scaffolds key factors that control translation initiation in higher eukaryotes, including humans. PMID:23623729
Slow Perceptual Processing at the Core of Developmental Dyslexia: A Parameter-Based Assessment of Visual Attention

ERIC Educational Resources Information Center

Stenneken, Prisca; Egetemeir, Johanna; Schulte-Korne, Gerd; Muller, Hermann J.; Schneider, Werner X.; Finke, Kathrin

2011-01-01

The cognitive causes as well as the neurological and genetic basis of developmental dyslexia, a complex disorder of written language acquisition, are intensely discussed with regard to multiple-deficit models. Accumulating evidence has revealed dyslexics' impairments in a variety of tasks requiring visual attention. The heterogeneity of these…
Molecular dynamics studies on the DNA-binding process of ERG.

PubMed

Beuerle, Matthias G; Dufton, Neil P; Randi, Anna M; Gould, Ian R

2016-11-15

The ETS family of transcription factors regulate gene targets by binding to a core GGAA DNA-sequence. The ETS factor ERG is required for homeostasis and lineage-specific functions in endothelial cells, some subset of haemopoietic cells and chondrocytes; its ectopic expression is linked to oncogenesis in multiple tissues. To date details of the DNA-binding process of ERG including DNA-sequence recognition outside the core GGAA-sequence are largely unknown. We combined available structural and experimental data to perform molecular dynamics simulations to study the DNA-binding process of ERG. In particular we were able to reproduce the ERG DNA-complex with a DNA-binding simulation starting in an unbound configuration with a final root-mean-square-deviation (RMSD) of 2.1 Å to the core ETS domain DNA-complex crystal structure. This allowed us to elucidate the relevance of amino acids involved in the formation of the ERG DNA-complex and to identify Arg385 as a novel key residue in the DNA-binding process. Moreover we were able to show that water-mediated hydrogen bonds are present between ERG and DNA in our simulations and that those interactions have the potential to achieve sequence recognition outside the GGAA core DNA-sequence. The methodology employed in this study shows the promising capabilities of modern molecular dynamics simulations in the field of protein DNA-interactions.
Color from hierarchy: Diverse optical properties of micron-sized spherical colloidal assemblies.

PubMed

Vogel, Nicolas; Utech, Stefanie; England, Grant T; Shirman, Tanya; Phillips, Katherine R; Koay, Natalie; Burgess, Ian B; Kolle, Mathias; Weitz, David A; Aizenberg, Joanna

2015-09-01

Materials in nature are characterized by structural order over multiple length scales have evolved for maximum performance and multifunctionality, and are often produced by self-assembly processes. A striking example of this design principle is structural coloration, where interference, diffraction, and absorption effects result in vivid colors. Mimicking this emergence of complex effects from simple building blocks is a key challenge for man-made materials. Here, we show that a simple confined self-assembly process leads to a complex hierarchical geometry that displays a variety of optical effects. Colloidal crystallization in an emulsion droplet creates micron-sized superstructures, termed photonic balls. The curvature imposed by the emulsion droplet leads to frustrated crystallization. We observe spherical colloidal crystals with ordered, crystalline layers and a disordered core. This geometry produces multiple optical effects. The ordered layers give rise to structural color from Bragg diffraction with limited angular dependence and unusual transmission due to the curved nature of the individual crystals. The disordered core contributes nonresonant scattering that induces a macroscopically whitish appearance, which we mitigate by incorporating absorbing gold nanoparticles that suppress scattering and macroscopically purify the color. With increasing size of the constituent colloidal particles, grating diffraction effects dominate, which result from order along the crystal's curved surface and induce a vivid polychromatic appearance. The control of multiple optical effects induced by the hierarchical morphology in photonic balls paves the way to use them as building blocks for complex optical assemblies--potentially as more efficient mimics of structural color as it occurs in nature.
Color from hierarchy: Diverse optical properties of micron-sized spherical colloidal assemblies

PubMed Central

Vogel, Nicolas; Utech, Stefanie; England, Grant T.; Shirman, Tanya; Phillips, Katherine R.; Koay, Natalie; Burgess, Ian B.; Kolle, Mathias; Weitz, David A.; Aizenberg, Joanna

2015-01-01

Materials in nature are characterized by structural order over multiple length scales have evolved for maximum performance and multifunctionality, and are often produced by self-assembly processes. A striking example of this design principle is structural coloration, where interference, diffraction, and absorption effects result in vivid colors. Mimicking this emergence of complex effects from simple building blocks is a key challenge for man-made materials. Here, we show that a simple confined self-assembly process leads to a complex hierarchical geometry that displays a variety of optical effects. Colloidal crystallization in an emulsion droplet creates micron-sized superstructures, termed photonic balls. The curvature imposed by the emulsion droplet leads to frustrated crystallization. We observe spherical colloidal crystals with ordered, crystalline layers and a disordered core. This geometry produces multiple optical effects. The ordered layers give rise to structural color from Bragg diffraction with limited angular dependence and unusual transmission due to the curved nature of the individual crystals. The disordered core contributes nonresonant scattering that induces a macroscopically whitish appearance, which we mitigate by incorporating absorbing gold nanoparticles that suppress scattering and macroscopically purify the color. With increasing size of the constituent colloidal particles, grating diffraction effects dominate, which result from order along the crystal’s curved surface and induce a vivid polychromatic appearance. The control of multiple optical effects induced by the hierarchical morphology in photonic balls paves the way to use them as building blocks for complex optical assemblies—potentially as more efficient mimics of structural color as it occurs in nature. PMID:26290583
Novel secretory granule morphology in physically fixed pancreatic islets.

PubMed

Dudek, R W; Boyne, A F; Charles, T M

1984-09-01

Protein A-gold immunocytochemistry has been applied to physically fixed beta cells from rat islets of Langerhans. The punctate nature of the gold particles permits improved resolution of the antigenic sites without obscuring the fine ultrastructural preservation obtained by physical fixation. There is a filamentous material within the halo of the secretory granules that is not preserved by aqueous, chemical fixation. When viewed in stereo the filaments appear as an annular cobweb or a series of wheel spokes attached to a centrally located hub (the dense core of the granule). The filaments demonstrate insulin-like immunoreactivity using the protein A-gold technique. The immunoreactivity appears to be restricted to the filaments and the surface of the dense cores. This may be a consequence of the preservation of a solid, insolubilized core state that resists penetration by the antibody and/or the protein A-gold complex. However, the evidence that there is a halo pool of insulin which is separate from the massive core aggregate suggests that i) correspondingly massive exocytotic pits may not be as mandatory for insulin release as has been assumed and ii) the complex kinetics of insulin secretion may be, in part, a reflection of multiple insulin compartments within secretory granules.
Reactions in trifluoroacetic acid (CF 3COOH) induced by low energy electron attachment

NASA Astrophysics Data System (ADS)

Langer, Judith; Stano, Michal; Gohlke, Sascha; Foltin, Victor; Matejcik, Stefan; Illenberger, Eugen

2006-02-01

Dissociative electron attachment to trifluoroacetic acid (CF 3COOH) is characterized by an intense low energy shape resonance located near 1 eV and a comparatively weaker core excited resonance located near 7 eV. The shape resonance decomposes into the fragment ions CF 3COO -, CF 2COO -, and CF2-. The underlying reactions include simple bond cleavage but also more complex sequences involving multiple bond cleavages, rearrangement in the precursor ion and formation of new molecules (HF, CO 2). The core excited resonance additionally decomposes into F -, CF3- and probably metastable CO2-.
Tetratricopeptide-motif-mediated interaction of FANCG with recombination proteins XRCC3 and BRCA2.

PubMed

Hussain, Shobbir; Wilson, James B; Blom, Eric; Thompson, Larry H; Sung, Patrick; Gordon, Susan M; Kupfer, Gary M; Joenje, Hans; Mathew, Christopher G; Jones, Nigel J

2006-05-10

Fanconi anaemia is an inherited chromosomal instability disorder characterised by cellular sensitivity to DNA interstrand crosslinkers, bone-marrow failure and a high risk of cancer. Eleven FA genes have been identified, one of which, FANCD1, is the breast cancer susceptibility gene BRCA2. At least eight FA proteins form a nuclear core complex required for monoubiquitination of FANCD2. The BRCA2/FANCD1 protein is connected to the FA pathway by interactions with the FANCG and FANCD2 proteins, both of which co-localise with the RAD51 recombinase, which is regulated by BRCA2. These connections raise the question of whether any of the FANC proteins of the core complex might also participate in other complexes involved in homologous recombination repair. We therefore tested known FA proteins for direct interaction with RAD51 and its paralogs XRCC2 and XRCC3. FANCG was found to interact with XRCC3, and this interaction was disrupted by the FA-G patient derived mutation L71P. FANCG was co-immunoprecipitated with both XRCC3 and BRCA2 from extracts of human and hamster cells. The FANCG-XRCC3 and FANCG-BRCA2 interactions did not require the presence of other FA proteins from the core complex, suggesting that FANCG also participates in a DNA repair complex that is downstream and independent of FANCD2 monoubiquitination. Additionally, XRCC3 and BRCA2 proteins co-precipitate in both human and hamster cells and this interaction requires FANCG. The FANCG protein contains multiple tetratricopeptide repeat motifs (TPRs), which function as scaffolds to mediate protein-protein interactions. Mutation of one or more of these motifs disrupted all of the known interactions of FANCG. We propose that FANCG, in addition to stabilising the FA core complex, may have a role in building multiprotein complexes that facilitate homologous recombination repair.
Engineering Promoter Architecture in Oleaginous Yeast Yarrowia lipolytica.

PubMed

Shabbir Hussain, Murtaza; Gambill, Lauren; Smith, Spencer; Blenner, Mark A

2016-03-18

Eukaryotic promoters have a complex architecture to control both the strength and timing of gene transcription spanning up to thousands of bases from the initiation site. This complexity makes rational fine-tuning of promoters in fungi difficult to predict; however, this very same complexity enables multiple possible strategies for engineering promoter strength. Here, we studied promoter architecture in the oleaginous yeast, Yarrowia lipolytica. While recent studies have focused on upstream activating sequences, we systematically examined various components common in fungal promoters. Here, we examine several promoter components including upstream activating sequences, proximal promoter sequences, core promoters, and the TATA box in autonomously replicating expression plasmids and integrated into the genome. Our findings show that promoter strength can be fine-tuned through the engineering of the TATA box sequence, core promoter, and upstream activating sequences. Additionally, we identified a previously unreported oleic acid responsive transcription enhancement in the XPR2 upstream activating sequences, which illustrates the complexity of fungal promoters. The promoters engineered here provide new genetic tools for metabolic engineering in Y. lipolytica and provide promoter engineering strategies that may be useful in engineering other non-model fungal systems.
X-Ray absorption spectroscopy quantitative analysis of biomimetic copper(II) complexes with tridentate nitrogen ligands mimicking the tris(imidazole) array of protein centres.

PubMed

Borghi, Elena; Casella, Luigi

2010-02-21

In this study copper(ii) complexes with the tridentate nitrogen ligand bis[2-(1-methylbenzimidazol-2-yl)ethyl]amine (2-BB) are considered as model compounds for the Cu-tris(imidazole) array found in several copper proteins. 2-BB chelates copper(ii) forming two six-membered rings and the complexes contain methanol, nitrite, azide and water as ancillary ligands; both the coordination numbers and stereochemistries differ in these complexes. Their key structural features were investigated by using full multiple-scattering theoretical analysis of the copper K-edge X-ray absorption spectrum with the MXAN code. We showed that using cluster sizes large enough to include all atoms of the ligand, the analysis of the XANES region can give both a structural model of the metal centre and map the structure of the 2-BB complexes. Complex [Cu(2-BB)(N(3))](+) provided a critical test through the comparison of the XANES simulation results with crystallographic data, thus permitting the extension of the method to the complex [Cu(2-BB)(H(2)O)(n)](+) (n = 1 or 2), for which crystallographic data are not available but is expected to bear a five-coordinated Cu(3N)(2O) core (n = 2). The structural data of [Cu(2-BB)(MeOH)(ClO(4))](+) and [Cu(2-BB)(NO(2))](+), both with a Cu(3N)(2O) core but with a different stereochemistry, were used as the starting parameters for two independent simulations of the XANES region of the [Cu(2-BB)(H(2)O)(2)](+) cation. The two structural models generated by simulation converge towards a structure for the aqua-cation with a lower coordination number. New calculations, where four-coordinated Cu(3N)(O) cores were considered as the starting structures, validated that the structure of the aqua-complex in the powder state has a copper(ii) centre with a four-coordinated Cu(3N)(O) core and a molecular formula [Cu(2-BB)(H(2)O)](ClO(4)).(H(2)O). A water solvation molecule, presumed to be disordered from the simulations with the two Cu(3N)(2O) cores, is present. The successful treatment of this Cu-2-BB complex system allows the extension of the method to other biomimetic compounds when a structural characterization is lacking.
At the Limit: Introducing Energy with Human Senses

ERIC Educational Resources Information Center

Stinken, Lisa; Heusler, Stefan; Carmesin, Hans-Otto

2016-01-01

Energy belongs to the core ideas of the physics curriculum. But at the same time, energy is one of the most complex topics in science education since it occurs in multiple ways, such as motion, sound, light, and thermal energy. It can neither be destroyed nor created, but only converted. Due to the variety of relevant scales and abstractness of…
Multiple tectonic mode switches indicate short-duration heat pulses in a Mio-Pliocene metamorphic core complex, West Papua, Indonesia

NASA Astrophysics Data System (ADS)

White, L. T.; Hall, R.; Gunawan, I.

2017-12-01

The Wandaman Peninsula is a narrow (<20 km), but mountainous (>2 km) promontory in remote western New Guinea. The peninsula is almost entirely composed of medium- to high-grade metamorphic rocks considered to be associated with a Mio-Pliocene metamorphic core complex. Previous work has shown that the uplift and exhumation of the core complex has potentially brought some extremely young eclogite to the surface. These might be comparable to the world's youngest (4.3 Ma) eclogites found in the D'Entrecasteaux Islands at the opposite end of New Guinea. We show that tectonic history of this region is complex. This is because the metamorphic sequences in the Wandaman Peninsula record multiple phases of deformation, all within the last few million years. This is demonstrated through methodical collation of cross-cutting relations from field and microstructural studies across the peninsula. The first phase of deformation and metamorphism is associated with crustal extension and partial melting that took place at 5-7 Ma according to new U-Pb data from metamorphic zircons. This extensional phase ceased after a tectonic mode switch and the region was shortened. This is demonstrated by two phases of folding (1. recumbent and 2. open) that overprint the earlier extensional fabrics. All previous structures were later overprinted by brittle extensional faults and uplift. This extensional phase is still taking place today, as is indicated by submerged forests exposed along the coastline associated with recent earthquakes and hot springs. The sequence of metamorphic rocks that are exposed in the Wandaman Peninsula show that stress and thermal conditions can change rapidly. If we consider that the present is a key to the past, then such results can identify the duration of deformation and metamorphic events more accurately than in much older orogenic systems.
TIMMDC1/C3orf1 functions as a membrane-embedded mitochondrial complex I assembly factor through association with the MCIA complex.

PubMed

Guarani, Virginia; Paulo, Joao; Zhai, Bo; Huttlin, Edward L; Gygi, Steven P; Harper, J Wade

2014-03-01

Complex I (CI) of the electron transport chain, a large membrane-embedded NADH dehydrogenase, couples electron transfer to the release of protons into the mitochondrial inner membrane space to promote ATP production through ATP synthase. In addition to being a central conduit for ATP production, CI activity has been linked to neurodegenerative disorders, including Parkinson's disease. CI is built in a stepwise fashion through the actions of several assembly factors. We employed interaction proteomics to interrogate the molecular associations of 15 core subunits and assembly factors previously linked to human CI deficiency, resulting in a network of 101 proteins and 335 interactions (edges). TIMMDC1, a predicted 4-pass membrane protein, reciprocally associated with multiple members of the MCIA CI assembly factor complex and core CI subunits and was localized in the mitochondrial inner membrane, and its depletion resulted in reduced CI activity and cellular respiration. Quantitative proteomics demonstrated a role for TIMMDC1 in assembly of membrane-embedded and soluble arms of the complex. This study defines a new membrane-embedded CI assembly factor and provides a resource for further analysis of CI biology.
Bromelain-Functionalized Multiple-Wall Lipid-Core Nanocapsules: Formulation, Chemical Structure and Antiproliferative Effect Against Human Breast Cancer Cells (MCF-7).

PubMed

Oliveira, Catiúscia P; Prado, Willian A; Lavayen, Vladimir; Büttenbender, Sabrina L; Beckenkamp, Aline; Martins, Bruna S; Lüdtke, Diogo S; Campo, Leandra F; Rodembusch, Fabiano S; Buffon, Andréia; Pessoa, Adalberto; Guterres, Silvia S; Pohlmann, Adriana R

2017-02-01

This study was conducted a promising approach to surface functionalization developed for lipid-core nanocapsules and the merit to pursue new strategies to treat solid tumors. Bromelain-functionalized multiple-wall lipid-core nanocapsules (Bro-MLNC-Zn) were produced by self-assembling following three steps of interfacial reactions. Physicochemical and structural characteristics, in vitro proteolytic activity (casein substrate) and antiproliferative activity (breast cancer cells, MCF-7) were determined. Bro-MLNC-Zn had z-average diameter of 135 nm and zeta potential of +23 mV. The complex is formed by a Zn-N chemical bond and a chelate with hydroxyl and carboxyl groups. Bromelain complexed at the nanocapsule surface maintained its proteolytic activity and showed anti-proliferative effect against human breast cancer cells (MCF-7) (72.6 ± 1.2% at 1.250 μg mL -1 and 65.5 ± 5.5% at 0.625 μg mL -1 ). Comparing Bro-MLNC-Zn and bromelain solution, the former needed a dose 160-folds lower than the latter for a similar effect. Tripan blue dye assay corroborated the results. The surface functionalization approach produced an innovative formulation having a much higher anti-proliferative effect than the bromelain solution, even though both in vitro proteolytic activity were similar, opening up a great opportunity for further studies in nanomedicine.
Study of a Fine Grained Threaded Framework Design

NASA Astrophysics Data System (ADS)

Jones, C. D.

2012-12-01

Traditionally, HEP experiments exploit the multiple cores in a CPU by having each core process one event. However, future PC designs are expected to use CPUs which double the number of processing cores at the same rate as the cost of memory falls by a factor of two. This effectively means the amount of memory per processing core will remain constant. This is a major challenge for LHC processing frameworks since the LHC is expected to deliver more complex events (e.g. greater pileup events) in the coming years while the LHC experiment's frameworks are already memory constrained. Therefore in the not so distant future we may need to be able to efficiently use multiple cores to process one event. In this presentation we will discuss a design for an HEP processing framework which can allow very fine grained parallelization within one event as well as supporting processing multiple events simultaneously while minimizing the memory footprint of the job. The design is built around the libdispatch framework created by Apple Inc. (a port for Linux is available) whose central concept is the use of task queues. This design also accommodates the reality that not all code will be thread safe and therefore allows one to easily mark modules or sub parts of modules as being thread unsafe. In addition, the design efficiently handles the requirement that events in one run must all be processed before starting to process events from a different run. After explaining the design we will provide measurements from simulating different processing scenarios where the processing times used for the simulation are drawn from processing times measured from actual CMS event processing.
Communication: Direct evidence for sequential dissociation of gas-phase Fe(CO)5 via a singlet pathway upon excitation at 266 nm

PubMed Central

Leitner, T.; Mazza, T.; Schröder, H.; Kunnus, K.; Schreck, S.; Radcliffe, P.; Düsterer, S.; Meyer, M.; Föhlisch, A.

2017-01-01

We prove the hitherto hypothesized sequential dissociation of Fe(CO)5 in the gas phase upon photoexcitation at 266 nm via a singlet pathway with time-resolved valence and core-level photoelectron spectroscopy with an x-ray free-electron laser. Valence photoelectron spectra are used to identify free CO molecules and to determine the time constants of stepwise dissociation to Fe(CO)4 within the temporal resolution of the experiment and further to Fe(CO)3 within 3 ps. Fe 3p core-level photoelectron spectra directly reflect the singlet spin state of the Fe center in Fe(CO)5, Fe(CO)4, and Fe(CO)3 showing that the dissociation exclusively occurs along a singlet pathway without triplet-state contribution. Our results are important for assessing intra- and intermolecular relaxation processes in the photodissociation dynamics of the prototypical Fe(CO)5 complex in the gas phase and in solution, and they establish time-resolved core-level photoelectron spectroscopy as a powerful tool for determining the multiplicity of transition metals in photochemical reactions of coordination complexes. PMID:28595420
Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.

PubMed

Cory, Seth A; Van Vranken, Jonathan G; Brignole, Edward J; Patra, Shachin; Winge, Dennis R; Drennan, Catherine L; Rutter, Jared; Barondeau, David P

2017-07-03

In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) complex forms the core of the iron-sulfur (Fe-S) assembly complex and associates with assembly proteins ISCU2, frataxin (FXN), and ferredoxin to synthesize Fe-S clusters. Here we present crystallographic and electron microscopic structures of the SDA complex coupled to enzyme kinetic and cell-based studies to provide structure-function properties of a mitochondrial cysteine desulfurase. Unlike prokaryotic cysteine desulfurases, the SDA structure adopts an unexpected architecture in which a pair of ISD11 subunits form the dimeric core of the SDA complex, which clarifies the critical role of ISD11 in eukaryotic assemblies. The different quaternary structure results in an incompletely formed substrate channel and solvent-exposed pyridoxal 5'-phosphate cofactor and provides a rationale for the allosteric activator function of FXN in eukaryotic systems. The structure also reveals the 4'-phosphopantetheine-conjugated acyl-group of ACP occupies the hydrophobic core of ISD11, explaining the basis of ACP stabilization. The unexpected architecture for the SDA complex provides a framework for understanding interactions with acceptor proteins for sulfur-containing biosynthetic pathways, elucidating mechanistic details of eukaryotic Fe-S cluster biosynthesis, and clarifying how defects in Fe-S cluster assembly lead to diseases such as Friedreich's ataxia. Moreover, our results support a lock-and-key model in which LYR proteins associate with acyl-ACP as a mechanism for fatty acid biosynthesis to coordinate the expression, Fe-S cofactor maturation, and activity of the respiratory complexes.
Development of core ion temperature gradients and edge sheared flows in a helicon plasma device investigated by laser induced fluorescence measurements

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

Thakur, S. C.; Tynan, G. R.; Center for Energy Research, University of California at San Diego, San Diego, California 92093

2016-08-15

We report experimental observation of ion heating and subsequent development of a prominent ion temperature gradient in the core of a linear magnetized plasma device, and the controlled shear de-correlation experiment. Simultaneously, we also observe the development of strong sheared flows at the edge of the device. Both the ion temperature and the azimuthal velocity profiles are quite flat at low magnetic fields. As the magnetic field is increased, the core ion temperature increases, producing centrally peaked ion temperature profiles and therefore strong radial gradients in the ion temperature. Similarly, we observe the development of large azimuthal flows at themore » edge, with increasing magnetic field, leading to strong radially sheared plasma flows. The ion velocities and temperatures are derived from laser induced fluorescence measurements of Doppler resolved velocity distribution functions of argon ions. These features are consistent with the previous observations of simultaneously existing radially separated multiple plasma instabilities that exhibit complex plasma dynamics in a very simple plasma system. The ion temperature gradients in the core and the radially sheared azimuthal velocities at the edge point to mechanisms that can drive the multiple plasma instabilities, that were reported earlier.« less
Regulation of flower development in Arabidopsis by SCF complexes.

PubMed

Ni, Weimin; Xie, Daoxin; Hobbie, Lawrence; Feng, Baomin; Zhao, Dazhong; Akkara, Joseph; Ma, Hong

2004-04-01

SCF complexes are the largest and best studied family of E3 ubiquitin protein ligases that facilitate the ubiquitylation of proteins targeted for degradation. The SCF core components Skp1, Cul1, and Rbx1 serve in multiple SCF complexes involving different substrate-specific F-box proteins that are involved in diverse processes including cell cycle and development. In Arabidopsis, mutations in the F-box gene UNUSUAL FLORAL ORGANS (UFO) result in a number of defects in flower development. However, functions of the core components Cul1 and Rbx1 in flower development are poorly understood. In this study we analyzed floral phenotypes caused by altering function of Cul1 or Rbx1, as well as the effects of mutations in ASK1 and ASK2. Plants homozygous for a point mutation in the AtCUL1 gene showed reduced floral organ number and several defects in each of the four whorls. Similarly, plants with reduced AtRbx1 expression due to RNA interference also exhibited floral morphological defects. In addition, compared to the ask1 mutant, plants homozygous for ask1 and heterozygous for ask2 displayed enhanced reduction of B function, as well as other novel defects of flower development, including carpelloid sepals and an inhibition of petal development. Genetic analyses demonstrate that AGAMOUS (AG) is required for the novel phenotypes observed in the first and second whorls. Furthermore, the genetic interaction between UFO and AtCUL1 supports the idea that UFO regulates multiple aspects of flower development as a part of SCF complexes. These results suggest that SCF complexes regulate several aspects of floral development in Arabidopsis.

Complex Pathologic Roles of RIPK1 and RIPK3: Moving Beyond Necroptosis

PubMed Central

Wegner, Kelby W.; Saleh, Danish; Degterev, Alexei

2017-01-01

A process of regulated necrosis, termed necroptosis, has been recognized as a major contributor to cell death and inflammation occurring under a wide range of pathologic settings. The core event in necroptosis is the formation of the detergent-insoluble “necrosome” complex of homologous Ser/Thr kinases Receptor Interacting Kinase 1 (RIPK1) and Receptor Interacting Kinase 3 (RIPK3), which promotes phosphorylation of a key pro-death effector Mixed Lineage Kinase Domain-like (MLKL) by RIPK3. Core necroptosis mediators are under multiple controls, which have been a subject of intense investigation. Additional, non-necroptotic functions of these factors, primarily in controlling apoptosis and inflammatory responses, have also begun to emerge. This review will provide an overview of the current understanding of the human disease relevance of this pathway, and potential therapeutic strategies, targeting necroptosis mediators in various pathologies. PMID:28126382
Effects of complex internal structures on rheology of multiple emulsions particles in 2D from a boundary integral method.

PubMed

Wang, Jingtao; Liu, Jinxia; Han, Junjie; Guan, Jing

2013-02-08

A boundary integral method is developed to investigate the effects of inner droplets and asymmetry of internal structures on rheology of two-dimensional multiple emulsion particles with arbitrary numbers of layers and droplets within each layer. Under a modest extensional flow, the number increment of layers and inner droplets, and the collision among inner droplets subject the particle to stronger shears. In addition, the coalescence or release of inner droplets changes the internal structure of the multiple emulsion particles. Since the rheology of such particles is sensitive to internal structures and their change, modeling them as the core-shell particles to obtain the viscosity equation of a single particle should be modified by introducing the time-dependable volume fraction Φ(t) of the core instead of the fixed Φ. An asymmetric internal structure induces an oriented contact and merging of the outer and inner interface. The start time of the interface merging is controlled by adjusting the viscosity ratio and enhancing the asymmetry, which is promising in the controlled release of inner droplets through hydrodynamics for targeted drug delivery.
Effect of bisecting GlcNAc and core fucosylation on conformational properties of biantennary complex-type N-glycans in solution.

PubMed

Nishima, Wataru; Miyashita, Naoyuki; Yamaguchi, Yoshiki; Sugita, Yuji; Re, Suyong

2012-07-26

The introduction of bisecting GlcNAc and core fucosylation in N-glycans is essential for fine functional regulation of glycoproteins. In this paper, the effect of these modifications on the conformational properties of N-glycans is examined at the atomic level by performing replica-exchange molecular dynamics (REMD) simulations. We simulate four biantennary complex-type N-glycans, namely, unmodified, two single-substituted with either bisecting GlcNAc or core fucose, and disubstituted forms. By using REMD as an enhanced sampling technique, five distinct conformers in solution, each of which is characterized by its local orientation of the Manα1-6Man glycosidic linkage, are observed for all four N-glycans. The chemical modifications significantly change their conformational equilibria. The number of major conformers is reduced from five to two and from five to four upon the introduction of bisecting GlcNAc and core fucosylation, respectively. The population change is attributed to specific inter-residue hydrogen bonds, including water-mediated ones. The experimental NMR data, including nuclear Overhauser enhancement and scalar J-coupling constants, are well reproduced taking the multiple conformers into account. Our structural model supports the concept of "conformer selection", which emphasizes the conformational flexibility of N-glycans in protein-glycan interactions.
Rubus: A compiler for seamless and extensible parallelism.

PubMed

Adnan, Muhammad; Aslam, Faisal; Nawaz, Zubair; Sarwar, Syed Mansoor

2017-01-01

Nowadays, a typical processor may have multiple processing cores on a single chip. Furthermore, a special purpose processing unit called Graphic Processing Unit (GPU), originally designed for 2D/3D games, is now available for general purpose use in computers and mobile devices. However, the traditional programming languages which were designed to work with machines having single core CPUs, cannot utilize the parallelism available on multi-core processors efficiently. Therefore, to exploit the extraordinary processing power of multi-core processors, researchers are working on new tools and techniques to facilitate parallel programming. To this end, languages like CUDA and OpenCL have been introduced, which can be used to write code with parallelism. The main shortcoming of these languages is that programmer needs to specify all the complex details manually in order to parallelize the code across multiple cores. Therefore, the code written in these languages is difficult to understand, debug and maintain. Furthermore, to parallelize legacy code can require rewriting a significant portion of code in CUDA or OpenCL, which can consume significant time and resources. Thus, the amount of parallelism achieved is proportional to the skills of the programmer and the time spent in code optimizations. This paper proposes a new open source compiler, Rubus, to achieve seamless parallelism. The Rubus compiler relieves the programmer from manually specifying the low-level details. It analyses and transforms a sequential program into a parallel program automatically, without any user intervention. This achieves massive speedup and better utilization of the underlying hardware without a programmer's expertise in parallel programming. For five different benchmarks, on average a speedup of 34.54 times has been achieved by Rubus as compared to Java on a basic GPU having only 96 cores. Whereas, for a matrix multiplication benchmark the average execution speedup of 84 times has been achieved by Rubus on the same GPU. Moreover, Rubus achieves this performance without drastically increasing the memory footprint of a program.
Rubus: A compiler for seamless and extensible parallelism

PubMed Central

Adnan, Muhammad; Aslam, Faisal; Sarwar, Syed Mansoor

2017-01-01

Nowadays, a typical processor may have multiple processing cores on a single chip. Furthermore, a special purpose processing unit called Graphic Processing Unit (GPU), originally designed for 2D/3D games, is now available for general purpose use in computers and mobile devices. However, the traditional programming languages which were designed to work with machines having single core CPUs, cannot utilize the parallelism available on multi-core processors efficiently. Therefore, to exploit the extraordinary processing power of multi-core processors, researchers are working on new tools and techniques to facilitate parallel programming. To this end, languages like CUDA and OpenCL have been introduced, which can be used to write code with parallelism. The main shortcoming of these languages is that programmer needs to specify all the complex details manually in order to parallelize the code across multiple cores. Therefore, the code written in these languages is difficult to understand, debug and maintain. Furthermore, to parallelize legacy code can require rewriting a significant portion of code in CUDA or OpenCL, which can consume significant time and resources. Thus, the amount of parallelism achieved is proportional to the skills of the programmer and the time spent in code optimizations. This paper proposes a new open source compiler, Rubus, to achieve seamless parallelism. The Rubus compiler relieves the programmer from manually specifying the low-level details. It analyses and transforms a sequential program into a parallel program automatically, without any user intervention. This achieves massive speedup and better utilization of the underlying hardware without a programmer’s expertise in parallel programming. For five different benchmarks, on average a speedup of 34.54 times has been achieved by Rubus as compared to Java on a basic GPU having only 96 cores. Whereas, for a matrix multiplication benchmark the average execution speedup of 84 times has been achieved by Rubus on the same GPU. Moreover, Rubus achieves this performance without drastically increasing the memory footprint of a program. PMID:29211758
Unprecedented linking of two polyoxometalate units with a metal-metal multiple bond.

PubMed

Sokolov, Maxim N; Korenev, Vladimir S; Izarova, Natalya V; Peresypkina, Eugenia V; Vicent, Cristian; Fedin, Vladimir P

2009-03-02

The reaction of (Bu(4)N)(2)[Re(2)Cl(8)] with lacunary Keggin polyoxometalate K(7)[PW(11)O(39)] in water produces a new dumbbell-shaped heteropolyoxometalate anion, [Re(2)(PW(11)O(39))(2)](8-), whose structure contains a central Re(2) core with a quadruple bond between Re atoms (Re-Re 2.25 A), coordinated to two polyoxometalate units. This complex represents the first example of the direct linking of two polyoxometalate units via a metal-metal multiple bond. The compounds were characterized by X-ray analysis, IR, and electrospray ionization mass spectrometry.
Photoenergy Harvesting Organic PV Cells Using Modified Photosynthetic Light-Harvesting Complex for Energy Harvesting Materials

DTIC Science & Technology

2008-07-03

complex is still unclear even in the crystal structure of RC-LH1 core complex from Rhodopseudomonas (Rps.) palustris [1]. In this study, we use a...complex of R. palustris . 16 The NIR absorption spectra of these core complexes on the electrode indicate that these complexes are stable when...as the LH or the core complex. For example, the core complex, isolated from the photosynthetic bacterium, Rps. palustris , was successfully
Emergence Processes up to Consciousness Using the Multiplicity Principle and Quantum Physics

NASA Astrophysics Data System (ADS)

Ehresmann, Andrée C.; Vanbremeersch, Jean-Paul

2002-09-01

Evolution is marked by the emergence of new objects and interactions. Pursuing our preceding work on Memory Evolutive Systems (MES; cf. our Internet site), we propose a general mathematical model for this process, based on Category Theory. Its main characteristics is the Multiplicity Principle (MP) which asserts the existence of complex objects with several possible configurations. The MP entails the emergence of non-reducible more and more complex objects (emergentist reductionism). From the laws of Quantum Physics, it follows that the MP is valid for the category of particles and atoms, hence, by complexification, for any natural autonomous anticipatory complex system, such as biological systems up to neural systems, or social systems. Applying the model to the MES of neurons, we describe the emergence of higher and higher cognitive processes and of a semantic memory. Consciousness is characterized by the development of a permanent `personal' memory, the archetypal core, which allows the formation of extended landscapes with an integration of the temporal dimensions.
Redefining self: patients' decision making about treatment for multiple sclerosis.

PubMed

Lowden, Diane; Lee, Virginia; Ritchie, Judith A

2014-08-01

The treatment of multiple sclerosis (MS) has become possible with the advent of disease-modifying therapies, but little is known about patients' experiences when faced with a complex array of treatment options. The purpose of this phenomenological study was to explore the lived experience of making a first decision about treatment with disease-modifying therapies for relapsing-remitting MS. Nine participants shared their perspectives on negotiating the decision to accept, refuse, or delay treatment. All individuals described a core theme in which decision making about treatment was part of a process of coming to a "redefined self." This core theme included reflections about self-image, quality of life, goals, and being a person with MS. Six common themes supporting this core theme were (a) weighing and deciding what's important, (b) acknowledging the illness as part of oneself, (c) playing the mental game, (d) seeking credible resources, (e) evaluating symptoms and fit with quality of life, and (f) managing the roles and involvement of family. The findings of this study provide a greater understanding about the experience of making a therapeutic choice for those with MS and offer insights for nurses when supporting patients faced with options about treatment.
Clinical efficacy of anti-glycopeptidolipid-core IgA test for diagnosing Mycobacterium avium complex infection in lung.

PubMed

Numata, Takanori; Araya, Jun; Yoshii, Yutaka; Shimizu, Kenichiro; Hara, Hiromichi; Nakayama, Katsutoshi; Kuwano, Kazuyoshi

2015-11-01

It is difficult to verify the bacteriological diagnosis of Mycobacterium avium complex (MAC) infection. The anti-glycopeptidolipid (GPL)-core IgA antibody test was recently developed as a diagnostic method for MAC pulmonary disease. Only a few studies evaluate its clinical efficacy. We conducted retrospective evaluations of clinical characteristics of patients suspected of MAC infection to explore the usefulness of the anti-GPL-core IgA antibody test. We retrospectively evaluated 296 patients who were suspected to have MAC infection and underwent anti-GPL-core IgA antibody test between March 2013 and July 2014 in Jikei University hospital. A total of 29 patients were diagnosed with 'definite MAC' based on the American Thoracic Society (ATS) criteria with multiple identifications of MAC. On the other hand, 106 patients were diagnosed with other pulmonary diseases than MAC. The sensitivity and specificity of anti-GPL-core IgA antibody test for MAC diagnosis were 58.6% and 98.1%, respectively. The definite MAC group showed no significant differences in strains, treatment history or number of segments involved. The duration of MAC disease in the positive-antibody group was significantly longer than in the negative-antibody group (P = 0.046). A significant increase in the false-negative rate was observed in patients with malignant disease (P = 0.029). The anti-GPL-core IgA antibody test demonstrated high sensitivity and specificity for the diagnosis of MAC infection especially in patients without malignant diseases. © 2015 Asian Pacific Society of Respirology.
SMA OBSERVATIONS OF THE W3(OH) COMPLEX: PHYSICAL AND CHEMICAL DIFFERENTIATION BETWEEN W3(H{sub 2}O) AND W3(OH)

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

Qin, Sheng-Li; Schilke, Peter; Sánchez-Monge, Álvaro

2015-04-10

We report on the Submillimeter Array (SMA) observations of molecular lines at 270 GHz toward the W3(OH) and W3(H{sub 2}O) complex. Although previous observations already resolved the W3(H{sub 2}O) into two or three sub-components, the physical and chemical properties of the two sources are not well constrained. Our SMA observations clearly resolved the W3(OH) and W3(H{sub 2}O) continuum cores. Taking advantage of the line fitting tool XCLASS, we identified and modeled a rich molecular spectrum in this complex, including multiple CH{sub 3}CN and CH{sub 3}OH transitions in both cores. HDO, C{sub 2}H{sub 5}CN, O{sup 13}CS, and vibrationally excited lines ofmore » HCN, CH{sub 3}CN, and CH{sub 3}OCHO were only detected in W3(H{sub 2}O). We calculate gas temperatures and column densities for both cores. The results show that W3(H{sub 2}O) has higher gas temperatures and larger column densities than W3(OH) as previously observed, suggesting physical and chemical differences between the two cores. We compare the molecular abundances in W3(H{sub 2}O) to those in the Sgr B2(N) hot core, the Orion KL hot core, and the Orion Compact Ridge, and discuss the chemical origin of specific species. An east–west velocity gradient is seen in W3(H{sub 2}O), and the extension is consistent with the bipolar outflow orientation traced by water masers and radio jets. A north–south velocity gradient across W3(OH) is also observed. However, with current observations we cannot be assured whether the velocity gradients are caused by rotation, outflow, or radial velocity differences of the sub-components of W3(OH)« less
RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations

PubMed Central

2012-01-01

Visualization and analysis of molecular networks are both central to systems biology. However, there still exists a large technological gap between them, especially when assessing multiple network levels or hierarchies. Here we present RedeR, an R/Bioconductor package combined with a Java core engine for representing modular networks. The functionality of RedeR is demonstrated in two different scenarios: hierarchical and modular organization in gene co-expression networks and nested structures in time-course gene expression subnetworks. Our results demonstrate RedeR as a new framework to deal with the multiple network levels that are inherent to complex biological systems. RedeR is available from http://bioconductor.org/packages/release/bioc/html/RedeR.html. PMID:22531049
Mediator complex dependent regulation of cardiac development and disease.

PubMed

Grueter, Chad E

2013-06-01

Cardiovascular disease (CVD) is a leading cause of morbidity and mortality. The risk factors for CVD include environmental and genetic components. Human mutations in genes involved in most aspects of cardiovascular function have been identified, many of which are involved in transcriptional regulation. The Mediator complex serves as a pivotal transcriptional regulator that functions to integrate diverse cellular signals by multiple mechanisms including recruiting RNA polymerase II, chromatin modifying proteins and non-coding RNAs to promoters in a context dependent manner. This review discusses components of the Mediator complex and the contribution of the Mediator complex to normal and pathological cardiac development and function. Enhanced understanding of the role of this core transcriptional regulatory complex in the heart will help us gain further insights into CVD. Copyright © 2013. Production and hosting by Elsevier Ltd.
The Detection of Hot Cores and Complex Organic Molecules in the Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

Sewilo, Marta; Indebetouw, Remy; Charnley, Steven; Zahorecz, Sarolta; Oliveira, Joana M.; van Loon, Jacco Th.; Ward, Jacob L.; Chen, C.-H. Rosie; Wiseman, Jennifer; Fukui, Yasuo; Kawamura, Akiko; Meixner, Margaret; Onishi, Toshikazu; Schilke, Peter

2018-01-01

We report the detection of the complex organic molecules (COMs) dimethyl ether (CH3OCH3) and methyl formate (CH3OCHO), and their parent species methanol (CH3OH), toward the N113 star-formation region in the Large Magellanic Cloud (LMC) with the Atacama Large Millimeter/submillimeter Array (ALMA). This constitutes the first detection of CH3OCH3 and CH3OCHO outside the Milky Way. We calculated the rotational temperatures (Trot ~ 130 K) and total column densities (Nrot ~ 1016 cm-2) for two sources in N113 with the COMs detection based on multiple transitions of CH3OH, and measured abundances for all detected species. The physical and chemical properties of these sources, and the association with H2O and OH maser emission indicate that they are hot molecular cores. The fractional abundances of COMs scaled by a factor of 2.5 to account for the lower metallicity in the LMC are comparable to those found at the lower end of the range in Galactic hot cores. Our results have important implications for studies of organic chemistry at higher redshift.
The Detection of Hot Cores and Complex Organic Molecules in the Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

Sewiło, Marta; Indebetouw, Remy; Charnley, Steven B.; Zahorecz, Sarolta; Oliveira, Joana M.; van Loon, Jacco Th.; Ward, Jacob L.; Chen, C.-H. Rosie; Wiseman, Jennifer; Fukui, Yasuo; Kawamura, Akiko; Meixner, Margaret; Onishi, Toshikazu; Schilke, Peter

2018-02-01

We report the first extragalactic detection of the complex organic molecules (COMs) dimethyl ether (CH3OCH3) and methyl formate (CH3OCHO) with the Atacama Large Millimeter/submillimeter Array (ALMA). These COMs, together with their parent species methanol (CH3OH), were detected toward two 1.3 mm continuum sources in the N 113 star-forming region in the low-metallicity Large Magellanic Cloud (LMC). Rotational temperatures ({T}{rot}∼ 130 K) and total column densities ({N}{rot}∼ {10}16 cm‑2) have been calculated for each source based on multiple transitions of CH3OH. We present the ALMA molecular emission maps for COMs and measured abundances for all detected species. The physical and chemical properties of two sources with COMs detection, and the association with H2O and OH maser emission, indicate that they are hot cores. The fractional abundances of COMs scaled by a factor of 2.5 to account for the lower metallicity in the LMC are comparable to those found at the lower end of the range in Galactic hot cores. Our results have important implications for studies of organic chemistry at higher redshift.
Development and Applications of Orthogonality Constrained Density Functional Theory for the Accurate Simulation of X-Ray Absorption Spectroscopy

NASA Astrophysics Data System (ADS)

Derricotte, Wallace D.

The aim of this dissertation is to address the theoretical challenges of calculating core-excited states within the framework of orthogonality constrained density functional theory (OCDFT). OCDFT is a well-established variational, time independent formulation of DFT for the computation of electronic excited states. In this work, the theory is first extended to compute core-excited states and generalized to calculate multiple excited state solutions. An initial benchmark is performed on a set of 40 unique core-excitations, highlighting that OCDFT excitation energies have a mean absolute error of 1.0 eV. Next, a novel implementation of the spin-free exact-two-component (X2C) one-electron treatment of scalar relativistic effects is presented and combined with OCDFT in an effort to calculate core excited states of transition metal complexes. The X2C-OCDFT spectra of three organotitanium complexes (TiCl4, TiCpCl3, and TiCp2Cl2) are shown to be in good agreement with experimental results and show a maximum absolute error of 5-6 eV. Next the issue of assigning core excited states is addressed by introducing an automated approach to analyzing the excited state MO by quantifying its local contributions using a unique orbital basis known as localized intrinsic valence virtual orbitals (LIVVOs). The utility of this approach is highlighted by studying sulfur core-excitations in ethanethiol and benzenethiol, as well as the hydrogen bonding in the water dimer. Finally, an approach to selectively target specic core-excited states in OCDFT based on atomic orbital subspace projection is presented in an effort to target core excited states of chemisorbed organic molecules. The core excitation spectrum of pyrazine chemisorbed on Si(100) is calculated using OCDFT and further characterized using the LIVVO approach.
Matching multiple rigid domain decompositions of proteins

PubMed Central

Flynn, Emily; Streinu, Ileana

2017-01-01

We describe efficient methods for consistently coloring and visualizing collections of rigid cluster decompositions obtained from variations of a protein structure, and lay the foundation for more complex setups that may involve different computational and experimental methods. The focus here is on three biological applications: the conceptually simpler problems of visualizing results of dilution and mutation analyses, and the more complex task of matching decompositions of multiple NMR models of the same protein. Implemented into the KINARI web server application, the improved visualization techniques give useful information about protein folding cores, help examining the effect of mutations on protein flexibility and function, and provide insights into the structural motions of PDB proteins solved with solution NMR. These tools have been developed with the goal of improving and validating rigidity analysis as a credible coarse-grained model capturing essential information about a protein’s slow motions near the native state. PMID:28141528
Parallel transformation of K-SVD solar image denoising algorithm

NASA Astrophysics Data System (ADS)

Liang, Youwen; Tian, Yu; Li, Mei

2017-02-01

The images obtained by observing the sun through a large telescope always suffered with noise due to the low SNR. K-SVD denoising algorithm can effectively remove Gauss white noise. Training dictionaries for sparse representations is a time consuming task, due to the large size of the data involved and to the complexity of the training algorithms. In this paper, an OpenMP parallel programming language is proposed to transform the serial algorithm to the parallel version. Data parallelism model is used to transform the algorithm. Not one atom but multiple atoms updated simultaneously is the biggest change. The denoising effect and acceleration performance are tested after completion of the parallel algorithm. Speedup of the program is 13.563 in condition of using 16 cores. This parallel version can fully utilize the multi-core CPU hardware resources, greatly reduce running time and easily to transplant in multi-core platform.
PCTO-SIM: Multiple-point geostatistical modeling using parallel conditional texture optimization

NASA Astrophysics Data System (ADS)

Pourfard, Mohammadreza; Abdollahifard, Mohammad J.; Faez, Karim; Motamedi, Sayed Ahmad; Hosseinian, Tahmineh

2017-05-01

Multiple-point Geostatistics is a well-known general statistical framework by which complex geological phenomena have been modeled efﬁciently. Pixel-based and patch-based are two major categories of these methods. In this paper, the optimization-based category is used which has a dual concept in texture synthesis as texture optimization. Our extended version of texture optimization uses the energy concept to model geological phenomena. While honoring the hard point, the minimization of our proposed cost function forces simulation grid pixels to be as similar as possible to training images. Our algorithm has a self-enrichment capability and creates a richer training database from a sparser one through mixing the information of all surrounding patches of the simulation nodes. Therefore, it preserves pattern continuity in both continuous and categorical variables very well. It also shows a fuzzy result in its every realization similar to the expected result of multi realizations of other statistical models. While the main core of most previous Multiple-point Geostatistics methods is sequential, the parallel main core of our algorithm enabled it to use GPU efficiently to reduce the CPU time. One new validation method for MPS has also been proposed in this paper.
Refractory Depression, Fatigue, Irritable Bowel Syndrome, and Chronic Pain: A Functional Medicine Case Report.

PubMed

Plotnikoff, Gregory; Barber, Melissa

2016-01-01

Single-disorder or single-organ-system clinical practice guidelines are often of limited usefulness in guiding effective management of patients with chronic multidimensional signs and symptoms. The presence of multiple long-standing medical problems in a given patient despite intensive medical effort suggests that addressing systemic core imbalances could complement more narrowly focused approaches. A 72-year-old man experiencing longstanding depression, fatigue, irritable bowel syndrome, and chronic pain in the context of additional refractory illnesses was assessed and treated, guided by a system-oriented approach to underlying core imbalances termed functional medicine. This patient was referred from a team of clinicians representing primary care, cardiology, gastroenterology, hematology, and psychology. Prior treatment had been unsuccessful in managing multiple chronic comorbidities. Diagnostic assessment included comprehensive stool and nutritional/metabolic laboratory testing. The blood-, urine-, or stool-based measurements of relevant markers for multiple systemic issues, including digestion/absorption, inflammation, oxidative stress, and methylation, identified previously unrecognized root causes of his constellation of symptoms. These functional measurements guided rational recommendations for dietary choices and supplementation. The patient experienced steady and significant improvement in his mental health, fatigue, chronic pain, and irritable bowel syndrome-as well as the unexpected resolution of his chronic idiopathic pancytopenia. The success in this case suggests that other patients with chronic, complex, and treatment-refractory illness may benefit from a system-oriented assessment of core imbalances guided by specialized nutritional/metabolic and digestive laboratory testing.

Computational Models and Emergent Properties of Respiratory Neural Networks

PubMed Central

Lindsey, Bruce G.; Rybak, Ilya A.; Smith, Jeffrey C.

2012-01-01

Computational models of the neural control system for breathing in mammals provide a theoretical and computational framework bringing together experimental data obtained from different animal preparations under various experimental conditions. Many of these models were developed in parallel and iteratively with experimental studies and provided predictions guiding new experiments. This data-driven modeling approach has advanced our understanding of respiratory network architecture and neural mechanisms underlying generation of the respiratory rhythm and pattern, including their functional reorganization under different physiological conditions. Models reviewed here vary in neurobiological details and computational complexity and span multiple spatiotemporal scales of respiratory control mechanisms. Recent models describe interacting populations of respiratory neurons spatially distributed within the Bötzinger and pre-Bötzinger complexes and rostral ventrolateral medulla that contain core circuits of the respiratory central pattern generator (CPG). Network interactions within these circuits along with intrinsic rhythmogenic properties of neurons form a hierarchy of multiple rhythm generation mechanisms. The functional expression of these mechanisms is controlled by input drives from other brainstem components, including the retrotrapezoid nucleus and pons, which regulate the dynamic behavior of the core circuitry. The emerging view is that the brainstem respiratory network has rhythmogenic capabilities at multiple levels of circuit organization. This allows flexible, state-dependent expression of different neural pattern-generation mechanisms under various physiological conditions, enabling a wide repertoire of respiratory behaviors. Some models consider control of the respiratory CPG by pulmonary feedback and network reconfiguration during defensive behaviors such as cough. Future directions in modeling of the respiratory CPG are considered. PMID:23687564
Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas.

PubMed

Łukasik, Piotr; Nazario, Katherine; Van Leuven, James T; Campbell, Matthew A; Meyer, Mariah; Michalik, Anna; Pessacq, Pablo; Simon, Chris; Veloso, Claudio; McCutcheon, John P

2018-01-09

Bacterial endosymbionts that provide nutrients to hosts often have genomes that are extremely stable in structure and gene content. In contrast, the genome of the endosymbiont Hodgkinia cicadicola has fractured into multiple distinct lineages in some species of the cicada genus Tettigades To better understand the frequency, timing, and outcomes of Hodgkinia lineage splitting throughout this cicada genus, we sampled cicadas over three field seasons in Chile and performed genomics and microscopy on representative samples. We found that a single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over the last 4 million years, resulting in complexes of between two and six distinct Hodgkinia lineages per host. Individual genomes in these symbiotic complexes differ dramatically in relative abundance, genome size, organization, and gene content. Each Hodgkinia lineage retains a small set of core genes involved in genetic information processing, but the high level of gene loss experienced by all genomes suggests that extensive sharing of gene products among symbiont cells must occur. In total, Hodgkinia complexes that consist of multiple lineages encode nearly complete sets of genes present on the ancestral single lineage and presumably perform the same functions as symbionts that have not undergone splitting. However, differences in the timing of the splits, along with dissimilar gene loss patterns on the resulting genomes, have led to very different outcomes of lineage splitting in extant cicadas.
The expanding syndrome of amyotrophic lateral sclerosis: a clinical and molecular odyssey

PubMed Central

Turner, Martin R; Swash, Michael

2015-01-01

Recent advances in understanding amyotrophic lateral sclerosis (ALS) have delivered new questions. Disappointingly, the initial enthusiasm for transgenic mouse models of the disease has not been followed by rapid advances in therapy or prevention. Monogenic models may have inadvertently masked the true complexity of the human disease. ALS has evolved into a multisystem disorder, involving a final common pathway accessible via multiple upstream aetiological tributaries. Nonetheless, there is a common clinical core to ALS, as clear today as it was to Charcot and others. We stress the continuing relevance of clinical observations amid the increasing molecular complexity of ALS. PMID:25644224
CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity

PubMed Central

Garrett, Roger A.; Shah, Shiraz A.; Erdmann, Susanne; Liu, Guannan; Mousaei, Marzieh; León-Sobrino, Carlos; Peng, Wenfang; Gudbergsdottir, Soley; Deng, Ling; Vestergaard, Gisle; Peng, Xu; She, Qunxin

2015-01-01

The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed. PMID:25764276
Individual and family environment correlates differ for consumption of core and non-core foods in children.

PubMed

Johnson, Laura; van Jaarsveld, Cornelia H M; Wardle, Jane

2011-03-01

Children's diets contain too few fruits and vegetables and too many foods high in saturated fat. Food intake is affected by multiple individual and family factors, which may differ for core foods (that are important to a healthy diet) and non-core foods (that are eaten more for pleasure than health). Data came from a sample of twins aged 11 years (n 342) and their parents from the Twins Early Development Study. Foods were categorised into two types: core (e.g. cereals, vegetables and dairy) and non-core (e.g. fats, crisps and biscuits). Parents' and children's intake was assessed by an FFQ. Mothers' and children's preference ratings and home availability were assessed for each food type. Parental feeding practices were assessed with the child feeding questionnaire and child television (TV) watching was maternally reported. Physical activity was measured using accelerometers. Correlates of the child's consumption of each food type were examined using a complex samples general linear model adjusted for potential confounders. Children's non-core food intake was associated with more TV watching, higher availability and greater maternal intake of non-core foods. Children's core food intake was associated with higher preferences for core foods and greater maternal intake of core foods. These results suggest that maternal intake influences both food types, while preferences affect intake of core foods but not of non-core foods, and availability and TV exposure were only important for non-core food intake. Cross-sectional studies cannot determine causality, but the present results suggest that different approaches may be needed to change the balance of core and non-core foods in children's diets.
A tethering complex drives the terminal stage of SNARE-dependent membrane fusion

NASA Astrophysics Data System (ADS)

D'Agostino, Massimo; Risselada, Herre Jelger; Lürick, Anna; Ungermann, Christian; Mayer, Andreas

2017-11-01

Membrane fusion in eukaryotic cells mediates the biogenesis of organelles, vesicular traffic between them, and exo- and endocytosis of important signalling molecules, such as hormones and neurotransmitters. Distinct tasks in intracellular membrane fusion have been assigned to conserved protein systems. Tethering proteins mediate the initial recognition and attachment of membranes, whereas SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein complexes are considered as the core fusion engine. SNARE complexes provide mechanical energy to distort membranes and drive them through a hemifusion intermediate towards the formation of a fusion pore. This last step is highly energy-demanding. Here we combine the in vivo and in vitro fusion of yeast vacuoles with molecular simulations to show that tethering proteins are critical for overcoming the final energy barrier to fusion pore formation. SNAREs alone drive vacuoles only into the hemifused state. Tethering proteins greatly increase the volume of SNARE complexes and deform the site of hemifusion, which lowers the energy barrier for pore opening and provides the driving force. Thereby, tethering proteins assume a crucial mechanical role in the terminal stage of membrane fusion that is likely to be conserved at multiple steps of vesicular traffic. We therefore propose that SNAREs and tethering proteins should be considered as a single, non-dissociable device that drives fusion. The core fusion machinery may then be larger and more complex than previously thought.
Dual-core mass-balance approach for evaluating mercury and210Pb atmospheric fallout and focusing to lakes

USGS Publications Warehouse

Van Metre, P.C.; Fuller, C.C.

2009-01-01

Determining atmospheric deposition rates of mercury and other contaminants using lake sediment cores requires a quantitative understanding of sediment focusing. Here we present a novel approach that solves mass-balance equations for two cores algebraically to estimate contaminant contributions to sediment from direct atmospheric fallout and from watershed and in-lake focusing. The model is applied to excess 210Pb and Hg in cores from Hobbs Lake, a high-altitude lake in Wyoming. Model results for excess 210Pb are consistent with estimates of fallout and focusing factors computed using excess 210Pb burdens in lake cores and soil cores from the watershed and model results for Hg fallout are consistent with fallout estimated using the soil-core-based 210Pb focusing factors. The lake cores indicate small increases in mercury deposition beginning in the late 1800s and large increases after 1940, with the maximum at the tops of the cores of 16-20 ??g/m 2year. These results suggest that global Hg emissions and possibly regional emissions in the western United States are affecting the north-central Rocky Mountains. Hg fallout estimates are generally consistent with fallout reported from an ice core from the nearby Upper Fremont Glacier, but with several notable differences. The model might not work for lakes with complex geometries and multiple sediment inputs, but for lakes with simple geometries, like Hobbs, it can provide a quantitative approach for evaluating sediment focusing and estimating contaminant fallout.
Hexanuclear gold(I) phosphide complexes as platforms for multiple redox-active ferrocenyl units.

PubMed

Lee, Terence Kwok-Ming; Cheng, Eddie Chung-Chin; Zhu, Nianyong; Yam, Vivian Wing-Wah

2014-01-03

The synthesis, X-ray crystal structures, electrochemical, and spectroscopic studies of a series of hexanuclear gold(I) μ(3)-ferrocenylmethylphosphido complexes stabilized by bridging phosphine ligands, [Au(6)(P-P)(n)(Fc-CH(2)-P)(2)][PF(6)](2) (n=3, P-P=dppm (bis(diphenylphosphino)methane) (1), dppe (1,2-bis(diphenylphosphino)ethane) (2), dppp (1,3-bis(diphenylphosphino)propane) (3), Ph(2)PN(C(3)H(7))-PPh(2) (4), Ph(2)PN(Ph-CH(3)-p)PPh(2) (5), dppf (1,1′-bis(diphenylphosphino)ferrocene) (6); n=2, P-P=dpepp (bis(2-diphenylphosphinoethyl)phenylphosphine) (7)), as platforms for multiple redox-active ferrocenyl units, are reported. The investigation of the structural changes of the clusters has been probed by introducing different bridging phosphine ligands. This class of gold(I) μ(3)-ferrocenylmethylphosphido complexes has been found to exhibit one reversible oxidation couple, suggestive of the absence of electronic communication between the ferrocene units through the Au(6)P(2) cluster core, providing an understanding of the electronic properties of the hexanuclear Au(I) cluster linkage. The present complexes also serve as an ideal system for the design of multi-electron reservoir and molecular battery systems.
Fundamental structures of dynamic social networks.

PubMed

Sekara, Vedran; Stopczynski, Arkadiusz; Lehmann, Sune

2016-09-06

Social systems are in a constant state of flux, with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding the spreading of influence or diseases, formation of friendships, and the productivity of teams. Although there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the microdynamics of social networks. Here, we explore the dynamic social network of a densely-connected population of ∼1,000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geolocation, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-min time slices, we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision.
Fundamental structures of dynamic social networks

PubMed Central

Sekara, Vedran; Stopczynski, Arkadiusz; Lehmann, Sune

2016-01-01

Social systems are in a constant state of flux, with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding the spreading of influence or diseases, formation of friendships, and the productivity of teams. Although there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the microdynamics of social networks. Here, we explore the dynamic social network of a densely-connected population of ∼1,000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geolocation, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-min time slices, we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision. PMID:27555584
Adaptation of Rhodopseudomonas acidophila strain 7050 to growth at different light intensities: what are the benefits to changing the type of LH2?

PubMed

Gardiner, A T; Niedzwiedzki, D M; Cogdell, R J

2018-04-01

Typical purple bacterial photosynthetic units consist of light harvesting one/reaction centre 'core' complexes surrounded by light harvesting two complexes. Factors such as the number and size of photosynthetic units per cell, as well as the type of light harvesting two complex that is produced, are controlled by environmental factors. In this paper, the change in the type of LH2 present in the Rhodopsuedomonas acidophila strain 7050 is described when cells are grown at a range of different light intensities. This species contains multiple pucBA genes that encode the apoproteins that form light-harvesting complex two, and a more complex mixture of spectroscopic forms of this complex has been found than was previously thought to be the case. Femto-second time resolved absorption has been used to investigate how the energy transfer properties in the membranes of high-light and low-light adapted cells change as the composition of the LH2 complexes varies.
In Vitro MRV-based Hemodynamic Study of Complex Helical Flow in a Patient-specific Jugular Model

NASA Astrophysics Data System (ADS)

Kefayati, Sarah; Acevedo-Bolton, Gabriel; Haraldsson, Henrik; Saloner, David

2014-11-01

Neurointerventional Radiologists are frequently requested to evaluate the venous side of the intracranial circulation for a variety of conditions including: Chronic Cerebrospinal Venous Insufficiency thought to play a role in the development of multiple sclerosis; sigmoid sinus diverticulum which has been linked to the presence of pulsatile tinnitus; and jugular vein distension which is related to cardiac dysfunction. Most approaches to evaluating these conditions rely on structural assessment or two dimensional flow analyses. This study was designed to investigate the highly complex jugular flow conditions using magnetic resonance velocimetry (MRV). A jugular phantom was fabricated based on the geometry of the dominant jugular in a tinnitus patient. Volumetric three-component time-resolved velocity fields were obtained using 4D PC-MRI -with the protocol enabling turbulence acquisition- and the patient-specific pulsatile waveform. Flow was highly complex exhibiting regions of jet, high swirling strength, and strong helical pattern with the core originating from the focal point of the jugular bulb. Specifically, flow was analyzed for helicity and the level of turbulence kinetic energy elevated in the core of helix and distally, in the post-narrowing region.
Turn Basin Construction

NASA Image and Video Library

2017-06-30

At NASA's Kennedy Space Center in Florida, cement is poured as part of a construction project to upgrade the turn basin wharf. The work includes driving multiple precast concrete piles to a depth of about 70 feet to accommodate arrival of the core stage for the agency's Space Launch System (SLS) rocket. When the stage for NASA's SLS departs the Michoud Assembly Facility in New Orleans, it will be shipped by the agency's modified barge to the Launch Complex 39 turn basin.
NEAMS-IPL MOOSE Midyear Framework Activities

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

Permann, Cody; Alger, Brian; Peterson, John

The MOOSE Framework is a modular pluggable framework for building complex simulations. The ability to add new objects with custom syntax is a core capability that makes MOOSE a powerful platform for coupling multiple applications together within a single environment. The creation of a new, more standardized JSON syntax output improves the external interfaces for generating graphical components or for validating input file syntax. The design of this interface and the requirements it satisfies are covered in this short report.
Fission yeast MOZART1/Mzt1 is an essential γ-tubulin complex component required for complex recruitment to the microtubule organizing center, but not its assembly

PubMed Central

Masuda, Hirohisa; Mori, Risa; Yukawa, Masashi; Toda, Takashi

2013-01-01

γ-Tubulin plays a universal role in microtubule nucleation from microtubule organizing centers (MTOCs) such as the animal centrosome and fungal spindle pole body (SPB). γ-Tubulin functions as a multiprotein complex called the γ-tubulin complex (γ-TuC), consisting of GCP1–6 (GCP1 is γ-tubulin). In fungi and flies, it has been shown that GCP1–3 are core components, as they are indispensable for γ-TuC complex assembly and cell division, whereas the other three GCPs are not. Recently a novel conserved component, MOZART1, was identified in humans and plants, but its precise functions remain to be determined. In this paper, we characterize the fission yeast homologue Mzt1, showing that it is essential for cell viability. Mzt1 is present in approximately equal stoichiometry with Alp4/GCP2 and localizes to all the MTOCs, including the SPB and interphase and equatorial MTOCs. Temperature-sensitive mzt1 mutants display varying degrees of compromised microtubule organization, exhibiting multiple defects during both interphase and mitosis. Mzt1 is required for γ-TuC recruitment, but not sufficient to localize to the SPB, which depends on γ-TuC integrity. Intriguingly, the core γ-TuC assembles in the absence of Mzt1. Mzt1 therefore plays a unique role within the γ-TuC components in attachment of this complex to the major MTOC site. PMID:23885124
Characterizing core-periphery structure of complex network by h-core and fingerprint curve

NASA Astrophysics Data System (ADS)

Li, Simon S.; Ye, Adam Y.; Qi, Eric P.; Stanley, H. Eugene; Ye, Fred Y.

2018-02-01

It is proposed that the core-periphery structure of complex networks can be simulated by h-cores and fingerprint curves. While the features of core structure are characterized by h-core, the features of periphery structure are visualized by rose or spiral curve as the fingerprint curve linking to entire-network parameters. It is suggested that a complex network can be approached by h-core and rose curves as the first-order Fourier-approach, where the core-periphery structure is characterized by five parameters: network h-index, network radius, degree power, network density and average clustering coefficient. The simulation looks Fourier-like analysis.
Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation

PubMed Central

Zhang, Yi; Ng, Huck-Hui; Erdjument-Bromage, Hediye; Tempst, Paul; Bird, Adrian; Reinberg, Danny

1999-01-01

ATP-dependent nucleosome remodeling and core histone acetylation and deacetylation represent mechanisms to alter nucleosome structure. NuRD is a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. The histone deacetylases HDAC1 and HDAC2 and the histone binding proteins RbAp48 and RbAp46 form a core complex shared between NuRD and Sin3-histone deacetylase complexes. The histone deacetylase activity of the core complex is severely compromised. A novel polypeptide highly related to the metastasis-associated protein 1, MTA2, and the methyl-CpG-binding domain-containing protein, MBD3, were found to be subunits of the NuRD complex. MTA2 modulates the enzymatic activity of the histone deacetylase core complex. MBD3 mediates the association of MTA2 with the core histone deacetylase complex. MBD3 does not directly bind methylated DNA but is highly related to MBD2, a polypeptide that binds to methylated DNA and has been reported to possess demethylase activity. MBD2 interacts with the NuRD complex and directs the complex to methylated DNA. NuRD may provide a means of gene silencing by DNA methylation. PMID:10444591
Assessment of multiple sources of anthropogenic and natural chemical inputs to a morphologically complex basin, Lake Mead, USA

USGS Publications Warehouse

Rosen, Michael R.; Van Metre, P.C.

2010-01-01

Lakes with complex morphologies and with different geologic and land-use characteristics in their sub-watersheds could have large differences in natural and anthropogenic chemical inputs to sub-basins in the lake. Lake Mead in southern Nevada and northern Arizona, USA, is one such lake. To assess variations in chemical histories from 1935 to 1998 for major sub-basins of Lake Mead, four sediment cores were taken from three different parts of the reservoir (two from Las Vegas Bay and one from the Overton Arm and Virgin Basin) and analyzed for major and trace elements, radionuclides, and organic compounds. As expected, anthropogenic contaminant inputs are greatest to Las Vegas Bay reflecting inputs from the Las Vegas urban area, although concentrations are low compared to sediment quality guidelines and to other USA lakes. One exception to this pattern was higher Hg in the Virgin Basin core. The Virgin Basin core is located in the main body of the lake (Colorado River channel) and is influenced by the hydrology of the Colorado River, which changed greatly with completion of Glen Canyon Dam upstream in 1963. Major and trace elements in the core show pronounced shifts in the early 1960s and, in many cases, gradually return to concentrations more typical of pre-1960s by the 1980s and 1990s, after the filling of Lake Powell. The Overton Arm is the sub-basin least effected by anthropogenic contaminant inputs but has a complex 137Cs profile with a series of large peaks and valleys over the middle of the core, possibly reflecting fallout from nuclear tests in the 1950s at the Nevada Test Site. The 137Cs profile suggests a much greater sedimentation rate during testing which we hypothesize results from greatly increased dust fall on the lake and Virgin and Muddy River watersheds. The severe drought in the southwestern USA during the 1950s might also have played a role in variations in sedimentation rate in all of the cores. ?? 2009.
Gold core/Ceria shell-based redox active nanozyme mimicking the biological multienzyme complex phenomenon

DOE PAGES

Bhagat, Stuti; Srikanth Vallabani, NV; Shutthanandan, Vaithiyalingam; ...

2017-12-02

Catalytically active individual gold (Au) and cerium oxide (CeO 2) nanoparticles (NPs) are well known to exhibit specific enzyme-like activities, such as natural catalase, oxidase, superoxide dismutase, and peroxidase enzymes. Our activities have been maneuvered to design several biological applications such as immunoassays, glucose detection, radiation and free radical protection and tissue engineering. In biological systems, multienzyme complexes are involved in catalyzing important reactions of essential metabolic processes such as respiration, biomolecule synthesis, and photosynthesis. It is well known that metabolic processes linked with multienzyme complexes offer several advantages over reactions catalyzed by individual enzymes. A functional nanozyme depicting multienzymemore » like properties has eluded the researchers in the nanoscience community for the past few decades. Here, we have designed a functional multienzyme in the form of Gold (core)-CeO 2 (shell) nanoparticles (Au/CeO 2 CSNPs) exhibiting excellent peroxidase, catalase, and superoxide dismutase enzyme-like activities that are controlled simply by tuning the pH. The reaction kinetic parameters reveal that the peroxidase-like activity of this core-shell nanozyme is comparable to natural horseradish peroxidase (HRP) enzyme. Unlike peroxidase-like activity exhibited by other nanomaterials, Au/CeO 2 CSNPs showed a decrease in hydroxyl radical formation, suggesting that the biocatalytic reactions are performed by efficient electron transfers. A significant enzyme-like activity of this core-shell nanoparticle was conserved at extreme pH (2 – 11) and temperatures (up to 90 °C), clearly suggesting the superiority over natural enzymes. Further, the utility of peroxidase-like activity of this core-shell nanoparticles was extended for the detection of glucose, which showed a linear range of detection between (100 µM – 1 mM). It is hypothesized that the proximity of the redox potentials of Au+/Au and Ce (III)/Ce (IV) may result in a redox couple promoting the multienzyme activity of core-shell nanoparticles. Au/CeO 2 CSNPs may open new directions for development of single platform sensors in multiple biosensing applications.« less
Gold core/Ceria shell-based redox active nanozyme mimicking the biological multienzyme complex phenomenon

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

Bhagat, Stuti; Srikanth Vallabani, NV; Shutthanandan, Vaithiyalingam

Catalytically active individual gold (Au) and cerium oxide (CeO 2) nanoparticles (NPs) are well known to exhibit specific enzyme-like activities, such as natural catalase, oxidase, superoxide dismutase, and peroxidase enzymes. Our activities have been maneuvered to design several biological applications such as immunoassays, glucose detection, radiation and free radical protection and tissue engineering. In biological systems, multienzyme complexes are involved in catalyzing important reactions of essential metabolic processes such as respiration, biomolecule synthesis, and photosynthesis. It is well known that metabolic processes linked with multienzyme complexes offer several advantages over reactions catalyzed by individual enzymes. A functional nanozyme depicting multienzymemore » like properties has eluded the researchers in the nanoscience community for the past few decades. Here, we have designed a functional multienzyme in the form of Gold (core)-CeO 2 (shell) nanoparticles (Au/CeO 2 CSNPs) exhibiting excellent peroxidase, catalase, and superoxide dismutase enzyme-like activities that are controlled simply by tuning the pH. The reaction kinetic parameters reveal that the peroxidase-like activity of this core-shell nanozyme is comparable to natural horseradish peroxidase (HRP) enzyme. Unlike peroxidase-like activity exhibited by other nanomaterials, Au/CeO 2 CSNPs showed a decrease in hydroxyl radical formation, suggesting that the biocatalytic reactions are performed by efficient electron transfers. A significant enzyme-like activity of this core-shell nanoparticle was conserved at extreme pH (2 – 11) and temperatures (up to 90 °C), clearly suggesting the superiority over natural enzymes. Further, the utility of peroxidase-like activity of this core-shell nanoparticles was extended for the detection of glucose, which showed a linear range of detection between (100 µM – 1 mM). It is hypothesized that the proximity of the redox potentials of Au+/Au and Ce (III)/Ce (IV) may result in a redox couple promoting the multienzyme activity of core-shell nanoparticles. Au/CeO 2 CSNPs may open new directions for development of single platform sensors in multiple biosensing applications.« less

Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

NASA Technical Reports Server (NTRS)

Ojha, R. P.; Dhingra, M. M.; Sarma, M. H.; Myer, Y. P.; Setlik, R. F.; Shibata, M.; Kazim, A. L.; Ornstein, R. L.; Rein, R.; Turner, C. J.;

1997-01-01

The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.

The Tom Core Complex

PubMed Central

Ahting, Uwe; Thun, Clemens; Hegerl, Reiner; Typke, Dieter; Nargang, Frank E.; Neupert, Walter; Nussberger, Stephan

1999-01-01

Translocation of nuclear-encoded preproteins across the outer membrane of mitochondria is mediated by the multicomponent transmembrane TOM complex. We have isolated the TOM core complex of Neurospora crassa by removing the receptors Tom70 and Tom20 from the isolated TOM holo complex by treatment with the detergent dodecyl maltoside. It consists of Tom40, Tom22, and the small Tom components, Tom6 and Tom7. This core complex was also purified directly from mitochondria after solubilization with dodecyl maltoside. The TOM core complex has the characteristics of the general insertion pore; it contains high-conductance channels and binds preprotein in a targeting sequence-dependent manner. It forms a double ring structure that, in contrast to the holo complex, lacks the third density seen in the latter particles. Three-dimensional reconstruction by electron tomography exhibits two open pores traversing the complex with a diameter of ∼2.1 nm and a height of ∼7 nm. Tom40 is the key structural element of the TOM core complex. PMID:10579717
Indirect fabrication of multiple post-and-core patterns with a vinyl polysiloxane matrix.

PubMed

Sabbak, Sahar Asaad

2002-11-01

In the described technique, a vinyl polysiloxane material is used as a matrix for the indirect fabrication of multiple custom-cast posts and cores. The matrix technique enables the clinician to fabricate multiple posts and cores in a short period of time. The form, harmony, and common axis of preparation for all cores are well controlled before the definitive crown/fixed partial denture restorations are fabricated. Oral tissues are not exposed to the heat of polymerization or the excess monomer of the resin material when this technique is used.
Enhancing oxidative stability in heated oils using core/shell structures of collagen and α-tocopherol complex.

PubMed

Gim, Seo Yeong; Hong, Seungmi; Kim, Jisu; Kwon, YongJun; Kim, Mi-Ja; Kim, GeunHyung; Lee, JaeHwan

2017-11-15

In this study, collagen mesh structure was prepared by carrying α-tocopherol in the form of core/shell complex. Antioxidant properties of α-tocopherol loaded carriers were tested in moisture added bulk oils at 140°C. From one gram of collagen core/shell complex, 138mg α-tocopherol was released in medium chain triacylglycerol (MCT). α-Tocopherol was substantially protected against heat treatment when α-tocopherol was complexed in collagen core/shell. Oxidative stability in bulk oil was significantly enhanced by added collagen mesh structure or collagen core/shell complex with α-tocopherol compared to that in control bulk oils (p<0.05), although no significant difference was observed between oils containing collagen mesh structure and collagen core/shell with α-tocopherol (p>0.05). Results of DPPH loss in methanol demonstrated that collagen core/shell with α-tocopherol had significantly (p<0.05) higher antioxidant properties than collagen mesh structure up to a certain period. Therefore, collagen core/shell complex is a promising way to enhance the stability of α-tocopherol and oxidative stability in oil-rich foods prepared at high temperature. Copyright © 2017 Elsevier Ltd. All rights reserved.
Multiple TPR motifs characterize the Fanconi anemia FANCG protein.

PubMed

Blom, Eric; van de Vrugt, Henri J; de Vries, Yne; de Winter, Johan P; Arwert, Fré; Joenje, Hans

2004-01-05

The genome protection pathway that is defective in patients with Fanconi anemia (FA) is controlled by at least eight genes, including BRCA2. A key step in the pathway involves the monoubiquitylation of FANCD2, which critically depends on a multi-subunit nuclear 'core complex' of at least six FANC proteins (FANCA, -C, -E, -F, -G, and -L). Except for FANCL, which has WD40 repeats and a RING finger domain, no significant domain structure has so far been recognized in any of the core complex proteins. By using a homology search strategy comparing the human FANCG protein sequence with its ortholog sequences in Oryzias latipes (Japanese rice fish) and Danio rerio (zebrafish) we identified at least seven tetratricopeptide repeat motifs (TPRs) covering a major part of this protein. TPRs are degenerate 34-amino acid repeat motifs which function as scaffolds mediating protein-protein interactions, often found in multiprotein complexes. In four out of five TPR motifs tested (TPR1, -2, -5, and -6), targeted missense mutagenesis disrupting the motifs at the critical position 8 of each TPR caused complete or partial loss of FANCG function. Loss of function was evident from failure of the mutant proteins to complement the cellular FA phenotype in FA-G lymphoblasts, which was correlated with loss of binding to FANCA. Although the TPR4 mutant fully complemented the cells, it showed a reduced interaction with FANCA, suggesting that this TPR may also be of functional importance. The recognition of FANCG as a typical TPR protein predicts this protein to play a key role in the assembly and/or stabilization of the nuclear FA protein core complex.
The effect of peculiar complex core balance training on isokinetic muscle functions of the knee and lumbus.

PubMed

Lee, Myungsun; Han, Gunsoo

2016-04-01

[Purpose] This study aimed to investigate the effect of peculiar complex core balance training on the isokinetic muscle function of the knee joint and lumbus to provide fundamental data for establishing a training program that focuses on improving the performance and prevention of injury by developing the core and low extremity muscles. [Subjects and Methods] The participants in this study included a total of ten high school athletes involved in a throwing event for over five years. The subjects were randomly divided into two groups: The experimental group (N=5) and the control group (N=5). The experimental group underwent peculiar complex core balance training. [Results] According to the analysis of covariance, there was a significant effect of peculiar complex core balance training. Therefore, the isokinetic muscle function of the knee joint and lumbus in the experimental group participating in peculiar complex core balance training was significantly increased compared to the control group. [Conclusion] It is concluded that peculiar complex core balance training had a positive effect on the isokinetic muscle function of the knee and lumbus in throwing event athletes.
Discovery and Mechanistic Study of Benzamide Derivatives That Modulate Hepatitis B Virus Capsid Assembly.

PubMed

Wu, Shuo; Zhao, Qiong; Zhang, Pinghu; Kulp, John; Hu, Lydia; Hwang, Nicky; Zhang, Jiming; Block, Timothy M; Xu, Xiaodong; Du, Yanming; Chang, Jinhong; Guo, Ju-Tao

2017-08-15

Chronic hepatitis B virus (HBV) infection is a global public health problem. Although the currently approved medications can reliably reduce the viral load and prevent the progression of liver diseases, they fail to cure the viral infection. In an effort toward discovery of novel antiviral agents against HBV, a group of benzamide (BA) derivatives that significantly reduced the amount of cytoplasmic HBV DNA were discovered. The initial lead optimization efforts identified two BA derivatives with improved antiviral activity for further mechanistic studies. Interestingly, similar to our previously reported sulfamoylbenzamides (SBAs), the BAs promote the formation of empty capsids through specific interaction with HBV core protein but not other viral and host cellular components. Genetic evidence suggested that both SBAs and BAs inhibited HBV nucleocapsid assembly by binding to the heteroaryldihydropyrimidine (HAP) pocket between core protein dimer-dimer interfaces. However, unlike SBAs, BA compounds uniquely induced the formation of empty capsids that migrated more slowly in native agarose gel electrophoresis from A36V mutant than from the wild-type core protein. Moreover, we showed that the assembly of chimeric capsids from wild-type and drug-resistant core proteins was susceptible to multiple capsid assembly modulators. Hence, HBV core protein is a dominant antiviral target that may suppress the selection of drug-resistant viruses during core protein-targeting antiviral therapy. Our studies thus indicate that BAs are a chemically and mechanistically unique type of HBV capsid assembly modulators and warranted for further development as antiviral agents against HBV. IMPORTANCE HBV core protein plays essential roles in many steps of the viral replication cycle. In addition to packaging viral pregenomic RNA (pgRNA) and DNA polymerase complex into nucleocapsids for reverse transcriptional DNA replication to take place, the core protein dimers, existing in several different quaternary structures in infected hepatocytes, participate in and regulate HBV virion assembly, capsid uncoating, and covalently closed circular DNA (cccDNA) formation. It is anticipated that small molecular core protein assembly modulators may disrupt one or multiple steps of HBV replication, depending on their interaction with the distinct quaternary structures of core protein. The discovery of novel core protein-targeting antivirals, such as benzamide derivatives reported here, and investigation of their antiviral mechanism may lead to the identification of antiviral therapeutics for the cure of chronic hepatitis B. Copyright © 2017 American Society for Microbiology.
Turn Basin Construction

NASA Image and Video Library

2017-06-30

Across from the Vehicle Assembly Building at NASA's Kennedy Space Center in Florida, cement trucks stand by to support a construction project to upgrade the turn basin wharf. The work includes driving multiple precast concrete piles to a depth of about 70 feet to accommodate arrival of the core stage for the agency's Space Launch System (SLS) rocket. When the stage for NASA's SLS departs the Michoud Assembly Facility in New Orleans, it will be shipped by the agency's modified barge to the Launch Complex 39 turn basin.
Turn Basin Construction

NASA Image and Video Library

2017-06-30

Across from the Vehicle Assembly Building at NASA's Kennedy Space Center in Florida, cement is poured as part of a construction project to upgrade the turn basin wharf. The work includes driving multiple precast concrete piles to a depth of about 70 feet to accommodate arrival of the core stage for the agency's Space Launch System (SLS) rocket. When the stage for NASA's SLS departs the Michoud Assembly Facility in New Orleans, it will be shipped by the agency's modified barge to the Launch Complex 39 turn basin.
Testing for Divergent Transmission Histories among Cultural Characters: A Study Using Bayesian Phylogenetic Methods and Iranian Tribal Textile Data

PubMed Central

Matthews, Luke J.; Tehrani, Jamie J.; Jordan, Fiona M.; Collard, Mark; Nunn, Charles L.

2011-01-01

Background Archaeologists and anthropologists have long recognized that different cultural complexes may have distinct descent histories, but they have lacked analytical techniques capable of easily identifying such incongruence. Here, we show how Bayesian phylogenetic analysis can be used to identify incongruent cultural histories. We employ the approach to investigate Iranian tribal textile traditions. Methods We used Bayes factor comparisons in a phylogenetic framework to test two models of cultural evolution: the hierarchically integrated system hypothesis and the multiple coherent units hypothesis. In the hierarchically integrated system hypothesis, a core tradition of characters evolves through descent with modification and characters peripheral to the core are exchanged among contemporaneous populations. In the multiple coherent units hypothesis, a core tradition does not exist. Rather, there are several cultural units consisting of sets of characters that have different histories of descent. Results For the Iranian textiles, the Bayesian phylogenetic analyses supported the multiple coherent units hypothesis over the hierarchically integrated system hypothesis. Our analyses suggest that pile-weave designs represent a distinct cultural unit that has a different phylogenetic history compared to other textile characters. Conclusions The results from the Iranian textiles are consistent with the available ethnographic evidence, which suggests that the commercial rug market has influenced pile-rug designs but not the techniques or designs incorporated in the other textiles produced by the tribes. We anticipate that Bayesian phylogenetic tests for inferring cultural units will be of great value for researchers interested in studying the evolution of cultural traits including language, behavior, and material culture. PMID:21559083
Jungle Computing: Distributed Supercomputing Beyond Clusters, Grids, and Clouds

NASA Astrophysics Data System (ADS)

Seinstra, Frank J.; Maassen, Jason; van Nieuwpoort, Rob V.; Drost, Niels; van Kessel, Timo; van Werkhoven, Ben; Urbani, Jacopo; Jacobs, Ceriel; Kielmann, Thilo; Bal, Henri E.

In recent years, the application of high-performance and distributed computing in scientific practice has become increasingly wide spread. Among the most widely available platforms to scientists are clusters, grids, and cloud systems. Such infrastructures currently are undergoing revolutionary change due to the integration of many-core technologies, providing orders-of-magnitude speed improvements for selected compute kernels. With high-performance and distributed computing systems thus becoming more heterogeneous and hierarchical, programming complexity is vastly increased. Further complexities arise because urgent desire for scalability and issues including data distribution, software heterogeneity, and ad hoc hardware availability commonly force scientists into simultaneous use of multiple platforms (e.g., clusters, grids, and clouds used concurrently). A true computing jungle.
Identifying Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks

PubMed Central

Li, Min; Chen, Weijie; Wang, Jianxin; Pan, Yi

2014-01-01

Identification of protein complexes from protein-protein interaction networks has become a key problem for understanding cellular life in postgenomic era. Many computational methods have been proposed for identifying protein complexes. Up to now, the existing computational methods are mostly applied on static PPI networks. However, proteins and their interactions are dynamic in reality. Identifying dynamic protein complexes is more meaningful and challenging. In this paper, a novel algorithm, named DPC, is proposed to identify dynamic protein complexes by integrating PPI data and gene expression profiles. According to Core-Attachment assumption, these proteins which are always active in the molecular cycle are regarded as core proteins. The protein-complex cores are identified from these always active proteins by detecting dense subgraphs. Final protein complexes are extended from the protein-complex cores by adding attachments based on a topological character of “closeness” and dynamic meaning. The protein complexes produced by our algorithm DPC contain two parts: static core expressed in all the molecular cycle and dynamic attachments short-lived. The proposed algorithm DPC was applied on the data of Saccharomyces cerevisiae and the experimental results show that DPC outperforms CMC, MCL, SPICi, HC-PIN, COACH, and Core-Attachment based on the validation of matching with known complexes and hF-measures. PMID:24963481
Orbital-angular-momentum mode-group multiplexed transmission over a graded-index ring-core fiber based on receive diversity and maximal ratio combining

NASA Astrophysics Data System (ADS)

Zhang, Junwei; Zhu, Guoxuan; Liu, Jie; Wu, Xiong; Zhu, Jiangbo; Du, Cheng; Luo, Wenyong; Chen, Yujie; Yu, Siyuan

2018-02-01

An orbital-angular-momentum (OAM) mode-group multiplexing (MGM) scheme based on a graded-index ring-core fiber (GIRCF) is proposed, in which a single-input two-output (or receive diversity) architecture is designed for each MG channel and simple digital signal processing (DSP) is utilized to adaptively resist the mode partition noise resulting from random intra-group mode crosstalk. There is no need of complex multiple-input multiple-output (MIMO) equalization in this scheme. Furthermore, the signal-to-noise ratio (SNR) of the received signals can be improved if a simple maximal ratio combining (MRC) technique is employed on the receiver side to efficiently take advantage of the diversity gain of receiver. Intensity-modulated direct-detection (IM-DD) systems transmitting three OAM mode groups with total 100-Gb/s discrete multi-tone (DMT) signals over a 1-km GIRCF and two OAM mode groups with total 40-Gb/s DMT signals over an 18-km GIRCF are experimentally demonstrated, respectively, to confirm the feasibility of our proposed OAM-MGM scheme.
Competition and cooperation among similar representations: toward a unified account of facilitative and inhibitory effects of lexical neighbors.

PubMed

Chen, Qi; Mirman, Daniel

2012-04-01

One of the core principles of how the mind works is the graded, parallel activation of multiple related or similar representations. Parallel activation of multiple representations has been particularly important in the development of theories and models of language processing, where coactivated representations (neighbors) have been shown to exhibit both facilitative and inhibitory effects on word recognition and production. Researchers generally ascribe these effects to interactive activation and competition, but there is no unified explanation for why the effects are facilitative in some cases and inhibitory in others. We present a series of simulations of a simple domain-general interactive activation and competition model that is broadly consistent with more specialized domain-specific models of lexical processing. The results showed that interactive activation and competition can indeed account for the complex pattern of reversals. Critically, the simulations revealed a core computational principle that determines whether neighbor effects are facilitative or inhibitory: strongly active neighbors exert a net inhibitory effect, and weakly active neighbors exert a net facilitative effect.
Core neuropathological abnormalities in progranulin-deficient mice are penetrant on multiple genetic backgrounds.

PubMed

Petkau, T L; Hill, A; Leavitt, B R

2016-02-19

Loss-of-function mutations in the progranulin gene (GRN) are a common cause of familial frontotemporal lobar degeneration (FTLD). A high degree of heterogeneity in the age-of-onset, duration of disease, and clinical presentation of FTLD, even among families carrying the same GRN mutation, suggests that additional modifying genes may be important to pathogenesis. Progranulin-knockout mice display subtle behavioral abnormalities and progressive neuropathological changes, as well as altered dendritic morphology and synaptic deficits in the hippocampus. In this study we evaluated multiple neuropathological endpoints in aged progranulin knockout mice and their wild-type littermates on two different genetic backgrounds: C57Bl/6 and 129/SvImJ. We find that in most brain regions, both strains are susceptible to progranulin-mediated neuropathological phenotypes, including astrogliosis, microgliosis, and highly accelerated deposition of the aging pigment lipofuscin. Neuroinflammation due to progranulin deficiency is exaggerated in the B6 strain and present, but less pronounced, in the 129 strain. Differences between the strains in hippocampal neuron counts and neuronal morphology suggest a complex role for progranulin in the hippocampus. We conclude that core progranulin-mediated neurodegenerative phenotypes are penetrant on multiple inbred mouse strains, but that genetic background modulates progranulin's role in neuroinflammation and hippocampal biology. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.
Evidence-based patient information about treatment of multiple sclerosis--a phase one study on comprehension and emotional responses.

PubMed

Kasper, Jürgen; Köpke, Sascha; Mühlhauser, Ingrid; Heesen, Christoph

2006-07-01

This study analysis the comprehension and emotional responses of people suffering from multiple sclerosis when provided with an evidence-based information module. It is a core module of a comprehensive decision aid about immunotherapy. The core module is designed to enable patients to process scientific uncertainty without adverse effects. It considers existing standards for risk communication and presentation of data. Using a mailing approach we investigated 169 patients with differing courses of disease in a before-after design. Items addressed the competence in processing relative and absolute risk information and patients' emotional response to the tool, comprising grade of familiarity with the information, understanding, relevance, emotional arousal, and certainty. Overall, numeracy improved (p < 0.001), although 99 of 169 patients did not complete the numeracy task correctly. Understanding depended on the relevance related to the course of disease. A moderate level of uncertainty was induced. No adverse emotional responses could be shown, neither in those who did comprehend the information, nor in those who did not develop numeracy skills. In conclusion, the tool supports people suffering from multiple sclerosis to process evidence-based medical information and scientific uncertainty without burdening them emotionally. This study is an example for the documentation of an important step in the development process of a complex intervention.
Exploiting MIC architectures for the simulation of channeling of charged particles in crystals

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Karpusenko, Vadim

2016-08-01

Coherent effects of ultra-relativistic particles in crystals is an area of science under development. DYNECHARM + + is a toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures. The particle trajectory in a crystal is computed through numerical integration of the equation of motion. The code was revised and improved in order to exploit parallelization on multi-cores and vectorization of single instructions on multiple data. An Intel Xeon Phi card was adopted for the performance measurements. The computation time was proved to scale linearly as a function of the number of physical and virtual cores. By enabling the auto-vectorization flag of the compiler a three time speedup was obtained. The performances of the card were compared to the Dual Xeon ones.
Dovetail spoke internal permanent magnet machine

DOEpatents

Alexander, James Pellegrino [Ballston Lake, NY; EL-Refaie, Ayman Mohamed Fawzi [Niskayuna, NY; Lokhandwalla, Murtuza [Clifton Park, NY; Shah, Manoj Ramprasad [Latham, NY; VanDam, Jeremy Daniel [West Coxsackie, NY

2011-08-23

An internal permanent magnet (IPM) machine is provided. The IPM machine includes a stator assembly and a stator core. The stator core also includes multiple stator teeth. The stator assembly is further configured with stator windings to generate a stator magnetic field when excited with alternating currents and extends along a longitudinal axis with an inner surface defining a cavity. The IPM machine also includes a rotor assembly and a rotor core. The rotor core is disposed inside the cavity and configured to rotate about the longitudinal axis. The rotor assembly further includes a shaft. The shaft further includes multiple protrusions alternately arranged relative to multiple bottom structures provided on the shaft. The rotor assembly also includes multiple stacks of laminations disposed on the protrusions and dovetailed circumferentially around the shaft. The rotor assembly further includes multiple pair of permanent magnets for generating a magnetic field, which magnetic field interacts with the stator magnetic field to produce a torque. The multiple pair of permanent magnets are disposed between the stacks. The rotor assembly also includes multiple middle wedges mounted between each pair of the multiple permanent magnets.
Construction of hybrid photosynthetic units using peripheral and core antennae from two different species of photosynthetic bacteria: detection of the energy transfer from bacteriochlorophyll a in LH2 to bacteriochlorophyll b in LH1.

PubMed

Fujii, Ritsuko; Shimonaka, Shozo; Uchida, Naoko; Gardiner, Alastair T; Cogdell, Richard J; Sugisaki, Mitsuru; Hashimoto, Hideki

2008-01-01

Typical purple bacterial photosynthetic units consist of supra-molecular arrays of peripheral (LH2) and core (LH1-RC) antenna complexes. Recent atomic force microscopy pictures of photosynthetic units in intact membranes have revealed that the architecture of these units is variable (Scheuring et al. (2005) Biochim Bhiophys Acta 1712:109-127). In this study, we describe methods for the construction of heterologous photosynthetic units in lipid-bilayers from mixtures of purified LH2 (from Rhodopseudomonas acidophila) and LH1-RC (from Rhodopseudomonas viridis) core complexes. The architecture of these reconstituted photosynthetic units can be varied by controlling ratio of added LH2 to core complexes. The arrangement of the complexes was visualized by electron-microscopy in combination with Fourier analysis. The regular trigonal array of the core complexes seen in the native photosynthetic membrane could be regenerated in the reconstituted membranes by temperature cycling. In the presence of added LH2 complexes, this trigonal symmetry was replaced with orthorhombic symmetry. The small lattice lengths for the latter suggest that the constituent unit of the orthorhombic lattice is the LH2. Fluorescence and fluorescence-excitation spectroscopy was applied to the set of the reconstituted membranes prepared with various proportions of LH2 to core complexes. Remarkably, even though the LH2 complexes contain bacteriochlorophyll a, and the core complexes contain bacteriochlorophyll b, it was possible to demonstrate energy transfer from LH2 to the core complexes. These experiments provide a first step along the path toward investigating how changing the architecture of purple bacterial photosynthetic units affects the overall efficiency of light-harvesting.
Atomic force microscopy reveals multiple patterns of antenna organization in purple bacteria: implications for energy transduction mechanisms and membrane modeling.

PubMed

Sturgis, James N; Niederman, Robert A

2008-01-01

Recent topographs of the intracytoplasmic membrane (ICM) of purple bacteria obtained by atomic force microscopy (AFM) have provided the first surface views of the native architecture of a multicomponent biological membrane at submolecular resolution, representing an important landmark in structural biology. A variety of species-dependent, closely packed arrangements of light-harvesting (LH) complexes was revealed: the most highly organized was found in Rhodobacter sphaeroides in which the peripheral LH2 antenna was seen either in large clusters or in fixed rows interspersed among ordered arrays of dimeric LH1-reaction center (RC) core complexes. A more random organization was observed in other species containing both the LH1 and LH2 complexes, as typified by Rhododspirillum photometricum with randomly packed monomeric LH1-RC core complexes intermingled with large, paracrystalline domains of LH2 antenna. Surprisingly, no structures that could be identified as the ATP synthase or cytochrome bc (1) complexes were observed, which may reflect their localization at ICM vesicle poles or in curved membrane areas, out of view from the flat regions imaged by AFM. This possible arrangement of energy transducing complexes has required a reassessment of energy tranduction mechanisms which place the cytochrome bc (1) complex in close association with the RC. Instead, more plausible proposals must account for the movement of quinone redox species over considerable membrane distances on appropriate time scales. AFM, together with atomic resolution structures are also providing the basis for molecular modeling of the ICM that is leading to an improved picture of the supramolecular organization of photosynthetic complexes, as well as the forces that drive their segregation into distinct domains.

Geochemical consequences of flow differentiation in a multiple injection dike (Trinity ophiolite, N. California)

USGS Publications Warehouse

Brouxel, M.

1991-01-01

A clinopyroxene-rich dike of the Trinity ophiolite sheeted-dike complex shows three different magmatic pulses, probably injected in a short period of time (no well developed chilled margin) and important variations of the clinopyroxene and plagioclase percentages between its core (highly porphyritic) and margins (aphyric). This variation, interpreted as related to a flow differentiation phenomenon (mechanical phenocryst redistribution), has important geochemical consequences. It produces increases in the FeO, MgO, CaO, Cr and Ni contents from the margin to the core, together with increases in the clinopyroxene percentage, and decreases in the SiO2, Zr, Y, Nb and REE contents together with a decrease in the percentage of the fine-grained groundmass toward the core of the dike. This mineralogical redistribution, which also affects the incompatible trace element ratios because of the difference in plagioclase and clinopyroxene mineral/liquid partition coefficients, illustrate the importance of fractionation processes outside of a magma chamber. ?? 1991.
Paleomagnetism of the Oman Ophiolite: New Results from Oman Drilling Project Cores

NASA Astrophysics Data System (ADS)

Horst, A. J.; Till, J. L.; Koornneef, L.; Usui, Y.; Kim, H.; Morris, A.

2017-12-01

The Oman Drilling Project drilled holes at four sites in a transect through the southern massifs of the Samail ophiolite, and recovered 1500 m of igneous and metamorphic rocks. We focus on three sites from the oceanic crustal section including lower layered gabbros (GT1A), the mid-crustal layered to foliated gabbro transition (GT2A), and the shallower transition from sheeted dikes to varitextured gabbros (GT3A). Detailed core descriptions, analyses, and paleomagnetic measurements, were made on D/V Chikyu from July to September 2017 to utilize the core laboratory facilities similar to IODP expeditions. Shipboard measurements included anisotropy of magnetic susceptibility (AMS) and alternating field and thermal demagnetization of 597 discrete samples. Sample demagnetization behavior is varied from each of the cores, with some revealing multiple components of magnetization, and others yielding nearly univectorial data. The interpretation of results from the lower crustal cores is complicated by the pervasive presence of secondary magnetite. In almost all samples, a stable component was resolved (interpreted as a characteristic remanent magnetization) after removal of a lower-coercivity or lower unblocking-temperature component. The inclinations of the stable components in the core reference frame are very consistent in Hole GT1A. However, a transition from negative to positive inclinations in GT2A suggests some structural complexity, possibly as a result of intense late faulting activity. Both abrupt and gradual transitions between multiple zones of negative and positive inclinations occur in Hole GT3A. Interpretation and direct comparison of remanence between drill sites is difficult as recovered core pieces currently remain azimuthally unoriented, and GT2A was drilled at a plunge of 60°, whereas GT1A and GT3A were both drilled vertically. Work is ongoing to use borehole imagery to reorient the core pieces and paleomagnetic data into a geographic in situ reference frame. We will present an overview of preliminary AMS and remanence data that will be used in the future to 1) document deformational histories, 2) characterize magmatic flow directions at different structural levels, and 3) identify the magnetic mineralogy of remanence carriers throughout the oceanic crustal section.
Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base.

PubMed

Funakoshi, Minoru; Tomko, Robert J; Kobayashi, Hideki; Hochstrasser, Mark

2009-05-29

The central protease of eukaryotes, the 26S proteasome, has a 20S proteolytic core particle (CP) and an attached 19S regulatory particle (RP). The RP is further subdivided into lid and base subcomplexes. Little is known about RP assembly. Here, we show that four conserved assembly factors govern biogenesis of the yeast RP base. Nas2 forms a complex with the Rpt4 and Rpt5 ATPases and enhances 26S proteasome formation in vivo and in vitro. Other RP subcomplexes contain Hsm3, which is related to mammalian proteasome subunit S5b. Hsm3 also contributes to base assembly. Larger Hsm3-containing complexes include two additional proteins, Nas6 and Rpn14, which function as assembly chaperones as well. Specific deletion combinations affecting these four factors cause severe perturbations to RP assembly. Our results demonstrate that proteasomal RP biogenesis requires multiple, functionally overlapping chaperones and suggest a model in which subunits form specific subcomplexes that then assemble into the base.
A defined role for multiple Fanconi anemia gene products in DNA-damage-associated ubiquitination.

PubMed

Tan, Winnie; Deans, Andrew J

2017-06-01

Fanconi anemia (FA) is an inherited blood disorder that causes bone marrow failure and high predisposition to cancers. The FA pathway guards the cell's genome stability by orchestrating the repair of interstrand cross-linking during the S phase of the cell cycle, preventing the chromosomal instability that is a key event in bone marrow failure syndrome. Central to the FA pathway is loss of monoubiquitinated forms of the Fanconi proteins FANCI and FANCD2, a process that is normally mediated by a "core complex" of seven other Fanconi proteins. Each protein, when mutated, can cause FA. The FA core-complex-catalyzed reaction is critical for signaling DNA cross-link damage such as that induced by chemotherapies. Here, we present a perspective on the current understanding of FANCI and FANCD2 monoubiquitination-mediated DNA repair. Our recent biochemical reconstitution of the monoubiquitination (and deubiquitination) reactions creates a paradigm for understanding FA. Further biochemical analysis will create new opportunities to address the leukemic phenotype of FA patients. Copyright © 2017 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.
Stream Processors

NASA Astrophysics Data System (ADS)

Erez, Mattan; Dally, William J.

Stream processors, like other multi core architectures partition their functional units and storage into multiple processing elements. In contrast to typical architectures, which contain symmetric general-purpose cores and a cache hierarchy, stream processors have a significantly leaner design. Stream processors are specifically designed for the stream execution model, in which applications have large amounts of explicit parallel computation, structured and predictable control, and memory accesses that can be performed at a coarse granularity. Applications in the streaming model are expressed in a gather-compute-scatter form, yielding programs with explicit control over transferring data to and from on-chip memory. Relying on these characteristics, which are common to many media processing and scientific computing applications, stream architectures redefine the boundary between software and hardware responsibilities with software bearing much of the complexity required to manage concurrency, locality, and latency tolerance. Thus, stream processors have minimal control consisting of fetching medium- and coarse-grained instructions and executing them directly on the many ALUs. Moreover, the on-chip storage hierarchy of stream processors is under explicit software control, as is all communication, eliminating the need for complex reactive hardware mechanisms.
The effect of peculiar complex core balance training on isokinetic muscle functions of the knee and lumbus

PubMed Central

Lee, Myungsun; Han, Gunsoo

2016-01-01

[Purpose] This study aimed to investigate the effect of peculiar complex core balance training on the isokinetic muscle function of the knee joint and lumbus to provide fundamental data for establishing a training program that focuses on improving the performance and prevention of injury by developing the core and low extremity muscles. [Subjects and Methods] The participants in this study included a total of ten high school athletes involved in a throwing event for over five years. The subjects were randomly divided into two groups: The experimental group (N=5) and the control group (N=5). The experimental group underwent peculiar complex core balance training. [Results] According to the analysis of covariance, there was a significant effect of peculiar complex core balance training. Therefore, the isokinetic muscle function of the knee joint and lumbus in the experimental group participating in peculiar complex core balance training was significantly increased compared to the control group. [Conclusion] It is concluded that peculiar complex core balance training had a positive effect on the isokinetic muscle function of the knee and lumbus in throwing event athletes. PMID:27190470
Structure of the Repulsive Guidance Molecule (RGM)—Neogenin Signaling Hub

PubMed Central

Bell, Christian H.; Bishop, Benjamin; Tang, Chenxiang; Gilbert, Robert J.C.; Aricescu, A. Radu; Pasterkamp, R. Jeroen; Siebold, Christian

2016-01-01

Repulsive guidance molecule family members (RGMs) control fundamental and diverse cellular processes, including motility and adhesion, immune cell regulation, and systemic iron metabolism. However, it is not known how RGMs initiate signaling through their common cell-surface receptor, neogenin (NEO1). Here, we present crystal structures of the NEO1 RGM-binding region and its complex with human RGMB (also called dragon). The RGMB structure reveals a previously unknown protein fold and a functionally important autocatalytic cleavage mechanism and provides a framework to explain numerous disease-linked mutations in RGMs. In the complex, two RGMB ectodomains conformationally stabilize the juxtamembrane regions of two NEO1 receptors in a pH-dependent manner. We demonstrate that all RGM-NEO1 complexes share this architecture, which therefore represents the core of multiple signaling pathways. PMID:23744777
Mathematical modeling and full-scale shaking table tests for multi-curve buckling restrained braces

NASA Astrophysics Data System (ADS)

Tsai, C. S.; Lin, Yungchang; Chen, Wenshin; Su, H. C.

2009-09-01

Buckling restrained braces (BRBs) have been widely applied in seismic mitigation since they were introduced in the 1970s. However, traditional BRBs have several disadvantages caused by using a steel tube to envelope the mortar to prevent the core plate from buckling, such as: complex interfaces between the materials used, uncertain precision, and time consumption during the manufacturing processes. In this study, a new device called the multi-curve buckling restrained brace (MC-BRB) is proposed to overcome these disadvantages. The new device consists of a core plate with multiple neck portions assembled to form multiple energy dissipation segments, and the enlarged segment, lateral support elements and constraining elements to prevent the BRB from buckling. The enlarged segment located in the middle of the core plate can be welded to the lateral support and constraining elements to increase buckling resistance and to prevent them from sliding during earthquakes. Component tests and a series of shaking table tests on a full-scale steel structure equipped with MC-BRBs were carried out to investigate the behavior and capability of this new BRB design for seismic mitigation. The experimental results illustrate that the MC-BRB possesses a stable mechanical behavior under cyclic loadings and provides good protection to structures during earthquakes. Also, a mathematical model has been developed to simulate the mechanical characteristics of BRBs.
High-speed, bi-directional dual-core fiber transmission system for high-density, short-reach optical interconnects

NASA Astrophysics Data System (ADS)

Geng, Ying; Li, Shenping; Li, Ming-Jun; Sutton, Clifford G.; McCollum, Robert L.; McClure, Randy L.; Koklyushkin, Alexander V.; Matthews, Karen I.; Luther, James P.; Butler, Douglas L.

2015-03-01

A complete single mode dual-core fiber system for short-reach optical interconnects is fabricated and tested for high-speed data transmission. It includes dual-core fibers capable of bi-directional data transmission, dual-core simplex LC connectors, and fan-outs. The transmission system offers simplified bi-directional traffic engineering with integrated bidirectional transceivers and compact system design, utilizing simplex dual-core LC connectors that use half the space while increasing the bandwidth density by a factor of two. The fiber has two cores that are compatible with single mode fiber and conforms to the industry standard outer diameter of 125 μm. This reduces operational complexity by reducing the size and number of fibers, cables and connectors. Measured OTDR loss for both cores was 0.34 dB/km at 1310 nm and 0.19 dB/km at 1550 nm. Crosstalk for a piece of 5.8 km long dual-core fiber was measured to be below -75 dB at 1310 nm, and below -40 dB at 1550 nm. Both free-space optics fan-outs and tapered-fiber-coupler based MCF fan-outs were evaluated for the transmission system. Error-free and penalty-free 25 Gb/s bi-directional transmission performance was demonstrated for three different fiber lengths, 200 m, 2 km and 10 km, using the complete all-fiber-based system including connectors and fan-outs. This single mode, dual-core fiber transmission system adds complementary value to systems where additional increases in bandwidth density can come from wavelength division multiplexing and multiple bits per symbol.
PFLOTRAN: Reactive Flow & Transport Code for Use on Laptops to Leadership-Class Supercomputers

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

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

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

NASA Astrophysics Data System (ADS)

Schroeder, T.; Cheadle, M. J.

2007-12-01

The Mid-Atlantic Ridge (MAR) 75km north and south of the 15-20 Fracture Zone (FZ) has produced upper oceanic lithosphere composed dominantly of mantle peridotite with gabbro intrusions. In the absence of diapirism, mantle peridotite can only be exposed on the seafloor by extensional faulting, thus the sea floor geology and bathymetry provide widespread evidence for extensive low-angle faulting. However, only 3% of the seafloor in this region has the domal morphology characteristic of features that have been termed oceanic core complexes; suggesting that other processes, in addition to low-angle faulting, are responsible for the generation of domal core complexes. Most low-angle faults near the 15-20 FZ form gently dipping (10-15°), 10-15km-wide dip slopes on the flanks of 2000m relief bathymetric ridges that are up to 15-40km long (parallel to the MAR). Core recovered from ODP Leg 209 drill holes in these ridges is dominantly peridotite with small (<50m thick) gabbro intrusions. The peridotite is cut by a very high density of brittle faults dipping at both steep and gentle angles. Several holes also contain long-lived shear zones/faults in their upper reaches in which strain was localized at granulite facies, indicated by mylonitic olivine and cpx, and remained active during cooling to sub-greenschist grade, indicated by cross-cutting of progressively lower-grade syn-deformation mineral assemblages. These observations suggest that seafloor spreading is largely accommodated here by slip on low-angle faults, and that these faults are correctly termed detachment faults. Holes drilled into a domal oceanic core complex north of the 15-20 FZ during Leg 209 (ODP Site 1275) recovered dominantly gabbro and not mantle peridotite. This hole is cut by significantly fewer brittle and ductile faults than the peridotite drilled at the non-core-complex detachment fault sites. The detachment fault in the upper reaches (50m) of Site 1275 was localized at temperatures near feldspar's ductile-to-brittle transition, indicated by cataclasis with minor crystal plastic flow in plagioclase, and a lack of pervasive pure-ductile deformation. Amphibole-plagioclase thermometry in the fault yields equilibrium temperatures from 600-650°C, compared to equilibrium temperatures of 750-850°C for the gabbro outside the fault. The presence of talc- chlorite schists and cataclasites cutting the higher-temperature deformation textures indicate fault activity down- temperature from amphibolite through greenschist facies. This core-complex-bounding fault contrasts with the fault that bounds the Atlantis Bank Core Complex on the Southwest Indian Ridge (SWIR). There, the fault is 100m thick and strain was initially localized at granulite grade (>800°C) (Mehl & Hirth, 2007); significantly hotter than the Site 1275 fault. Therefore, the formation of core-complex morphology does not seem to depend on the initial faulting conditions. Both oceanic core complexes that have been drilled besides Site 1275, Atlantis Massif at 30°N (IODP Hole 1309D) on the MAR and Atlantis Bank on the SWIR (ODP Hole 735B), are also comprised dominantly of gabbro. This suggests that magma supply may be an essential requirement for core complex formation and raises the question whether all domal oceanic core complexes are cored by gabbro? We also ask whether the term 'oceanic core complex' should be restricted to these domal features and not applied to detachment-bound, non- domal, peridotite-cored ridges; or if these should be considered two sub-classes of oceanic core complexes.
SQL is Dead; Long-live SQL: Relational Database Technology in Science Contexts

NASA Astrophysics Data System (ADS)

Howe, B.; Halperin, D.

2014-12-01

Relational databases are often perceived as a poor fit in science contexts: Rigid schemas, poor support for complex analytics, unpredictable performance, significant maintenance and tuning requirements --- these idiosyncrasies often make databases unattractive in science contexts characterized by heterogeneous data sources, complex analysis tasks, rapidly changing requirements, and limited IT budgets. In this talk, I'll argue that although the value proposition of typical relational database systems are weak in science, the core ideas that power relational databases have become incredibly prolific in open source science software, and are emerging as a universal abstraction for both big data and small data. In addition, I'll talk about two open source systems we are building to "jailbreak" the core technology of relational databases and adapt them for use in science. The first is SQLShare, a Database-as-a-Service system supporting collaborative data analysis and exchange by reducing database use to an Upload-Query-Share workflow with no installation, schema design, or configuration required. The second is Myria, a service that supports much larger scale data, complex analytics, and supports multiple back end systems. Finally, I'll describe some of the ways our collaborators in oceanography, astronomy, biology, fisheries science, and more are using these systems to replace script-based workflows for reasons of performance, flexibility, and convenience.
Differential global structural changes in the core particle of yeast and mouse proteasome induced by ligand binding

PubMed Central

Arciniega, Marcelino; Beck, Philipp; Lange, Oliver F.; Groll, Michael; Huber, Robert

2014-01-01

Two clusters of configurations of the main proteolytic subunit β5 were identified by principal component analysis of crystal structures of the yeast proteasome core particle (yCP). The apo-cluster encompasses unliganded species and complexes with nonpeptidic ligands, and the pep-cluster comprises complexes with peptidic ligands. The murine constitutive CP structures conform to the yeast system, with the apo-form settled in the apo-cluster and the PR-957 (a peptidic ligand) complex in the pep-cluster. In striking contrast, the murine immune CP classifies into the pep-cluster in both the apo and the PR-957–liganded species. The two clusters differ essentially by multiple small structural changes and a domain motion enabling enclosure of the peptidic ligand and formation of specific hydrogen bonds in the pep-cluster. The immune CP species is in optimal peptide binding configuration also in its apo form. This favors productive ligand binding and may help to explain the generally increased functional activity of the immunoproteasome. Molecular dynamics simulations of the representative murine species are consistent with the experimentally observed configurations. A comparison of all 28 subunits of the unliganded species with the peptidic liganded forms demonstrates a greatly enhanced plasticity of β5 and suggests specific signaling pathways to other subunits. PMID:24979800
Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures

PubMed Central

Manolakos, Elias S.

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub. PMID:26605332
Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures.

PubMed

Sharma, Anuj; Manolakos, Elias S

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub.
F3D Image Processing and Analysis for Many - and Multi-core Platforms

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

F3D is written in OpenCL, so it achieve[sic] platform-portable parallelism on modern mutli-core CPUs and many-core GPUs. The interface and mechanims to access F3D core are written in Java as a plugin for Fiji/ImageJ to deliver several key image-processing algorithms necessary to remove artifacts from micro-tomography data. The algorithms consist of data parallel aware filters that can efficiently utilizes[sic] resources and can work on out of core datasets and scale efficiently across multiple accelerators. Optimizing for data parallel filters, streaming out of core datasets, and efficient resource and memory and data managements over complex execution sequence of filters greatly expeditesmore » any scientific workflow with image processing requirements. F3D performs several different types of 3D image processing operations, such as non-linear filtering using bilateral filtering and/or median filtering and/or morphological operators (MM). F3D gray-level MM operators are one-pass constant time methods that can perform morphological transformations with a line-structuring element oriented in discrete directions. Additionally, MM operators can be applied to gray-scale images, and consist of two parts: (a) a reference shape or structuring element, which is translated over the image, and (b) a mechanism, or operation, that defines the comparisons to be performed between the image and the structuring element. This tool provides a critical component within many complex pipelines such as those for performing automated segmentation of image stacks. F3D is also called a "descendent" of Quant-CT, another software we developed in the past. These two modules are to be integrated in a next version. Further details were reported in: D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J. Sethian. Structure recognition from high-resolution images of ceramic composites. IEEE International Conference on Big Data, October 2014.« less
High speed internal permanent magnet machine and method of manufacturing the same

DOEpatents

Alexander, James Pellegrino [Ballston Lake, NY; EL-Refaie, Ayman Mohamed Fawzi [Niskayuna, NY; Lokhandwalla, Murtuza [Clifton Park, NY; Shah, Manoj Ramprasad [Latham, NY; VanDam, Jeremy Daniel [West Coxsackie, NY

2011-09-13

An internal permanent magnet (IPM) machine is provided. The IPM machine includes a stator assembly and a stator core. The stator core also includes multiple stator teeth. The stator assembly is further configured with stator windings to generate a magnetic field when excited with alternating currents and extends along a longitudinal axis with an inner surface defining a cavity. The IPM machine also includes a rotor assembly and a rotor core. The rotor core is disposed inside the cavity and configured to rotate about the longitudinal axis. The rotor assembly further includes a shaft. The shaft further includes multiple protrusions alternately arranged relative to multiple bottom structures provided on the shaft. The rotor assembly also includes multiple stacks of laminations disposed on the protrusions and dovetailed circumferentially around the shaft. The rotor assembly further includes multiple permanent magnets for generating a magnetic field, which interacts with the stator magnetic field to produce torque. The permanent magnets are disposed between the stacks. The rotor assembly also includes multiple bottom wedges disposed on the bottom structures of the shaft and configured to hold the multiple stacks and the multiple permanent magnets.
Molecular structure of the pyruvate dehydrogenase complex from Escherichia coli K-12.

PubMed

Vogel, O; Hoehn, B; Henning, U

1972-06-01

The pyruvate dehydrogenase core complex from E. coli K-12, defined as the multienzyme complex that can be obtained with a unique polypeptide chain composition, has a molecular weight of 3.75 x 10(6). All results obtained agree with the following numerology. The core complex consists of 48 polypeptide chains. There are 16 chains (molecular weight = 100,000) of the pyruvate dehydrogenase component, 16 chains (molecular weight = 80,000) of the dihydrolipoamide dehydrogenase component, and 16 chains (molecular weight = 56,000) of the dihydrolipoamide dehydrogenase component. Usually, but not always, pyruvate dehydrogenase complex is produced in vivo containing at least 2-3 mol more of dimers of the pyruvate dehydrogenase component than the stoichiometric ratio with respect to the core complex. This "excess" component is bound differently than are the eight dimers in the core complex.
Modeling Multiple-Core Updraft Plume Rise for an Aerial Ignition Prescribed Burn by Coupling Daysmoke with a Cellular Automata Fire Model

Treesearch

G. L Achtemeier; S. L. Goodrick; Y. Liu

2012-01-01

Smoke plume rise is critically dependent on plume updraft structure. Smoke plumes from landscape burns (forest and agricultural burns) are typically structured into âsub-plumesâ or multiple-core updrafts with the number of updraft cores depending on characteristics of the landscape, fire, fuels, and weather. The number of updraft cores determines the efficiency of...
THE ABUNDANCE, ORTHO/PARA RATIO, AND DEUTERATION OF WATER IN THE HIGH-MASS STAR-FORMING REGION NGC 6334 I

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

Emprechtinger, M.; Lis, D. C.; Monje, R. R.

2013-03-01

We present Herschel/HIFI observations of 30 transitions of water isotopologues toward the high-mass star-forming region NGC 6334 I. The line profiles of H{sup 16} {sub 2}O, H{sup 17} {sub 2}O, H{sup 18} {sub 2}O, and HDO show a complex pattern of emission and absorption components associated with the embedded hot cores, a lower-density envelope, two outflow components, and several foreground clouds, some associated with the NGC 6334 complex, others seen in projection against the strong continuum background of the source. Our analysis reveals an H{sub 2}O ortho/para ratio of 3 {+-} 0.5 in the foreground clouds, as well as themore » outflow. The water abundance varies from {approx}10{sup -8} in the foreground clouds and the outer envelope to {approx}10{sup -6} in the hot core. The hot core abundance is two orders of magnitude below the chemical model predictions for dense, warm gas, but within the range of values found in other Herschel/HIFI studies of hot cores and hot corinos. This may be related to the relatively low gas and dust temperature ({approx}100 K), or time-dependent effects, resulting in a significant fraction of water molecules still locked up in dust grain mantles. The HDO/H{sub 2}O ratio in NGC 6334 I, {approx}2 Multiplication-Sign 10{sup -4}, is also relatively low, but within the range found in other high-mass star-forming regions.« less

Connecting Core Percolation and Controllability of Complex Networks

PubMed Central

Jia, Tao; Pósfai, Márton

2014-01-01

Core percolation is a fundamental structural transition in complex networks related to a wide range of important problems. Recent advances have provided us an analytical framework of core percolation in uncorrelated random networks with arbitrary degree distributions. Here we apply the tools in analysis of network controllability. We confirm analytically that the emergence of the bifurcation in control coincides with the formation of the core and the structure of the core determines the control mode of the network. We also derive the analytical expression related to the controllability robustness by extending the deduction in core percolation. These findings help us better understand the interesting interplay between the structural and dynamical properties of complex networks. PMID:24946797
Evidence that the assembly of the yeast cytochrome bc1 complex involves the formation of a large core structure in the inner mitochondrial membrane.

PubMed

Zara, Vincenzo; Conte, Laura; Trumpower, Bernard L

2009-04-01

The assembly status of the cytochrome bc(1) complex has been analyzed in distinct yeast deletion strains in which genes for one or more of the bc(1) subunits were deleted. In all the yeast strains tested, a bc(1) sub-complex of approximately 500 kDa was found when the mitochondrial membranes were analyzed by blue native electrophoresis. The subsequent molecular characterization of this sub-complex, carried out in the second dimension by SDS/PAGE and immunodecoration, revealed the presence of the two catalytic subunits, cytochrome b and cytochrome c(1), associated with the noncatalytic subunits core protein 1, core protein 2, Qcr7p and Qcr8p. Together, these bc(1) subunits build up the core structure of the cytochrome bc(1) complex, which is then able to sequentially bind the remaining subunits, such as Qcr6p, Qcr9p, the Rieske iron-sulfur protein and Qcr10p. This bc(1) core structure may represent a true assembly intermediate during the maturation of the bc(1) complex; first, because of its wide distribution in distinct yeast deletion strains and, second, for its characteristics of stability, which resemble those of the intact homodimeric bc(1) complex. By contrast, the bc(1) core structure is unable to interact with the cytochrome c oxidase complex to form respiratory supercomplexes. The characterization of this novel core structure of the bc(1) complex provides a number of new elements clarifying the molecular events leading to the maturation of the yeast cytochrome bc(1) complex in the inner mitochondrial membrane.
Evidence that assembly of the yeast cytochrome bc1 complex involves formation of a large core structure in the inner mitochondrial membrane

PubMed Central

Zara, Vincenzo; Conte, Laura; Trumpower, Bernard L.

2009-01-01

The assembly status of the cytochrome bc1 complex has been analyzed in distinct yeast deletion strains in which genes for one or more of the bc1 subunits had been deleted. In all the yeast strains tested a bc1 sub-complex of about 500 kDa was found when the mitochondrial membranes were analyzed by blue native electrophoresis. The subsequent molecular characterization of this sub-complex, carried out in the second dimension by SDS-PAGE and immunodecoration, revealed the presence of the two catalytic subunits cytochrome b and cytochrome c1, associated with the non catalytic subunits core protein 1, core protein 2, Qcr7p and Qcr8p. Altogether these bc1 subunits build up the core structure of the cytochrome bc1 complex which is then able to sequentially bind the remaining subunits, such as Qcr6p, Qcr9p, the Rieske iron-sulfur protein and Qcr10p. This bc1 core structure may represent a true assembly intermediate during the maturation of the bc1 complex, first because of its wide distribution in distinct yeast deletion strains and second for its characteristics of stability which resemble those of the intact homodimeric bc1 complex. Differently from this latter, however, the bc1 core structure is not able to interact with the cytochrome c oxidase complex to form respiratory supercomplexes. The characterization of this novel core structure of the bc1 complex provides a number of new elements for clarification of the molecular events leading to the maturation of the yeast cytochrome bc1 complex in the inner mitochondrial membrane. PMID:19236481
Activities for Challenging Gifted Learners by Increasing Complexity in the Common Core

ERIC Educational Resources Information Center

McKeone, Alyssa; Caruso, Lenora; Bettle, Kailyn; Chase, Ashley; Bryson, Bridget; Schneider, Jean S.; Rule, Audrey C.

2015-01-01

Gifted learners need opportunities for critical and creative thinking to stretch their minds and imaginations. Strategies for increasing complexity in the four core areas of language arts, mathematics, science, and social studies were addressed using the Common Core and Iowa Core Standards through several methods. Descriptive adjective object…
Characterization of Hepatitis C Virus Core Protein Multimerization and Membrane Envelopment: Revelation of a Cascade of Core-Membrane Interactions ▿

PubMed Central

Ai, Li-Shuang; Lee, Yu-Wen; Chen, Steve S.-L.

2009-01-01

The molecular basis underlying hepatitis C virus (HCV) core protein maturation and morphogenesis remains elusive. We characterized the concerted events associated with core protein multimerization and interaction with membranes. Analyses of core proteins expressed from a subgenomic system showed that the signal sequence located between the core and envelope glycoprotein E1 is critical for core association with endoplasmic reticula (ER)/late endosomes and the core's envelopment by membranes, which was judged by the core's acquisition of resistance to proteinase K digestion. Despite exerting an inhibitory effect on the core's association with membranes, (Z-LL)2-ketone, a specific inhibitor of signal peptide peptidase (SPP), did not affect core multimeric complex formation, suggesting that oligomeric core complex formation proceeds prior to or upon core attachment to membranes. Protease-resistant core complexes that contained both innate and processed proteins were detected in the presence of (Z-LL)2-ketone, implying that core envelopment occurs after intramembrane cleavage. Mutations of the core that prevent signal peptide cleavage or coexpression with an SPP loss-of-function D219A mutant decreased the core's envelopment, demonstrating that SPP-mediated cleavage is required for core envelopment. Analyses of core mutants with a deletion in domain I revealed that this domain contains sequences crucial for core envelopment. The core proteins expressed by infectious JFH1 and Jc1 RNAs in Huh7 cells also assembled into a multimeric complex, associated with ER/late-endosomal membranes, and were enveloped by membranes. Treatment with (Z-LL)2-ketone or coexpression with D219A mutant SPP interfered with both core envelopment and infectious HCV production, indicating a critical role of core envelopment in HCV morphogenesis. The results provide mechanistic insights into the sequential and coordinated processes during the association of the HCV core protein with membranes in the early phase of virus maturation and morphogenesis. PMID:19605478
Detection of core-periphery structure in networks based on 3-tuple motifs

NASA Astrophysics Data System (ADS)

Ma, Chuang; Xiang, Bing-Bing; Chen, Han-Shuang; Small, Michael; Zhang, Hai-Feng

2018-05-01

Detecting mesoscale structure, such as community structure, is of vital importance for analyzing complex networks. Recently, a new mesoscale structure, core-periphery (CP) structure, has been identified in many real-world systems. In this paper, we propose an effective algorithm for detecting CP structure based on a 3-tuple motif. In this algorithm, we first define a 3-tuple motif in terms of the patterns of edges as well as the property of nodes, and then a motif adjacency matrix is constructed based on the 3-tuple motif. Finally, the problem is converted to find a cluster that minimizes the smallest motif conductance. Our algorithm works well in different CP structures: including single or multiple CP structure, and local or global CP structures. Results on the synthetic and the empirical networks validate the high performance of our method.
A Paleomagnetic and Diagenetic Study of the Woodford Shale, Oklahoma, U.S.A.: The Timing of Hydrothermal Alteration

NASA Astrophysics Data System (ADS)

Roberts, J.; Elmore, R. D.

2017-12-01

An oriented Woodford Shale core from the Ardmore Basin near the Ouachita thrust zone (Core B) was sampled to identify diagenetic events and interpret their origin, and to test if a magnetization was present that can be used to date the altering event(s). The shale is extensively altered, exhibiting a complex paragenesis with multiple fractures and brecciated intervals. Multiple hydrothermal minerals, including biotite, magnesite, norsethite, witherite, gorceixite, potassium feldspar, sphalerite, chalcopyrite, and saddle dolomite, are present in and around fractures and in the matrix. Vitrinite and bitumen reflectance measurements indicate VRo values of 1.82% ( 230°C). Two other Woodford Shale cores (A and C) from the Anadarko Basin also contain hydrothermal minerals. Vitrinite and bitumen reflectance data reveal trends between thermal maturity and the level of hydrothermal alteration, with Core A (0.80% VRo ( 125°C) displaying the lowest alteration, and Core C ( 1.5% VRo ( 210°C) displaying intermediate alteration compared to core B. Paleomagnetic analysis of Core B reveals the presence of a characteristic remanent magnetization (ChRM) with south-southeasterly declinations and shallow inclinations that is unblocked by 450°C and is interpreted to reside in magnetite. This ChRM is interpreted to be either a chemical remanent magnetization (CRM) or a thermochemical remanent magnetization (TCRM) acquired during the Late Permian based on the pole position. The presence of specimens with the CRM/TCRM in altered rock and high thermal maturities suggests that this CRM/TCRM originated from alteration by hydrothermal fluids. These results suggest that the Woodford Shale evolved into an open diagenetic system. In addition to causing heightened thermal maturities, these hydrothermal fluids both increased porosity through dissolution and decreased porosity through precipitation of minerals. The Late Permian timing agrees with the dating of hydrothermal alteration found within the Ouachita and Arbuckle Mountains in other studies. The timing for these events is postcollisional, and the most consistent model for the origin of the hydrothermal minerals is fluid flow as a result of faulting that accessed reservoir(s) of warm fluids.
Transcription co-activator SAYP mediates the action of STAT activator.

PubMed

Panov, Vladislav V; Kuzmina, Julia L; Doronin, Semen A; Kopantseva, Marina R; Nabirochkina, Elena N; Georgieva, Sofia G; Vorobyeva, Nadezhda E; Shidlovskii, Yulii V

2012-03-01

Jak/STAT is an important signaling pathway mediating multiple events in development. We describe participation of metazoan co-activator SAYP/PHF10 in this pathway downstream of STAT. The latter, via its activation domain, interacts with the conserved core of SAYP. STAT is associated with the SAYP-containing co-activator complex BTFly and recruits BTFly onto genes. SAYP is necessary for stimulating STAT-driven transcription of numerous genes. Mutation of SAYP leads to maldevelopments similar to those observed in STAT mutants. Thus, SAYP is a novel co-activator mediating the action of STAT.
Social networks and family violence in cross-cultural perspective.

PubMed

Korbin, J E

1995-01-01

The purpose of this chapter was twofold. First, the chapter put forward a brief cross-cultural perspective indicating that multiple types of intrafamilial violence occur cross-culturally. Second, the chapter placed social networks at the core of a complex etiology of intrafamilial violence. The purpose of giving centrality to social networks is not to suggest that social networks are the sole or primary agent contributing to family violence but to broaden the context in which family violence is viewed beyond that of the perpetrator, the victim/survivor, or the violent dyad.
Molecular Structure of the Pyruvate Dehydrogenase Complex from Escherichia coli K-12

PubMed Central

Vogel, Otto; Hoehn, Barbara; Henning, Ulf

1972-01-01

The pyruvate dehydrogenase core complex from E. coli K-12, defined as the multienzyme complex that can be obtained with a unique polypeptide chain composition, has a molecular weight of 3.75 × 106. All results obtained agree with the following numerology. The core complex consists of 48 polypeptide chains. There are 16 chains (molecular weight = 100,000) of the pyruvate dehydrogenase component, 16 chains (molecular weight = 80,000) of the dihydrolipoamide dehydrogenase component, and 16 chains (molecular weight = 56,000) of the dihydrolipoamide dehydrogenase component. Usually, but not always, pyruvate dehydrogenase complex is produced in vivo containing at least 2-3 mol more of dimers of the pyruvate dehydrogenase component than the stoichiometric ratio with respect to the core complex. This “excess” component is bound differently than are the eight dimers in the core complex. Images PMID:4556465
Common and distinctive localization patterns of Crumbs polarity complex proteins in the mammalian eye.

PubMed

Kim, Jin Young; Song, Ji Yun; Karnam, Santi; Park, Jun Young; Lee, Jamie J H; Kim, Seonhee; Cho, Seo-Hee

2015-01-01

Crumbs polarity complex proteins are essential for cellular and tissue polarity, and for adhesion of epithelial cells. In epithelial tissues deletion of any of three core proteins disrupts localization of the other proteins, indicating structural and functional interdependence among core components. Despite previous studies of function and co-localization that illustrated the properties that these proteins share, it is not known whether an individual component of the complex plays a distinct role in a unique cellular and developmental context. In order to investigate this question, we primarily used confocal imaging to determine the expression and subcellular localization of the core Crumbs polarity complex proteins during ocular development. Here we show that in developing ocular tissues core Crumbs polarity complex proteins, Crb, Pals1 and Patj, generally appear in an overlapping pattern with some exceptions. All three core complex proteins localize to the apical junction of the retinal and lens epithelia. Pals1 is also localized in the Golgi of the retinal cells and Patj localizes to the nuclei of the apically located subset of progenitor cells. These findings suggest that core Crumbs polarity complex proteins exert common and independent functions depending on cellular context. Copyright © 2015 Elsevier B.V. All rights reserved.
Structure of the dimeric PufX-containing core complex of Rhodobacter blasticus by in situ atomic force microscopy.

PubMed

Scheuring, Simon; Busselez, Johan; Lévy, Daniel

2005-01-14

We have studied photosynthetic membranes of wild type Rhodobacter blasticus, a closely related strain to the well studied Rhodobacter sphaeroides, using atomic force microscopy. High-resolution atomic force microscopy topographs of both cytoplasmic and periplasmic surfaces of LH2 and RC-LH1-PufX (RC, reaction center) complexes were acquired in situ. The LH2 is a nonameric ring inserted into the membrane with the 9-fold axis perpendicular to the plane. The core complex is an S-shaped dimer composed of two RCs, each encircled by 13 LH1 alpha/beta-heterodimers, and two PufXs. The LH1 assembly is an open ellipse with a topography-free gap of approximately 25 A. The two PufXs, one of each core, are located at the dimer center. Based on our data, we propose a model of the core complex, which provides explanation for the PufX-induced dimerization of the Rhodobacter core complex. The QB site is located facing a approximately 25-A wide gap within LH1, explaining the PufX-favored quinone passage in and out of the core complex.
TOWARD A DETERMINISTIC MODEL OF PLANETARY FORMATION. VII. ECCENTRICITY DISTRIBUTION OF GAS GIANTS

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

Ida, S.; Lin, D. N. C.; Nagasawa, M., E-mail: ida@geo.titech.ac.jp, E-mail: lin@ucolick.org, E-mail: nagasawa.m.ad@m.titech.ac.jp

2013-09-20

The ubiquity of planets and diversity of planetary systems reveal that planet formation encompasses many complex and competing processes. In this series of papers, we develop and upgrade a population synthesis model as a tool to identify the dominant physical effects and to calibrate the range of physical conditions. Recent planet searches have led to the discovery of many multiple-planet systems. Any theoretical models of their origins must take into account dynamical interactions between emerging protoplanets. Here, we introduce a prescription to approximate the close encounters between multiple planets. We apply this method to simulate the growth, migration, and dynamicalmore » interaction of planetary systems. Our models show that in relatively massive disks, several gas giants and rocky/icy planets emerge, migrate, and undergo dynamical instability. Secular perturbation between planets leads to orbital crossings, eccentricity excitation, and planetary ejection. In disks with modest masses, two or less gas giants form with multiple super-Earths. Orbital stability in these systems is generally maintained and they retain the kinematic structure after gas in their natal disks is depleted. These results reproduce the observed planetary mass-eccentricity and semimajor axis-eccentricity correlations. They also suggest that emerging gas giants can scatter residual cores to the outer disk regions. Subsequent in situ gas accretion onto these cores can lead to the formation of distant (∼> 30 AU) gas giants with nearly circular orbits.« less
Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways

PubMed Central

Kawakami, Eiryo; Singh, Vivek K; Matsubara, Kazuko; Ishii, Takashi; Matsuoka, Yukiko; Hase, Takeshi; Kulkarni, Priya; Siddiqui, Kenaz; Kodilkar, Janhavi; Danve, Nitisha; Subramanian, Indhupriya; Katoh, Manami; Shimizu-Yoshida, Yuki; Ghosh, Samik; Jere, Abhay; Kitano, Hiroaki

2016-01-01

Cellular stress responses require exquisite coordination between intracellular signaling molecules to integrate multiple stimuli and actuate specific cellular behaviors. Deciphering the web of complex interactions underlying stress responses is a key challenge in understanding robust biological systems and has the potential to lead to the discovery of targeted therapeutics for diseases triggered by dysregulation of stress response pathways. We constructed large-scale molecular interaction maps of six major stress response pathways in Saccharomyces cerevisiae (baker’s or budding yeast). Biological findings from over 900 publications were converted into standardized graphical formats and integrated into a common framework. The maps are posted at http://www.yeast-maps.org/yeast-stress-response/ for browse and curation by the research community. On the basis of these maps, we undertook systematic analyses to unravel the underlying architecture of the networks. A series of network analyses revealed that yeast stress response pathways are organized in bow–tie structures, which have been proposed as universal sub-systems for robust biological regulation. Furthermore, we demonstrated a potential role for complexes in stabilizing the conserved core molecules of bow–tie structures. Specifically, complex-mediated reversible reactions, identified by network motif analyses, appeared to have an important role in buffering the concentration and activity of these core molecules. We propose complex-mediated reactions as a key mechanism mediating robust regulation of the yeast stress response. Thus, our comprehensive molecular interaction maps provide not only an integrated knowledge base, but also a platform for systematic network analyses to elucidate the underlying architecture in complex biological systems. PMID:28725465
Accelerating the Mining of Influential Nodes in Complex Networks through Community Detection

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

Halappanavar, Mahantesh; Sathanur, Arun V.; Nandi, Apurba

Computing the set of influential nodes with a given size to ensure maximal spread of influence on a complex network is a challenging problem impacting multiple applications. A rigorous approach to influence maximization involves utilization of optimization routines that comes with a high computational cost. In this work, we propose to exploit the existence of communities in complex networks to accelerate the mining of influential seeds. We provide intuitive reasoning to explain why our approach should be able to provide speedups without significantly degrading the extent of the spread of influence when compared to the case of influence maximization withoutmore » using the community information. Additionally, we have parallelized the complete workflow by leveraging an existing parallel implementation of the Louvain community detection algorithm. We then conduct a series of experiments on a dataset with three representative graphs to first verify our implementation and then demonstrate the speedups. Our method achieves speedups ranging from 3x - 28x for graphs with small number of communities while nearly matching or even exceeding the activation performance on the entire graph. Complexity analysis reveals that dramatic speedups are possible for larger graphs that contain a correspondingly larger number of communities. In addition to the speedups obtained from the utilization of the community structure, scalability results show up to 6.3x speedup on 20 cores relative to the baseline run on 2 cores. Finally, current limitations of the approach are outlined along with the planned next steps.« less
Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants.

PubMed

Hunt, Arthur G; Xing, Denghui; Li, Qingshun Q

2012-11-20

Polyadenylation, an essential step in eukaryotic gene expression, requires both cis-elements and a plethora of trans-acting polyadenylation factors. The polyadenylation factors are largely conserved across mammals and fungi. The conservation seems also extended to plants based on the analyses of Arabidopsis polyadenylation factors. To extend this observation, we systemically identified the orthologs of yeast and human polyadenylation factors from 10 plant species chosen based on both the availability of their genome sequences and their positions in the evolutionary tree, which render them representatives of different plant lineages. The evolutionary trajectories revealed several interesting features of plant polyadenylation factors. First, the number of genes encoding plant polyadenylation factors was clearly increased from "lower" to "higher" plants. Second, the gene expansion in higher plants was biased to some polyadenylation factors, particularly those involved in RNA binding. Finally, while there are clear commonalities, the differences in the polyadenylation apparatus were obvious across different species, suggesting an ongoing process of evolutionary change. These features lead to a model in which the plant polyadenylation complex consists of a conserved core, which is rather rigid in terms of evolutionary conservation, and a panoply of peripheral subunits, which are less conserved and associated with the core in various combinations, forming a collection of somewhat distinct complex assemblies. The multiple forms of plant polyadenylation complex, together with the diversified polyA signals may explain the intensive alternative polyadenylation (APA) and its regulatory role in biological functions of higher plants.
Scheduler for multiprocessor system switch with selective pairing

DOEpatents

Gara, Alan; Gschwind, Michael Karl; Salapura, Valentina

2015-01-06

System, method and computer program product for scheduling threads in a multiprocessing system with selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). The method configures the selective pairing facility to use checking provide one highly reliable thread for high-reliability and allocate threads to corresponding processor cores indicating need for hardware checking. The method configures the selective pairing facility to provide multiple independent cores and allocate threads to corresponding processor cores indicating inherent resilience.
Monomeric RC-LH1 core complexes retard LH2 assembly and intracytoplasmic membrane formation in PufX-minus mutants of Rhodobacter sphaeroides.

PubMed

Adams, Peter G; Mothersole, David J; Ng, Irene W; Olsen, John D; Hunter, C Neil

2011-09-01

In the model photosynthetic bacterium Rhodobacter sphaeroides domains of light-harvesting 2 (LH2) complexes surround and interconnect dimeric reaction centre-light-harvesting 1-PufX (RC-LH1-PufX) 'core' complexes, forming extensive networks for energy transfer and trapping. These complexes are housed in spherical intracytoplasmic membranes (ICMs), which are assembled in a stepwise process where biosynthesis of core complexes tends to dominate the early stages of membrane invagination. The kinetics of LH2 assembly were measured in PufX mutants that assemble monomeric core complexes, as a consequence of either a twelve-residue N-terminal truncation of PufX (PufXΔ12) or the complete removal of PufX (PufX(-)). Lower rates of LH2 assembly and retarded maturation of membrane invagination were observed for the larger and less curved ICM from the PufX(-) mutant, consistent with the proposition that local membrane curvature, initiated by arrays of bent RC-LH1-PufX dimers, creates a favourable environment for stable assembly of LH2 complexes. Transmission electron microscopy and high-resolution atomic force microscopy were used to examine ICM morphology and membrane protein organisation in these mutants. Some partitioning of core and LH2 complexes was observed in PufX(-) membranes, resulting in locally ordered clusters of monomeric RC-LH1 complexes. The distribution of core and LH2 complexes in the three types of membrane examined is consistent with previous models of membrane curvature and domain formation (Frese et al., 2008), which demonstrated that a combination of crowding and asymmetries in sizes and shapes of membrane protein complexes drives membrane organisation. 2011 Elsevier B.V. All rights reserved.
Evaluating the core microbiota in complex communities: A systematic investigation.

PubMed

Astudillo-García, Carmen; Bell, James J; Webster, Nicole S; Glasl, Bettina; Jompa, Jamaluddin; Montoya, Jose M; Taylor, Michael W

2017-04-01

The study of complex microbial communities poses unique conceptual and analytical challenges, with microbial species potentially numbering in the thousands. With transient or allochthonous microorganisms often adding to this complexity, a 'core' microbiota approach, focusing only on the stable and permanent members of the community, is becoming increasingly popular. Given the various ways of defining a core microbiota, it is prudent to examine whether the definition of the core impacts upon the results obtained. Here we used complex marine sponge microbiotas and undertook a systematic evaluation of the degree to which different factors used to define the core influenced the conclusions. Significant differences in alpha- and beta-diversity were detected using some but not all core definitions. However, findings related to host specificity and environmental quality were largely insensitive to major changes in the core microbiota definition. Furthermore, none of the applied definitions altered our perception of the ecological networks summarising interactions among bacteria within the sponges. These results suggest that, while care should still be taken in interpretation, the core microbiota approach is surprisingly robust, at least for comparing microbiotas of closely related samples. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.
Unsymmetrical Bimetallic Complexes with MII–(μ-OH)–MII Cores (MIIMIII = FeIIFeIII, MnIIFeIII, MnIIMnIII): Structural, Magnetic, and Redox Properties

PubMed Central

Sano, Yohei; Weitz, Andrew C.; Ziller, Joseph W.; Hendrich, Michael P.; Borovik, A.S.

2013-01-01

Heterobimetallic cores are important unit within the active sites of metalloproteins, but are often difficult to duplicate in synthetic systems. We have developed a synthetic approach for the preparation of a complex with a MnII–(μ-OH)–FeIII core, in which the metal centers have different coordination environments. Structural and physical data support the assignment of this complex as a heterobimetallic system. Comparison with the analogous homobimetallic complexes, those containing MnII–(μ-OH)–MnIII and FeII–(μ-OH)–FeIII cores, further supports this assignment. PMID:23992041

Education research: a case-based bioethics curriculum for neurology residents.

PubMed

Tolchin, Benjamin; Willey, Joshua Z; Prager, Kenneth

2015-03-31

In 2012, the American Academy of Neurology (AAN) updated and expanded its ethics curriculum into Practical Ethics in Clinical Neurology, a case-based ethics curriculum for neurologists. We piloted a case-based bioethics curriculum for neurology residents using the framework and topics recommended by the AAN, matched to clinical cases drawn from Columbia's neurologic services. Our primary outcome was residents' ability to analyze and manage ethically complex cases as measured on precurriculum and postcurriculum multiple-choice quizzes. Secondary outcomes included precurriculum and postcurriculum self-assessed comfort in discussing and managing ethically complex cases, as well as attendance at ethics discussion sessions as compared to attendance at other didactic sessions. Resident performance on quizzes improved from 75.8% to 86.7% (p = 0.02). Comfort in discussing ethically complex cases improved from 6.4 to 7.4 on a 10-point scale (p = 0.03). Comfort in managing such cases trended toward improvement but did not reach statistical significance. Attendance was significantly better at ethics discussions (73.5%) than at other didactic sessions (61.7%, p = 0.04). Our formal case-based ethics curriculum for neurology residents, based on core topics drawn from the AAN's published curricula, was successfully piloted. Our study showed a statistically significant improvement in residents' ability to analyze and manage ethically complex cases as measured by multiple-choice tests and self-assessments. © 2015 American Academy of Neurology.
Results of the Simulation of the HTR-Proteus Core 4.2 Using PEBBED-COMBINE: FY10 Report

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

Hans Gougar

2010-07-01

ABSTRACT The Idaho National Laboratory’s deterministic neutronics analysis codes and methods were applied to the computation of the core multiplication factor of the HTR-Proteus pebble bed reactor critical facility. This report is a follow-on to INL/EXT-09-16620 in which the same calculation was performed but using earlier versions of the codes and less developed methods. In that report, results indicated that the cross sections generated using COMBINE-7.0 did not yield satisfactory estimates of keff. It was concluded in the report that the modeling of control rods was not satisfactory. In the past year, improvements to the homogenization capability in COMBINE havemore » enabled the explicit modeling of TRIS particles, pebbles, and heterogeneous core zones including control rod regions using a new multi-scale version of COMBINE in which the 1-dimensional discrete ordinate transport code ANISN has been integrated. The new COMBINE is shown to yield benchmark quality results for pebble unit cell models, the first step in preparing few-group diffusion parameters for core simulations. In this report, the full critical core is modeled once again but with cross sections generated using the capabilities and physics of the improved COMBINE code. The new PEBBED-COMBINE model enables the exact modeling of the pebbles and control rod region along with better approximation to structures in the reflector. Initial results for the core multiplication factor indicate significant improvement in the INL’s tools for modeling the neutronic properties of a pebble bed reactor. Errors on the order of 1.6-2.5% in keff are obtained; a significant improvement over the 5-6% error observed in the earlier This is acceptable for a code system and model in the early stages of development but still too high for a production code. Analysis of a simpler core model indicates an over-prediction of the flux in the low end of the thermal spectrum. Causes of this discrepancy are under investigation. New homogenization techniques and assumptions were used in this analysis and as such, they require further confirmation and validation. Further refinement and review of the complex Proteus core model are likely to reduce the errors even further.« less
Chemical complexity induced by efficient ice evaporation in the Barnard 5 molecular cloud

NASA Astrophysics Data System (ADS)

Taquet, V.; Wirström, E. S.; Charnley, S. B.; Faure, A.; López-Sepulcre, A.; Persson, C. M.

2017-10-01

Cold gas-phase water has recently been detected in a cold dark cloud, Barnard 5 located in the Perseus complex, by targeting methanol peaks as signposts for ice mantle evaporation. Observed morphology and abundances of methanol and water are consistent with a transient non-thermal evaporation process only affecting the outermost ice mantle layers, possibly triggering a more complex chemistry. Here we present the detection of the complex organic molecules (COMs) acetaldehyde (CH3CHO) and methyl formate (CH3OCHO), as well as formic acid (HCOOH) and ketene (CH2CO), and the tentative detection of di-methyl ether (CH3OCH3) towards the "methanol hotspot" of Barnard 5 located between two dense cores using the single dish OSO 20 m, IRAM 30 m, and NRO 45 m telescopes. The high energy cis-conformer of formic acid is detected, suggesting that formic acid is mostly formed at the surface of interstellar grains and then evaporated. The detection of multiple transitions for each species allows us to constrain their abundances through LTE and non-LTE methods. All the considered COMs show similar abundances between 1 and 10% relative to methanol depending on the assumed excitation temperature. The non-detection of glycolaldehyde, an isomer of methyl formate, with a [glycolaldehyde]/[methyl formate] abundance ratio lower than 6%, favours gas phase formation pathways triggered by methanol evaporation. According to their excitation temperatures derived in massive hot cores, formic acid, ketene, and acetaldehyde have been designated as "lukewarm" COMs whereas methyl formate and di-methyl ether were defined as "warm" species. Comparison with previous observations of other types of sources confirms that lukewarm and warm COMs show similar abundances in low-density cold gas whereas the warm COMs tend to be more abundant than the lukewarm species in warm protostellar cores. This abundance evolution suggests either that warm COMs are indeed mostly formed in protostellar environments and/or that lukewarm COMs are efficiently depleted by increased hydrogenation efficiency around protostars.
Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network.

PubMed

Shen, Xianjun; Yi, Li; Jiang, Xingpeng; He, Tingting; Yang, Jincai; Xie, Wei; Hu, Po; Hu, Xiaohua

2017-01-01

How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI) data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes. In order to achieve this goal, this paper proposes a novel algorithm DCA (Dynamic Core-Attachment). It detects protein-complex core comprising of continually expressed and highly connected proteins in dynamic PPI network, and then the protein complex is formed by including the attachments with high adhesion into the core. The integration of core-attachment feature into the dynamic PPI network is responsible for the superiority of our algorithm. DCA has been applied on two different yeast dynamic PPI networks and the experimental results show that it performs significantly better than the state-of-the-art techniques in terms of prediction accuracy, hF-measure and statistical significance in biology. In addition, the identified complexes with strong biological significance provide potential candidate complexes for biologists to validate.
Multi-view L2-SVM and its multi-view core vector machine.

PubMed

Huang, Chengquan; Chung, Fu-lai; Wang, Shitong

2016-03-01

In this paper, a novel L2-SVM based classifier Multi-view L2-SVM is proposed to address multi-view classification tasks. The proposed Multi-view L2-SVM classifier does not have any bias in its objective function and hence has the flexibility like μ-SVC in the sense that the number of the yielded support vectors can be controlled by a pre-specified parameter. The proposed Multi-view L2-SVM classifier can make full use of the coherence and the difference of different views through imposing the consensus among multiple views to improve the overall classification performance. Besides, based on the generalized core vector machine GCVM, the proposed Multi-view L2-SVM classifier is extended into its GCVM version MvCVM which can realize its fast training on large scale multi-view datasets, with its asymptotic linear time complexity with the sample size and its space complexity independent of the sample size. Our experimental results demonstrated the effectiveness of the proposed Multi-view L2-SVM classifier for small scale multi-view datasets and the proposed MvCVM classifier for large scale multi-view datasets. Copyright © 2015 Elsevier Ltd. All rights reserved.
Symbolic bones and interethnic violence in a frontier zone, northwest Mexico, ca. 500–900 C.E.

PubMed Central

Nelson, Ben A.; Martin, Debra L.

2015-01-01

Although extensive deposits of disarticulated, commingled human bones are common in the prehispanic Northern Frontier of Mesoamerica, detailed bioarchaeological analyses of them are not. To our knowledge, this article provides the first such analysis of bone from a full residential-ceremonial complex and evaluates multiple hypotheses about its significance, concluding that the bones actively represented interethnic violence as well as other relationships among persons living and dead. Description of these practices is important to the discussion of multiethnic societies because the frontier was a context where urbanism and complexity were emerging and groups with the potential to form multiethnic societies were interacting, possibly in the same ways that groups did before the formation of larger multiethnic city-states in the core of Mesoamerica. PMID:25941398
Symbolic bones and interethnic violence in a frontier zone, northwest Mexico, ca. 500-900 C.E.

PubMed

Nelson, Ben A; Martin, Debra L

2015-07-28

Although extensive deposits of disarticulated, commingled human bones are common in the prehispanic Northern Frontier of Mesoamerica, detailed bioarchaeological analyses of them are not. To our knowledge, this article provides the first such analysis of bone from a full residential-ceremonial complex and evaluates multiple hypotheses about its significance, concluding that the bones actively represented interethnic violence as well as other relationships among persons living and dead. Description of these practices is important to the discussion of multiethnic societies because the frontier was a context where urbanism and complexity were emerging and groups with the potential to form multiethnic societies were interacting, possibly in the same ways that groups did before the formation of larger multiethnic city-states in the core of Mesoamerica.
Enantioselective synthesis of pactamycin, a complex antitumor antibiotic.

PubMed

Malinowski, Justin T; Sharpe, Robert J; Johnson, Jeffrey S

2013-04-12

Medicinal application of many complex natural products is precluded by the impracticality of their chemical synthesis. Pactamycin, the most structurally intricate aminocyclopentitol antibiotic, displays potent antiproliferative properties across multiple phylogenetic domains, but it is highly cytotoxic. A limited number of analogs produced by genetic engineering technologies show reduced cytotoxicity against mammalian cells, renewing promise for therapeutic applications. For decades, an efficient synthesis of pactamycin amenable to analog derivatizations has eluded researchers. Here, we present a short asymmetric total synthesis of pactamycin. An enantioselective Mannich reaction and symmetry-breaking reduction sequence was designed to enable assembly of the entire carbon core skeleton in under five steps and control critical three-dimensional (stereochemical) functional group relationships. This modular route totals 15 steps and is immediately amenable for structural analog synthesis.
Multiphase boudinage: a case study of amphibolites in marble in the Naxos migmatite core

NASA Astrophysics Data System (ADS)

Virgo, Simon; von Hagke, Christoph; Urai, Janos L.

2018-02-01

In multiply deformed terrains multiphase boudinage is common, but identification and analysis of these is difficult. Here we present an analysis of multiphase boudinage and fold structures in deformed amphibolite layers in marble from the migmatitic centre of the Naxos metamorphic core complex. Overprinting between multiple boudinage generations is shown in exceptional 3-D outcrop. We identify five generations of boudinage, reflecting the transition from high-strain high-temperature ductile deformation to medium- to low-strain brittle boudins formed during cooling and exhumation. All boudin generations indicate E-W horizontal shortening and variable direction of bedding parallel extension, evolving from subvertical extension in the earliest boudins to subhorizontal N-S extension during exhumation. Two phases of E-W shortening can be inferred, the first associated with lower crustal synmigmatic convergent flow and the second associated with exhumation and N-S extension, possibly related to movement of the North Anatolian Fault.
Optic Atrophy 1 Is Epistatic to the Core MICOS Component MIC60 in Mitochondrial Cristae Shape Control.

PubMed

Glytsou, Christina; Calvo, Enrique; Cogliati, Sara; Mehrotra, Arpit; Anastasia, Irene; Rigoni, Giovanni; Raimondi, Andrea; Shintani, Norihito; Loureiro, Marta; Vazquez, Jesùs; Pellegrini, Luca; Enriquez, Jose Antonio; Scorrano, Luca; Soriano, Maria Eugenia

2016-12-13

The mitochondrial contact site and cristae organizing system (MICOS) and Optic atrophy 1 (OPA1) control cristae shape, thus affecting mitochondrial function and apoptosis. Whether and how they physically and functionally interact is unclear. Here, we provide evidence that OPA1 is epistatic to MICOS in the regulation of cristae shape. Proteomic analysis identifies multiple MICOS components in native OPA1-containing high molecular weight complexes disrupted during cristae remodeling. MIC60, a core MICOS protein, physically interacts with OPA1, and together, they control cristae junction number and stability, OPA1 being epistatic to MIC60. OPA1 defines cristae width and junction diameter independently of MIC60. Our combination of proteomics, biochemistry, genetics, and electron tomography provides a unifying model for mammalian cristae biogenesis by OPA1 and MICOS. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.
Multiple Small Diameter Drillings Increase Femoral Neck Stability Compared with Single Large Diameter Femoral Head Core Decompression Technique for Avascular Necrosis of the Femoral Head.

PubMed

Brown, Philip J; Mannava, Sandeep; Seyler, Thorsten M; Plate, Johannes F; Van Sikes, Charles; Stitzel, Joel D; Lang, Jason E

2016-10-26

Femoral head core decompression is an efficacious joint-preserving procedure for treatment of early stage avascular necrosis. However, postoperative fractures have been described which may be related to the decompression technique used. Femoral head decompressions were performed on 12 matched human cadaveric femora comparing large 8mm single bore versus multiple 3mm small drilling techniques. Ultimate failure strength of the femora was tested using a servo-hydraulic material testing system. Ultimate load to failure was compared between the different decompression techniques using two paired ANCOVA linear regression models. Prior to biomechanical testing and after the intervention, volumetric bone mineral density was determined using quantitative computed tomography to account for variation between cadaveric samples and to assess the amount of bone disruption by the core decompression. Core decompression, using the small diameter bore and multiple drilling technique, withstood significantly greater load prior to failure compared with the single large bore technique after adjustment for bone mineral density (p< 0.05). The 8mm single bore technique removed a significantly larger volume of bone compared to the 3mm multiple drilling technique (p< 0.001). However, total fracture energy was similar between the two core decompression techniques. When considering core decompression for the treatment of early stage avascular necrosis, the multiple small bore technique removed less bone volume, thereby potentially leading to higher load to failure.
The Conceptual Complexity of Vocabulary in Elementary-Grades Core Science Program Textbooks

ERIC Educational Resources Information Center

Fitzgerald, W. Jill; Elmore, Jeff; Kung, Melody; Stenner, A. Jackson

2017-01-01

The researchers explored the conceptual complexity of vocabulary in contemporary elementary-grades core science program textbooks to address two research questions: (1) Can a progression of concepts' complexity level be described across grades? (2) Was there gradual developmental growth of the most complex concepts' networks of associated concepts…
Calcified cartilage or bone? Collagens in the tessellated endoskeletons of cartilaginous fish (sharks and rays).

PubMed

Seidel, Ronald; Blumer, Michael; Pechriggl, Elisabeth-Judith; Lyons, Kady; Hall, Brian K; Fratzl, Peter; Weaver, James C; Dean, Mason N

2017-10-01

The primary skeletal tissue in elasmobranchs -sharks, rays and relatives- is cartilage, forming both embryonic and adult endoskeletons. Only the skeletal surface calcifies, exhibiting mineralized tiles (tesserae) sandwiched between a cartilage core and overlying fibrous perichondrium. These two tissues are based on different collagens (Coll II and I, respectively), fueling a long-standing debate as to whether tesserae are more like calcified cartilage or bone (Coll 1-based) in their matrix composition. We demonstrate that stingray (Urobatis halleri) tesserae are bipartite, having an upper Coll I-based 'cap' that merges into a lower Coll II-based 'body' zone, although tesserae are surrounded by cartilage. We identify a 'supratesseral' unmineralized cartilage layer, between tesserae and perichondrium, distinguished from the cartilage core in containing Coll I and X (a common marker for mammalian mineralization), in addition to Coll II. Chondrocytes within tesserae appear intact and sit in lacunae filled with Coll II-based matrix, suggesting tesserae originate in cartilage, despite comprising a diversity of collagens. Intertesseral joints are also complex in their collagenous composition, being similar to supratesseral cartilage closer to the perichondrium, but containing unidentified fibrils nearer the cartilage core. Our results indicate a unique potential for tessellated cartilage in skeletal biology research, since it lacks features believed diagnostic for vertebrate cartilage mineralization (e.g. hypertrophic and apoptotic chondrocytes), while offering morphologies amenable for investigating the regulation of complex mineralized ultrastructure and tissues patterned on multiple collagens. Copyright © 2017 Elsevier Inc. All rights reserved.
Mediator independently orchestrates multiple steps of preinitiation complex assembly in vivo

PubMed Central

Eyboulet, Fanny; Wydau-Dematteis, Sandra; Eychenne, Thomas; Alibert, Olivier; Neil, Helen; Boschiero, Claire; Nevers, Marie-Claire; Volland, Hervé; Cornu, David; Redeker, Virginie; Werner, Michel; Soutourina, Julie

2015-01-01

Mediator is a large multiprotein complex conserved in all eukaryotes, which has a crucial coregulator function in transcription by RNA polymerase II (Pol II). However, the molecular mechanisms of its action in vivo remain to be understood. Med17 is an essential and central component of the Mediator head module. In this work, we utilised our large collection of conditional temperature-sensitive med17 mutants to investigate Mediator's role in coordinating preinitiation complex (PIC) formation in vivo at the genome level after a transfer to a non-permissive temperature for 45 minutes. The effect of a yeast mutation proposed to be equivalent to the human Med17-L371P responsible for infantile cerebral atrophy was also analyzed. The ChIP-seq results demonstrate that med17 mutations differentially affected the global presence of several PIC components including Mediator, TBP, TFIIH modules and Pol II. Our data show that Mediator stabilizes TFIIK kinase and TFIIH core modules independently, suggesting that the recruitment or the stability of TFIIH modules is regulated independently on yeast genome. We demonstrate that Mediator selectively contributes to TBP recruitment or stabilization to chromatin. This study provides an extensive genome-wide view of Mediator's role in PIC formation, suggesting that Mediator coordinates multiple steps of a PIC assembly pathway. PMID:26240385
Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes

PubMed Central

Benjamino, Jacquelynn; Graf, Joerg

2016-01-01

The hindgut of the termite Reticulitermes flavipes harbors a complex symbiotic community consisting of protists, bacteria, and archaea. These symbionts aid in the digestion of lignocellulose from the termite’s wood meal. Termite hindguts were sampled and the V4 hyper-variable region of the 16S rRNA gene was sequenced and analyzed from individual termites. The core microbiota of worker termites consisted of 69 OTUs at the 97% identity level, grouped into 16 taxa, and together accounted for 67.05% of the sequences from the bacterial community. The core was dominated by Treponema, which contained 36 different OTUs and accounted for ∼32% of the sequences, which suggests Treponema sp. have an important impact on the overall physiology in the hindgut. Bray–Curtis beta diversity metrics showed that hindgut samples from termites of the same colony were more similar to each other than to samples from other colonies despite possessing a core that accounted for the majority of the sequences. The specific tasks and dietary differences of the termite castes could have an effect on the composition of the microbial community. The hindgut microbiota of termites from the alate castes differed from the worker caste with significantly lower abundances of Treponema and Endomicrobia, which dominated the hindgut microbiota in workers and soldiers. Protist abundances were also quantified in the same samples using qPCR of the 18S rRNA gene. Parabasalia abundances dropped significantly in the winged alates and the Oxymonadida abundances dropped in both alate castes. These data suggest that the changes in diet or overall host physiology affected the protist and bacterial populations in the hindgut. The in-depth bacterial characterization and protist quantification in this study sheds light on the potential community dynamics within the R. flavipes hindgut and identified a large and complex core microbiota in termites obtained from multiple colonies and castes. PMID:26925043
MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity

NASA Astrophysics Data System (ADS)

Zheng, Jingjing; Mielke, Steven L.; Clarkson, Kenneth L.; Truhlar, Donald G.

2012-08-01

We present a Fortran program package, MSTor, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsional motions by the recently proposed MS-T method. This method interpolates between the local harmonic approximation in the low-temperature limit, and the limit of free internal rotation of all torsions at high temperature. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes six utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Catalogue identifier: AEMF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 77 434 No. of bytes in distributed program, including test data, etc.: 3 264 737 Distribution format: tar.gz Programming language: Fortran 90, C, and Perl Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), Elmo (Sun Fire X4600 Linux cluster with AMD Opteron cores), and Mac Pro (two 2.8 GHz Quad-core Intel Xeon processors) Operating system: Linux/Unix/Mac OS RAM: 2 Mbytes Classification: 16.3, 16.12, 23 Nature of problem: Calculation of the partition functions and thermodynamic functions (standard-state energy, enthalpy, entropy, and free energy as functions of temperatures) of complex molecules involving multiple torsional motions. Solution method: The multi-structural approximation with torsional anharmonicity (MS-T). The program also provides results for the multi-structural local harmonic approximation [1]. Restrictions: There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multi-torsional problems for which one can afford to calculate all the conformations and their frequencies. Unusual features: The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes and six utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomain defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Additional comments: The program package includes a manual, installation script, and input and output files for a test suite. Running time: There are 24 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 seconds. J. Zheng, T. Yu, E. Papajak, I.M. Alecu, S.L. Mielke, D.G. Truhlar, Practical methods for including torsional anharmonicity in thermochemical calculations of complex molecules: The internal-coordinate multi-structural approximation, Phys. Chem. Chem. Phys. 13 (2011) 10885-10907.
P- T- t constraints on the development of the Doi Inthanon metamorphic core complex domain and implications for the evolution of the western gneiss belt, northern Thailand

NASA Astrophysics Data System (ADS)

Macdonald, A. S.; Barr, S. M.; Miller, B. V.; Reynolds, P. H.; Rhodes, B. P.; Yokart, B.

2010-01-01

The western gneiss belt in northern Thailand is exposed within two overlapping Cenozoic structural domains: the extensional Doi Inthanon metamorphic core complex domain located west of the Chiang Mai basin, and the Mae Ping strike-slip fault domain located west of the Tak batholith. New P- T estimates and U-Pb and 40Ar/ 39Ar age determinations from the Doi Inthanon domain show that the gneiss there records a complex multi-stage history that can be represented by a clockwise P- T- t path. U-Pb zircon and titanite dating of mylonitic calc-silicate gneiss from the Mae Wang area of the complex indicates that the paragneissic sequence experienced high-grade, medium-pressure metamorphism (M1) in the Late Triassic - Early Jurassic (ca. 210 Ma), in good agreement with previously determined zircon ages from the underlying core orthogneiss exposed on Doi Inthanon. Late Cretaceous monazite ages of 84 and 72 Ma reported previously from the core orthogneiss are attributed to a thermal overprint (M2) to upper-amphibolite facies in the sillimanite field. U-Pb zircon and monazite dating of granitic mylonite from the Doi Suthep area of the complex provides an upper age limit of 40 Ma (Late Eocene) for the early stage(s) of development of the actual core complex, by initially ductile, low-angle extensional shearing under lower amphibolite-facies conditions (M3), accompanied by near-isothermal diapiric rise and decompression melting. 40Ar/ 39Ar laserprobe dating of muscovite from both Doi Suthep and Doi Inthanon provided Miocene ages of ca. 26-15 Ma, representing cooling through the ca. 350 °C isotherm and marking late-stage development of the core complex by detachment faulting of the cover rocks and isostatic uplift of the sheared core zone and mantling gneisses in the footwall. Similarities in the thermochronology of high-grade gneisses exposed in the core complex and shear zone domains in the western gneiss belt of northern Thailand (and also in northern Vietnam, Laos, Yunnan, and central Myanmar) suggest a complex regional response to indentation of Southeast Asia by India.
Genetic Pedagogical Content Knowledge (PCK) Ability Profile of Prospective Biology Teacher

NASA Astrophysics Data System (ADS)

Purwianingsih, W.; Muthmainnah, E.; Hidayat, T.

2017-02-01

Genetics is one of the topics or subject matter in biology that are considered difficult. Student difficulties of understanding genetics, can be caused by lack of understanding this concept and the way of teachers teach. Pedagogical Content Knowledge (PCK) is a way to understand the complex relationships between teaching and content taught through the use of specific teaching approaches. The aims of study was to analyze genetic PCK ability profile of prospective biology teacher.13 student of sixth semester Biology education department who learned Kapita Selekta Biologi SMA course, participated in this study. PCK development was measured by CoRes (Content Representation). Before students fill CoRes, students are tested mastery genetic concepts through a multiple-choice test with three tier-test. Data was obtained from the prior CoRes and its revisions, as well as the mastery concept in pre and post test. Results showed that pre-test of genetic mastery concepts average on 55.4% (low category) and beginning of the writing CoRes, student get 43.2% (Pra PCK). After students get lecture and simulating learning, the post-test increased to 63.8% (sufficient category) and PCK revision is also increase 58.1% (growing PCK). It can be concluded that mastery of subject matter could affects the ability of genetic PCK.
Implementation of kernels on the Maestro processor

NASA Astrophysics Data System (ADS)

Suh, Jinwoo; Kang, D. I. D.; Crago, S. P.

Currently, most microprocessors use multiple cores to increase performance while limiting power usage. Some processors use not just a few cores, but tens of cores or even 100 cores. One such many-core microprocessor is the Maestro processor, which is based on Tilera's TILE64 processor. The Maestro chip is a 49-core, general-purpose, radiation-hardened processor designed for space applications. The Maestro processor, unlike the TILE64, has a floating point unit (FPU) in each core for improved floating point performance. The Maestro processor runs at 342 MHz clock frequency. On the Maestro processor, we implemented several widely used kernels: matrix multiplication, vector add, FIR filter, and FFT. We measured and analyzed the performance of these kernels. The achieved performance was up to 5.7 GFLOPS, and the speedup compared to single tile was up to 49 using 49 tiles.
The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles

PubMed Central

Topalidou, Irini; Cattin-Ortolá, Jérôme; MacCoss, Michael J.

2016-01-01

The dense-core vesicle is a secretory organelle that mediates the regulated release of peptide hormones, growth factors, and biogenic amines. Dense-core vesicles originate from the trans-Golgi of neurons and neuroendocrine cells, but it is unclear how this specialized organelle is formed and acquires its specific cargos. To identify proteins that act in dense-core vesicle biogenesis, we performed a forward genetic screen in Caenorhabditis elegans for mutants defective in dense-core vesicle function. We previously reported the identification of two conserved proteins that interact with the small GTPase RAB-2 to control normal dense-core vesicle cargo-sorting. Here we identify several additional conserved factors important for dense-core vesicle cargo sorting: the WD40 domain protein EIPR-1 and the endosome-associated recycling protein (EARP) complex. By assaying behavior and the trafficking of dense-core vesicle cargos, we show that mutants that lack EIPR-1 or EARP have defects in dense-core vesicle cargo-sorting similar to those of mutants in the RAB-2 pathway. Genetic epistasis data indicate that RAB-2, EIPR-1 and EARP function in a common pathway. In addition, using a proteomic approach in rat insulinoma cells, we show that EIPR-1 physically interacts with the EARP complex. Our data suggest that EIPR-1 is a new interactor of the EARP complex and that dense-core vesicle cargo sorting depends on the EARP-dependent trafficking of cargo through an endosomal sorting compartment. PMID:27191843

Mexican Ridges passive margin foldbelt of western Gulf of Mexico detached along the top of an extensive, Oligocene mass transport complex

NASA Astrophysics Data System (ADS)

Fick, A.; Mann, P.

2016-12-01

The Mexican Ridges fold-thrust belt (MRFTB) is a 110-210-km-wide and 500-600-km long passive margin, deep-water fold belt fringing the eastern Mexico continental shelf and deepwater western Gulf of Mexico (WGOM). Previous workers determined: 1) that the MRFTB formed in response to multiple gravity sliding events along multiple, Paleogene shale horizons during the Neogene and 2) that down-dip, east-west shortening ranges from 12-22 km in the deep western GOM basin is paired with updip extension of 9-10 km along the Mexican shelf. We have used a grid of 9,440 km's of 2D seismic lines tied to 2 wells to better constrain the detachment underlying the MRFTB. In the northern fold belt, fault detachment and detachment folds in the competent Neogene stratigraphy are cored by a ductile wedge of finer-grained Oligocene sediment ranging in thickness from 0-900 meters. The wedge covers approximately 81,750 km2 and extends 300 kilometers from its onlap onto the Eocene shelf to its downdip pinchout in the deepwater GOM basin. Previous workers have interpreted the Oligocene strata coring the folds to be composed of finer grained sediments with some chaotic seismic facies or homogeneous shales but have not mapped this detachment surface in detail. Our new 2D seismic reflection data tied to wells shows that the basal detachment of the MRFTB is a thickening-landward, wedge of stacked, fine-grained mass transport complexes (MTCs). This Oligocene aged MTC has experienced significant internal deformation in the proximal shelf area while its depositional facies are well preserved in the more distal deepwater areas of the GOM. Elevated pore and fluid pressure in the MTC complex may have contributed to its role as a regional detachment underlying the Mexican Ridges fold-thrust belt along with defining the regional, lobate geometry of the MRFTB.
Asteroid family dynamics in the inner main belt

NASA Astrophysics Data System (ADS)

Dykhuis, Melissa Joy

The inner main asteroid belt is an important source of near-Earth objects and terrestrial planet impactors; however, the dynamics and history of this region are challenging to understand, due to its high population density and the presence of multiple orbital resonances. This dissertation explores the properties of two of the most populous inner main belt family groups --- the Flora family and the Nysa-Polana complex --- investigating their memberships, ages, spin properties, collision dynamics, and range in orbital and reflectance parameters. Though diffuse, the family associated with asteroid (8) Flora dominates the inner main belt in terms of the extent of its members in orbital parameter space, resulting in its significant overlap with multiple neighboring families. This dissertation introduces a new method for membership determination (the core sample method) which enables the distinction of the Flora family from the background, permitting its further analysis. The Flora family is shown to have a signature in plots of semimajor axis vs. size consistent with that expected for a collisional family dispersed as a result of the Yarkovsky radiation effect. The family's age is determined from the Yarkovsky dispersion to be 950 My. Furthermore, a survey of the spin sense of 21 Flora-region asteroids, accomplished via a time-efficient modification of the epoch method for spin sense determination, confirms the single-collision Yarkovsky-dispersed model for the family's origin. The neighboring Nysa-Polana complex is the likely source region for many of the carbonaceous near-Earth asteroids, several of which are important targets for spacecraft reconnaissance and sample return missions. Family identification in the Nysa-Polana complex via the core sample method reveals two families associated with asteroid (135) Hertha, both with distinct age and reflectance properties. The larger of these two families demonstrates a correlation in semimajor axis and eccentricity indicating that its family-forming collision occurred near the parent body's aphelion. In addition, the Eulalia family is connected with a possible second component, suggesting an anisotropic distribution of ejecta from its collision event.
Predicting MHC-II binding affinity using multiple instance regression

PubMed Central

EL-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant

2011-01-01

Reliably predicting the ability of antigen peptides to bind to major histocompatibility complex class II (MHC-II) molecules is an essential step in developing new vaccines. Uncovering the amino acid sequence correlates of the binding affinity of MHC-II binding peptides is important for understanding pathogenesis and immune response. The task of predicting MHC-II binding peptides is complicated by the significant variability in their length. Most existing computational methods for predicting MHC-II binding peptides focus on identifying a nine amino acids core region in each binding peptide. We formulate the problems of qualitatively and quantitatively predicting flexible length MHC-II peptides as multiple instance learning and multiple instance regression problems, respectively. Based on this formulation, we introduce MHCMIR, a novel method for predicting MHC-II binding affinity using multiple instance regression. We present results of experiments using several benchmark datasets that show that MHCMIR is competitive with the state-of-the-art methods for predicting MHC-II binding peptides. An online web server that implements the MHCMIR method for MHC-II binding affinity prediction is freely accessible at http://ailab.cs.iastate.edu/mhcmir. PMID:20855923
Evolution of an RNP assembly system: A minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster

PubMed Central

Kroiss, Matthias; Schultz, Jörg; Wiesner, Julia; Chari, Ashwin; Sickmann, Albert; Fischer, Utz

2008-01-01

In vertebrates, assembly of spliceosomal uridine-rich small nuclear ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a macromolecular entity composed of the proteins SMN and Gemins 2–8. Here we have studied the evolution of this machinery using complete genome assemblies of multiple model organisms. The SMN complex has gained complexity in evolution by a blockwise addition of Gemins onto an ancestral core complex composed of SMN and Gemin2. In contrast to this overall evolutionary trend to more complexity in metazoans, orthologs of most Gemins are missing in dipterans. In accordance with these bioinformatic data a previously undescribed biochemical purification strategy elucidated that the dipteran Drosophila melanogaster contains an SMN complex of remarkable simplicity. Surprisingly, this minimal complex not only mediates the assembly reaction in a manner very similar to its vertebrate counterpart, but also prevents misassembly onto nontarget RNAs. Our data suggest that only a minority of Gemins are required for the assembly reaction per se, whereas others may serve additional functions in the context of UsnRNP biogenesis. The evolution of the SMN complex is an interesting example of how the simplification of a biochemical process contributes to genome compaction. PMID:18621711
GBT Observations of the Star-Forming Regions DR21 and MonR2 with the new Argus Instrument

NASA Astrophysics Data System (ADS)

Linville, Dylan; Frayer, David; Cunningham, Nichol; Maddalena, Ronald

2018-01-01

We present GBT molecular line observations of DR21 and MonR2 with the new 16 element 75--115 GHz Argus instrument. Both molecular cloud complexes are associated with regions of high-mass star formation. We present the results of our 13CO, C18O, and HCO+ observations. Both MonR2 and DR21 show multiple velocity components, and the data suggest that the core of MonR2 is collapsing, while DR21 contains a region with a strong outflow traced by HCO+.
Transcription co-activator SAYP mediates the action of STAT activator

PubMed Central

Panov, Vladislav V.; Kuzmina, Julia L.; Doronin, Semen A.; Kopantseva, Marina R.; Nabirochkina, Elena N.; Georgieva, Sofia G.; Vorobyeva, Nadezhda E.; Shidlovskii, Yulii V.

2012-01-01

Jak/STAT is an important signaling pathway mediating multiple events in development. We describe participation of metazoan co-activator SAYP/PHF10 in this pathway downstream of STAT. The latter, via its activation domain, interacts with the conserved core of SAYP. STAT is associated with the SAYP-containing co-activator complex BTFly and recruits BTFly onto genes. SAYP is necessary for stimulating STAT-driven transcription of numerous genes. Mutation of SAYP leads to maldevelopments similar to those observed in STAT mutants. Thus, SAYP is a novel co-activator mediating the action of STAT. PMID:22123744
Native structure of a type IV secretion system core complex essential for Legionella pathogenesis.

PubMed

Kubori, Tomoko; Koike, Masafumi; Bui, Xuan Thanh; Higaki, Saori; Aizawa, Shin-Ichi; Nagai, Hiroki

2014-08-12

Bacterial type IV secretion systems are evolutionarily related to conjugation systems and play a pivotal role in infection by delivering numerous virulence factors into host cells. Using transmission electron microscopy, we report the native molecular structure of the core complex of the Dot/Icm type IV secretion system encoded by Legionella pneumophila, an intracellular human pathogen. The biochemically isolated core complex, composed of at least five proteins--DotC, DotD, DotF, DotG, and DotH--has a ring-shaped structure. Intriguingly, morphologically distinct premature complexes are formed in the absence of DotG or DotF. Our data suggest that DotG forms a central channel spanning inner and outer membranes. DotF, a component dispensable for type IV secretion, plays a role in efficient embedment of DotG into the functional core complex. These results highlight a common scheme for the biogenesis of transport machinery.
Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition

PubMed Central

Madina, Bhaskara R.; Kumar, Vikas; Metz, Richard; Mooers, Blaine H.M.; Bundschuh, Ralf; Cruz-Reyes, Jorge

2014-01-01

Mitochondrial mRNAs in kinetoplastids require extensive U-insertion/deletion editing that progresses 3′-to-5′ in small blocks, each directed by a guide RNA (gRNA), and exhibits substrate and developmental stage-specificity by unsolved mechanisms. Here, we address compositionally related factors, collectively known as the mitochondrial RNA-binding complex 1 (MRB1) or gRNA-binding complex (GRBC), that contain gRNA, have a dynamic protein composition, and transiently associate with several mitochondrial factors including RNA editing core complexes (RECC) and ribosomes. MRB1 controls editing by still unknown mechanisms. We performed the first next-generation sequencing study of native subcomplexes of MRB1, immunoselected via either RNA helicase 2 (REH2), that binds RNA and associates with unwinding activity, or MRB3010, that affects an early editing step. The particles contain either REH2 or MRB3010 but share the core GAP1 and other proteins detected by RNA photo-crosslinking. Analyses of the first editing blocks indicate an enrichment of several initiating gRNAs in the MRB3010-purified complex. Our data also indicate fast evolution of mRNA 3′ ends and strain-specific alternative 3′ editing within 3′ UTR or C-terminal protein-coding sequence that could impact mitochondrial physiology. Moreover, we found robust specific copurification of edited and pre-edited mRNAs, suggesting that these particles may bind both mRNA and gRNA editing substrates. We propose that multiple subcomplexes of MRB1 with different RNA/protein composition serve as a scaffold for specific assembly of editing substrates and RECC, thereby forming the editing holoenzyme. The MRB3010-subcomplex may promote early editing through its preferential recruitment of initiating gRNAs. PMID:24865612
Node Resource Manager: A Distributed Computing Software Framework Used for Solving Geophysical Problems

NASA Astrophysics Data System (ADS)

Lawry, B. J.; Encarnacao, A.; Hipp, J. R.; Chang, M.; Young, C. J.

2011-12-01

With the rapid growth of multi-core computing hardware, it is now possible for scientific researchers to run complex, computationally intensive software on affordable, in-house commodity hardware. Multi-core CPUs (Central Processing Unit) and GPUs (Graphics Processing Unit) are now commonplace in desktops and servers. Developers today have access to extremely powerful hardware that enables the execution of software that could previously only be run on expensive, massively-parallel systems. It is no longer cost-prohibitive for an institution to build a parallel computing cluster consisting of commodity multi-core servers. In recent years, our research team has developed a distributed, multi-core computing system and used it to construct global 3D earth models using seismic tomography. Traditionally, computational limitations forced certain assumptions and shortcuts in the calculation of tomographic models; however, with the recent rapid growth in computational hardware including faster CPU's, increased RAM, and the development of multi-core computers, we are now able to perform seismic tomography, 3D ray tracing and seismic event location using distributed parallel algorithms running on commodity hardware, thereby eliminating the need for many of these shortcuts. We describe Node Resource Manager (NRM), a system we developed that leverages the capabilities of a parallel computing cluster. NRM is a software-based parallel computing management framework that works in tandem with the Java Parallel Processing Framework (JPPF, http://www.jppf.org/), a third party library that provides a flexible and innovative way to take advantage of modern multi-core hardware. NRM enables multiple applications to use and share a common set of networked computers, regardless of their hardware platform or operating system. Using NRM, algorithms can be parallelized to run on multiple processing cores of a distributed computing cluster of servers and desktops, which results in a dramatic speedup in execution time. NRM is sufficiently generic to support applications in any domain, as long as the application is parallelizable (i.e., can be subdivided into multiple individual processing tasks). At present, NRM has been effective in decreasing the overall runtime of several algorithms: 1) the generation of a global 3D model of the compressional velocity distribution in the Earth using tomographic inversion, 2) the calculation of the model resolution matrix, model covariance matrix, and travel time uncertainty for the aforementioned velocity model, and 3) the correlation of waveforms with archival data on a massive scale for seismic event detection. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
The Common Core State Standards' Quantitative Text Complexity Trajectory: Figuring out How Much Complexity Is Enough

ERIC Educational Resources Information Center

Williamson, Gary L.; Fitzgerald, Jill; Stenner, A. Jackson

2013-01-01

The Common Core State Standards (CCSS) set a controversial aspirational, quantitative trajectory for text complexity exposure for readers throughout the grades, aiming for all high school graduates to be able to independently read complex college and workplace texts. However, the trajectory standard is presented without reference to how the…
Integrally cored ceramic investment casting mold fabricated by ceramic stereolithography

NASA Astrophysics Data System (ADS)

Bae, Chang-Jun

Superalloy airfoils are produced by investment casting (IC), which uses ceramic cores and wax patterns with ceramic shell molds. Hollow cored superalloy airfoils in a gas turbine engine are an example of complex IC parts. The complex internal hollow cavities of the airfoil are designed to conduct cooling air through one or more passageways. These complex internal passageways have been fabricated by a lost wax process requiring several processing steps; core preparation, injection molding for wax pattern, and dipping process for ceramic shell molds. Several steps generate problems such as high cost and decreased accuracy of the ceramic mold. For example, costly tooling and production delay are required to produce mold dies for complex cores and wax patterns used in injection molding, resulting in a big obstacle for prototypes and smaller production runs. Rather than using separate cores, patterns, and shell molds, it would be advantageous to directly produce a mold that has the casting cavity and the ceramic core by one process. Ceramic stereolithography (CerSLA) can be used to directly fabricate the integrally cored ceramic casting mold (ICCM). CerSLA builds ceramic green objects from CAD files from many thin liquid layers of powder in monomer, which are solidified by polymerization with a UV laser, thereby "writing" the design for each slice. This dissertation addresses the integrally cored casting ceramic mold (ICCM), the ceramic core with a ceramic mold shell in a single patternless construction, fabricated by ceramic stereolithography (CerSLA). CerSLA is considered as an alternative method to replace lost wax processes, for small production runs or designs too complex for conventional cores and patterns. The main topic is the development of methods to successfully fabricate an ICCM by CerSLA from refractory silica, as well as related issues. The related issues are the segregation of coarse fused silica powders in a layer, the degree of segregation parameter to prevent segregation, and sintering and cristobalite transformation in fused silica compacts.
Has First-Grade Core Reading Program Text Complexity Changed across Six Decades?

ERIC Educational Resources Information Center

Fitzgerald, Jill; Elmore, Jeff; Relyea, Jackie Eunjung; Hiebert, Elfrieda H.; Stenner, A. Jackson

2016-01-01

The purpose of the study was to address possible text complexity shifts across the past six decades for a continually best-selling first-grade core reading program. The anthologies of one publisher's seven first-grade core reading programs were examined using computer-based analytics, dating from 1962 to 2013. Variables were Overall Text…
Three nested randomized controlled trials of peer-only or multiple stakeholder group feedback within Delphi surveys during core outcome and information set development.

PubMed

Brookes, Sara T; Macefield, Rhiannon C; Williamson, Paula R; McNair, Angus G; Potter, Shelley; Blencowe, Natalie S; Strong, Sean; Blazeby, Jane M

2016-08-17

Methods for developing a core outcome or information set require involvement of key stakeholders to prioritise many items and achieve agreement as to the core set. The Delphi technique requires participants to rate the importance of items in sequential questionnaires (or rounds) with feedback provided in each subsequent round such that participants are able to consider the views of others. This study examines the impact of receiving feedback from different stakeholder groups, on the subsequent rating of items and the level of agreement between stakeholders. Randomized controlled trials were nested within the development of three core sets each including a Delphi process with two rounds of questionnaires, completed by patients and health professionals. Participants rated items from 1 (not essential) to 9 (absolutely essential). For round 2, participants were randomized to receive feedback from their peer stakeholder group only (peer) or both stakeholder groups separately (multiple). Decisions as to which items to retain following each round were determined by pre-specified criteria. Whilst type of feedback did not impact on the percentage of items for which a participant subsequently changed their rating, or the magnitude of change, it did impact on items retained at the end of round 2. Each core set contained discordant items retained by one feedback group but not the other (3-22 % discordant items). Consensus between patients and professionals in items to retain was greater amongst those receiving multiple group feedback in each core set (65-82 % agreement for peer-only feedback versus 74-94 % for multiple feedback). In addition, differences in round 2 scores were smaller between stakeholder groups receiving multiple feedback than between those receiving peer group feedback only. Variability in item scores across stakeholders was reduced following any feedback but this reduction was consistently greater amongst the multiple feedback group. In the development of a core outcome or information set, providing feedback within Delphi questionnaires from all stakeholder groups separately may influence the final core set and improve consensus between the groups. Further work is needed to better understand how participants rate and re-rate items within a Delphi process. The three randomized controlled trials reported here were each nested within the development of a core information or outcome set to investigate processes in core outcome and information set development. Outcomes were not health-related and therefore trial registration was not applicable.
Melting of Fe-Si-O alloys: the Fate of Coexisting Si and O in the Core

NASA Astrophysics Data System (ADS)

Arveson, S. M.; Lee, K. K. M.

2017-12-01

The light element budget of Earth's core plays an integral role in sustaining outer core convection, which powers the geodynamo. Many experiments have been performed on binary iron compounds, but the results do not robustly agree with seismological observations and geochemical constraints. Earth's core is almost certainly made up of multiple light elements, so the future of core composition studies lies in ternary (or higher order) systems in order to examine interactions between light elements. We perform melting experiments on Fe-Si-O alloys in a laser-heated diamond-anvil cell to 80 GPa and 4000 K. Using 2D multi- wavelength imaging radiometry together with textural and chemical analysis of quenched samples, we measure the high-pressure melting curves and determine partitioning of light elements between the melt and the coexisting solid. Quenched samples are analyzed both in map view and in cross section using scanning electron microscopy (SEM) and electron microprobe analysis (EPMA) to examine the 3D melt structure and composition. Partitioning of light elements between molten and solid alloys dictates (1) the density contrast at the ICB, which drives compositional convection in the outer core and (2) the temperature of the CMB, an integral parameter for understanding the deep Earth. Our experiments suggest silicon and oxygen do not simply coexist in the melt and instead show complex solubility based on temperature. Additionally, we do not find evidence of crystallization of SiO2 at low oxygen content as was recently reported.11 Hirose, K., et al., Crystallization of silicon dioxide and compositional evolution of the Earth's core. Nature, 2017. 543(7643): p. 99-102.
The six most essential questions in psychiatric diagnosis: a pluralogue. Part 4: general conclusion

PubMed Central

2012-01-01

In the conclusion to this multi-part article I first review the discussions carried out around the six essential questions in psychiatric diagnosis – the position taken by Allen Frances on each question, the commentaries on the respective question along with Frances’ responses to the commentaries, and my own view of the multiple discussions. In this review I emphasize that the core question is the first – what is the nature of psychiatric illness – and that in some manner all further questions follow from the first. Following this review I attempt to move the discussion forward, addressing the first question from the perspectives of natural kind analysis and complexity analysis. This reflection leads toward a view of psychiatric disorders – and future nosologies – as far more complex and uncertain than we have imagined. PMID:23249629
Modeling Smoke Plume-Rise and Dispersion from Southern United States Prescribed Burns with Daysmoke.

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

Achtemeier, Gary, L.; Goodrick, Scott, A.; Liu, Yongqiang

2011-08-19

We present Daysmoke, an empirical-statistical plume rise and dispersion model for simulating smoke from prescribed burns. Prescribed fires are characterized by complex plume structure including multiple-core updrafts which makes modeling with simple plume models difficult. Daysmoke accounts for plume structure in a three-dimensional veering/sheering atmospheric environment, multiple-core updrafts, and detrainment of particulate matter. The number of empirical coefficients appearing in the model theory is reduced through a sensitivity analysis with the Fourier Amplitude Sensitivity Test (FAST). Daysmoke simulations for 'bent-over' plumes compare closely with Briggs theory although the two-thirds law is not explicit in Daysmoke. However, the solutions for themore » 'highly-tilted' plume characterized by weak buoyancy, low initial vertical velocity, and large initial plume diameter depart considerably from Briggs theory. Results from a study of weak plumes from prescribed burns at Fort Benning GA showed simulated ground-level PM2.5 comparing favorably with observations taken within the first eight kilometers of eleven prescribed burns. Daysmoke placed plume tops near the lower end of the range of observed plume tops for six prescribed burns. Daysmoke provides the levels and amounts of smoke injected into regional scale air quality models. Results from CMAQ with and without an adaptive grid are presented.« less
What does music express? Basic emotions and beyond.

PubMed

Juslin, Patrik N

2013-01-01

Numerous studies have investigated whether music can reliably convey emotions to listeners, and-if so-what musical parameters might carry this information. Far less attention has been devoted to the actual contents of the communicative process. The goal of this article is thus to consider what types of emotional content are possible to convey in music. I will argue that the content is mainly constrained by the type of coding involved, and that distinct types of content are related to different types of coding. Based on these premises, I suggest a conceptualization in terms of "multiple layers" of musical expression of emotions. The "core" layer is constituted by iconically-coded basic emotions. I attempt to clarify the meaning of this concept, dispel the myths that surround it, and provide examples of how it can be heuristic in explaining findings in this domain. However, I also propose that this "core" layer may be extended, qualified, and even modified by additional layers of expression that involve intrinsic and associative coding. These layers enable listeners to perceive more complex emotions-though the expressions are less cross-culturally invariant and more dependent on the social context and/or the individual listener. This multiple-layer conceptualization of expression in music can help to explain both similarities and differences between vocal and musical expression of emotions.
Simultaneous Optimization of Multiple Response Variables for the Gelatin-chitosan Microcapsules Containing Angelica Essential Oil.

PubMed

Li, Qiang; Sun, Li-Jian; Gong, Xian-Feng; Wang, Yang; Zhao, Xue-Ling

2017-01-01

Angelica essential oil (AO), a major pharmacologically active component of Angelica sinensis (Oliv.) Diels, possesses hemogenesis, analgesic activities, and sedative effect. The application of AO in pharmaceutical systems had been limited because of its low oxidative stability. The AO-loaded gelatin-chitosan microcapsules with prevention from oxidation were developed and optimized using response surface methodology. The effects of formulation variables (pH at complex coacervation, gelatin concentration, and core/wall ratio) on multiple response variables (yield, encapsulation efficiency, antioxidation rate, percent of drug released in 1 h, and time to 85% drug release) were systemically investigated. A desirability function that combined these five response variables was constructed. All response variables investigated were found to be highly dependent on the formulation variables, with strong interactions observed between the formulation variables. It was found that optimum overall desirability of AO microcapsules could be obtained at pH 6.20, gelatin concentration 25.00%, and core/wall ratio 40.40%. The experimental values of the response variables highly agreed with the predicted values. The antioxidation rate of optimum formulation was approximately 8 times higher than that of AO. The in-vitro drug release from microcapsules was followed Higuchi model with super case-II transport mechanism.
Monomeric RC-LH1 core complexes retard LH2 assembly and intracytoplasmic membrane formation in PufX-minus mutants of Rhodobacter sphaeroides

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

Adams, Peter G.; Mothersole, David J.; Ng, Irene W.

2011-01-01

In the model photosynthetic bacterium Rhodobacter sphaeroides domains of light-harvesting 2 (LH2) complexes surround and interconnect dimeric reaction centre–light-harvesting 1–PufX (RC–LH1–PufX) ‘core’ complexes, forming extensive networks for energy transfer and trapping. These complexes are housed in spherical intracytoplasmic membranes (ICMs), which are assembled in a stepwise process where biosynthesis of core complexes tends to dominate the early stages of membrane invagination. The kinetics of LH2 assembly were measured in PufX mutants that assemble monomeric core complexes, as a consequence of either a twelve-residue N-terminal truncation of PufX (PufXΔ12) or the complete removal of PufX (PufX -). Lower rates of LH2more » assembly and retarded maturation of membrane invagination were observed for the larger and less curved ICM from the PufX - mutant, consistent with the proposition that local membrane curvature, initiated by arrays of bent RC–LH1–PufX dimers, creates a favourable environment for stable assembly of LH2 complexes. Transmission electron microscopy and high-resolution atomic force microscopy were used to examine ICM morphology and membrane protein organisation in these mutants. Some partitioning of core and LH2 complexes was observed in PufX - membranes, resulting in locally ordered clusters of monomeric RC–LH1 complexes. The distribution of core and LH2 complexes in the three types of membrane examined is consistent with previous models of membrane curvature and domain formation (Frese et al., 2008), which demonstrated that a combination of crowding and asymmetries in sizes and shapes of membrane protein complexes drives membrane organisation.« less
Controlling energy transfer between multiple dopants within a single nanoparticle

PubMed Central

DiMaio, Jeffrey R.; Sabatier, Clément; Kokuoz, Baris; Ballato, John

2008-01-01

Complex core-shell architectures are implemented within LaF3 nanoparticles to allow for a tailored degree of energy transfer (ET) between different rare earth dopants. By constraining specific dopants to individual shells, their relative distance to one another can be carefully controlled. Core-shell LaF3 nanoparticles doped with Tb3+ and Eu3+ and consisting of up to four layers were synthesized with an outer diameter of ≈10 nm. It is found that by varying the thicknesses of an undoped layer between a Tb3+-doped layer and a Eu3+-doped layer, the degree of ET can be engineered to allow for zero, partial, or total ET from a donor ion to an acceptor ion. More specifically, the ratio of the intensities of the 541-nm Tb3+ and 590 nm Eu3+ peaks was tailored from <0.2 to ≈2.4 without changing the overall composition of the particles but only by changing the internal structure. Further, the emission spectrum of a blend of singly doped nanoparticles is shown to be equivalent to the spectra of co-doped particles when a core-shell configuration that restricts ET is used. Beyond simply controlling ET, which can be limiting when designing materials for optical applications, this approach can be used to obtain truly engineered spectral features from nanoparticles and composites made from them. Further, it allows for a single excitation source to yield multiple discrete emissions from numerous lanthanide dopants that heretofore would have been quenched in a more conventional active optical material. PMID:18250307

Interactions of Escherichia coli σ70 within the transcription elongation complex

PubMed Central

Daube, Shirley S.; von Hippel, Peter H.

1999-01-01

A functional transcription elongation complex can be formed without passing through a promoter by adding a complementary RNA primer and core Escherichia coli RNA polymerase in trans to an RNA-primed synthetic bubble-duplex DNA framework. This framework consists of a double-stranded DNA sequence with an internal noncomplementary DNA “bubble” containing a hybridized RNA primer. On addition of core polymerase and the requisite NTPs, the RNA primer is extended in a process that manifests most of the properties of in vitro transcription elongation. This synthetic elongation complex can also be assembled by using holo rather than core RNA polymerase, and in this study we examine the interactions and fate of the σ70 specificity subunit of the holopolymerase in the assembly process. We show that the addition of holopolymerase to the bubble-duplex construct triggers the dissociation of the sigma factor from some complexes, whereas in others the RNA oligomer is released into solution instead. These results are consistent with an allosteric competition between σ70 and the nascent RNA strand within the elongation complex and suggest that both cannot be bound to the core polymerase simultaneously. However, the dissociation of σ70 from the complex can also be stimulated by binding of the holopolymerase to the DNA bubble duplex in the absence of a hybridized RNA primer, suggesting that the binding of the core polymerase to the bubble-duplex construct also triggers a conformational change that additionally weakens the sigma–core interaction. PMID:10411885
The rheology and processing of “edge sheared” colloidal polymer opals

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

Wong, Hon Sum; Mackley, Malcolm, E-mail: mrm5@cam.ac.uk; Butler, Simon

This paper is concerned with the rheology and processing of solvent-free core shell “polymer opals” that consist of a soft outer shell grafted to hard colloidal polymer core particles. Strong iridescent colors can be produced by shearing the material in a certain way that causes the initially disordered spheres to rearrange into ordered crystalline structures and produce colors by diffraction and interference of multiple light scattering, similar to gemstone opals. The basic linear viscoelastic rheology of a polymer opal sample was determined as a function of temperature, and the material was found to be highly viscoelastic at all tested temperatures.more » A Cambridge multipass rheometer was specifically modified in order to make controlled mechanical measurements of initially disordered polymer opal tapes that were sandwiched between protective polyethylene terephthalate sheets. Axial extension, simple shear, and a novel “edge shearing” geometry were all evaluated, and multiple successive experiments of the edge shearing test were carried out at different temperatures. The optical development of colloidal ordering, measured as optical opalescence, was quantified by spectroscopy using visible backscattered light. The development of opalescence was found to be sensitive to the geometry of deformation and a number of process variables suggesting a complex interaction of parameters that caused the opalescence. In order to identify aspects of the deformation mechanism of the edge shearing experiment, a separate series of in situ optical experiments were carried out and this helped indicate the extent of simple shear generated with each edge shear deformation. The results show that strong ordering can be induced by successive edge shearing deformation. The results are relevant to polymer opal rheology, processing, and mechanisms relating to ordering within complex viscoelastic fluids.« less
Evidences of Multiple Magma Injections in Quaternary Balerang and Rajabasa Volcanoes, Indonesia

NASA Astrophysics Data System (ADS)

Hasibuan, R. F.; Ohba, T.; Abdurrachman, M.

2016-12-01

Quaternary Balerang and Rajabasa volcanoes are situated along the nearly north-south lineament with a most explosive Krakatau volcanic complex in the south and effusive Sukadana basalt plateau in the north. Some studies have elucidated that Krakatau volcano has multiple magma storage regions beneath together with evidences of magma mixing process. By considering these circumstances, it is necessary to know lateral variations of magmas and to characterize volcanic rocks from Rajabasa volcanic complex which is located between these distinct magmatic systems, in terms of magmatic processes and evolution. Methodologies we used are X-ray fluorescence to determine the whole rock chemistry, K-Ar isotope dating to determine the lifespan of the volcano, as well as EPMA analysis to obtain the chemical composition of minerals. The rock chemistry or TAS plot shows a linear trend, ranging from basaltic (51 wt.%) to rhyolitic (75 wt.%), indicating a chemical heterogeneity of magma. When SiO2 contents are correlated with the relative ages, we found a broad tendency that SiO2 contents progressively decrease with age. The Rajabasa volcano lifespan is known formed at 0.31 Ma while one of the youngest lava is identified erupted at 0.12 Ma. Some plagioclase crystals exhibit disequilibrium textures, like highly sieved core and clear rim regions, also overgrowth rim on the plagioclase and pyroxene crystals whose composition more primitive than the core's composition, indicating magmatic recharge events. Reverse zoning and resorption textures associated with compositional step zoning or progressive zoning are quite common as well in clinopyroxene and plagioclase crystals. By considering these evidences, we conclude that injection of a hotter basaltic magma into colder and more felsic magma occurred beneath the volcanoes.
Complex and noncentrosymmetric stacking of layered metal dichalcogenide materials created by screw dislocations

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

Shearer, Melinda J.; Samad, Leith; Zhang, Yi

The interesting and tunable properties of layered metal dichalcogenides heavily depend on their phase and layer stacking. Here, we show and explain how the layer stacking and physical properties of WSe 2 are influenced by screw dislocations. A one-to-one correlation of atomic force microscopy and high- and low-frequency Raman spectroscopy of many dislocated WSe 2 nanoplates reveals variations in the number and shapes of dislocation spirals and different layer stackings that are determined by the number, rotation, and location of the dislocations. Plates with triangular dislocation spirals form noncentrosymmetric stacking that gives rise to strong second-harmonic generation and enhanced photoluminescence,more » plates with hexagonal dislocation spirals form the bulk 2H layer stacking commonly observed, and plates containing mixed dislocation shapes have intermediate noncentrosymmetric stackings with mixed properties. Multiple dislocation cores and other complexities can lead to more complex stackings and properties. Finally, these previously unobserved properties and layer stackings in WSe 2 will be interesting for spintronics and valleytronics.« less
Complex and noncentrosymmetric stacking of layered metal dichalcogenide materials created by screw dislocations

DOE PAGES

Shearer, Melinda J.; Samad, Leith; Zhang, Yi; ...

2017-02-08

The interesting and tunable properties of layered metal dichalcogenides heavily depend on their phase and layer stacking. Here, we show and explain how the layer stacking and physical properties of WSe 2 are influenced by screw dislocations. A one-to-one correlation of atomic force microscopy and high- and low-frequency Raman spectroscopy of many dislocated WSe 2 nanoplates reveals variations in the number and shapes of dislocation spirals and different layer stackings that are determined by the number, rotation, and location of the dislocations. Plates with triangular dislocation spirals form noncentrosymmetric stacking that gives rise to strong second-harmonic generation and enhanced photoluminescence,more » plates with hexagonal dislocation spirals form the bulk 2H layer stacking commonly observed, and plates containing mixed dislocation shapes have intermediate noncentrosymmetric stackings with mixed properties. Multiple dislocation cores and other complexities can lead to more complex stackings and properties. Finally, these previously unobserved properties and layer stackings in WSe 2 will be interesting for spintronics and valleytronics.« less
A pathway-based network analysis of hypertension-related genes

NASA Astrophysics Data System (ADS)

Wang, Huan; Hu, Jing-Bo; Xu, Chuan-Yun; Zhang, De-Hai; Yan, Qian; Xu, Ming; Cao, Ke-Fei; Zhang, Xu-Sheng

2016-02-01

Complex network approach has become an effective way to describe interrelationships among large amounts of biological data, which is especially useful in finding core functions and global behavior of biological systems. Hypertension is a complex disease caused by many reasons including genetic, physiological, psychological and even social factors. In this paper, based on the information of biological pathways, we construct a network model of hypertension-related genes of the salt-sensitive rat to explore the interrelationship between genes. Statistical and topological characteristics show that the network has the small-world but not scale-free property, and exhibits a modular structure, revealing compact and complex connections among these genes. By the threshold of integrated centrality larger than 0.71, seven key hub genes are found: Jun, Rps6kb1, Cycs, Creb312, Cdk4, Actg1 and RT1-Da. These genes should play an important role in hypertension, suggesting that the treatment of hypertension should focus on the combination of drugs on multiple genes.
Probing lysine mono-methylation in histone H3 tail peptides with an abiotic receptor coupled to a non-plasmonic resonator.

PubMed

Bontempi, N; Biavardi, E; Bordiga, D; Candiani, G; Alessandri, I; Bergese, P; Dalcanale, E

2017-06-29

Binder and effector molecules that allow studying and manipulating epigenetic processes are of biological relevance and pose severe technical challenges. We report the first example of a synthetic receptor able to recognize mono-methylated lysines in a histone H3 tail peptide, which has relevant functions in epigenetic regulation. Recognition is robust and specific regardless of the position and the number of mono-methylated lysines along the polypeptide chain. The peptide is first captured in solution by a tetraphosphonate cavitand (Tiiii) that selectively binds its Lys-NMe + moieties. Separation from solution and detection of the peptide-Tiiii complexes is then enabled in one single step by an all dielectric SiO 2 -TiO 2 core-shell resonator (T-rex), which captures the complex and operates fully reproducible signal transduction by non-plasmonic surface enhanced Raman scattering (SERS) without degrading the complex. The realized abiotic probe is able to distinguish multiple mono-methylated peptides from the single mono-methylated ones.
Multiple core-hole formation by free-electron laser radiation in molecular nitrogen

NASA Astrophysics Data System (ADS)

Banks, H. I. B.; Little, D. A.; Emmanouilidou, A.

2018-05-01

We investigate the formation of multiple-core-hole states of molecular nitrogen interacting with a free-electron laser pulse. In previous work, we obtained bound and continuum molecular orbitals in the single-center expansion scheme and used these orbitals to calculate photo-ionization and auger decay rates. We extend our formulation to track the proportion of the population that accesses single-site versus two-site double-core-hole (TSDCH) states, before the formation of the final atomic ions. We investigate the pulse parameters that favor the formation of the single-site and TSDCH as well as triple-core-hole states for 525 and 1100 eV photons.
Student Reading Growth Illuminates the Common Core Text-Complexity Standard: Raising Both Bars

ERIC Educational Resources Information Center

Williamson, Gary L.; Fitzgerald, Jill; Stenner, Jackson A.

2014-01-01

The Common Core State Standards (CCSS) establish a challenging text-complexity standard for all high school graduates to read at college and workplace text-complexity levels. We argue that implementation of the CCSS standard requires concurrent examination of historical student reading-growth trends. An example of a historical student average…
Structural and functional organization of the ESCRT-I trafficking complex

PubMed Central

Kostelansky, Michael S.; Sun, Ji; Lee, Sangho; Kim, Jaewon; Ghirlando, Rodolfo; Hierro, Aitor; Emr, Scott D.; Hurley, James H.

2006-01-01

Summary The Endosomal Sorting Complex Required for Transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37. The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 Å resolution. Each subunit contains a structurally similar pair of helices that form the core. The N-terminal domain of Vps28 has a hydrophobic binding site on its surface that is conformationally dynamic. The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEVdomain, the Vps28 C-domain, and other domains project to bind their partners. PMID:16615894
Revealing the Structural Complexity of Component Interactions of Topic-Specific PCK when Planning to Teach

NASA Astrophysics Data System (ADS)

Mavhunga, Elizabeth

2018-04-01

Teaching pedagogical content knowledge (PCK) at a topic-specific level requires clarity on the content-specific nature of the components employed, as well as the specific features that bring about the desirable depth in teacher explanations. Such understanding is often hazy; yet, it influences the nature of teacher tasks and learning opportunities afforded to pre-service teachers in a teaching program. The purpose of this study was twofold: firstly, to illuminate the emerging complexity when content-specific components of PCK interact when planning to teach a chemistry topic; and secondly, to identify the kinds of teacher tasks that promote the emergence of such complexity. Data collected were content representations (CoRes) in chemical equilibrium accompanied by expanded lesson outlines from 15 pre-service teachers in their final year of study towards a first degree in teaching (B Ed). The analysis involved extraction of episodes that exhibited component interaction by using a qualitative in-depth analysis method. The results revealed the structure in which the components of PCK in a topic interact among each other to be linear, interwoven, or a combination of the two. The interwoven interactions contained multiple components that connected explanations on different aspects of a concept, all working in a complementary manner. The most sophisticated component interactions emerged from teacher tasks on descriptions of a lesson sequence and a summary of a lesson. Recommendations in this study highlight core practices for making pedagogical transformation of topic content knowledge more accessible.
Unravelling the Paleoenvironmental and Diagenetic History of Fluviolacustrine Sediments from a Northern Kenya Rift Basin Through Analysis of HSPDP West Turkana-Kaitio Core Material

NASA Astrophysics Data System (ADS)

Rabideaux, N. M.; Chaudhary, M. S.; Deocampo, D.; Feibel, C. S.; Cohen, A. S.

2016-12-01

The Hominin Sites and Paleolakes Drilling Project (HSPDP) collected sediment cores from six rift basins in Ethiopia and Kenya. The goal of HSPDP is to construct high-resolution records of environmental change, and to understand how those changes relate to early human evolution and cultural adaptations. The West Turkana-Kaitio (WTK) site was targeted due to the abundant archeological and paleontological artifacts and fossils discovered around the basin. We conducted XRD and XRF analyses on HSPDP-WTK core material to construct a high-resolution record of paleoenvironmental conditions in the Kenya Rift during the Early Pleistocene ( 1.9-1.35 Ma). Mineralogical and geochemical trends were also used to identify the diagenetic history of fluviolacustrine sediments in the basin. The bulk mineralogy is comprised of mostly detrital feldspars, muscovite, α-quartz, and carbonates. Zeolites are present in intervals throughout the core, possibly suggesting pulses of increased salinity. Oxides and S-bearing minerals are abundant from 100-170 mbs, which may be indicative of redox and or hydrothermal processes in that interval. The lowermost portion of the core contains α- and β-quartz, pyrite and zeolites, suggesting either low-oxygen saline conditions or hydrothermal activity. Oriented clay analysis indicated multiple intervals of diagenesis, with the illitization of smectite related to hydrothermal and or microbial activity. Clay analysis provided evidence for a low degree of illitization in the upper portion of the core, whereas mixed-layered illite-smectite (I/S) contained 30-50% illite proximal to fault breccia and up to 70% illite below the faulted section, indicative of significant alteration in the lowermost portion of the core. Coupled mineralogical and geochemical analysis revealed a complex alteration history in the basin indicated by: 1) the presence of mixed-layer I/S throughout the 216 m core; 2) pronounced alteration proximal to faulting; and 3) authigenic silicates and pyrite in the basal section of the core.
A core hSSB1–INTS complex participates in the DNA damage response

PubMed Central

Zhang, Feng; Ma, Teng; Yu, Xiaochun

2013-01-01

Summary Human single-stranded DNA-binding protein 1 (hSSB1) plays an important role in the DNA damage response and the maintenance of genomic stability. It has been shown that the core hSSB1 complex contains hSSB1, INTS3 and C9orf80. Using protein affinity purification, we have identified integrator complex subunit 6 (INTS6) as a major subunit of the core hSSB1 complex. INTS6 forms a stable complex with INTS3 and hSSB1 both in vitro and in vivo. In this complex, INTS6 directly interacts with INTS3. In response to the DNA damage response, along with INTS3 and hSSB1, INTS6 relocates to the DNA damage sites. Moreover, the hSSB1–INTS complex regulates the accumulation of RAD51 and BRCA1 at DNA damage sites and the correlated homologous recombination. PMID:23986477
Atomic structure of the Y complex of the nuclear pore

DOE PAGES

Kelley, Kotaro; Knockenhauer, Kevin E.; Kabachinski, Greg; ...

2015-03-30

The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. In this paper, we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved coremore » of the Y complex has six rather than seven members. Finally, evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.« less
On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods

PubMed Central

Lee, Anthony; Yau, Christopher; Giles, Michael B.; Doucet, Arnaud; Holmes, Christopher C.

2011-01-01

We present a case-study on the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods. Graphics cards, containing multiple Graphics Processing Units (GPUs), are self-contained parallel computational devices that can be housed in conventional desktop and laptop computers and can be thought of as prototypes of the next generation of many-core processors. For certain classes of population-based Monte Carlo algorithms they offer massively parallel simulation, with the added advantage over conventional distributed multi-core processors that they are cheap, easily accessible, easy to maintain, easy to code, dedicated local devices with low power consumption. On a canonical set of stochastic simulation examples including population-based Markov chain Monte Carlo methods and Sequential Monte Carlo methods, we nd speedups from 35 to 500 fold over conventional single-threaded computer code. Our findings suggest that GPUs have the potential to facilitate the growth of statistical modelling into complex data rich domains through the availability of cheap and accessible many-core computation. We believe the speedup we observe should motivate wider use of parallelizable simulation methods and greater methodological attention to their design. PMID:22003276
Unit: Making Life Easier, Inspection Pack, National Trial Print.

ERIC Educational Resources Information Center

Australian Science Education Project, Toorak, Victoria.

As a part of the unit materials in the series produced by the Australian Science Education Project, this teacher edition is primarily composed of three sections: a core relating to a bicycle, tests, and options. The core is concerned with basic properties of a machine such as force multiplication, speed multiplication, energy dissipation, and…
Content Validity of the Comprehensive ICF Core Set for Multiple Sclerosis from the Perspective of Speech and Language Therapists

ERIC Educational Resources Information Center

Renom, Marta; Conrad, Andrea; Bascuñana, Helena; Cieza, Alarcos; Galán, Ingrid; Kesselring, Jürg; Coenen, Michaela

2014-01-01

Background: The Comprehensive International Classification of Functioning, Disability and Health (ICF) Core Set for Multiple Sclerosis (MS) is a comprehensive framework to structure the information obtained in multidisciplinary clinical settings according to the biopsychosocial perspective of the International Classification of Functioning,…
The need for a prescribing competency framework to address the burden of complex polypharmacy among multiple long-term conditions.

PubMed

Picton, Catherine; Loughrey, Claire; Webb, Andrew

2016-10-01

The original requirement for a competency framework for prescribers was to identify the essential skills for non-medical prescribers. However, core prescribing competencies are relevant to any prescriber. The new, revised version is especially relevant for doctors/physicians. Doctors are the most frequent prescribers - prescribing is the most common therapeutic intervention. The quantity and complexity of medicine use is increasing through multiple treatment strategies/pathways for multiple comorbidities, resulting in polypharmacy - especially with long-term conditions. This is against a background of the ongoing introduction of new drugs with novel mechanisms of action with increased risks of adverse effects, compounded by drug-drug and disease-drug interactions. This has increased the need for monitoring and follow-up, including identification and management of poor adherence. It is challenging for doctors to maintain safe and effective prescribing and train other doctors and non-medical prescribers within the multidisciplinary team. The prescribing competency framework provides a systematic approach to support doctors to prescribe safely and effectively. It can be used by medical schools to teach prescribing, including preparation for the prescribing safety assessment; by F1/F2 doctors to support prescribing in early years; as part of prescribing quality improvement initiatives and as a continuing professional development framework in general practice or acute care settings. © Royal College of Physicians 2016. All rights reserved.
A mass spectrometry proteomics data management platform.

PubMed

Sharma, Vagisha; Eng, Jimmy K; Maccoss, Michael J; Riffle, Michael

2012-09-01

Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the volume and complexity are only increasing with time. There exist many software pipelines for analyzing these data (each typically with its own file formats), and as technology improves, these file formats change and new formats are developed. Files produced from these myriad software programs may accumulate on hard disks or tape drives over time, with older files being rendered progressively more obsolete and unusable with each successive technical advancement and data format change. Although initiatives exist to standardize the file formats used in proteomics, they do not address the core failings of a file-based data management system: (1) files are typically poorly annotated experimentally, (2) files are "organically" distributed across laboratory file systems in an ad hoc manner, (3) files formats become obsolete, and (4) searching the data and comparing and contrasting results across separate experiments is very inefficient (if possible at all). Here we present a relational database architecture and accompanying web application dubbed Mass Spectrometry Data Platform that is designed to address the failings of the file-based mass spectrometry data management approach. The database is designed such that the output of disparate software pipelines may be imported into a core set of unified tables, with these core tables being extended to support data generated by specific pipelines. Because the data are unified, they may be queried, viewed, and compared across multiple experiments using a common web interface. Mass Spectrometry Data Platform is open source and freely available at http://code.google.com/p/msdapl/.
Biogenesis of the yeast cytochrome bc1 complex.

PubMed

Zara, Vincenzo; Conte, Laura; Trumpower, Bernard L

2009-01-01

The mitochondrial respiratory chain is composed of four different protein complexes that cooperate in electron transfer and proton pumping across the inner mitochondrial membrane. The cytochrome bc1 complex, or complex III, is a component of the mitochondrial respiratory chain. This review will focus on the biogenesis of the bc1 complex in the mitochondria of the yeast Saccharomyces cerevisiae. In wild type yeast mitochondrial membranes the major part of the cytochrome bc1 complex was found in association with one or two copies of the cytochrome c oxidase complex. The analysis of several yeast mutant strains in which single genes or pairs of genes encoding bc1 subunits had been deleted revealed the presence of a common set of bc1 sub-complexes. These sub-complexes are represented by the central core of the bc1 complex, consisting of cytochrome b bound to subunit 7 and subunit 8, by the two core proteins associated with each other, by the Rieske protein associated with subunit 9, and by those deriving from the unexpected interaction of each of the two core proteins with cytochrome c1. Furthermore, a higher molecular mass sub-complex is that composed of cytochrome b, cytochrome c1, core protein 1 and 2, subunit 6, subunit 7 and subunit 8. The identification and characterization of all these sub-complexes may help in defining the steps and the molecular events leading to bc1 assembly in yeast mitochondria.

A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex.

PubMed

Armour, Sean M; Bennett, Eric J; Braun, Craig R; Zhang, Xiao-Yong; McMahon, Steven B; Gygi, Steven P; Harper, J Wade; Sinclair, David A

2013-04-01

Although many functions and targets have been attributed to the histone and protein deacetylase SIRT1, a comprehensive analysis of SIRT1 binding proteins yielding a high-confidence interaction map has not been established. Using a comparative statistical analysis of binding partners, we have assembled a high-confidence SIRT1 interactome. Employing this method, we identified the deubiquitinating enzyme ubiquitin-specific protease 22 (USP22), a component of the deubiquitinating module (DUBm) of the SAGA transcriptional coactivating complex, as a SIRT1-interacting partner. We found that this interaction is highly specific, requires the ZnF-UBP domain of USP22, and is disrupted by the inactivating H363Y mutation within SIRT1. Moreover, we show that USP22 is acetylated on multiple lysine residues and that alteration of a single lysine (K129) within the ZnF-UBP domain is sufficient to alter interaction of the DUBm with the core SAGA complex. Furthermore, USP22-mediated recruitment of SIRT1 activity promotes the deacetylation of individual SAGA complex components. Our results indicate an important role of SIRT1-mediated deacetylation in regulating the formation of DUBm subcomplexes within the larger SAGA complex.
Electrophysiological models of neural processing.

PubMed

Nelson, Mark E

2011-01-01

The brain is an amazing information processing system that allows organisms to adaptively monitor and control complex dynamic interactions with their environment across multiple spatial and temporal scales. Mathematical modeling and computer simulation techniques have become essential tools in understanding diverse aspects of neural processing ranging from sub-millisecond temporal coding in the sound localization circuity of barn owls to long-term memory storage and retrieval in humans that can span decades. The processing capabilities of individual neurons lie at the core of these models, with the emphasis shifting upward and downward across different levels of biological organization depending on the nature of the questions being addressed. This review provides an introduction to the techniques for constructing biophysically based models of individual neurons and local networks. Topics include Hodgkin-Huxley-type models of macroscopic membrane currents, Markov models of individual ion-channel currents, compartmental models of neuronal morphology, and network models involving synaptic interactions among multiple neurons.
Rab protein evolution and the history of the eukaryotic endomembrane system

PubMed Central

Brighouse, Andrew; Dacks, Joel B.

2010-01-01

Spectacular increases in the quantity of sequence data genome have facilitated major advances in eukaryotic comparative genomics. By exploiting homology with classical model organisms, this makes possible predictions of pathways and cellular functions currently impossible to address in intractable organisms. Echoing realization that core metabolic processes were established very early following evolution of life on earth, it is now emerging that many eukaryotic cellular features, including the endomembrane system, are ancient and organized around near-universal principles. Rab proteins are key mediators of vesicle transport and specificity, and via the presence of multiple paralogues, alterations in interaction specificity and modification of pathways, contribute greatly to the evolution of complexity of membrane transport. Understanding system-level contributions of Rab proteins to evolutionary history provides insight into the multiple processes sculpting cellular transport pathways and the exciting challenges that we face in delving further into the origins of membrane trafficking specificity. PMID:20582450
Mediator independently orchestrates multiple steps of preinitiation complex assembly in vivo.

PubMed

Eyboulet, Fanny; Wydau-Dematteis, Sandra; Eychenne, Thomas; Alibert, Olivier; Neil, Helen; Boschiero, Claire; Nevers, Marie-Claire; Volland, Hervé; Cornu, David; Redeker, Virginie; Werner, Michel; Soutourina, Julie

2015-10-30

Mediator is a large multiprotein complex conserved in all eukaryotes, which has a crucial coregulator function in transcription by RNA polymerase II (Pol II). However, the molecular mechanisms of its action in vivo remain to be understood. Med17 is an essential and central component of the Mediator head module. In this work, we utilised our large collection of conditional temperature-sensitive med17 mutants to investigate Mediator's role in coordinating preinitiation complex (PIC) formation in vivo at the genome level after a transfer to a non-permissive temperature for 45 minutes. The effect of a yeast mutation proposed to be equivalent to the human Med17-L371P responsible for infantile cerebral atrophy was also analyzed. The ChIP-seq results demonstrate that med17 mutations differentially affected the global presence of several PIC components including Mediator, TBP, TFIIH modules and Pol II. Our data show that Mediator stabilizes TFIIK kinase and TFIIH core modules independently, suggesting that the recruitment or the stability of TFIIH modules is regulated independently on yeast genome. We demonstrate that Mediator selectively contributes to TBP recruitment or stabilization to chromatin. This study provides an extensive genome-wide view of Mediator's role in PIC formation, suggesting that Mediator coordinates multiple steps of a PIC assembly pathway. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Magnetism and Mössbauer study of formation of multi-core γ -Fe2O3 nanoparticles

NASA Astrophysics Data System (ADS)

Kamali, Saeed; Bringas, Eugenio; Hah, Hien-Yoong; Bates, Brian; Johnson, Jacqueline A.; Johnson, Charles E.; Stroeve, Pieter

2018-04-01

A systematic investigation of magnetic nanoparticles and the formation of a core-shell structure, consisting of multiple maghemite (γ -Fe2O3) nanoparticles as the core and silica as the shell, has been performed using various techniques. High-resolution transmission electron microscopy clearly shows isolated maghemite nanoparticles with an average diameter of 13 nm and the formation of a core-shell structure. Low temperature Mössbauer spectroscopy reveals the presence of pure maghemite nanoparticles with all vacancies at the B-sites. Isothermal magnetization and zero-field-cooled and field-cooled measurements are used for investigating the magnetic properties of the nanoparticles. The magnetization results are in good accordance with the contents of the magnetic core and the non-magnetic shell. The multiple-core γ -Fe2O3 nanoparticles show similar behavior to isolated particles of the same size.
Transitions between multiple equilibria of paleo climate: a glimpse in to the dynamics of abrupt climate change

NASA Astrophysics Data System (ADS)

Ferreira, David; Marshall, John; Ito, Takamitsu; McGee, David; Moreno-Chamarro, Eduardo

2017-04-01

The dynamics regulating large climatic transitions such as glacial-interglacial cycles or DO events remains a puzzle. Forcings behind these transitions are not robustly identified and potential candidates (e.g. Milankovitch cycles, freshwater perturbations) often appear too weak to explain such dramatic transitions. A potential solution to this long-standing puzzle is that Earth's climate is endowed with multiple equilibrium states of global extent. Such states are commonly found in low-order or conceptual climate models, but it is unclear whether a system as complex as Earth's climate can sustain multiple equilibrium states. Here we report that multiple equilibrium states of the climate system are also possible in a complex, fully dynamical coupled ocean-atmosphere-sea ice GCM with idealized Earth-like geometry, resolved weather systems and a hydrological cycle. In our model, two equilibrium states coexist for the same parameters and external forcings: a Warm climate with a small Northern hemisphere sea ice cap and a large southern one and a Cold climate with large ice caps at both poles. The dynamical states of the Warm and Cold solutions exhibit striking similarities with our present-day climate and the climate of the Last Glacial Maximum, respectively. A carbon cycle model driven by the two dynamical states produces an atmospheric pCO2 draw-down of about 110 pm between the Warm and Cold states, close to Glacial-Interglacial differences found in ice cores. Mechanism controlling the existence of the multiple states and changes in the atmospheric CO2 will be briefly presented. Finally we willdescribe transition experiments from the Cold to the Warm state, focusing on the lead-lags in the system, notably between the Northern and Southern Hemispheres climates.
The Effects of Non-Redox Active Metal Ions on the Activation of Dioxygen: Isolation and Characterization of a Heterobimetallic Complex Containing a MnIII–(μ-OH)–CaII core

PubMed Central

Park, Young Jun; Ziller, Joseph W.; Borovik, A. S.

2011-01-01

Rate enhancements for the reduction of dioxygen by a MnII complex were observed in the presence of redox inactive Group 2 metal ions. The rate changes correlated with an increase in the Lewis acidity of the Group 2 metal ions. These studies led to the isolation of heterobimetallic complexes that contain MnIII-(μ-OH)-MII cores (MII = CaII, BaII), in which the hydroxo oxygen atom is derived from O2. This type of core structure has relevance to the oxygen evolving complexes within photosystem II. PMID:21595481
Shell thickness-dependent microwave absorption of core-shell Fe3O4@C composites.

PubMed

Du, Yunchen; Liu, Wenwen; Qiang, Rong; Wang, Ying; Han, Xijiang; Ma, Jun; Xu, Ping

2014-08-13

Core-shell composites, Fe3O4@C, with 500 nm Fe3O4 microspheres as cores have been successfully prepared through in situ polymerization of phenolic resin on the Fe3O4 surface and subsequent high-temperature carbonization. The thickness of carbon shell, from 20 to 70 nm, can be well controlled by modulating the weight ratio of resorcinol and Fe3O4 microspheres. Carbothermic reduction has not been triggered at present conditions, thus the crystalline phase and magnetic property of Fe3O4 micropsheres can be well preserved during the carbonization process. Although carbon shells display amorphous nature, Raman spectra reveal that the presence of Fe3O4 micropsheres can promote their graphitization degree to a certain extent. Coating Fe3O4 microspheres with carbon shells will not only increase the complex permittivity but also improve characteristic impedance, leading to multiple relaxation processes in these composites, thus the microwave absorption properties of these composites are greatly enhanced. Very interestingly, a critical thickness of carbon shells leads to an unusual dielectric behavior of the core-shell structure, which endows these composites with strong reflection loss, especially in the high frequency range. By considering good chemical homogeneity and microwave absorption, we believe the as-fabricated Fe3O4@C composites can be promising candidates as highly effective microwave absorbers.
Dynamic musical communication of core affect

PubMed Central

Flaig, Nicole K.; Large, Edward W.

2013-01-01

Is there something special about the way music communicates feelings? Theorists since Meyer (1956) have attempted to explain how music could stimulate varied and subtle affective experiences by violating learned expectancies, or by mimicking other forms of social interaction. Our proposal is that music speaks to the brain in its own language; it need not imitate any other form of communication. We review recent theoretical and empirical literature, which suggests that all conscious processes consist of dynamic neural events, produced by spatially dispersed processes in the physical brain. Intentional thought and affective experience arise as dynamical aspects of neural events taking place in multiple brain areas simultaneously. At any given moment, this content comprises a unified “scene” that is integrated into a dynamic core through synchrony of neuronal oscillations. We propose that (1) neurodynamic synchrony with musical stimuli gives rise to musical qualia including tonal and temporal expectancies, and that (2) music-synchronous responses couple into core neurodynamics, enabling music to directly modulate core affect. Expressive music performance, for example, may recruit rhythm-synchronous neural responses to support affective communication. We suggest that the dynamic relationship between musical expression and the experience of affect presents a unique opportunity for the study of emotional experience. This may help elucidate the neural mechanisms underlying arousal and valence, and offer a new approach to exploring the complex dynamics of the how and why of emotional experience. PMID:24672492
Dynamic musical communication of core affect.

PubMed

Flaig, Nicole K; Large, Edward W

2014-01-01

Is there something special about the way music communicates feelings? Theorists since Meyer (1956) have attempted to explain how music could stimulate varied and subtle affective experiences by violating learned expectancies, or by mimicking other forms of social interaction. Our proposal is that music speaks to the brain in its own language; it need not imitate any other form of communication. We review recent theoretical and empirical literature, which suggests that all conscious processes consist of dynamic neural events, produced by spatially dispersed processes in the physical brain. Intentional thought and affective experience arise as dynamical aspects of neural events taking place in multiple brain areas simultaneously. At any given moment, this content comprises a unified "scene" that is integrated into a dynamic core through synchrony of neuronal oscillations. We propose that (1) neurodynamic synchrony with musical stimuli gives rise to musical qualia including tonal and temporal expectancies, and that (2) music-synchronous responses couple into core neurodynamics, enabling music to directly modulate core affect. Expressive music performance, for example, may recruit rhythm-synchronous neural responses to support affective communication. We suggest that the dynamic relationship between musical expression and the experience of affect presents a unique opportunity for the study of emotional experience. This may help elucidate the neural mechanisms underlying arousal and valence, and offer a new approach to exploring the complex dynamics of the how and why of emotional experience.
Cold fronts and shocks formed by gas streams in galaxy clusters

NASA Astrophysics Data System (ADS)

Zinger, E.; Dekel, A.; Birnboim, Y.; Nagai, D.; Lau, E.; Kravtsov, A. V.

2018-05-01

Cold fronts (CFs) and shocks are hallmarks of the complex intra-cluster medium (ICM) in galaxy clusters. They are thought to occur due to gas motions within the ICM and are often attributed to galaxy mergers within the cluster. Using hydro-cosmological simulations of clusters of galaxies, we show that collisions of inflowing gas streams, seen to penetrate to the very centre of about half the clusters, offer an additional mechanism for the formation of shocks and CFs in cluster cores. Unlike episodic merger events, a gas stream inflow persists over a period of several Gyr and it could generate a particular pattern of multiple CFs and shocks.
Enantioselective Rhodium-Catalyzed Dimerization of ω-Allenyl Carboxylic Acids: Straightforward Synthesis of C2 -Symmetric Macrodiolides.

PubMed

Steib, Philip; Breit, Bernhard

2018-04-19

Herein, we report on the first enantioselective and atom-efficient catalytic one-step dimerization method to selectively transform ω-allenyl carboxylic acids into C 2 -symmetric 14- to 28-membered bismacrolactones (macrodiolides). This convenient asymmetric access serves as an attractive route towards multiple naturally occuring homodimeric macrocyclic scaffolds and demonstrates excellent efficiency to construct the complex, symmetric core structures. By utilizing a rhodium catalyst with a modified chiral cyclopentylidene-diop ligand, the desired diolides were obtained in good to high yields, high diastereoselectivity, and excellent enantioselectivity. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Multilayer checkpoints for microRNA authenticity during RISC assembly.

PubMed

Kawamata, Tomoko; Yoda, Mayuko; Tomari, Yukihide

2011-09-01

MicroRNAs (miRNAs) function through the RNA-induced silencing complex (RISC), which contains an Argonaute (Ago) protein at the core. RISC assembly follows a two-step pathway: miRNA/miRNA* duplex loading into Ago, and separation of the two strands within Ago. Here we show that the 5' phosphate of the miRNA strand is essential for duplex loading into Ago, whereas the preferred 5' nucleotide of the miRNA strand and the base-pairing status in the seed region and the middle of the 3' region function as additive anchors to Ago. Consequently, the miRNA authenticity is inspected at multiple steps during RISC assembly.
Flexible Stoichiometry and Asymmetry of the PIDDosome Core Complex by Heteronuclear NMR Spectroscopy and Mass Spectrometry

PubMed Central

Nematollahi, Lily A.; Garza-Garcia, Acely; Bechara, Chérine; Esposito, Diego; Morgner, Nina; Robinson, Carol V.; Driscoll, Paul C.

2015-01-01

Homotypic death domain (DD)–DD interactions are important in the assembly of oligomeric signaling complexes such as the PIDDosome that acts as a platform for activation of caspase-2-dependent apoptotic signaling. The structure of the PIDDosome core complex exhibits an asymmetric three-layered arrangement containing five PIDD-DDs in one layer, five RAIDD-DDs in a second layer and an additional two RAIDD-DDs. We addressed complex formation between PIDD-DD and RAIDD-DD in solution using heteronuclear nuclear magnetic resonance (NMR) spectroscopy, nanoflow electrospray ionization mass spectrometry and size-exclusion chromatography with multi-angle light scattering. The DDs assemble into complexes displaying molecular masses in the range 130–158 kDa and RAIDD-DD:PIDD-DD stoichiometries of 5:5, 6:5 and 7:5. These data suggest that the crystal structure is representative of only the heaviest species in solution and that two RAIDD-DDs are loosely attached to the 5:5 core. Two-dimensional 1H,15N-NMR experiments exhibited signal loss upon complexation consistent with the formation of high-molecular-weight species. 13C-Methyl-transverse relaxation optimized spectroscopy measurements of the PIDDosome core exhibit signs of differential line broadening, cross-peak splitting and chemical shift heterogeneity that reflect the presence of non-equivalent sites at interfaces within an asymmetric complex. Experiments using a mutant RAIDD-DD that forms a monodisperse 5:5 complex with PIDD-DD show that the spectroscopic signature derives from the quasi- but non-exact equivalent environments of each DD. Since this characteristic was previously demonstrated for the complex between the DDs of CD95 and FADD, the NMR data for this system are consistent with the formation of a structure homologous to the PIDDosome core. PMID:25528640
Geochemistry of glacial sediments in the area of the Bend massive sulfide deposit, north-central Wisconsin

USGS Publications Warehouse

Woodruff, L.G.; Attig, J.W.; Cannon, W.F.

2004-01-01

Geochemical exploration in northern Wisconsin has been problematic because of thick glacial overburden and complex stratigraphic record of glacial history. To assess till geochemical exploration in an area of thick glacial cover and complex stratigraphy samples of glacial materials were collected from cores from five rotasonic boreholes near a known massive sulfide deposit, the Bend deposit in north-central Wisconsin. Diamond drilling in the Bend area has defined a long, thin zone of mineralization at least partly intersected at the bedrock surface beneath 30-40 m of unconsolidated glacial sediments. The bedrock surface has remnant regolith and saprolite resulting from pre-Pleistocene weathering. Massive sulfide and mineralized rock collected from diamond drill core from the deposit contain high (10s to 10,000s ppm) concentrations of Ag, As, Au, Bi, Cu, Hg, Se, Te, and Tl. Geochemical properties of the glacial stratigraphic units helped clarify the sequence and source areas of several glacial ice advances preserved in the section. At least two till sheets are recognized. Over the zone of mineralization, saprolite and preglacial alluvial and lacustrine samples are preserved on the bedrock surface in a paleoriver valley. The overlying till sheet is a gray, silty carbonate till with a source hundreds of kilometers to the northwest of the study area. This gray till is overlain by red, sandy till with a source to the north in Proterozoic rocks of the Lake Superior area. The complex glacial stratigraphy confounds down-ice geochemical till exploration. The presence of remnant saprolite, preglacial sediment, and far-traveled carbonate till minimized glacial erosion of mineralized material. As a result, little evidence of down-ice glacial dispersion of lithologic or mineralogic indicators of Bend massive sulfide mineralization was found in the samples from the rotasonic cores. This study points out the importance of determining glacial stratigraphy and history, and identifying favorable lithologies required for geochemical exploration. Drift prospecting in Wisconsin and other areas near the outer limits of the Pleistocene ice sheets may not be unsuccessful, in part, because of complex stratigraphic sequences of multiple glaciations where deposition dominates over erosion. ?? 2004 Elsevier B.V. All rights reserved.
The Arabidopsis THO/TREX component TEX1 functionally interacts with MOS11 and modulates mRNA export and alternative splicing events.

PubMed

Sørensen, Brian B; Ehrnsberger, Hans F; Esposito, Silvia; Pfab, Alexander; Bruckmann, Astrid; Hauptmann, Judith; Meister, Gunter; Merkl, Rainer; Schubert, Thomas; Längst, Gernot; Melzer, Michael; Grasser, Marion; Grasser, Klaus D

2017-02-01

We identify proteins that associate with the THO core complex, and show that the TEX1 and MOS11 components functionally interact, affecting mRNA export and splicing as well as plant development. TREX (TRanscription-EXport) is a multiprotein complex that plays a central role in the coordination of synthesis, processing and nuclear export of mRNAs. Using targeted proteomics, we identified proteins that associate with the THO core complex of Arabidopsis TREX. In addition to the RNA helicase UAP56 and the mRNA export factors ALY2-4 and MOS11 we detected interactions with the mRNA export complex TREX-2 and multiple spliceosomal components. Plants defective in the THO component TEX1 or in the mRNA export factor MOS11 (orthologue of human CIP29) are mildly affected. However, tex1 mos11 double-mutant plants show marked defects in vegetative and reproductive development. In tex1 plants, the levels of tasiRNAs are reduced, while miR173 levels are decreased in mos11 mutants. In nuclei of mos11 cells increased mRNA accumulation was observed, while no mRNA export defect was detected with tex1 cells. Nevertheless, in tex1 mos11 double-mutants, the mRNA export defect was clearly enhanced relative to mos11. The subnuclear distribution of TEX1 substantially overlaps with that of splicing-related SR proteins and in tex1 plants the ratio of certain alternative splicing events is altered. Our results demonstrate that Arabidopsis TEX1 and MOS11 are involved in distinct steps of the biogenesis of mRNAs and small RNAs, and that they interact regarding some aspects, but act independently in others.
Multiple slope failures shaped the lower continental slope offshore NW Svalbard in the Fram Strait

NASA Astrophysics Data System (ADS)

Osti, Giacomo; Mienert, Jürgen; Forwick, Matthias; Sverre Laberg, Jan

2016-04-01

Bathymetry data show that the lower slope (between 1300 m and 3000 m water depth) of the NW-Svalbard passive margin has been affected by multiple slope failure events. The single events differ in terms of extension, volume of mobilized sediments, morphology of the slide scar, run-out distance and age. As for several mega-scale and minor Arctic slides, the trigger mechanism is still speculative and may include high sedimentation rates, dissociation of gas hydrates, excess pore pressure, or earthquakes caused by isostatic rebound. In this study, we discuss the potential trigger mechanisms that have led to the multiple slope failure events within what we suggest to be named the Fram Strait Slide Complex. The slide complex lies in proximity to the tectonically active Spitsbergen Fracture Zone where earthquakes events, occurrences of potential weak layers in the sediment column, low sedimentation rates, and extended gas hydrate-bearing sediments may all have contributed to the causes leading to multiple slope failures. Preliminary results obtained from 14C dating on N. pachyderma sin. from sediment cores from the Spitsbergen Fracture Zone slides (SFZS 1 and 2), coupled with sub-bottom profiler data (frequency 9 to 15 KHz) show that the two shallowest glide planes within one of the observed slide scars failed ~100,000 and ~115,000 yr BP. Whilst SFZS 1 affected an area of 750 km2 mobilizing a total sediment volume of 40 km3, SFZS 2 moved an area of 230 km2 with a sediment volume of 4.5 km3.
Onset and Multiple Fluctuations of Holocene Glaciation in the Sierra Nevada, California

NASA Astrophysics Data System (ADS)

Bowerman, N. D.; Clark, D. H.

2004-12-01

Multiple sediment cores from two paternoster tarns (First and Second lakes) in North Fork Big Pine Creek, Sierra Nevada, preserve the most detailed and complete record of Holocene glaciation yet recovered in the range; they indicate that the glacier was absent during the early Holocene, reformed in the late Holocene, and experienced several expansions and contractions, culminating with the Matthes maximum during the last ˜200 years. The lakes are fed by outwash from the Palisade Glacier, the largest ( ˜1.3 km2) and presumably longest-lived glacier in the Sierra Nevada, and capture essentially all of the rock flour produced by the glacier. Distinct late-Holocene (Matthes) and late-Pleistocene (Recess Peak) moraines lie between the modern glacier and the lakes. Thus, the lakes have received continuous sedimentation since the retreat of the Tioga glacier ( ˜15,000 yr B.P.), and therefore capture rock flour related to all subsequent advances. First and Second lakes occupy relatively deep bedrock basins at 3036 m and 3066 m asl., respectively. Third Lake, a shallow (<3 m deep), moraine-dammed lake that lies directly above Second Lake, is the only lake between the Palisade Glacier and the lower lakes. As such, it captures the coarsest (sand/gravel bedload) outwash, but abundant suspended sediment (silt/clay) continues to the lower lakes. We cored the lakes using both Reasoner and Livingston corers, to sediment depths of up to ˜5 m. The deepest cores bottomed in coarse, inorganic sand and silt that we interpret as outwash or slopewash related to Tioga deglaciation. Magnetic susceptibility (MS) analyses of the sediment cores indicate that both lakes record multiple late-Holocene peaks in MS, with the most recent peak being the largest. They also retain outwash near the base related to the more extensive Recess Peak advance. MS peaks in Sierran lakes typically indicate greater abundances of clastic (vs. organic) sediment. The peaks in our cores thus imply 4-5 periods of increased flux of rock flour (outwash) from the upstream Palisade Glacier, most likely related to formation and expansions of the glacier in the late Holocene. The maximum peak at the top of the cores confirms the moraine record, which indicates that the maximum Holocene advance of Sierran glaciers occurred during the late Little Ice Age (last ˜200 yr) At least one tephra layer, possibly related to the Mono/Inyo dome complexes, occurs in the middle depths of the First Lake cores. Other narrow peaks in MS may also be associated with tephra deposits. Ongoing detailed analyses of the sediments, including AMS radiocarbon dating, visual and x-ray imaging, particle size analysis, organic content, tephrochronology, diatom assemblages, and palynology will constrain the timing and character of the environmental fluctuations related to the rock-flour flux. We will present results of these analyses at the meeting.
Pre-eruptive Magnetic Reconnection within a Multi-flux-rope System in the Solar Corona

NASA Astrophysics Data System (ADS)

Awasthi, Arun Kumar; Liu, Rui; Wang, Haimin; Wang, Yuming; Shen, Chenglong

2018-04-01

The solar corona is frequently disrupted by coronal mass ejections (CMEs), whose core structure is believed to be a flux rope made of helical magnetic field. This has become a “standard” picture; though, it remains elusive how the flux rope forms and evolves toward eruption. While one-third of the ejecta passing through spacecraft demonstrate a flux-rope structure, the rest have complex magnetic fields. Are they originating from a coherent flux rope, too? Here we investigate the source region of a complex ejecta, focusing on a flare precursor with definitive signatures of magnetic reconnection, i.e., nonthermal electrons, flaring plasma, and bidirectional outflowing blobs. Aided by nonlinear force-free field modeling, we conclude that the reconnection occurs within a system of multiple braided flux ropes with different degrees of coherency. The observation signifies the importance of internal structure and dynamics in understanding CMEs and in predicting their impacts on Earth.
Prison prescribing practice: practitioners' perspectives on why prison is different.

PubMed

Bartlett, A; Dholakia, N; England, R; Hales, H; van Horn, E; McGeorge, T; Moss, B; Ovaisi, S; Tukmachi, E; Patel, S

2014-04-01

The current prison population in England and Wales has multiple, complex healthcare needs, presenting unique challenges to those caring for prisoners. Prison numbers have increased dramatically in the last 10 years. There are now approximately 84,000 prisoners in England and Wales and 120,000 new episodes of imprisonment each year . The authors all contribute to prison healthcare. Below, we discuss a key issue arising from first-hand experience of prisoners' health and social care needs, the prescription of psycho-active drugs by primary and secondary care practitioners. This is a core medical task, but beset with difficulties. These difficulties are not necessarily encountered in other areas of prison healthcare. However, they do illustrate how providing healthcare to prisoners is complex, often lacking a research base and can have pitfalls that are not obvious to the outsider. © 2014 John Wiley & Sons Ltd.

RTEMS SMP and MTAPI for Efficient Multi-Core Space Applications on LEON3/LEON4 Processors

NASA Astrophysics Data System (ADS)

Cederman, Daniel; Hellstrom, Daniel; Sherrill, Joel; Bloom, Gedare; Patte, Mathieu; Zulianello, Marco

2015-09-01

This paper presents the final result of an European Space Agency (ESA) activity aimed at improving the software support for LEON processors used in SMP configurations. One of the benefits of using a multicore system in a SMP configuration is that in many instances it is possible to better utilize the available processing resources by load balancing between cores. This however comes with the cost of having to synchronize operations between cores, leading to increased complexity. While in an AMP system one can use multiple instances of operating systems that are only uni-processor capable, a SMP system requires the operating system to be written to support multicore systems. In this activity we have improved and extended the SMP support of the RTEMS real-time operating system and ensured that it fully supports the multicore capable LEON processors. The targeted hardware in the activity has been the GR712RC, a dual-core core LEON3FT processor, and the functional prototype of ESA's Next Generation Multiprocessor (NGMP), a quad core LEON4 processor. The final version of the NGMP is now available as a product under the name GR740. An implementation of the Multicore Task Management API (MTAPI) has been developed as part of this activity to aid in the parallelization of applications for RTEMS SMP. It allows for simplified development of parallel applications using the task-based programming model. An existing space application, the Gaia Video Processing Unit, has been ported to RTEMS SMP using the MTAPI implementation to demonstrate the feasibility and usefulness of multicore processors for space payload software. The activity is funded by ESA under contract 4000108560/13/NL/JK. Gedare Bloom is supported in part by NSF CNS-0934725.
Coordination of Hepatitis C Virus Assembly by Distinct Regulatory Regions in Nonstructural Protein 5A

PubMed Central

Zayas, Margarita; Long, Gang; Madan, Vanesa; Bartenschlager, Ralf

2016-01-01

Hepatitis C virus (HCV) nonstructural protein (NS)5A is a RNA-binding protein composed of a N-terminal membrane anchor, a structured domain I (DI) and two intrinsically disordered domains (DII and DIII) interacting with viral and cellular proteins. While DI and DII are essential for RNA replication, DIII is required for assembly. How these processes are orchestrated by NS5A is poorly understood. In this study, we identified a highly conserved basic cluster (BC) at the N-terminus of DIII that is critical for particle assembly. We generated BC mutants and compared them with mutants that are blocked at different stages of the assembly process: a NS5A serine cluster (SC) mutant blocked in NS5A-core interaction and a mutant lacking the envelope glycoproteins (ΔE1E2). We found that BC mutations did not affect core-NS5A interaction, but strongly impaired core–RNA association as well as virus particle envelopment. Moreover, BC mutations impaired RNA-NS5A interaction arguing that the BC might be required for loading of core protein with viral RNA. Interestingly, RNA-core interaction was also reduced with the ΔE1E2 mutant, suggesting that nucleocapsid formation and envelopment are coupled. These findings argue for two NS5A DIII determinants regulating assembly at distinct, but closely linked steps: (i) SC-dependent recruitment of replication complexes to core protein and (ii) BC-dependent RNA genome delivery to core protein, triggering encapsidation that is tightly coupled to particle envelopment. These results provide a striking example how a single viral protein exerts multiple functions to coordinate the steps from RNA replication to the assembly of infectious virus particles. PMID:26727512
Genome-Wide Analysis of the Core DNA Replication Machinery in the Higher Plants Arabidopsis and Rice1[W][OA

PubMed Central

Shultz, Randall W.; Tatineni, Vinaya M.; Hanley-Bowdoin, Linda; Thompson, William F.

2007-01-01

Core DNA replication proteins mediate the initiation, elongation, and Okazaki fragment maturation functions of DNA replication. Although this process is generally conserved in eukaryotes, important differences in the molecular architecture of the DNA replication machine and the function of individual subunits have been reported in various model systems. We have combined genome-wide bioinformatic analyses of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) with published experimental data to provide a comprehensive view of the core DNA replication machinery in plants. Many components identified in this analysis have not been studied previously in plant systems, including the GINS (go ichi ni san) complex (PSF1, PSF2, PSF3, and SLD5), MCM8, MCM9, MCM10, NOC3, POLA2, POLA3, POLA4, POLD3, POLD4, and RNASEH2. Our results indicate that the core DNA replication machinery from plants is more similar to vertebrates than single-celled yeasts (Saccharomyces cerevisiae), suggesting that animal models may be more relevant to plant systems. However, we also uncovered some important differences between plants and vertebrate machinery. For example, we did not identify geminin or RNASEH1 genes in plants. Our analyses also indicate that plants may be unique among eukaryotes in that they have multiple copies of numerous core DNA replication genes. This finding raises the question of whether specialized functions have evolved in some cases. This analysis establishes that the core DNA replication machinery is highly conserved across plant species and displays many features in common with other eukaryotes and some characteristics that are unique to plants. PMID:17556508
Controlled Synthesis and Utilization of Metal and Oxide Hybrid Nanoparticles

NASA Astrophysics Data System (ADS)

Crane, Cameron

This dissertation reports the development of synthetic methods concerning rationally-designed, hybrid, and multifunctional nanomaterials. These methods are based on a wet chemical, solution phase approach that utilizes the knowledge of synthetic organic and inorganic chemistry to generate building blocks in solution for the growth of nanocrystals and hybrid nanostructures. This work builds on the prior knowledge of shape-controlled synthesis of noble metal nanocrystals and expands into the challenging realm of the more reactive first row transition metals. Specifically, a microemulsion sol-gel method was developed to synthesize Au-SiO2 dimers as precursors for the synthesis of segmented heterostructures of noble metals that can be used for catalysis. This microemulsion sol-gel method was modified to synthesize an aqueous suspension of oxidation-resistant Cu-SiO2 core-shell nanoparticles that can be used for sensing and catalysis. A thermal decomposition approach was developed, wherein zero-valence metal precursor complexes in the presence of seed nanoparticles produced metal-metal oxide core-shell structures with well-controlled shell thickness. This method was demonstrated on AuCu 3-Fe3O4, AuCu3-NiO, and AuCu3 -MnO core-shell systems. Switching the core from AuCu3 alloy to pure Cu, this method could extend to Cu-Fe3O4 and Cu-MnO systems. Further etching the Cu core in these core-shell structures led to the formation of the hollow metal oxides which provides a versatile route to hollow nanostructures of metal oxides. This work develops the synthetic library of tools for the production of hybrid nanostructures with multiple functionalities.
Integrated core-log petrofacies analysis in the construction of a reservoir geomodel: A case study of a mature Mississippian carbonate reservoir using limited data

USGS Publications Warehouse

Bhattacharya, S.; Doveton, J.H.; Carr, T.R.; Guy, W.R.; Gerlach, P.M.

2005-01-01

Small independent operators produce most of the Mississippian carbonate fields in the United States mid-continent, where a lack of integrated characterization studies precludes maximization of hydrocarbon recovery. This study uses integrative techniques to leverage extant data in an Osagian and Meramecian (Mississippian) cherty carbonate reservoir in Kansas. Available data include petrophysical logs of varying vintages, limited number of cores, and production histories from each well. A consistent set of assumptions were used to extract well-level porosity and initial saturations, from logs of different types and vintages, to build a geomodel. Lacking regularly recorded well shut-in pressures, an iterative technique, based on material balance formulations, was used to estimate average reservoir-pressure decline that matched available drillstem test data and validated log-analysis assumptions. Core plugs representing the principal reservoir petrofacies provide critical inputs for characterization and simulation studies. However, assigning plugs among multiple reservoir petrofacies is difficult in complex (carbonate) reservoirs. In a bottom-up approach, raw capillary pressure (Pc) data were plotted on the Super-Pickett plot, and log- and core-derived saturation-height distributions were reconciled to group plugs by facies, to identify core plugs representative of the principal reservoir facies, and to discriminate facies in the logged interval. Pc data from representative core plugs were used for effective pay evaluation to estimate water cut from completions, in infill and producing wells, and guide-selective perforations for economic exploitation of mature fields. The results from this study were used to drill 22 infill wells. Techniques demonstrated here can be applied in other fields and reservoirs. Copyright ?? 2005. The American Association of Petroleum Geologists. All rights reserved.
Integrative FourD omics approach profiles the target network of the carbon storage regulatory system

PubMed Central

Sowa, Steven W.; Gelderman, Grant; Leistra, Abigail N.; Buvanendiran, Aishwarya; Lipp, Sarah; Pitaktong, Areen; Vakulskas, Christopher A.; Romeo, Tony; Baldea, Michael

2017-01-01

Abstract Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets. PMID:28126921
Bonding quandary in the [Cu3S2]3+ core: insights from the analysis of domain averaged fermi holes and the local spin.

PubMed

Ponec, Robert; Ramos-Cordoba, Eloy; Salvador, Pedro

2013-03-07

The electronic structure of the trinuclear symmetric complex [(tmedaCu)3S2 ](3+), whose Cu3S2 core represents a model of the active site of metalloenzymes involved in biological processes, has been in recent years the subject of vigorous debate. The complex exists as an open-shell triplet, and discussions concerned the question whether there is a direct S-S bond in the [Cu3S2](3+) core, whose answer is closely related to the problem of the formal oxidation state of Cu atoms. In order to contribute to the elucidation of the serious differences in the conclusions of earlier studies, we report in this study the detailed comprehensive analysis of the electronic structure of the [Cu3S2](3+) core using the methodologies that are specifically designed to address three particular aspects of the bonding in the core of the above complex, namely, the presence and/or absence of direct S-S bond, the existence and the nature of spin-spin interactions among the atoms in the core, and the formal oxidation state of Cu atoms in the core. Using such a combined approach, it was possible to conclude that the picture of bonding consistently indicates the existence of a weak direct two-center-three-electron (2c-3e) S-S bond, but at the same time, the observed lack of any significant local spin in the core of the complex is at odds with the suggested existence of antiferromagnetic coupling among the Cu and S atoms, so that the peculiarities of the bonding in the complex seem to be due to extensive delocalization of the unpaired spin in the [Cu3S2](3+) core. Finally, a scrutiny of the effective atomic hybrids and their occupations points to a predominant formal Cu(II) oxidation state, with a weak contribution of partial Cu(I) character induced mainly by the partial flow of electrons from S to Cu atoms and high delocalization of the unpaired spin in the [Cu3S2](3+) core.
Core outcome measures for exercise studies in people with multiple sclerosis: recommendations from a multidisciplinary consensus meeting.

PubMed

Paul, Lorna; Coote, Susan; Crosbie, Jean; Dixon, Diane; Hale, Leigh; Holloway, Ed; McCrone, Paul; Miller, Linda; Saxton, John; Sincock, Caroline; White, Lesley

2014-10-01

Evidence shows that exercise is beneficial for people with multiple sclerosis (MS); however, statistical pooling of data is difficult because of the diversity of outcome measures used. The objective of this review is to report the recommendations of an International Consensus Meeting for a core set of outcome measures for use in exercise studies in MS. From the 100 categories of the International Classification of Function Core Sets for MS, 57 categories were considered as likely/potentially likely to be affected by exercise and were clustered into seven core groups. Outcome measures to address each group were evaluated regarding, for example, psychometric properties. The following are recommended: Modified Fatigue Impact Scale (MFIS) or Fatigue Severity Scale (FSS) for energy and drive, 6-Minute Walk Test (6MWT) for exercise tolerance, Timed Up and Go (TUG) for muscle function and moving around, Multiple Sclerosis Impact Scale (MSIS-29) or Multiple Sclerosis Quality of Life-54 Instrument (MSQoL54) for quality of life and body mass index (BMI) or waist-hip ratio (WHR) for the health risks associated with excess body fat. A cost effectiveness analysis and qualitative evaluation should be included where possible. Using these core measures ensures that future meta-analyses of exercise studies in MS are more robust and thus more effectively inform practice. © The Author(s) 2014.
The dynamics of health care reform--learning from a complex adaptive systems theoretical perspective.

PubMed

Sturmberg, Joachim P; Martin, Carmel M

2010-10-01

Health services demonstrate key features of complex adaptive systems (CAS), they are dynamic and unfold in unpredictable ways, and unfolding events are often unique. To better understand the complex adaptive nature of health systems around a core attractor we propose the metaphor of the health care vortex. We also suggest that in an ideal health care system the core attractor would be personal health attainment. Health care reforms around the world offer an opportunity to analyse health system change from a complex adaptive perspective. At large health care reforms have been pursued disregarding the complex adaptive nature of the health system. The paper details some recent reforms and outlines how to understand their strategies and outcomes, and what could be learnt for future efforts, utilising CAS principles. Current health systems show the inherent properties of a CAS driven by a core attractor of disease and cost containment. We content that more meaningful health systems reform requires the delicate task of shifting the core attractor from disease and cost containment towards health attainment.
Understanding the implementation of evidence-based care: a structural network approach.

PubMed

Parchman, Michael L; Scoglio, Caterina M; Schumm, Phillip

2011-02-24

Recent study of complex networks has yielded many new insights into phenomenon such as social networks, the internet, and sexually transmitted infections. The purpose of this analysis is to examine the properties of a network created by the 'co-care' of patients within one region of the Veterans Health Affairs. Data were obtained for all outpatient visits from 1 October 2006 to 30 September 2008 within one large Veterans Integrated Service Network. Types of physician within each clinic were nodes connected by shared patients, with a weighted link representing the number of shared patients between each connected pair. Network metrics calculated included edge weights, node degree, node strength, node coreness, and node betweenness. Log-log plots were used to examine the distribution of these metrics. Sizes of k-core networks were also computed under multiple conditions of node removal. There were 4,310,465 encounters by 266,710 shared patients between 722 provider types (nodes) across 41 stations or clinics resulting in 34,390 edges. The number of other nodes to which primary care provider nodes have a connection (172.7) is 42% greater than that of general surgeons and two and one-half times as high as cardiology. The log-log plot of the edge weight distribution appears to be linear in nature, revealing a 'scale-free' characteristic of the network, while the distributions of node degree and node strength are less so. The analysis of the k-core network sizes under increasing removal of primary care nodes shows that about 10 most connected primary care nodes play a critical role in keeping the k-core networks connected, because their removal disintegrates the highest k-core network. Delivery of healthcare in a large healthcare system such as that of the US Department of Veterans Affairs (VA) can be represented as a complex network. This network consists of highly connected provider nodes that serve as 'hubs' within the network, and demonstrates some 'scale-free' properties. By using currently available tools to explore its topology, we can explore how the underlying connectivity of such a system affects the behavior of providers, and perhaps leverage that understanding to improve quality and outcomes of care.
Understanding Why Students Participate in Multiple Surveys: Who are the Hard-Core Responders?

ERIC Educational Resources Information Center

Porter, Stephen R.; Whitcomb, Michael E.

2004-01-01

What causes a student to participate in a survey? This paper looks at survey response across multiple surveys to understand who the hard-core survey responders and non-responders are. Students at a selective liberal arts college were administered four different surveys throughout the 2002-2003 academic year, and we use the number of surveys…
Evaluation of a Multiple Mediator Model of the Relationship between Core Self-Evaluations and Job Satisfaction in Employed Individuals with Disabilities

ERIC Educational Resources Information Center

Smedema, Susan Miller; Kesselmayer, Rachel Friefeld; Peterson, Lauren

2018-01-01

Purpose: To test a meditation model of the relationship between core self-evaluations (CSE) and job satisfaction in employed individuals with disabilities. Method: A quantitative descriptive design using Hayes's (2012) PROCESS macro for SPSS and multiple regression analysis. Two-hundred fifty-nine employed persons with disabilities were recruited…
Experiments on Lunar Core Composition: Phase Equilibrium Analysis of A Multi-Element (Fe-Ni-S-C) System

NASA Technical Reports Server (NTRS)

Go, B. M.; Righter, K.; Danielson, L.; Pando, K.

2015-01-01

Previous geochemical and geophysical experiments have proposed the presence of a small, metallic lunar core, but its composition is still being investigated. Knowledge of core composition can have a significant effect on understanding the thermal history of the Moon, the conditions surrounding the liquid-solid or liquid-liquid field, and siderophile element partitioning between mantle and core. However, experiments on complex bulk core compositions are very limited. One limitation comes from numerous studies that have only considered two or three element systems such as Fe-S or Fe-C, which do not supply a comprehensive understanding for complex systems such as Fe-Ni-S-Si-C. Recent geophysical data suggests the presence of up to 6% lighter elements. Reassessments of Apollo seismological analyses and samples have also shown the need to acquire more data for a broader range of pressures, temperatures, and compositions. This study considers a complex multi-element system (Fe-Ni-S-C) for a relevant pressure and temperature range to the Moon's core conditions.
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.

PubMed

Van Leene, Jelle; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Stals, Hilde; Van Isterdael, Gert; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; De Bodt, Stefanie; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo C G; Eloy, Nubia; Renne, Charlotte; Meyer, Christian; Faure, Jean-Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C; Van de Peer, Yves; Hilson, Pierre; Kuiper, Martin; De Veylder, Lieven; Van Onckelen, Harry; Inzé, Dirk; Witters, Erwin; De Jaeger, Geert

2010-08-10

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)-cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK-cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants.
Parallel seed-based approach to multiple protein structure similarities detection

DOE PAGES

Chapuis, Guillaume; Le Boudic-Jamin, Mathilde; Andonov, Rumen; ...

2015-01-01

Finding similarities between protein structures is a crucial task in molecular biology. Most of the existing tools require proteins to be aligned in order-preserving way and only find single alignments even when multiple similar regions exist. We propose a new seed-based approach that discovers multiple pairs of similar regions. Its computational complexity is polynomial and it comes with a quality guarantee—the returned alignments have both root mean squared deviations (coordinate-based as well as internal-distances based) lower than a given threshold, if such exist. We do not require the alignments to be order preserving (i.e., we consider nonsequential alignments), which makesmore » our algorithm suitable for detecting similar domains when comparing multidomain proteins as well as to detect structural repetitions within a single protein. Because the search space for nonsequential alignments is much larger than for sequential ones, the computational burden is addressed by extensive use of parallel computing techniques: a coarse-grain level parallelism making use of available CPU cores for computation and a fine-grain level parallelism exploiting bit-level concurrency as well as vector instructions.« less
Minimally Disruptive Medicine: A Pragmatically Comprehensive Model for Delivering Care to Patients with Multiple Chronic Conditions

PubMed Central

Leppin, Aaron L.; Montori, Victor M.; Gionfriddo, Michael R.

2015-01-01

An increasing proportion of healthcare resources in the United States are directed toward an expanding group of complex and multimorbid patients. Federal stakeholders have called for new models of care to meet the needs of these patients. Minimally Disruptive Medicine (MDM) is a theory-based, patient-centered, and context-sensitive approach to care that focuses on achieving patient goals for life and health while imposing the smallest possible treatment burden on patients’ lives. The MDM Care Model is designed to be pragmatically comprehensive, meaning that it aims to address any and all factors that impact the implementation and effectiveness of care for patients with multiple chronic conditions. It comprises core activities that map to an underlying and testable theoretical framework. This encourages refinement and future study. Here, we present the conceptual rationale for and a practical approach to minimally disruptive care for patients with multiple chronic conditions. We introduce some of the specific tools and strategies that can be used to identify the right care for these patients and to put it into practice. PMID:27417747
Multiple ash layers in late Quaternary sediments from the Central Indian Basin

NASA Astrophysics Data System (ADS)

Mascarenhas-Pereira, M. B. L.; Nagender Nath, B.; Iyer, S. D.; Borole, D. V.; Parthiban, G.; Jijin, R.; Khedekar, V.

2016-04-01

We have investigated three sediment cores collected from water depths > 5000 m along the transect 76°30‧E in close proximity to a fracture zone in the Central Indian Basin (CIB). The cores yielded five volcanic horizons of which four have visual and dispersed shards. Rhyolitic glass shards of bubble wall, platy, angular and blocky types were retrieved from various stratigraphic horizons in the cores. The abundance of glass shards, composition of bulk sediments, and 230Thexcess ages of the host sediments were used to distinguish the volcanic horizons. Of the four volcanic horizons, three are now newly reported and correspond to ages of ~ 85, 107-109 and 142-146 ka while the fourth horizon is of 70-75 ka. By using trace element ratios and Cr and Nb-based normative calculations, cryptotephra has been identified for the first time from the CIB sediment. The cryptotephra forms the fifth ash horizon and is of ~ 34 ka. A comparison with the published data on volcanic tephra in and around the Indian Ocean indicate the shard rich horizon (SRH) of 70-75 ka to resemble the Younger Toba Tuffs (YTT), while the other volcanic horizons that were deposited during different time periods do not correlate with any known marine or terrestrial records. These tephra layers have produced a tephrostratigraphic framework across the tectonically and volcanically complex regions of the CIB. Due to the lack of terrestrial equivalents of these tephra, it is hypothesized that the newly found volcanic horizons may have been derived from submarine volcanic eruptions. Multiple layers of submarine volcaniclastic deposits found at water depths as great as 5300 m reaffirm the growing belief that submarine phreatomagmatic eruptions are much more common in the intraplate region of the Indian Ocean than previously reported.
Evolution of oceanic core complex domes and corrugations

NASA Astrophysics Data System (ADS)

Cann, J.; Escartin, J.; Smith, D.; Schouten, H.

2007-12-01

In regions of the oceans where detachment faulting is developed widely, individual core complex domes (elevated massifs capped by corrugated detachment surfaces) show a consistent morphology. At their outward sides, most core complex domes are attached to a planar slope, interpreted (Smith et al., 2006) as an originally steep inward-facing normal fault that has been rotated to shallower angles. We suggest that the break in slope where the originally steep normal fault meets the domal corrugated surface marks the trace of the brittle-ductile transition at the base of the original normal fault. The steep faults originate within a short distance of the spreading axis. This means that the arcuate shape of the intersection of the steep fault with the dome must indicate the shape of the brittle-ductile transition very close to the spreading axis. The transition must be very shallow close to the summit of the dome and deeper on each flank. Evidence from drilling of some core complexes (McCaig et al, 2007) shows that while the domal detachment faults are active they may channel hydrothermal flow at black smoker temperatures and may be simultaneously injected by magma from below. This indicates a close link between igneous activity, hydrothermal flow and deformation while a core complex is forming. Once the shape of the core complex dome is established, it persists as the ductile footwall mantle rising from below is shaped by the overlying brittle hanging wall that has been cooled by the hydrothermal circulation. The corrugations in the footwall must be moulded into it by irregularities in the brittle hanging wall, as suggested by Spencer (1999). The along-axis arched shape of the hanging wall helps to stabilise the domal shape of the footwall as it rises and cools.
The foot core system: a new paradigm for understanding intrinsic foot muscle function.

PubMed

McKeon, Patrick O; Hertel, Jay; Bramble, Dennis; Davis, Irene

2015-03-01

The foot is a complex structure with many articulations and multiple degrees of freedom that play an important role in static posture and dynamic activities. The evolutionary development of the arch of the foot was coincident with the greater demands placed on the foot as humans began to run. The movement and stability of the arch is controlled by intrinsic and extrinsic muscles. However, the intrinsic muscles are largely ignored by clinicians and researchers. As such, these muscles are seldom addressed in rehabilitation programmes. Interventions for foot-related problems are more often directed at externally supporting the foot rather than training these muscles to function as they are designed. In this paper, we propose a novel paradigm for understanding the function of the foot. We begin with an overview of the evolution of the human foot with a focus on the development of the arch. This is followed by a description of the foot intrinsic muscles and their relationship to the extrinsic muscles. We draw the parallels between the small muscles of the trunk region that make up the lumbopelvic core and the intrinsic foot muscles, introducing the concept of the foot core. We then integrate the concept of the foot core into the assessment and treatment of the foot. Finally, we call for an increased awareness of the importance of the foot core stability to normal foot and lower extremity function. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
The CoreWall Project: An Update for 2007

NASA Astrophysics Data System (ADS)

Yu-Chung Chen, J.; Higgins, S.; Hur, H.; Ito, E.; Jenkins, C. J.; Johnson, A.; Leigh, J.; Morin, P.; Lee, J.

2007-12-01

The CoreWall Suite is a NSF-supported collaborative development for a real-time core description (Corelyzer), stratigraphic correlation (Correlater), and data visualization (CoreNavigator) software to be used by the marine, terrestrial and Antarctic science communities. The overall goal of the Corewall software development is to bring portable cross-platform tools to the broader drilling and coring communities to expand and enhance data visualization and enhance collaborative integration of multiple datasets. The CoreWall Project is now in its second year and significant progress has been made on all 3 software components. Corelyzer has undergone 2 field deployments and testing by ANDRILL program in 2006 (and again in Fall 2007) and by ICDP's SAFOD project (summer 2007). In addition, Corewall group and ICDP are working together so that the core description (DIS) system can expose DIS core data directly into Corelyzer seamlessly and be available to future ICDP and IODP-Mission Specific Platform expeditions. Educators have also taken note of the software's ease of use and strong visualization capabilities to begin exploring curriculum projects with Corelyzer software. To ensure that the software development is integrated with other community IT activities the development of the U.S. IODP-Phase 2 Scientific Ocean Drilling Vessel (SODV), a Steering Committee was constituted. It is composed of key U.S. IODP and related database (e.g., CHRONOS, SedDB) developers and users as well as representatives of other core-based enterprises (e.g., ANDRILL, ICDP, LacCore). Corelyzer (CoreWall's main visual core description tool) software displays digital core images from one or more cores along with discrete data streams (eg. physical properties, downhole logs) and nested images (eg. thin sections, fossils) to provide a robust approach to the description of sediment cores. Corelyzer's digital image handling allows the cores to be viewed from micron to km scale determined by the image resolution along a sliding plane, effectively making it a "digital microscope". Detailed features such as lithologic variation, macroscopic grain size variation, bioturbation intensity, chemical composition and micropaleontology are easier to interpret and annotate. Significant new capabilities have been added to allow for importing multiple images and data types, sharing/exporting Corelyzer "work sessions" for multiple users, enhanced annotations, as well as support for other activities like examining clasts, and sample requests. The new Correlator software, the updated version of Splicer/Sagan software used by ODP for over 10 years, has been ported into a single new analysis tool that will work across multiple platforms and interact seamlessly with both JANUS (ODP's relational database), CHRONOS, PetDB, SedDB, dbSEABED and other databases. This functionality will result in a CoreWall Suite module that can be used and distributed anywhere for stratigraphic and age correlation tasks. CoreNavigator, a spatial data discovery tool, has taken on a virtual Globe interface that allows users to enter Corelyzer from a geographic-visual standpoint.

Contemporary prostate biopsy reporting: insights from a survey of clinicians' use of pathology data.

PubMed

Varma, Murali; Narahari, Krishna; Mason, Malcolm; Oxley, Jon D; Berney, Daniel M

2018-05-02

To determine how clinicians use data in contemporary prostate biopsy reports. A survey was circulated to members of the British Association of Urological Surgeons and the British Uro-oncology Group. Responses were received from 114 respondents (88 urologists, 26 oncologists). Ninety-seven (94%) use the number of positive cores from each side and 43 (42%) use the % number of positive cores. When determining the number and percentage of positive cores, 72 (71%) would not differentiate between targeted and non-targeted samples. If multiple Gleason Scores (GS) were included in a report, 77 (78%) would use the worst GS even if present in a core with very little tumour, 12% would use the global GS and 10% the GS in the core most involved by tumour. Fifty-five (55%) either never or rarely used perineural invasion for patient management. The number of positive cores is an important parameter for patient management but may be difficult to determine in the laboratory due to core fragmentation so the biopsy taker must indicate the number of biopsies obtained. Multiple biopsies taken from a single site are often interpreted by clinicians as separate cores when determining the number of positive cores so pathologists should also report the number of sites positive. Clinicians have a non-uniform approach to the interpretation of multiple GS in prostate biopsy reports so we recommend that pathologists also include a single 'bottom-line' GS for each case to direct the clinician's treatment decision. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.
Aligning "TextEvaluator"® Scores with the Accelerated Text Complexity Guidelines Specified in the Common Core State Standards. Research Report. ETS RR-15-21

ERIC Educational Resources Information Center

Sheehan, Kathleen M.

2015-01-01

The "TextEvaluator"® text analysis tool is a fully automated text complexity evaluation tool designed to help teachers, curriculum specialists, textbook publishers, and test developers select texts that are consistent with the text complexity guidelines specified in the Common Core State Standards.This paper documents the procedure used…
A novel complex networks clustering algorithm based on the core influence of nodes.

PubMed

Tong, Chao; Niu, Jianwei; Dai, Bin; Xie, Zhongyu

2014-01-01

In complex networks, cluster structure, identified by the heterogeneity of nodes, has become a common and important topological property. Network clustering methods are thus significant for the study of complex networks. Currently, many typical clustering algorithms have some weakness like inaccuracy and slow convergence. In this paper, we propose a clustering algorithm by calculating the core influence of nodes. The clustering process is a simulation of the process of cluster formation in sociology. The algorithm detects the nodes with core influence through their betweenness centrality, and builds the cluster's core structure by discriminant functions. Next, the algorithm gets the final cluster structure after clustering the rest of the nodes in the network by optimizing method. Experiments on different datasets show that the clustering accuracy of this algorithm is superior to the classical clustering algorithm (Fast-Newman algorithm). It clusters faster and plays a positive role in revealing the real cluster structure of complex networks precisely.
Numerical simulation of the multiple core localized low shear toroidal Alfvenic eigenmodes

NASA Astrophysics Data System (ADS)

Wang, Wenjia; Zhou, Deng; Hu, Youjun; Ming, Yue

2018-03-01

In modern tokamak experiments, scenarios with weak central magnetic shear has been proposed. It is necessary to study the Alfvenic mode activities in such scenarios. Theoretical researches have predicted the multiplicity of core-localized toroidally induced Alfvenic eigenmodes for ɛ/s > 1, where ɛ is the inverse aspect ratio and s is magnetic shear. We numerically investigate the existence of multiplicity of core-localized TAEs and mode characteristics using NOVA code in the present work. We firstly verify the existence of the multiplicity for zero beta plasma and the even mode at the forbidden zone. For finite beta plasma, the mode parities become more distinguishable, and the frequencies of odd modes are close to the upper tip of the continuum, while the frequencies of even modes are close to the lower tip of the continuum. Their frequencies are well separated by the forbidden zone. With the increasing value of ɛ/s, more modes with multiple radial nodes will appear, which is in agreement with theoretical prediction. The discrepancy between theoretical prediction and our numerical simulation is also discussed in the main text.
Multiple cores of Gleason score 6 correlate with favourable findings at radical prostatectomy

PubMed Central

Ellis, Carla L.; Walsh, Patrick C.; Partin, Alan W.; Epstein, Jonathan I.

2014-01-01

Objective To establish whether the good prognosis of Gleason score 6 (GS6) is maintained in the setting of multiple involved cores. Patients and Methods In total, 6156 men (from 1 April 2000 to 30 April 2007) with GS6 on biopsy underwent radical prostatectomy (RP) at our institution. The number of positive cores was correlated with the outcome at RP. Results More positive cores correlated with less organ-confined disease (P < 0.001), positive margins (P < 0.012), increasing RP grade (P < 0.001) and increased seminal vesicles/lymph node involvement (P = 0.012). For men with data available, the actuarial risk of being biochemically free of disease at 5 years was 93.2% when ≤6 cores were positive (812 men followed to 5 years) vs 89.1% if >6 cores were positive (41 men followed to 2 years) (P = 0.6). Although the predicted ‘cure rate’ of >75% probability of a tumour showing no evidence of biochemical recurrence at 10 years after RP was statistically different between cases with ≤6 vs >6 positive cores (P < 0.0001), the outcome in both groups was still favourable (90.5% vs 84%). Partin-like tables were generated factoring in the number of positive cores to predict organ-confined disease as a guide for urologists to perform nerve-sparing surgery. For example, with T1c disease, there was a ≥75% probability of organ-confined disease with one to three positive cores regardless of prostate-specific antigen (PSA) level, and the same probability was present with four to six positive cores and a PSA level of 0–4 ng/mL. Conclusion A low Gleason score on biopsy is a powerful prognostic finding, such that this favourable outcome is maintained even in the setting of multiple positive cores with GS6. PMID:23350787
Multiple cores of Gleason score 6 correlate with favourable findings at radical prostatectomy.

PubMed

Ellis, Carla L; Walsh, Patrick C; Partin, Alan W; Epstein, Jonathan I

2013-06-01

To establish whether the good prognosis of Gleason score 6 (GS6) is maintained in the setting of multiple involved cores. In total, 6156 men (from 1 April 2000 to 30 April 2007) with GS6 on biopsy underwent radical prostatectomy (RP) at our institution. The number of positive cores was correlated with the outcome at RP. More positive cores correlated with less organ-confined disease (P < 0.001), positive margins (P < 0.012), increasing RP grade (P < 0.001) and increased seminal vesicles/lymph node involvement (P = 0.012). For men with data available, the actuarial risk of being biochemically free of disease at 5 years was 93.2% when ≤6 cores were positive (812 men followed to 5 years) vs 89.1% if >6 cores were positive (41 men followed to 2 years) (P = 0.6). Although the predicted 'cure rate' of >75% probability of a tumour showing no evidence of biochemical recurrence at 10 years after RP was statistically different between cases with ≤6 vs >6 positive cores (P < 0.0001), the outcome in both groups was still favourable (90.5% vs 84%). Partin-like tables were generated factoring in the number of positive cores to predict organ-confined disease as a guide for urologists to perform nerve-sparing surgery. For example, with T1c disease, there was a ≥75% probability of organ-confined disease with one to three positive cores regardless of prostate-specific antigen (PSA) level, and the same probability was present with four to six positive cores and a PSA level of 0-4 ng/mL. A low Gleason score on biopsy is a powerful prognostic finding, such that this favourable outcome is maintained even in the setting of multiple positive cores with GS6. © 2013 BJU International.
A facile single-step synthesis of ternary multicore magneto-plasmonic nanoparticles.

PubMed

Benelmekki, Maria; Bohra, Murtaza; Kim, Jeong-Hwan; Diaz, Rosa E; Vernieres, Jerome; Grammatikopoulos, Panagiotis; Sowwan, Mukhles

2014-04-07

We report a facile single-step synthesis of ternary hybrid nanoparticles (NPs) composed of multiple dumbbell-like iron-silver (FeAg) cores encapsulated by a silicon (Si) shell using a versatile co-sputter gas-condensation technique. In comparison to previously reported binary magneto-plasmonic NPs, the advantage conferred by a Si shell is to bind the multiple magneto-plasmonic (FeAg) cores together and prevent them from aggregation at the same time. Further, we demonstrate that the size of the NPs and number of cores in each NP can be modulated over a wide range by tuning the experimental parameters.
Managing hospitals in turbulent times: do organizational changes improve hospital survival?

PubMed Central

Lee, S Y; Alexander, J A

1999-01-01

OBJECTIVE: To examine (1) the degree to which organizational changes affected hospital survival; (2) whether core and peripheral organizational changes affected hospital survival differently; and (3) how simultaneous organizational changes affected hospital survival. DATA SOURCES: AHA Hospital Surveys, the Area Resource File, and the AHA Hospital Guides, Part B: Multihospital Systems. STUDY DESIGN: The study employed a longitudinal panel design. We followed changes in all community hospitals in the continental United States from 1981 through 1994. The dependent variable, hospital closure, was examined as a function of multiple changes in a hospital's core and peripheral structures as well as the hospital's organizational and environmental characteristics. Cox regression models were used to test the expectations that core changes increased closure risk while peripheral changes decreased such risk, and that simultaneous core and peripheral changes would lead to higher risk of closure. PRINCIPAL FINDINGS: Results indicated more peripheral than core changes in community hospitals. Overall, findings contradicted our expectations. Change in specialty, a core change, was beneficial for hospitals, because it reduced closure risk. The two most frequent peripheral changes, downsizing and leadership change, were positively associated with closure. Simultaneous organizational changes displayed a similar pattern: multiple core changes reduced closure risk, while multiple peripheral changes increased the risk. These patterns held regardless of the level of uncertainty in hospital environments. CONCLUSIONS: Organizational changes are not all beneficial for hospitals, suggesting that hospital leaders should be both cautious and selective in their efforts to turn their hospitals around. PMID:10536977
Early Tertiary Anaconda metamorphic core complex, southwestern Montana

USGS Publications Warehouse

O'Neill, J. M.; Lonn, J.D.; Lageson, D.R.; Kunk, Michael J.

2004-01-01

A sinuous zone of gently southeast-dipping low-angle Tertiary normal faults is exposed for 100 km along the eastern margins of the Anaconda and Flint Creek ranges in southwest Montana. Faults in the zone variously place Mesoproterozoic through Paleozoic sedimentary rocks on younger Tertiary granitic rocks or on sedimentary rocks older than the overlying detached rocks. Lower plate rocks are lineated and mylonitic at the main fault and, below the mylonitic front, are cut by mylonitic mesoscopic to microscopic shear zones. The upper plate consists of an imbricate stack of younger-on-older sedimentary rocks that are locally mylonitic at the main, lowermost detachment fault but are characteristically strongly brecciated or broken. Kinematic indicators in the lineated mylonite indicate tectonic transport to the east-southeast. Syntectonic sedimentary breccia and coarse conglomerate derived solely from upper plate rocks were deposited locally on top of hanging-wall rocks in low-lying areas between fault blocks and breccia zones. Muscovite occurs locally as mica fish in mylonitic quartzites at or near the main detachment. The 40Ar/39Ar age spectrum obtained from muscovite in one mylonitic quartzite yielded an age of 47.2 + 0.14 Ma, interpreted to be the age of mylonitization. The fault zone is interpreted as a detachment fault that bounds a metamorphic core complex, here termed the Anaconda metamorphic core complex, similar in age and character to the Bitterroot mylonite that bounds the Bitterroot metamorphic core complex along the Idaho-Montana state line 100 km to the west. The Bitterroot and Anaconda core complexes are likely components of a continuous, tectonically integrated system. Recognition of this core complex expands the region of known early Tertiary brittle-ductile crustal extension eastward into areas of profound Late Cretaceous contractile deformation characterized by complex structural interactions between the overthrust belt and Laramide basement uplifts, overprinted by late Tertiary Basin and Range faulting. ?? 2004 NRC Canada.
The source of high signal cooperativity in bacterial chemosensory arrays

PubMed Central

Piñas, Germán E.; Frank, Vered; Vaknin, Ady; Parkinson, John S.

2016-01-01

The Escherichia coli chemosensory system consists of large arrays of transmembrane chemoreceptors associated with a dedicated histidine kinase, CheA, and a linker protein, CheW, that couples CheA activity to receptor control. The kinase activity responses to receptor ligand occupancy changes can be highly cooperative, reflecting allosteric coupling of multiple CheA and receptor molecules. Recent structural and functional studies have led to a working model in which receptor core complexes, the minimal units of signaling, are linked into hexagonal arrays through a unique interface 2 interaction between CheW and the P5 domain of CheA. To test this array model, we constructed and characterized CheA and CheW mutants with amino acid replacements at key interface 2 residues. The mutant proteins proved defective in interface 2-specific in vivo cross-linking assays, and formed signaling complexes that were dispersed around the cell membrane rather than clustered at the cell poles as in wild type chemosensory arrays. Interface 2 mutants down-regulated CheA activity in response to attractant stimuli in vivo, but with much less cooperativity than the wild type. Moreover, mutant cells containing fluorophore-tagged receptors exhibited greater basal anisotropy that changed rapidly in response to attractant stimuli, consistent with facile changes in loosely packed receptors. We conclude that interface 2 lesions disrupt important network connections between core complexes, preventing receptors from operating in large, allosteric teams. This work confirms the critical role of interface 2 in organizing the chemosensory array, in directing the clustered array to the cell poles, and in producing its highly cooperative signaling properties. PMID:26951681
ETD QA CORE TEAM: AN ELOQUENT SOLUTION TO A COMPLEX PROBLEM

EPA Science Inventory

ETD QA CORE TEAM: AN ELOQUENT SOLUTION TO A COMPLEX PROBLEMThomas J. Hughes, QA and Records Manager, Experimental Toxicology Division (ETD), National Health and Environmental Effects Research Laboratory (NHEERL), ORD, U.S. EPA, RTP, NC 27709

ETD is the largest health divis...
The lateral boundary of a metamorphic core complex: the Moutsounas shear zone on Naxos, Cyclades, Greece

NASA Astrophysics Data System (ADS)

Cao, S.; Neubauer, F.

2012-04-01

One of the apparently best investigated metamorphic core complexes all over world is that of Naxos in the Aegean Sea and numerous high-quality data on structures and microfabrics have been published. Among these structures is the Naxos-Paros ductile low-angle fault (Gautier et al., 1993), which is located along the northern margin of Naxos and which is part of the North Cycladic Detachment System (Jolivet et al., 2010). There, structural evidence indicates that the hanging wall of the core complex experienced large-scale top-to-the-north (ca. 010°) transport along a low-angle detachment fault. Interestingly no attention has been paid on the well exposed boundary fault on the eastern margin of the Naxos Island, which is even not mentioned in the lierarure. We denote this fault as Moutsounas shear zone, which represents the lateral boundary of the Naxos metamorphic core complex. The Naxos metamorphic core complex is a N-trending elongated dome, which exposes on its eastern side moderately E-dipping micaschists and marbles, which are largely well annealed due to late heating. These annealed rocks grade towards the Moutsounas Peninsula in retrogressed sheared rocks, mostly phyllonitic micaschists and phyllites with an E-dipping foliation and a ca. NNE-trending subhorizontal stretching lineation. Shear bands, asymmetric fringes around rigid clasts and oblique mineralized extension veins consistently indicate top-to-the-NNE shear. The shear zone is structurally overlain by hydrothermally altered Miocene conglomerates, which contain no pebbles from the Naxos metamorphic core complex but exclusively from the ophiolitic hangingwall unit. Miocene rocks are exposed both on the northern and southern edge of the Moutsounas Peninsula. Their bedding is variable but dips generally towards NW, oblique to the detachment fault, which dips with a medium-angle towards east indicating therefore a rollover structure. The Miocene succession is overlain by subhorizontal conglomerates of Pliocene age, which form the main portion of the Moutsounas Peninsula and which contain numerous clasts, mainly marble, of the metamorphic core complex. These sedimentary data indicate that exhumation of the Naxos metamorphic core complex postdate deposition of Miocene successions and predate Pliocene rocks. We interpret the Moutsounas shear zone as a lateral boundary of the Naxos migmatite dome and relate their main activity with top NNE-shear with the main stage of updoming during migmatite formation and granite uplift between ca. 15 and 11 Ma.
Effect of interactions between multiple interfaces on the rheological characteristics of double emulsions

NASA Astrophysics Data System (ADS)

Choi, Se Bin; Park, Jae Yong; Moon, Ji Young; Lee, Joon Sang

2018-06-01

In this study, we analyzed the rheological characteristics of double emulsions by using a three-dimensional lattice Boltzmann model. Numerical simulations indicate that interactions between multiple interfaces play a vital role in determining the shear stress on interfaces and affect deformations, which influence the relative viscosity of double emulsions. The large shear stress induced by droplets in contact increases the relative viscosity for high volume fractions. The double emulsions also show shear-thinning behavior, which corresponds with the Carreau model. The interfacial interference between the core and the deforming shell cause the relative viscosity to increase with increasing core-droplet radius. Finally, we investigated the dependence of the double-emulsion viscosity on the core-droplet viscosity. At high shear rates, the relative viscosity increases with increasing core-droplet viscosity. However, the trend is opposite at low shear rates, which results from the high inward flow (Marangoni flow) at low core-droplet viscosity.
Isolation and characterization of PSI-LHCI super-complex and their sub-complexes from a red alga Cyanidioschyzon merolae.

PubMed

Tian, Lirong; Liu, Zheyi; Wang, Fangjun; Shen, Liangliang; Chen, Jinghua; Chang, Lijing; Zhao, Songhao; Han, Guangye; Wang, Wenda; Kuang, Tingyun; Qin, Xiaochun; Shen, Jian-Ren

2017-09-01

Photosystem I (PSI)-light-harvesting complex I (LHCI) super-complex and its sub-complexes PSI core and LHCI, were purified from a unicellular red alga Cyanidioschyzon merolae and characterized. PSI-LHCI of C. merolae existed as a monomer with a molecular mass of 580 kDa. Mass spectrometry analysis identified 11 subunits (PsaA, B, C, D, E, F, I, J, K, L, O) in the core complex and three LHCI subunits, CMQ142C, CMN234C, and CMN235C in LHCI, indicating that at least three Lhcr subunits associate with the red algal PSI core. PsaG was not found in the red algae PSI-LHCI, and we suggest that the position corresponding to Lhca1 in higher plant PSI-LHCI is empty in the red algal PSI-LHCI. The PSI-LHCI complex was separated into two bands on native PAGE, suggesting that two different complexes may be present with slightly different protein compositions probably with respective to the numbers of Lhcr subunits. Based on the results obtained, a structural model was proposed for the red algal PSI-LHCI. Furthermore, pigment analysis revealed that the C. merolae PSI-LHCI contained a large amount of zeaxanthin, which is mainly associated with the LHCI complex whereas little zeaxanthin was found in the PSI core. This indicates a unique feature of the carotenoid composition of the Lhcr proteins and may suggest an important role of Zea in the light-harvesting and photoprotection of the red algal PSI-LHCI complex.
A Mass Spectrometry Proteomics Data Management Platform*

PubMed Central

Sharma, Vagisha; Eng, Jimmy K.; MacCoss, Michael J.; Riffle, Michael

2012-01-01

Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the volume and complexity are only increasing with time. There exist many software pipelines for analyzing these data (each typically with its own file formats), and as technology improves, these file formats change and new formats are developed. Files produced from these myriad software programs may accumulate on hard disks or tape drives over time, with older files being rendered progressively more obsolete and unusable with each successive technical advancement and data format change. Although initiatives exist to standardize the file formats used in proteomics, they do not address the core failings of a file-based data management system: (1) files are typically poorly annotated experimentally, (2) files are “organically” distributed across laboratory file systems in an ad hoc manner, (3) files formats become obsolete, and (4) searching the data and comparing and contrasting results across separate experiments is very inefficient (if possible at all). Here we present a relational database architecture and accompanying web application dubbed Mass Spectrometry Data Platform that is designed to address the failings of the file-based mass spectrometry data management approach. The database is designed such that the output of disparate software pipelines may be imported into a core set of unified tables, with these core tables being extended to support data generated by specific pipelines. Because the data are unified, they may be queried, viewed, and compared across multiple experiments using a common web interface. Mass Spectrometry Data Platform is open source and freely available at http://code.google.com/p/msdapl/. PMID:22611296
Widespread active detachment faulting and core complex formation near 13 degrees N on the Mid-Atlantic Ridge.

PubMed

Smith, Deborah K; Cann, Johnson R; Escartín, Javier

2006-07-27

Oceanic core complexes are massifs in which lower-crustal and upper-mantle rocks are exposed at the sea floor. They form at mid-ocean ridges through slip on detachment faults rooted below the spreading axis. To date, most studies of core complexes have been based on isolated inactive massifs that have spread away from ridge axes. Here we present a survey of the Mid-Atlantic Ridge near 13 degrees N containing a segment in which a number of linked detachment faults extend for 75 km along one flank of the spreading axis. The detachment faults are apparently all currently active and at various stages of development. A field of extinct core complexes extends away from the axis for at least 100 km. Our observations reveal the topographic characteristics of actively forming core complexes and their evolution from initiation within the axial valley floor to maturity and eventual inactivity. Within the surrounding region there is a strong correlation between detachment fault morphology at the ridge axis and high rates of hydroacoustically recorded earthquake seismicity. Preliminary examination of seismicity and seafloor morphology farther north along the Mid-Atlantic Ridge suggests that active detachment faulting is occurring in many segments and that detachment faulting is more important in the generation of ocean crust at this slow-spreading ridge than previously suspected.
Mass spectrometry of Escherichia coli RNA polymerase: interactions of the core enzyme with sigma70 and Rsd protein.

PubMed

Ilag, Leopold L; Westblade, Lars F; Deshayes, Caroline; Kolb, Annie; Busby, Stephen J W; Robinson, Carol V

2004-02-01

The E. coli RNA polymerase core enzyme is a multisubunit complex of 388,981 Da. To initiate transcription at promoters, the core enzyme associates with a sigma subunit to form holo RNA polymerase. Here we have used nanoflow electrospray mass spectrometry, coupled with tandem mass spectrometry, to probe the interaction of the RNA polymerase core enzyme with the most abundant sigma factor, sigma70. The results show remarkably well-resolved spectra for both the core and holo RNA polymerases. The regulator of sigma70, Rsd protein, has previously been identified as a protein that binds to free sigma70. We show that Rsd also interacts with core enzyme. In addition, by adding increasing amounts of Rsd, we show that sigma70 is displaced from holo RNA polymerase, resulting in complexes of Rsd with core and sigma70. The results argue for a model in which Rsd not only sequesters sigma70, but is also an effector of core RNA polymerase.
Novel Binding Motif and New Flexibility Revealed by Structural Analyses of a Pyruvate Dehydrogenase-Dihydrolipoyl Acetyltransferase Subcomplex from the Escherichia coli Pyruvate Dehydrogenase Multienzyme Complex*

PubMed Central

Arjunan, Palaniappa; Wang, Junjie; Nemeria, Natalia S.; Reynolds, Shelley; Brown, Ian; Chandrasekhar, Krishnamoorthy; Calero, Guillermo; Jordan, Frank; Furey, William

2014-01-01

The Escherichia coli pyruvate dehydrogenase multienzyme complex contains multiple copies of three enzymatic components, E1p, E2p, and E3, that sequentially carry out distinct steps in the overall reaction converting pyruvate to acetyl-CoA. Efficient functioning requires the enzymatic components to assemble into a large complex, the integrity of which is maintained by tethering of the displaced, peripheral E1p and E3 components to the E2p core through non-covalent binding. We here report the crystal structure of a subcomplex between E1p and an E2p didomain containing a hybrid lipoyl domain along with the peripheral subunit-binding domain responsible for tethering to the core. In the structure, a region at the N terminus of each subunit in the E1p homodimer previously unseen due to crystallographic disorder was observed, revealing a new folding motif involved in E1p-E2p didomain interactions, and an additional, unexpected, flexibility was discovered in the E1p-E2p didomain subcomplex, both of which probably have consequences in the overall multienzyme complex assembly. This represents the first structure of an E1p-E2p didomain subcomplex involving a homodimeric E1p, and the results may be applicable to a large range of complexes with homodimeric E1 components. Results of HD exchange mass spectrometric experiments using the intact, wild type 3-lipoyl E2p and E1p are consistent with the crystallographic data obtained from the E1p-E2p didomain subcomplex as well as with other biochemical and NMR data reported from our groups, confirming that our findings are applicable to the entire E1p-E2p assembly. PMID:25210042
Novel binding motif and new flexibility revealed by structural analyses of a pyruvate dehydrogenase-dihydrolipoyl acetyltransferase subcomplex from the Escherichia coli pyruvate dehydrogenase multienzyme complex.

PubMed

Arjunan, Palaniappa; Wang, Junjie; Nemeria, Natalia S; Reynolds, Shelley; Brown, Ian; Chandrasekhar, Krishnamoorthy; Calero, Guillermo; Jordan, Frank; Furey, William

2014-10-24

The Escherichia coli pyruvate dehydrogenase multienzyme complex contains multiple copies of three enzymatic components, E1p, E2p, and E3, that sequentially carry out distinct steps in the overall reaction converting pyruvate to acetyl-CoA. Efficient functioning requires the enzymatic components to assemble into a large complex, the integrity of which is maintained by tethering of the displaced, peripheral E1p and E3 components to the E2p core through non-covalent binding. We here report the crystal structure of a subcomplex between E1p and an E2p didomain containing a hybrid lipoyl domain along with the peripheral subunit-binding domain responsible for tethering to the core. In the structure, a region at the N terminus of each subunit in the E1p homodimer previously unseen due to crystallographic disorder was observed, revealing a new folding motif involved in E1p-E2p didomain interactions, and an additional, unexpected, flexibility was discovered in the E1p-E2p didomain subcomplex, both of which probably have consequences in the overall multienzyme complex assembly. This represents the first structure of an E1p-E2p didomain subcomplex involving a homodimeric E1p, and the results may be applicable to a large range of complexes with homodimeric E1 components. Results of HD exchange mass spectrometric experiments using the intact, wild type 3-lipoyl E2p and E1p are consistent with the crystallographic data obtained from the E1p-E2p didomain subcomplex as well as with other biochemical and NMR data reported from our groups, confirming that our findings are applicable to the entire E1p-E2p assembly. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA.

PubMed

Dale, Ryan K; Matzat, Leah H; Lei, Elissa P

2014-08-01

Here we introduce metaseq, a software library written in Python, which enables loading multiple genomic data formats into standard Python data structures and allows flexible, customized manipulation and visualization of data from high-throughput sequencing studies. We demonstrate its practical use by analyzing multiple datasets related to chromatin insulators, which are DNA-protein complexes proposed to organize the genome into distinct transcriptional domains. Recent studies in Drosophila and mammals have implicated RNA in the regulation of chromatin insulator activities. Moreover, the Drosophila RNA-binding protein Shep has been shown to antagonize gypsy insulator activity in a tissue-specific manner, but the precise role of RNA in this process remains unclear. Better understanding of chromatin insulator regulation requires integration of multiple datasets, including those from chromatin-binding, RNA-binding, and gene expression experiments. We use metaseq to integrate RIP- and ChIP-seq data for Shep and the core gypsy insulator protein Su(Hw) in two different cell types, along with publicly available ChIP-chip and RNA-seq data. Based on the metaseq-enabled analysis presented here, we propose a model where Shep associates with chromatin cotranscriptionally, then is recruited to insulator complexes in trans where it plays a negative role in insulator activity. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization

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

Guan, Jian; Bywaters, Stephanie M.; Brendle, Sarah A.

2015-09-15

Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope.more » Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays. - Highlights: • We present HPV16-Fab complexes from neutralizing mAbs: H16.1A, H16.14J, and H263.A2. • The structure-function analysis revealed predominantly monovalent binding of each mAb. • Capsid–Fab interactions involved multiple loops from symmetry related L1 proteins. • Besides the known FG and HI loops, epitope mapping also identified DE, EF, and BC loops. • Neutralizing assays complement the structures to show multiple neutralization mechanisms.« less
Litho- and chemostratigraphy of the Flatreef PGE deposit, northern Bushveld Complex

NASA Astrophysics Data System (ADS)

Grobler, D. F.; Brits, J. A. N.; Maier, W. D.; Crossingham, A.

2018-05-01

The Flatreef is a world-class platinum-group element (PGE) deposit recently discovered down-dip from existing mining and exploration operations on the northern limb of the Bushveld Complex. Current indicated resources stand at 42 Moz PGE (346 Mt with 3.8 g/t Pt+Pd+Rh+Au, 0.32% Ni and 0.16% Cu) which, in the case of Pt, is equivalent to 10 years global annual production, making it one of the largest PGE deposits on earth. The grade and thickness of the Flatreef mineralised interval is highly unusual, with some drill core intersections containing up to 4.5 g/t Pt+Pd+Rh+Au over 90 m in drill core. Here, we document the down-dip and along-strike litho- and chemostratigraphy of the Flatreef and its footwall and hanging wall rocks, based on a diamond drill core database totalling > 720 km. At the base of the sequence intersected in the drill cores are up to 700-m-thick sills of ultramafic rocks (dunite, harzburgite, pyroxenite) emplaced into pelitic, dolomitic, and locally quartzitic and evaporitic rocks belonging to the Duitschland Formation of the Transvaal Supergroup. Next is an approximately 100-200-m sequence of low-grade-sulphide-mineralised, layered mafic-ultramafic rocks containing abundant sedimentary xenoliths and, in places, several chromite seams or stringers. This is overlain by a 100-m-thick sequence of well-mineralised mafic-ultramafic rocks (the Flatreef sensu strictu), overlain by a laterally persistent mottled compositional analogies at the base of > 1 km of homogenous Main Zone gabbronorite. Based on stratigraphic, lithological and compositional alanalogies to the layered rocks in the eastern and western Bushveld Complex, we correlate the Flatreef and its chromite bearing footwall rocks with the Upper Critical Zone, notably the interval between the UG2 chromitite and the Bastard Reef as found elsewhere in the Bushveld Complex. This includes recognition of a Merensky Reef correlative. The ultramafic rocks below the main chromitite seam (UG2 correlative) in the Flatreef footwall are correlated with the Lower Critical and Lower zones. However, compared to the western and eastern Bushveld limbs, the studied sequence is strongly enriched in sulphide and PGE, many of the rocks show elevated CaO, K2O, Rb and Zr contents, and lateral continuity of layers between drill cores is less pronounced than elsewhere in the Bushveld, whereas ultramafic units are locally considerably thickened. These compositional and lithological traits are interpreted to result from a range of processes which include contamination with calcsilicate and hornfels, intrusion of granitic magmas, and the influence of multiple structural events such as pre- to syn-emplacement regional-scale open folding and growth faults. Evidence for the existence of potholes also exists. In the shallow, up-dip portions of the project area, the entire magmatic sequence below the Main Zone becomes increasingly contaminated to the extent that individual units are somewhat more difficult to correlate between drill cores. This package represents the Platreef as exposed in outcrop and shallow bore holes across much of the northern limb of the Bushveld Complex. The new data presented here thus indicate that the Platreef is a relatively more contaminated up-dip extension of parts of the Critical and Lower zones.
Upping the Ante of Text Complexity in the Common Core State Standards: Examining Its Potential Impact on Young Readers

ERIC Educational Resources Information Center

Hiebert, Elfrieda H.; Mesmer, Heidi Anne E.

2013-01-01

The Common Core Standards for the English Language Arts (CCSS) provide explicit guidelines matching grade-level bands (e.g., 2-3, 4-5) with targeted text complexity levels. The CCSS staircase accelerates text expectations for students across Grades 2-12 in order to close a gap in the complexity of texts typically used in high school and those of…
Pan- and core- network analysis of co-expression genes in a model plant

DOE PAGES

He, Fei; Maslov, Sergei

2016-12-16

Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single coexpression network by combining multiple expression datasets generated in different labs. We advocate a complementary approach in which we construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications. To this end we reanalyzed public expression data. To describe this collection of networks we introduced concepts of ‘pan-network’ andmore » ‘core-network’ representing union and intersection between a sizeable fractions of individual networks, respectively. Here, we showed that these two types of networks are different both in terms of their topology and biological function of interacting genes. For example, the modules of the pan-network are enriched in regulatory and signaling functions, while the modules of the core-network tend to include components of large macromolecular complexes such as ribosomes and photosynthetic machinery. Our analysis is aimed to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.« less
Pan- and core- network analysis of co-expression genes in a model plant

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

He, Fei; Maslov, Sergei

Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single coexpression network by combining multiple expression datasets generated in different labs. We advocate a complementary approach in which we construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications. To this end we reanalyzed public expression data. To describe this collection of networks we introduced concepts of ‘pan-network’ andmore » ‘core-network’ representing union and intersection between a sizeable fractions of individual networks, respectively. Here, we showed that these two types of networks are different both in terms of their topology and biological function of interacting genes. For example, the modules of the pan-network are enriched in regulatory and signaling functions, while the modules of the core-network tend to include components of large macromolecular complexes such as ribosomes and photosynthetic machinery. Our analysis is aimed to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.« less
Inviscid and Viscous CFD Analysis of Booster Separation for the Space Launch System Vehicle

NASA Technical Reports Server (NTRS)

Dalle, Derek J.; Rogers, Stuart E.; Chan, William M.; Lee, Henry C.

2016-01-01

This paper presents details of Computational Fluid Dynamic (CFD) simulations of the Space Launch System during solid-rocket booster separation using the Cart3D inviscid and Overflow viscous CFD codes. The discussion addresses the use of multiple data sources of computational aerodynamics, experimental aerodynamics, and trajectory simulations for this critical phase of flight. Comparisons are shown between Cart3D simulations and a wind tunnel test performed at NASA Langley Research Center's Unitary Plan Wind Tunnel, and further comparisons are shown between Cart3D and viscous Overflow solutions for the flight vehicle. The Space Launch System (SLS) is a new exploration-class launch vehicle currently in development that includes two Solid Rocket Boosters (SRBs) modified from Space Shuttle hardware. These SRBs must separate from the SLS core during a phase of flight where aerodynamic loads are nontrivial. The main challenges for creating a separation aerodynamic database are the large number of independent variables (including orientation of the core, relative position and orientation of the boosters, and rocket thrust levels) and the complex flow caused by exhaust plumes of the booster separation motors (BSMs), which are small rockets designed to push the boosters away from the core by firing partially in the direction opposite to the motion of the vehicle.
Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes.

PubMed

Dygut, Jacek; Kalinowska, Barbara; Banach, Mateusz; Piwowar, Monika; Konieczny, Leszek; Roterman, Irena

2016-10-18

The presented analysis concerns the inter-domain and inter-protein interface in protein complexes. We propose extending the traditional understanding of the protein domain as a function of local compactness with an additional criterion which refers to the presence of a well-defined hydrophobic core. Interface areas in selected homodimers vary with respect to their contribution to share as well as individual (domain-specific) hydrophobic cores. The basic definition of a protein domain, i.e., a structural unit characterized by tighter packing than its immediate environment, is extended in order to acknowledge the role of a structured hydrophobic core, which includes the interface area. The hydrophobic properties of interfaces vary depending on the status of interacting domains-In this context we can distinguish: (1) Shared hydrophobic cores (spanning the whole dimer); (2) Individual hydrophobic cores present in each monomer irrespective of whether the dimer contains a shared core. Analysis of interfaces in dystrophin and utrophin indicates the presence of an additional quasi-domain with a prominent hydrophobic core, consisting of fragments contributed by both monomers. In addition, we have also attempted to determine the relationship between the type of interface (as categorized above) and the biological function of each complex. This analysis is entirely based on the fuzzy oil drop model.
Morphosyntax of Complex Predicates in South Caucasian Languages

ERIC Educational Resources Information Center

Lomashvili, Leila

2010-01-01

The argument structure of complex predicates such as causatives and applicatives is closely associated with the functional heads that introduce core and non-core arguments: Voice, causative and applicative. These elements merge in a sentence structure at various cycles of derivation and take complements whose "size" accounts for the meaning and…
Multilayer checkpoints for microRNA authenticity during RISC assembly

PubMed Central

Kawamata, Tomoko; Yoda, Mayuko; Tomari, Yukihide

2011-01-01

MicroRNAs (miRNAs) function through the RNA-induced silencing complex (RISC), which contains an Argonaute (Ago) protein at the core. RISC assembly follows a two-step pathway: miRNA/miRNA* duplex loading into Ago, and separation of the two strands within Ago. Here we show that the 5′ phosphate of the miRNA strand is essential for duplex loading into Ago, whereas the preferred 5′ nucleotide of the miRNA strand and the base-pairing status in the seed region and the middle of the 3′ region function as additive anchors to Ago. Consequently, the miRNA authenticity is inspected at multiple steps during RISC assembly. PMID:21738221
Performance of GeantV EM Physics Models

NASA Astrophysics Data System (ADS)

Amadio, G.; Ananya, A.; Apostolakis, J.; Aurora, A.; Bandieramonte, M.; Bhattacharyya, A.; Bianchini, C.; Brun, R.; Canal, P.; Carminati, F.; Cosmo, G.; Duhem, L.; Elvira, D.; Folger, G.; Gheata, A.; Gheata, M.; Goulas, I.; Iope, R.; Jun, S. Y.; Lima, G.; Mohanty, A.; Nikitina, T.; Novak, M.; Pokorski, W.; Ribon, A.; Seghal, R.; Shadura, O.; Vallecorsa, S.; Wenzel, S.; Zhang, Y.

2017-10-01

The recent progress in parallel hardware architectures with deeper vector pipelines or many-cores technologies brings opportunities for HEP experiments to take advantage of SIMD and SIMT computing models. Launched in 2013, the GeantV project studies performance gains in propagating multiple particles in parallel, improving instruction throughput and data locality in HEP event simulation on modern parallel hardware architecture. Due to the complexity of geometry description and physics algorithms of a typical HEP application, performance analysis is indispensable in identifying factors limiting parallel execution. In this report, we will present design considerations and preliminary computing performance of GeantV physics models on coprocessors (Intel Xeon Phi and NVidia GPUs) as well as on mainstream CPUs.
[Autism in children. Speech, behavior and motor activity point to diagnosis].

PubMed

Neumärker, K J

2001-02-01

Austistic disorders characteristically involve specific impairments of social skills, of the language and of stereotyped body movements. L Kanner and H. Asperger were the first to describe these psychopathologic features, which still form the core of the diagnostic criteria of contemporary psychiatric classification systems, ICD-10 and DSM-IV, in the category pervasive developmental disorders. Useful diagnostic tools have been developed to establish the clinical diagnosis. The results of research point to a predominantly genetic pathogenesis involving a complex interaction of multiple genes. While no causal treatments are available for these heterogenic disorders, there are many therapeutic concepts. Although some treatments may achieve significant improvements, autistic disorders usually mean a lifelong individual impairment.
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

PubMed Central

Van Leene, Jelle; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Stals, Hilde; Van Isterdael, Gert; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; De Bodt, Stefanie; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo C G; Eloy, Nubia; Renne, Charlotte; Meyer, Christian; Faure, Jean-Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C; Van de Peer, Yves; Hilson, Pierre; Kuiper, Martin; De Veylder, Lieven; Van Onckelen, Harry; Inzé, Dirk; Witters, Erwin; De Jaeger, Geert

2010-01-01

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)–cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK–cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants. PMID:20706207
Quantum electron tunneling in respiratory complex I.

PubMed

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A

2011-05-12

We have simulated the atomistic details of electronic wiring of all Fe/S clusters in complex I, a key enzyme in the respiratory electron transport chain. The tunneling current theory of many-electron systems is applied to the broken-symmetry (BS) states of the protein at the ZINDO level. While the one-electron tunneling approximation is found to hold in electron tunneling between the antiferromagnetic binuclear and tetranuclear Fe/S clusters without major orbital or spin rearrangement of the core electrons, induced polarization of the core electrons contributes significantly to decrease the electron transfer rates to 19-56 %. Calculated tunneling energy is about 3 eV higher than Fermi level in the band gap of the protein, which supports that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of the electron transport chain. Resulting electron tunneling pathways consist of up to three key contributing protein residues between neighboring Fe/S clusters. A signature of the wave properties of electrons is observed as distinct quantum interferences when multiple tunneling pathways exist. In N6a-N6b, electron tunnels along different pathways depending on the involved BS states, suggesting possible fluctuations of the tunneling pathways driven by the local protein environment. The calculated distance dependence of the electron transfer rates with internal water molecules included is in good agreement with a reported phenomenological relation.
Low-energy Control of Electrical Turbulence in the Heart

PubMed Central

Luther, Stefan; Fenton, Flavio H.; Kornreich, Bruce G.; Squires, Amgad; Bittihn, Philip; Hornung, Daniel; Zabel, Markus; Flanders, James; Gladuli, Andrea; Campoy, Luis; Cherry, Elizabeth M.; Luther, Gisa; Hasenfuss, Gerd; Krinsky, Valentin I.; Pumir, Alain; Gilmour, Robert F.; Bodenschatz, Eberhard

2011-01-01

Controlling the complex spatio-temporal dynamics underlying life-threatening cardiac arrhythmias such as fibrillation is extremely difficult due to the nonlinear interaction of excitation waves within a heterogeneous anatomical substrate1–4. Lacking a better strategy, strong, globally resetting electrical shocks remain the only reliable treatment for cardiac fibrillation5–7. Here, we establish the relation between the response of the tissue to an electric field and the spatial distribution of heterogeneities of the scale-free coronary vascular structure. We show that in response to a pulsed electric field E, these heterogeneities serve as nucleation sites for the generation of intramural electrical waves with a source density ρ(E), and a characteristic time τ for tissue depolarization that obeys a power law τ∝Eα. These intramural wave sources permit targeting of electrical turbulence near the cores of the vortices of electrical activity that drive complex fibrillatory dynamics. We show in vitro that simultaneous and direct access to multiple vortex cores results in rapid synchronization of cardiac tissue and therefore efficient termination of fibrillation. Using this novel control strategy, we demonstrate, for the first time, low-energy termination of fibrillation in vivo. Our results give new insights into the mechanisms and dynamics underlying the control of spatio-temporal chaos in heterogeneous excitable media and at the same time provide new research perspectives towards alternative, life-saving low-energy defibrillation techniques. PMID:21753855
Fanconi anemia (FA) binding protein FAAP20 stabilizes FA complementation group A (FANCA) and participates in interstrand cross-link repair.

PubMed

Leung, Justin Wai Chung; Wang, Yucai; Fong, Ka Wing; Huen, Michael Shing Yan; Li, Lei; Chen, Junjie

2012-03-20

The Fanconi anemia (FA) pathway participates in interstrand cross-link (ICL) repair and the maintenance of genomic stability. The FA core complex consists of eight FA proteins and two Fanconi anemia-associated proteins (FAAP24 and FAAP100). The FA core complex has ubiquitin ligase activity responsible for monoubiquitination of the FANCI-FANCD2 (ID) complex, which in turn initiates a cascade of biochemical events that allow processing and removal of cross-linked DNA and thereby promotes cell survival following DNA damage. Here, we report the identification of a unique component of the FA core complex, namely, FAAP20, which contains a RAD18-like ubiquitin-binding zinc-finger domain. Our data suggest that FAAP20 promotes the functional integrity of the FA core complex via its direct interaction with the FA gene product, FANCA. Indeed, somatic knockout cells devoid of FAAP20 displayed the hallmarks of FA cells, including hypersensitivity to DNA cross-linking agents, chromosome aberrations, and reduced FANCD2 monoubiquitination. Taking these data together, our study indicates that FAAP20 is an important player involved in the FA pathway.
Fanconi anemia (FA) binding protein FAAP20 stabilizes FA complementation group A (FANCA) and participates in interstrand cross-link repair

PubMed Central

Leung, Justin Wai Chung; Wang, Yucai; Fong, Ka Wing; Huen, Michael Shing Yan; Li, Lei; Chen, Junjie

2012-01-01

The Fanconi anemia (FA) pathway participates in interstrand cross-link (ICL) repair and the maintenance of genomic stability. The FA core complex consists of eight FA proteins and two Fanconi anemia-associated proteins (FAAP24 and FAAP100). The FA core complex has ubiquitin ligase activity responsible for monoubiquitination of the FANCI-FANCD2 (ID) complex, which in turn initiates a cascade of biochemical events that allow processing and removal of cross-linked DNA and thereby promotes cell survival following DNA damage. Here, we report the identification of a unique component of the FA core complex, namely, FAAP20, which contains a RAD18-like ubiquitin-binding zinc-finger domain. Our data suggest that FAAP20 promotes the functional integrity of the FA core complex via its direct interaction with the FA gene product, FANCA. Indeed, somatic knockout cells devoid of FAAP20 displayed the hallmarks of FA cells, including hypersensitivity to DNA cross-linking agents, chromosome aberrations, and reduced FANCD2 monoubiquitination. Taking these data together, our study indicates that FAAP20 is an important player involved in the FA pathway. PMID:22396592
s-core network decomposition: A generalization of k-core analysis to weighted networks

NASA Astrophysics Data System (ADS)

Eidsaa, Marius; Almaas, Eivind

2013-12-01

A broad range of systems spanning biology, technology, and social phenomena may be represented and analyzed as complex networks. Recent studies of such networks using k-core decomposition have uncovered groups of nodes that play important roles. Here, we present s-core analysis, a generalization of k-core (or k-shell) analysis to complex networks where the links have different strengths or weights. We demonstrate the s-core decomposition approach on two random networks (ER and configuration model with scale-free degree distribution) where the link weights are (i) random, (ii) correlated, and (iii) anticorrelated with the node degrees. Finally, we apply the s-core decomposition approach to the protein-interaction network of the yeast Saccharomyces cerevisiae in the context of two gene-expression experiments: oxidative stress in response to cumene hydroperoxide (CHP), and fermentation stress response (FSR). We find that the innermost s-cores are (i) different from innermost k-cores, (ii) different for the two stress conditions CHP and FSR, and (iii) enriched with proteins whose biological functions give insight into how yeast manages these specific stresses.
Igneous stratigraphy and rock-types from a deep transect of the gabbroic lower crust of the Atlantis Bank core complex (SW Indian Ridge): preliminary results from IODP Expedition 360

NASA Astrophysics Data System (ADS)

Sanfilippo, A.; France, L.; Ghosh, B.; Liu, C. Z.; Morishita, T.; Natland, J. H.; Dick, H. J.; MacLeod, C. J.; Expedition 360 Scientists, I.

2016-12-01

International Ocean Discovery Program (IODP) Expedition 360 represents the first leg of a multi-phase drilling programme ('SloMo' project) aimed at investigating the nature of the lower crust and Moho at slow spreading ridges. As an initial phase of the SloMo project, IODP Exp. 360 intended to recover a representative transect of the lower oceanic crust formed at Atlantis Bank, an oceanic core complex on the SW Indian Ridge. During this expedition, 89 cores of gabbroic rocks were recovered at Hole U1473A, drilled to 789.7 m below seafloor. This hole was subsequently deepened to 809.4 mbsf during transit Expedition 362T, which recovered additional 7 cores. The gabbroic section recovered at Hole U1473A consists of several types of gabbro, diabase, and felsic veins. The main lithology is dominated by olivine gabbro (76.5% in abundance), followed by gabbro containing 1-2% oxide (9.5%), gabbro with >2% oxide (7.4%), gabbro sensu stricto (5.1%), felsic veins (1.5%) and diabase (<0.5%). The different lithologies appear randomly distributed throughout the section, although oxide abundance seems to decrease slightly downhole, except for the lowermost intervals where oxide gabbros are more abundant. Based on changes in rock types, grain size, texture, and the occurrence of felsic material, we identified eight lithologic units, which locally define separate geochemical trends. Each unit is characterized by meter-scale heterogeneity which classically characterizes gabbros formed at slow spreading ridges. Reaction textures in olivine gabbros, crosscutting relationships between oxide gabbros and host rocks, the presence of intrusive to sutured contacts, igneous layering and the widespread occurrence of felsic veins and segregations indicate that the evolution of this section was controlled by complicated interactions of magmatic processes, e.g., fractional crystallization, melt-rock reaction, late-stage melt migration, which were active in a crystal mush formed by multiple injections of magma. This contribution describes the main features of these rocks and discusses the complexity of the igneous processes producing this 800 m-long transect of oceanic crust that was formed in a robust magmatic segment of an ultraslow spreading ridge.
A High-Confidence Interaction Map Identifies SIRT1 as a Mediator of Acetylation of USP22 and the SAGA Coactivator Complex

PubMed Central

Armour, Sean M.; Bennett, Eric J.; Braun, Craig R.; Zhang, Xiao-Yong; McMahon, Steven B.; Gygi, Steven P.; Harper, J. Wade

2013-01-01

Although many functions and targets have been attributed to the histone and protein deacetylase SIRT1, a comprehensive analysis of SIRT1 binding proteins yielding a high-confidence interaction map has not been established. Using a comparative statistical analysis of binding partners, we have assembled a high-confidence SIRT1 interactome. Employing this method, we identified the deubiquitinating enzyme ubiquitin-specific protease 22 (USP22), a component of the deubiquitinating module (DUBm) of the SAGA transcriptional coactivating complex, as a SIRT1-interacting partner. We found that this interaction is highly specific, requires the ZnF-UBP domain of USP22, and is disrupted by the inactivating H363Y mutation within SIRT1. Moreover, we show that USP22 is acetylated on multiple lysine residues and that alteration of a single lysine (K129) within the ZnF-UBP domain is sufficient to alter interaction of the DUBm with the core SAGA complex. Furthermore, USP22-mediated recruitment of SIRT1 activity promotes the deacetylation of individual SAGA complex components. Our results indicate an important role of SIRT1-mediated deacetylation in regulating the formation of DUBm subcomplexes within the larger SAGA complex. PMID:23382074
G-actin provides substrate-specificity to eukaryotic initiation factor 2α holophosphatases

PubMed Central

Chen, Ruming; Rato, Cláudia; Yan, Yahui; Crespillo-Casado, Ana; Clarke, Hanna J; Harding, Heather P; Marciniak, Stefan J; Read, Randy J; Ron, David

2015-01-01

Dephosphorylation of eukaryotic translation initiation factor 2a (eIF2a) restores protein synthesis at the waning of stress responses and requires a PP1 catalytic subunit and a regulatory subunit, PPP1R15A/GADD34 or PPP1R15B/CReP. Surprisingly, PPP1R15-PP1 binary complexes reconstituted in vitro lacked substrate selectivity. However, selectivity was restored by crude cell lysate or purified G-actin, which joined PPP1R15-PP1 to form a stable ternary complex. In crystal structures of the non-selective PPP1R15B-PP1G complex, the functional core of PPP1R15 made multiple surface contacts with PP1G, but at a distance from the active site, whereas in the substrate-selective ternary complex, actin contributes to one face of a platform encompassing the active site. Computational docking of the N-terminal lobe of eIF2a at this platform placed phosphorylated serine 51 near the active site. Mutagenesis of predicted surface-contacting residues enfeebled dephosphorylation, suggesting that avidity for the substrate plays an important role in imparting specificity on the PPP1R15B-PP1G-actin ternary complex. DOI: http://dx.doi.org/10.7554/eLife.04871.001 PMID:25774600

Polymer optical waveguide with multiple graded-index cores for on-board interconnects fabricated using soft-lithography.

PubMed

Ishigure, Takaaki; Nitta, Yosuke

2010-06-21

We successfully fabricate a polymer optical waveguide with multiple graded-index (GI) cores directly on a substrate utilizing the soft-lithography method. A UV-curable polymer (TPIR-202) supplied from Tokyo Ohka Kogyo Co., Ltd. is used, and the GI cores are formed during the curing process of the core region, which is similar to the preform process we previously reported. We experimentally confirm that near parabolic refractive index profiles are formed in the parallel cores (more than 50 channels) with 40 microm x 40 microm size at 250-microm pitch. Although the loss is still as high as 0.1 approximately 0.3 dB/cm at 850 nm, which is mainly due to scattering loss inherent to the polymer matrix, the scattering loss attributed to the waveguide's structural irregularity could be sufficiently reduced by a graded refractive index profile. For comparison, we fabricate step-index (SI)-core waveguides with the same materials by means of the same process. Then, we evaluate the inter-channel crosstalk in the SI- and GI-core waveguides under almost the same conditions. It is noteworthy that remarkable crosstalk reduction (5 dB and beyond) is confirmed in the GI-core waveguides, since the propagating modes in GI-cores are tightly confined near the core center and less optical power is found near the core cladding boundary. This significant improvement in the inter-channel crosstalk allows the GI-core waveguides to be utilized for extra high-density on-board optical interconnections.
Fundamentals of Marketing Core Curriculum. Test Items and Assessment Techniques.

ERIC Educational Resources Information Center

Smith, Clifton L.; And Others

This document contains multiple choice test items and assessment techniques for Missouri's fundamentals of marketing core curriculum. The core curriculum is divided into these nine occupational duties: (1) communications in marketing; (2) economics and marketing; (3) employment and advancement; (4) human relations in marketing; (5) marketing…
Thermionic nuclear reactor with internal heat distribution and multiple duct cooling

DOEpatents

Fisher, C.R.; Perry, L.W. Jr.

1975-11-01

A Thermionic Nuclear Reactor is described having multiple ribbon-like coolant ducts passing through the core, intertwined among the thermionic fuel elements to provide independent cooling paths. Heat pipes are disposed in the core between and adjacent to the thermionic fuel elements and the ribbon ducting, for the purpose of more uniformly distributing the heat of fission among the thermionic fuel elements and the ducts.
Results of multiple drilling compared with those of conventional methods of core decompression.

PubMed

Song, Won Seok; Yoo, Jeong Joon; Kim, Young-Min; Kim, Hee Joong

2007-01-01

We performed multiple drilling as a femoral head-preserving procedure for osteonecrosis of the femoral head thinking the therapeutic effects of core decompression could be achieved by this simpler procedure than core decompression. We retrospectively reviewed 136 patients (163 hips) who had multiple drilling using 9/64-inch Steinmann pins for treatment of nontraumatic osteonecrosis of the femoral head. The mean followup for patients who did not require additional surgery (113 hips) was 87 months (range, 60-134 months). We defined failure as the need for additional surgery or a Harris hip score less than 75. After a minimum 5-year followup, 79% (31/39) of patients with Stage I disease and 77% (62/81) of patients with Stage II disease had no additional surgery. All (15/15) small lesions (<25% involvement) and 84% (37/44) of medium-sized lesions (25-50% involvement) were considered successful. Survival rates of patients with Ficat Stages I or II lesions were greater than survival rates for patients with Stage III lesions. Hips with a large necrotic area had poor results. We had one instance of subtrochanteric fracture through drill entry holes. Multiple drilling is straightforward with few complications and produces results comparable to results of other core decompression techniques.
The role of interbasin groundwater transfers in geologically complex terranes, demonstrated by the Great Basin in the western United States

NASA Astrophysics Data System (ADS)

Nelson, Stephen T.; Mayo, Alan L.

2014-06-01

In the Great Basin, USA, bedrock interbasin flow is conceptualized as the mechanism by which large groundwater fluxes flow through multiple basins and intervening mountains. Interbasin flow is propounded based on: (1) water budget imbalances, (2) potential differences between basins, (3) stable isotope evidence, and (4) modeling studies. However, water budgets are too imprecise to discern interbasin transfers and potential differences may exist with or without interbasin fluxes. Potentiometric maps are dependent on conceptual underpinnings, leading to possible false inferences regarding interbasin transfers. Isotopic evidence is prone to non-unique interpretation and may be confounded by the effects of climate change. Structural and stratigraphic considerations in a geologically complex region like the Great Basin should produce compartmentalization, where increasing aquifer size increases the odds of segmentation along a given flow path. Initial conceptual hypotheses should explain flow with local recharge and short flow paths. Where bedrock interbasin flow is suspected, it is most likely controlled by diversion of water into the damage zones of normal faults, where fault cores act as barriers. Large-scale bedrock interbasin flow where fluxes must transect multiple basins, ranges, and faults at high angles should be the conceptual model of last resort.
Dosage changes of a segment at 17p13.1 lead to intellectual disability and microcephaly as a result of complex genetic interaction of multiple genes.

PubMed

Carvalho, Claudia M B; Vasanth, Shivakumar; Shinawi, Marwan; Russell, Chad; Ramocki, Melissa B; Brown, Chester W; Graakjaer, Jesper; Skytte, Anne-Bine; Vianna-Morgante, Angela M; Krepischi, Ana C V; Patel, Gayle S; Immken, LaDonna; Aleck, Kyrieckos; Lim, Cynthia; Cheung, Sau Wai; Rosenberg, Carla; Katsanis, Nicholas; Lupski, James R

2014-11-06

The 17p13.1 microdeletion syndrome is a recently described genomic disorder with a core clinical phenotype of intellectual disability, poor to absent speech, dysmorphic features, and a constellation of more variable clinical features, most prominently microcephaly. We identified five subjects with copy-number variants (CNVs) on 17p13.1 for whom we performed detailed clinical and molecular studies. Breakpoint mapping and retrospective analysis of published cases refined the smallest region of overlap (SRO) for microcephaly to a genomic interval containing nine genes. Dissection of this phenotype in zebrafish embryos revealed a complex genetic architecture: dosage perturbation of four genes (ASGR1, ACADVL, DVL2, and GABARAP) impeded neurodevelopment and decreased dosage of the same loci caused a reduced mitotic index in vitro. Moreover, epistatic analyses in vivo showed that dosage perturbations of discrete gene pairings induce microcephaly. Taken together, these studies support a model in which concomitant dosage perturbation of multiple genes within the CNV drive the microcephaly and possibly other neurodevelopmental phenotypes associated with rearrangements in the 17p13.1 SRO. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
Investigating the role of Clinical Nurse Consultants in one health district from multiple stakeholder perspectives: a cooperative inquiry.

PubMed

Walsh, Kenneth; Bothe, Janine; Edgar, Denise; Beaven, Geraldine; Burgess, Bernadette; Dickson, Vhari; Dunn, Stephen; Horning, Lynda; Jensen, Janice; Kandl, Bronia; Nonu, Miriam; Owen, Fran; Moss, Cheryle

2015-01-01

The impetus for this research came from a group of 11 Clinical Nurse Consultants (CNCs) within a health service in NSW, Australia, who wanted to investigate the CNC role from multiple stakeholder perspectives. With support from academic researchers, the CNCs designed and implemented the study. The aim of this research project was to investigate the role of the CNC from the multiple perspectives of CNCs and other stakeholders who work with CNCs in the Health District. This was a co-operative inquiry that utilised qualitative descriptive research approach. Co-operative inquiry methods enabled 11 CNCs to work as co-researchers and to conduct the investigation. The co-researchers implemented a qualitative descriptive design for the research and used interviews (7) and focus groups (16) with CNC stakeholders (n = 103) to gather sufficient data to investigate the role of the CNC in the organisation. Thematic analysis was undertaken to obtain the results. The CNC role is invaluable to all stakeholders and it was seen as the "glue" which holds teams together. Stakeholder expectations of the CNC role were multiple and generally agreed. Five themes derived from the data are reported as "clinical leadership as core", "making a direct difference to patient care", "service development as an outcome", "role breadth or narrowness and boundaries", and "career development". There was clear appreciation of the work that CNCs do in their roles, and the part that the CNC role plays in achieving quality health outcomes. The role of the CNC is complex and the CNCs themselves often negotiate these complexities to ensure beneficial outcomes for the patient and organisation. For the wider audience this study has given further insights into the role of these nurses and the perspectives of those with whom they work.
Brightness analysis of an electron beam with a complex profile

NASA Astrophysics Data System (ADS)

Maesaka, Hirokazu; Hara, Toru; Togawa, Kazuaki; Inagaki, Takahiro; Tanaka, Hitoshi

2018-05-01

We propose a novel analysis method to obtain the core bright part of an electron beam with a complex phase-space profile. This method is beneficial to evaluate the performance of simulation data of a linear accelerator (linac), such as an x-ray free electron laser (XFEL) machine, since the phase-space distribution of a linac electron beam is not simple, compared to a Gaussian beam in a synchrotron. In this analysis, the brightness of undulator radiation is calculated and the core of an electron beam is determined by maximizing the brightness. We successfully extracted core electrons from a complex beam profile of XFEL simulation data, which was not expressed by a set of slice parameters. FEL simulations showed that the FEL intensity was well remained even after extracting the core part. Consequently, the FEL performance can be estimated by this analysis without time-consuming FEL simulations.
Supplemental Information for Appendix A of the Common Core State Standards for English Language Arts and Literacy: New Research on Text Complexity

ERIC Educational Resources Information Center

Council of Chief State School Officers, 2017

2017-01-01

Appendix A of the Common Core State Standards (hereafter CCSS) contains a review of the research stressing the importance of being able to read complex text for success in college and career. The research shows that while the complexity of reading demands for college, career, and citizenship have held steady or risen over the past half century,…
Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments

PubMed Central

Wei, Jyh-Da; Cheng, Hui-Jun; Lin, Chun-Yuan; Ye, Jin; Yeh, Kuan-Yu

2017-01-01

High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs). Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform) was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform). Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments. PMID:28835734
Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments.

PubMed

Wei, Jyh-Da; Cheng, Hui-Jun; Lin, Chun-Yuan; Ye, Jin; Yeh, Kuan-Yu

2017-01-01

High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs). Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform) was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform). Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments.
Disentangling formation of multiple-core holes in aminophenol molecules exposed to bright X-FEL radiation

NASA Astrophysics Data System (ADS)

Zhaunerchyk, V.; Kamińska, M.; Mucke, M.; Squibb, R. J.; Eland, J. H. D.; Piancastelli, M. N.; Frasinski, L. J.; Grilj, J.; Koch, M.; McFarland, B. K.; Sistrunk, E.; Gühr, M.; Coffee, R. N.; Bostedt, C.; Bozek, J. D.; Salén, P.; Meulen, P. v. d.; Linusson, P.; Thomas, R. D.; Larsson, M.; Foucar, L.; Ullrich, J.; Motomura, K.; Mondal, S.; Ueda, K.; Richter, R.; Prince, K. C.; Takahashi, O.; Osipov, T.; Fang, L.; Murphy, B. F.; Berrah, N.; Feifel, R.

2015-12-01

Competing multi-photon ionization processes, some leading to the formation of double core hole states, have been examined in 4-aminophenol. The experiments used the linac coherent light source (LCLS) x-ray free electron laser, in combination with a time-of-flight magnetic bottle electron spectrometer and the correlation analysis method of covariance mapping. The results imply that 4-aminophenol molecules exposed to the focused x-ray pulses of the LCLS sequentially absorb more than two x-ray photons, resulting in the formation of multiple core holes as well as in the sequential removal of photoelectrons and Auger electrons (so-called PAPA sequences).
Disentangling formation of multiple-core holes in aminophenol molecules exposed to bright X-FEL radiation

DOE PAGES

Zhaunerchyk, V.; Kaminska, M.; Mucke, M.; ...

2015-10-28

Competing multi-photon ionization processes, some leading to the formation of double core hole states, have been examined in 4-aminophenol. The experiments used the linac coherent light source (LCLS) x-ray free electron laser, in combination with a time-of-flight magnetic bottle electron spectrometer and the correlation analysis method of covariance mapping. Furthermore, the results imply that 4-aminophenol molecules exposed to the focused x-ray pulses of the LCLS sequentially absorb more than two x-ray photons, resulting in the formation of multiple core holes as well as in the sequential removal of photoelectrons and Auger electrons (so-called PAPA sequences).
Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.

PubMed

Bausewein, Thomas; Mills, Deryck J; Langer, Julian D; Nitschke, Beate; Nussberger, Stephan; Kühlbrandt, Werner

2017-08-10

The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the α-helical subunits Tom5, Tom6, and Tom7. Tom22, the central preprotein receptor, connects the two Tom40 pores at the dimer interface. Our structure offers detailed insights into the molecular architecture of the mitochondrial preprotein import machinery. Copyright © 2017 Elsevier Inc. All rights reserved.
DNA compaction by poly (amido amine) dendrimers of ammonia cored and ethylene diamine cored

NASA Astrophysics Data System (ADS)

Qamhieh, K.; Al-Shawwa, J.

2017-06-01

The complexes build-up of DNA and soft particles poly amidoamine (PAMAM) dendrimers of ammonia cored of generations (G1-G6) and ethylenediamine cored of generations (G1-G10) have been studied, using a new theoretical model developed by Qamhieh and coworkers. The model describes the interaction between linear polyelectrolyte (LPE) chain and ion-penetrable spheres. Many factors affecting LPE/dendrimer complex have been investigated such as dendrimer generation, the Bjerrum length, salt concentration, and rigidity of the LPE chain represented by the persistence length. It is found that the wrapping chain length around dendrimer increases by increasing dendrimer`s generation, Bjerrum length, and salt concentration, while decreases by increasing the persistence length of the LPE chain. Also we can conclude that the wrapping length of LPE chain around ethylenediamine cored dendrimers is larger than its length around ammonia cored dendrimers.
Trichloroethylene (TCE) in tree cores to complement a subsurface investigation on residential property near a former electroplating facility.

PubMed

Wilcox, Jeffrey D; Johnson, Kathy M

2016-10-01

Tree cores were collected and analyzed for trichloroethylene (TCE) on a private property between a former electroplating facility in Asheville, North Carolina (USA), and a contaminated wetland/spring complex. TCE was detected in 16 of 31 trees, the locations of which were largely consistent with a "plume core" delineated by a more detailed subsurface investigation nearly 2 years later. Concentrations in tree cores and nearby soil borings were not correlated, perhaps due to heterogeneities in both geologic and tree root structure, spatial and temporal variability in transpiration rates, or interferences caused by other contaminants at the site. Several tree cores without TCE provided evidence for significantly lower TCE concentrations in shallow groundwater along the margins of the contaminated spring complex in an area with limited accessibility. This study demonstrates that tree core analyses can complement a more extensive subsurface investigation, particularly in residential or ecologically sensitive areas.
Inhibiting core fucosylation attenuates glucose-induced peritoneal fibrosis in rats.

PubMed

Li, Longkai; Shen, Nan; Wang, Nan; Wang, Weidong; Tang, Qingzhu; Du, Xiangning; Carrero, Juan Jesus; Wang, Keping; Deng, Yiyao; Li, Zhitong; Lin, Hongli; Wu, Taihua

2018-06-01

Ultrafiltration failure is a major complication of long-term peritoneal dialysis, resulting in dialysis failure. Peritoneal fibrosis induced by continuous exposure to high glucose dialysate is the major contributor of ultrafiltration failure, for which there is no effective treatment. Overactivation of several signaling pathways, including transforming growth factor-β1 (TGF-β1) and platelet-derived growth factor (PDGF) pathways, contribute to the development of peritoneal fibrosis. Therefore, simultaneously blocking multiple signaling pathways might be a potential novel method of treating peritoneal fibrosis. Previously, we showed that core fucosylation, an important posttranslational modification of the TGF-β1 receptors, can regulate the activation of TGF-β1 signaling in renal interstitial fibrosis. However, it remains unclear whether core fucosylation affects the progression of peritoneal fibrosis. Herein, we show that core fucosylation was enriched in the peritoneal membrane of rats accompanied by peritoneal fibrosis induced by a high glucose dialysate. Blocking core fucosylation dramatically attenuated peritoneal fibrosis in the rat model achieved by simultaneously inactivating the TGF-β1 and PDGF signaling pathways. Next the protective effects of blocking core fucosylation and imatinib (a selective PDGF receptor inhibitor) on peritoneal fibrosis were compared and found to exhibit a greater inhibitory effect over imatinib alone, suggesting that blocking activation of multiple signaling pathways may have superior inhibitory effects on the development of peritoneal fibrosis. Thus, core fucosylation is essential for the development of peritoneal fibrosis by regulating the activation of multiple signaling pathways. This may be a potential novel target for drug development to treat peritoneal fibrosis. Copyright © 2018 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.
Complicating Canons: A Critical Literacy Challenge to Common Core Assessment

ERIC Educational Resources Information Center

Peel, Anne

2017-01-01

The widespread adoption of the Common Core State Standards in the US has prioritized rigorous reading of complex texts. The emphasis on text complexity has led to instructional and assessment materials that constrain critical literacy practices by emphasizing quantitative features of text, such as sentence length, and a static list of text…
Structures of transcription pre-initiation complex with TFIIH and Mediator.

PubMed

Schilbach, S; Hantsche, M; Tegunov, D; Dienemann, C; Wigge, C; Urlaub, H; Cramer, P

2017-11-09

For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.
Effect of an adhesive resin luting agent on the dowel-head retention of three different core materials.

PubMed

Aksoy, Gokhan; Cotert, H Serdar; Korkut, Levent

2005-05-01

A dowel-and-core restoration may fail due to failure at either the dowel-tooth or dowel head-core material interface. Long-term clinical success of a dowel-and-core restoration depends on retention of both the dowel to the tooth and the dowel head to the core material. Thus, strengthening of the dowel head-core interface is important. This study evaluated the retention between a prefabricated dowel and 3 different core materials with or without a dual-polymerized adhesive resin luting agent. Sixty prefabricated dowels (Gold Plated Anchorage Post) were divided into 3 groups (n=20) consisting of 1 of 3 core materials, amalgam (Standalloy F), light-polymerized resin composite (Clearfil Ray), or glass ionomer (Chelon-Silver). Each core group was divided into 2 subgroups (n=10), and a dual-polymerized adhesive resin luting agent (Panavia F) was applied to the dowel heads of 1 of these subgroups before application of the core material. The manufacturing procedure was standardized by using a plastic index (4.5-mm internal diameter and 5-mm height) and a custom-made dowel holder, which held the dowel head. Prepared specimens were stored in water at room temperature for 3 months and then loaded to fracture in a universal testing machine with a crosshead speed of 0.05 mm/min until failure. Bond strengths were recorded (MPa). Data were analyzed with 2-way analysis of variance (ANOVA) in a 2 x 3 factorial randomized design (alpha=.05). Afterward, core material differences were computed with 1-way ANOVA for both of the bonded and nonbonded groups. Post hoc multiple comparisons were made with the Dunnett C multiple range test. Dowel-head retention values (MPa) of the tested core materials (mean +/- SD) from the highest to the lowest were as follows: bonded amalgam core, 296.1 +/- 108; bonded composite core, 284.3 +/- 38.3; nonbonded composite core, 177.0 +/- 53.7; nonbonded amalgam core, 128.5 +/- 35.0; bonded glass-ionomer core (GIC), 128.0 +/- 24.5; nonbonded GIC, 61.8 +/- 13.3. Two-way ANOVA revealed significant differences between the core material groups and between the bonded and nonbonded groups (P <.001). The interaction between the core material and bond variables was also significant (P =.018). One-way ANOVA revealed statistically significant differences between the bonded (P <.001) and also between the nonbonded core material groups (P <.001). Post hoc multiple comparisons showed that the dowel-head retention of the GIC was significantly weaker than the post-head retention for amalgam and resin composite, whether bonded or not. Within the limitations of this study, the adhesive resin luting agent tested appeared to have a significant strengthening effect on the dowel-head retention of the core materials.

Characterization of the low-temperature triplet state of chlorophyll in photosystem II core complexes: Application of phosphorescence measurements and Fourier transform infrared spectroscopy.

PubMed

Zabelin, Alexey A; Neverov, Konstantin V; Krasnovsky, Alexander A; Shkuropatova, Valentina A; Shuvalov, Vladimir A; Shkuropatov, Anatoly Ya

2016-06-01

Phosphorescence measurements at 77 K and light-induced FTIR difference spectroscopy at 95 K were applied to study of the triplet state of chlorophyll a ((3)Chl) in photosystem II (PSII) core complexes isolated from spinach. Using both methods, (3)Chl was observed in the core preparations with doubly reduced primary quinone acceptor QA. The spectral parameters of Chl phosphorescence resemble those in the isolated PSII reaction centers (RCs). The main spectral maximum and the lifetime of the phosphorescence corresponded to 955±1 nm and of 1.65±0.05 ms respectively; in the excitation spectrum, the absorption maxima of all core complex pigments (Chl, pheophytin a (Pheo), and β-carotene) were observed. The differential signal at 1667(-)/1628(+)cm(-1) reflecting a downshift of the stretching frequency of the 13(1)-keto C=O group of Chl was found to dominate in the triplet-minus-singlet FTIR difference spectrum of core complexes. Based on FTIR results and literature data, it is proposed that (3)Chl is mostly localized on the accessory chlorophyll that is in triplet equilibrium with P680. Analysis of the data suggests that the Chl triplet state responsible for the phosphorescence and the FTIR difference spectrum is mainly generated due to charge recombination in the reaction center radical pair P680(+)PheoD1(-), and the energy and temporal parameters of this triplet state as well as the molecular environment and interactions of the triplet-bearing Chl molecule are similar in the PSII core complexes and isolated PSII RCs. Copyright © 2016 Elsevier B.V. All rights reserved.
[Medicinal laws and application examples of traditional Chinese medicine prescriptions for multiple aorto-arteritis].

PubMed

Zhang, Xin-Gen; Cai, Hai-Ying

2016-05-01

To collect the literature on traditional Chinese medicine treatment for multiple aorto-arteritis from China National Knowledge Infrastructure(CNKI), establish prescriptions database after screening and normalizing the prescriptions reported in these literature, and analyze their medicinal rules by using traditional Chinese medicine inheritance support system. A total of 126 prescriptions for multiple aorto-arteritis were screened, containing 212 kinds of Chinese herbs. 26 core herb combinations were obtained by analysis of the commonly used herbs and their use frequencies. The treatment for multiple aorto-arteritis was manly of tonifying qi to nourish blood, promoting blood circulation to remove blood stasis, warming yang to dredge collaterals, and four new prescriptions were obtained. On this basis, two clinical cases were taken as the examples by analyzing the medicinal rules and the features of multiple aorto-arteritis. The first case showed that the herb combination of this study conformed to the basic core drug application mode and the core pathogenesis of multiple aorto-arteritis. The second case reflected the characteristics of the new prescriptions' herb combinations based on entropy hierarchical clustering. The practical analysis of the two clinical cases further indicated the reliability of the results. This study has certain guiding significance and reference value on new medicine research and development as well as clinical traditional Chinese medicine treatment for multiple aorto-arteritis. Copyright© by the Chinese Pharmaceutical Association.
Design, synthesis and applications of core-shell, hollow core, and nanorattle multifunctional nanostructures.

PubMed

El-Toni, Ahmed Mohamed; Habila, Mohamed A; Labis, Joselito Puzon; ALOthman, Zeid A; Alhoshan, Mansour; Elzatahry, Ahmed A; Zhang, Fan

2016-02-07

With the evolution of nanoscience and nanotechnology, studies have been focused on manipulating nanoparticle properties through the control of their size, composition, and morphology. As nanomaterial research has progressed, the foremost focus has gradually shifted from synthesis, morphology control, and characterization of properties to the investigation of function and the utility of integrating these materials and chemical sciences with the physical, biological, and medical fields, which therefore necessitates the development of novel materials that are capable of performing multiple tasks and functions. The construction of multifunctional nanomaterials that integrate two or more functions into a single geometry has been achieved through the surface-coating technique, which created a new class of substances designated as core-shell nanoparticles. Core-shell materials have growing and expanding applications due to the multifunctionality that is achieved through the formation of multiple shells as well as the manipulation of core/shell materials. Moreover, core removal from core-shell-based structures offers excellent opportunities to construct multifunctional hollow core architectures that possess huge storage capacities, low densities, and tunable optical properties. Furthermore, the fabrication of nanomaterials that have the combined properties of a core-shell structure with that of a hollow one has resulted in the creation of a new and important class of substances, known as the rattle core-shell nanoparticles, or nanorattles. The design strategies of these new multifunctional nanostructures (core-shell, hollow core, and nanorattle) are discussed in the first part of this review. In the second part, different synthesis and fabrication approaches for multifunctional core-shell, hollow core-shell and rattle core-shell architectures are highlighted. Finally, in the last part of the article, the versatile and diverse applications of these nanoarchitectures in catalysis, energy storage, sensing, and biomedicine are presented.
Assessment of the core learning objectives curriculum for the urology clerkship.

PubMed

Rapp, David E; Gong, Edward M; Reynolds, W Stuart; Lucioni, Alvaro; Zagaja, Gregory P

2007-11-01

The traditional approach to the surgical clerkship has limitations, including variability of clinical exposure. To optimize student education we developed and introduced the core learning objectives curriculum, which is designed to allow students freedom to direct their learning and focus on core concepts. We performed a prospective, randomized, controlled study to compare the efficacy of core learning objectives vs traditional curricula through objective and subjective measures. Medical students were randomly assigned to the core learning objectives or traditional curricula during the 2-week urology clerkship. Faculty was blinded to student assignment. Upon rotation completion all students were given a 20-question multiple choice examination covering basic urology concepts. In addition, students completed a questionnaire addressing subjective clerkship satisfaction, comprising 15 questions. Between June 2005 and January 2007, 10 core learning objectives students and 10 traditional students completed the urology clerkship. The average +/- SEM multiple choice examination score was 12.1 +/- 0.87 and 9.8 +/- 0.59 for students assigned to the core learning objectives and traditional curricula, respectively (p <0.05). Subjective scores were higher in the core learning objectives cohort, although this result did not attain statistical significance (124.9 +/- 3.72 vs 114.3 +/- 4.96, p = 0.1). Core learning objectives students reported higher satisfaction in all 15 assessed subjective end points. Our experience suggests that the core learning objectives model may be an effective educational tool to help students achieve a broad and directed exposure to the core urological concepts.
Lysosomal multienzyme complex: pros and cons of working together.

PubMed

Bonten, Erik J; Annunziata, Ida; d'Azzo, Alessandra

2014-06-01

The ubiquitous distribution of lysosomes and their heterogeneous protein composition reflects the versatility of these organelles in maintaining cell homeostasis and their importance in tissue differentiation and remodeling. In lysosomes, the degradation of complex, macromolecular substrates requires the synergistic action of multiple hydrolases that usually work in a stepwise fashion. This catalytic machinery explains the existence of lysosomal enzyme complexes that can be dynamically assembled and disassembled to efficiently and quickly adapt to the pool of substrates to be processed or degraded, adding extra tiers to the regulation of the individual protein components. An example of such a complex is the one composed of three hydrolases that are ubiquitously but differentially expressed: the serine carboxypeptidase, protective protein/cathepsin A (PPCA), the sialidase, neuraminidase-1 (NEU1), and the glycosidase β-galactosidase (β-GAL). Next to this 'core' complex, the existence of sub-complexes, which may contain additional components, and function at the cell surface or extracellularly, suggests as yet unexplored functions of these enzymes. Here we review how studies of basic biological processes in the mouse models of three lysosomal storage disorders, galactosialidosis, sialidosis, and GM1-gangliosidosis, revealed new and unexpected roles for the three respective affected enzymes, Ppca, Neu1, and β-Gal, that go beyond their canonical degradative activities. These findings have broadened our perspective on their functions and may pave the way for the development of new therapies for these lysosomal storage disorders.
Development and validation of a low-frequency modeling code for high-moment transmitter rod antennas

NASA Astrophysics Data System (ADS)

Jordan, Jared Williams; Sternberg, Ben K.; Dvorak, Steven L.

2009-12-01

The goal of this research is to develop and validate a low-frequency modeling code for high-moment transmitter rod antennas to aid in the design of future low-frequency TX antennas with high magnetic moments. To accomplish this goal, a quasi-static modeling algorithm was developed to simulate finite-length, permeable-core, rod antennas. This quasi-static analysis is applicable for low frequencies where eddy currents are negligible, and it can handle solid or hollow cores with winding insulation thickness between the antenna's windings and its core. The theory was programmed in Matlab, and the modeling code has the ability to predict the TX antenna's gain, maximum magnetic moment, saturation current, series inductance, and core series loss resistance, provided the user enters the corresponding complex permeability for the desired core magnetic flux density. In order to utilize the linear modeling code to model the effects of nonlinear core materials, it is necessary to use the correct complex permeability for a specific core magnetic flux density. In order to test the modeling code, we demonstrated that it can accurately predict changes in the electrical parameters associated with variations in the rod length and the core thickness for antennas made out of low carbon steel wire. These tests demonstrate that the modeling code was successful in predicting the changes in the rod antenna characteristics under high-current nonlinear conditions due to changes in the physical dimensions of the rod provided that the flux density in the core was held constant in order to keep the complex permeability from changing.
Methodological and hermeneutic reduction - a study of Finnish multiple-birth families.

PubMed

Heinonen, Kristiina

2015-07-01

To describe reduction as a method in methodological and hermeneutic reduction and the hermeneutic circle using van Manen's principles, with the empirical example of the lifeworlds of multiple-birth families in Finland. Reduction involves several levels that can be distinguished for their methodological usefulness. Researchers can use reduction in different ways and dimensions for their methodological needs. Open interviews with public health nurses, family care workers and parents of twins. The systematic literature and knowledge review shows there were no articles on multiple-birth families that used van Manen's method. This paper presents reduction as a method that uses the hermeneutic circle. The lifeworlds of multiple-birth families consist of three core themes: 'A state of constant vigilance'; 'Ensuring that they can continue to cope'; and 'Opportunities to share with other people'. Reduction allows us to perform deep phenomenological-hermeneutic research and understand people's lifeworlds. It helps to keep research stages separate but also enables a consolidated view. Social care and healthcare professionals have to hear parents' voices better to comprehensively understand their situation; they also need further tools and training to be able to empower parents of twins. The many variations in adapting reduction mean its use can be very complex and confusing. This paper adds to the discussion of phenomenology, hermeneutic study and reduction.
Microstructural and paleomagnetic insight into the cooling history of the IAB parent body

NASA Astrophysics Data System (ADS)

Nichols, Claire I. O.; Krakow, Robert; Herrero-Albillos, Julia; Kronast, Florian; Northwood-Smith, Geraint; Harrison, Richard J.

2018-05-01

The IABs represent one of only two groups of iron meteorites that did not form by fractional crystallization of liquid Fe-Ni in the core of a differentiated planetesimal. Instead, they are believed to originate from a partially differentiated body that was severely disrupted by one or more impacts during its early history. We present a detailed microstructural and paleomagnetic study of the Odessa and Toluca IAB meteorites, with a view to further constraining the complex history of the IAB parent body. X-ray photoemission electron microscopy and energy dispersive spectroscopy were used to generate high-resolution Ni/Fe maps. The crystallographic architecture of Odessa was analysed using electron backscatter diffraction. Paleomagnetic signals and the magnetic properties of several microstructures were also assessed using X-ray magnetic circular dichroism. Odessa exhibits a complex series of microstructures, requiring an unusual evolution during slow cooling. A conventional Widmanstätten microstructure, consisting of multiple generations of kamacite lamellae surrounded by M-shaped diffusion profiles, developed via continuous precipitation to temperatures below ∼400 °C. Multiple generations of pearlitic plessite nucleated from kamacite/taenite (T > 400 °C) and tetrataenite rim/taenite interfaces (T < 400 °C), via a process of discontinuous precipitation. Rounded rafts of Ni-rich taenite, observed within some regions of pearlitic plessite, are shown to have the same crystallographic orientation as the parental taenite, and a non-standard orientation relationship with the enclosing kamacite. Contrary to current theories, these rafts cannot have formed by coarsening of pre-existing pearlitic plessite. A new bowing mechanism is proposed, whereby rafts of Ni-enriched taenite form between advancing lobes of an irregular reaction front during discontinuous precipitation. Subsequent coarsening leads to the growth of the taenite rafts, and the partial or complete removal of pearlite lamellae, resulting in spheroidised plessite with a crystallographic architecture matching the experimental observations. We find no evidence for a strong magnetic field on the IAB parent body, suggesting it did not have an active core dynamo at the time of cloudy zone formation. This supports the prediction that the IAB parent body was unable to form a significant core due to the redistribution of metal during an earlier impact event.
Integrative FourD omics approach profiles the target network of the carbon storage regulatory system.

PubMed

Sowa, Steven W; Gelderman, Grant; Leistra, Abigail N; Buvanendiran, Aishwarya; Lipp, Sarah; Pitaktong, Areen; Vakulskas, Christopher A; Romeo, Tony; Baldea, Michael; Contreras, Lydia M

2017-02-28

Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Arthroscopic-assisted core decompression of the humeral head.

PubMed

Dines, Joshua S; Strauss, Eric J; Fealy, Stephen; Craig, Edward V

2007-01-01

Humeral head osteonecrosis is a progressive disease that requires prompt diagnosis and treatment. Core decompression is a viable treatment option for early-stage cases. Most surgeons perform core decompression by arthroscopically visualizing the necrotic area of bone and using a cannulated drill to take a core. Several attempts are frequently needed to reach the proper location. In the hip multiple passes are associated with complications. We describe the use of an anterior cruciate ligament (ACL) tibial drill guide to precisely localize the area of necrotic bone. Diagnostic arthroscopy is performed to assess the areas of osteonecrosis. Core decompression is performed by use of an ACL tibial guide, brought in through the anterior or posterior portal to precisely localize the necrotic area in preparation for drilling. Under image intensification, Steinmann pins are advanced into the area of osteonecrosis. Once positioned, several 4-mm cores are made. We treated 3 patients with this technique, and all had immediate pain relief. The use of the ACL guide allows precise localization of the area of humeral head involvement and avoids multiple drillings into unaffected areas. Initial indications are that arthroscopic-assisted core decompression with an ACL guide is an effective alternative to previously used methods.
Harmonic Quantum Coherence of Multiple Excitons in PbS/CdS Core-Shell Nanocrystals

NASA Astrophysics Data System (ADS)

Tahara, Hirokazu; Sakamoto, Masanori; Teranishi, Toshiharu; Kanemitsu, Yoshihiko

2017-12-01

The generation and recombination dynamics of multiple excitons in nanocrystals (NCs) have attracted much attention from the viewpoints of fundamental physics and device applications. However, the quantum coherence of multiple exciton states in NCs still remains unclear due to a lack of experimental support. Here, we report the first observation of harmonic dipole oscillations in PbS/CdS core-shell NCs using a phase-locked interference detection method for transient absorption. From the ultrafast coherent dynamics and excitation-photon-fluence dependence of the oscillations, we found that multiple excitons cause the harmonic dipole oscillations with ω , 2 ω , and 3 ω oscillations, even though the excitation pulse energy is set to the exciton resonance frequency, ω . This observation is closely related to the quantum coherence of multiple exciton states in NCs, providing important insights into multiple exciton generation mechanisms.
Scalable Synthesis of Triple-Core-Shell Nanostructures of TiO2 @MnO2 @C for High Performance Supercapacitors Using Structure-Guided Combustion Waves.

PubMed

Shin, Dongjoon; Shin, Jungho; Yeo, Taehan; Hwang, Hayoung; Park, Seonghyun; Choi, Wonjoon

2018-03-01

Core-shell nanostructures of metal oxides and carbon-based materials have emerged as outstanding electrode materials for supercapacitors and batteries. However, their synthesis requires complex procedures that incur high costs and long processing times. Herein, a new route is proposed for synthesizing triple-core-shell nanoparticles of TiO 2 @MnO 2 @C using structure-guided combustion waves (SGCWs), which originate from incomplete combustion inside chemical-fuel-wrapped nanostructures, and their application in supercapacitor electrodes. SGCWs transform TiO 2 to TiO 2 @C and TiO 2 @MnO 2 to TiO 2 @MnO 2 @C via the incompletely combusted carbonaceous fuels under an open-air atmosphere, in seconds. The synthesized carbon layers act as templates for MnO 2 shells in TiO 2 @C and organic shells of TiO 2 @MnO 2 @C. The TiO 2 @MnO 2 @C-based electrodes exhibit a greater specific capacitance (488 F g -1 at 5 mV s -1 ) and capacitance retention (97.4% after 10 000 cycles at 1.0 V s -1 ), while the absence of MnO 2 and carbon shells reveals a severe degradation in the specific capacitance and capacitance retention. Because the core-TiO 2 nanoparticles and carbon shell prevent the deformation of the inner and outer sides of the MnO 2 shell, the nanostructures of the TiO 2 @MnO 2 @C are preserved despite the long-term cycling, giving the superior performance. This SGCW-driven fabrication enables the scalable synthesis of multiple-core-shell structures applicable to diverse electrochemical applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Wireline Deep Drill for the Exploration of Icy Bodies

NASA Technical Reports Server (NTRS)

Paulsen, G.; Zacny, K.; Mellerowicz, B.; Craft, J.; Bar-Cohen, Y.; Beegle, L.; Sherrit, S.; Badescu, M.; Corsetti, F.; Ibarra, Y.

2013-01-01

One of the most pressing current questions in space science is whether life has ever arisen anywhere else in the universe. Water is a critical prerequisite for all life-as-we-know-it, thus the possible exploration targets for extraterrestrial life are bodies that have or had copious liquid: Mars, Europa, and Enceladus. Due to the oxidizing nature of Mars' surface, as well as subsurface liquid water reservoirs present on Europa and Enceladus, the search for evidence of existing life must likely focus on subsurface locations, at depths sufficient to support liquid water or retain biologic signatures. To address these questions, an Auto-Gopher sampler has been developed that is a wireline type drill. This drill is suspended on a tether and its motors and mechanisms are built into a tube that ends with a coring bit. The tether provides the mechanical connection to a rover/lander on a surface as well as power and data communication. Upon penetrating to a target depth, the drill is retracted from the borehole, the core is deposited into a sample transfer system, and the drill is lowered back into the hole. Wireline operation sidesteps one of the major drawbacks of traditional continuous drill string systems by obviating the need for multiple drill sections, which add significantly to the mass and the complexity of the system (i.e. penetration rate was 40 cm per hour). Drilling to 2 meter depth and recovering of cores every 10 cm took a total time of 15 hours (a single step of drilling 10 cm and retrieving the core was 45 minutes). Total energy to reach the 2 m depth was 500 Whr. The Weight on Bit was limited to less than 70 Newton. The core recovery was 100%.
Sample Acquisition and Caching architecture for the Mars Sample Return mission

NASA Astrophysics Data System (ADS)

Zacny, K.; Chu, P.; Cohen, J.; Paulsen, G.; Craft, J.; Szwarc, T.

This paper presents a Mars Sample Return (MSR) Sample Acquisition and Caching (SAC) study developed for the three rover platforms: MER, MER+, and MSL. The study took into account 26 SAC requirements provided by the NASA Mars Exploration Program Office. For this SAC architecture, the reduction of mission risk was chosen by us as having greater priority than mass or volume. For this reason, we selected a “ One Bit per Core” approach. The enabling technology for this architecture is Honeybee Robotics' “ eccentric tubes” core breakoff approach. The breakoff approach allows the drill bits to be relatively small in diameter and in turn lightweight. Hence, the bits could be returned to Earth with the cores inside them with only a modest increase to the total returned mass, but a significant decrease in complexity. Having dedicated bits allows a reduction in the number of core transfer steps and actuators. It also alleviates the bit life problem, eliminates cross contamination, and aids in hermetic sealing. An added advantage is faster drilling time, lower power, lower energy, and lower Weight on Bit (which reduces Arm preload requirements). Drill bits are based on the BigTooth bit concept, which allows re-use of the same bit multiple times, if necessary. The proposed SAC consists of a 1) Rotary-Percussive Core Drill, 2) Bit Storage Carousel, 3) Cache, 4) Robotic Arm, and 5) Rock Abrasion and Brushing Bit (RABBit), which is deployed using the Drill. The system also includes PreView bits (for viewing of cores prior to caching) and Powder bits for acquisition of regolith or cuttings. The SAC total system mass is less than 22 kg for MER and MER+ size rovers and less than 32 kg for the MSL-size rover.
MetaCoMET: a web platform for discovery and visualization of the core microbiome

USDA-ARS?s Scientific Manuscript database

A key component of the analysis of microbiome datasets is the identification of OTUs shared between multiple experimental conditions, commonly referred to as the core microbiome. Results: We present a web platform named MetaCoMET that enables the discovery and visualization of the core microbiome an...
Challenges to Common Core State Standards Implementation: Views from Six States

ERIC Educational Resources Information Center

Smith, Joanna; Thier, Michael

2017-01-01

The implementation of the Common Core State Standards has posed a number of challenges for school leaders. This study applies a policy implementation conceptual framework to analyze data gathered from 46 interviews in six states. Findings suggest the existence of multiple barriers to Common Core State Standards implementation. To promote…
Pricing the Services of Scientific Cores. Part II: Charging Outside Users.

ERIC Educational Resources Information Center

Fife, Jerry; Forrester, Robert

2002-01-01

Explaining that scientific cores at research institutions support shared resources and facilities, considers pricing of services to users from outside the institution. Proposes a method of allocating charges from the cores to projects with multiple funding sources through program-based management. Describes aspects of an example program: price of…
Advanced Marketing Core Curriculum. Test Items and Assessment Techniques.

ERIC Educational Resources Information Center

Smith, Clifton L.; And Others

This document contains duties and tasks, multiple-choice test items, and other assessment techniques for Missouri's advanced marketing core curriculum. The core curriculum begins with a list of 13 suggested textbook resources. Next, nine duties with their associated tasks are given. Under each task appears one or more citations to appropriate…
Multiple network interface core apparatus and method

DOEpatents

Underwood, Keith D [Albuquerque, NM; Hemmert, Karl Scott [Albuquerque, NM

2011-04-26

A network interface controller and network interface control method comprising providing a single integrated circuit as a network interface controller and employing a plurality of network interface cores on the single integrated circuit.
A coarse grained molecular dynamics simulation study on the structural properties of carbon nanotube-dendrimer composites.

PubMed

Kavyani, Sajjad; Dadvar, Mitra; Modarress, Hamid; Amjad-Iranagh, Sepideh

2018-04-25

By employing coarse grained (CG) molecular dynamics (MD) simulation, the effect of the size and hydrophilic/hydrophobic properties of the interior/exterior structures of the dendrimers in carbon nanotube (CNT)-dendrimer composites has been studied, to find a stable composite with high solubility in water and the capability to be used in drug delivery applications. For this purpose, composites consisting of core-shell dendrimer complexes including: [PPI{core}-PAMAM{shell}], [PAMAM{core}-polyethyleneglycol (PEG){shell}] and [PAMAM{core}-fattyacid (FTA){shell}] were constructed. A new CG model for the fatty acid (FTA) molecules as functionalized to the dendrimer was developed, which, unlike the previous models, could generate the structural conformations of the FTA properly. The obtained results indicated that the dendrimer complexes with short FTA chains can form stable composites with the CNT. Also, it was found that the pristine PAMAM and PPI-PAMAM with small PPI, and PAMAM-PEG dendrimers with short PEG chains, can distribute their chains into the water medium and interact with the CNT efficiently, to form a stable water-soluble CNT-dendrimer composite. The results demonstrated that the structural difference between the interior and exterior of a core-shell dendrimer complex can prevent the core and the interior layers of the dendrimer complex from interacting with the CNT. An overall analysis of the results manifested that the CNT-PAMAM:4-PEG:4 is the most stable composite, due to strong binding of the dendrimer with the CNT while also having high solubility in water, and its core retains its structure properly and unchanged, suitable for encapsulating drugs in the targeted delivery applications.

Continuous Wave Stimulated Raman Spectroscopy Inside a Hollow Core Photonic Crystal Fiber

NASA Astrophysics Data System (ADS)

Domenech, Jose L.; Cueto, Maite

2013-06-01

Hollow-core photonic crystal fibers (HCPCF) have raised new opportunities to study light-matter interaction. Dielectric or metallic capillaries are intrinsically lossy, making poor light guides. In contrast, HCPCFs can guide light quite efficiently, due to the band-gap effect produced by an array of smaller channels which surrounds a central hollow core with a few μm diameter. The tight confinement of light inside the core, that can be filled with gases, as well as a long interaction length, enhance multiple nonlinear phenomena, making it possible to devise new ways to do low signal level spectroscopy, as is the case of high resolution stimulated Raman spectroscopy (SRS). A. Owyoung demonstrated high resolution continuous wave SRS in 1978. Shortly afterwards, seeking higher sensitivity, he developed the quasi-continuous SRS technique (a high peak power pump laser, interacting with a low power cw probe laser). That variant remains today the best compromise between resolution and sensitivity for gas-phase Raman spectroscopy. In this work, we show the possibility of fully cw stimulated Raman spectroscopy, using a gas cell built around a HCPCF to overcome the limitations posed by the weakness of the stimulated Raman effect when not using pulsed sources. The interaction length (1.2 m), longer than that of a multiple pass refocusing cell, and the narrow diameter of the core (4.8 μm), can compensate for the much lower laser powers used in the cw set-up. The experimental complexity is considerably reduced and the instrumental resolution is at the 10's of MHz level, limited, with our fiber, by transit time effects. At present, we have demonstrated the feasibility of the experiment, a sensitivity enhancement of ˜ 6000 over the single focus regime, and a spectral resolution better than 0.005 wn in the unresolved Q-branch of the ν_1 component of the Fermi dyad of CO_2 at 1388 wn. Other examples of rotationally resolved spectra will be shown: the Q branch of O_2 at 1555 wn, and the 2ν_2 component of the Fermi dyad of CO_2 at 1285 wn. P. St. Russell, Science {299}, 358, 2003. A.Owyoung, C. W. Patterson, R S. McDowell, Chem. Phys. Lett. {59}, 156, 1978
Experimental implementation of fiber optic bundle array wide FOV free space optical communications receiver.

PubMed

Brown, Andrea M; Hahn, Daniel V; Brown, David M; Rolander, Nathan W; Bair, Chun-Huei; Sluz, Joseph E

2012-06-20

A gimbal-free wide field-of-regard (FOR) optical receiver has been built in a laboratory setting for proof-of-concept testing. Multiple datasets are presented that examine the overall FOR of the system and the receiver's ability to track and collect a signal from a moving source. The design is not intended to compete with traditional free space optical communication systems, but rather offer an alternative design that minimizes the number and complexity of mechanical components required at the surface of a small mobile platform. The receiver is composed of a micro-lens array and hexagonal bundles of large core optical fibers that route the optical signal to remote detectors and electronics. Each fiber in the bundle collects power from a distinct solid angle of space and a piezo-electric transducer is used to translate the micro-lens array and optimize coupling into a given fiber core in the bundle. The micro-lens to fiber bundle design is scalable, modular, and can be replicated in an array to increase aperture size.
The optimal community detection of software based on complex networks

NASA Astrophysics Data System (ADS)

Huang, Guoyan; Zhang, Peng; Zhang, Bing; Yin, Tengteng; Ren, Jiadong

2016-02-01

The community structure is important for software in terms of understanding the design patterns, controlling the development and the maintenance process. In order to detect the optimal community structure in the software network, a method Optimal Partition Software Network (OPSN) is proposed based on the dependency relationship among the software functions. First, by analyzing the information of multiple execution traces of one software, we construct Software Execution Dependency Network (SEDN). Second, based on the relationship among the function nodes in the network, we define Fault Accumulation (FA) to measure the importance of the function node and sort the nodes with measure results. Third, we select the top K(K=1,2,…) nodes as the core of the primal communities (only exist one core node). By comparing the dependency relationships between each node and the K communities, we put the node into the existing community which has the most close relationship. Finally, we calculate the modularity with different initial K to obtain the optimal division. With experiments, the method OPSN is verified to be efficient to detect the optimal community in various softwares.
[Negative symptoms of schizophrenia: historical aspects].

PubMed

Pringuey, D; Paquin, N; Cherikh, F; Giordana, B; Belzeaux, R; Cermolacce, M; Adida, M; Azorin, J-M

2015-12-01

The history of negative symptoms of schizophrenia rises early days of medicine in clinical and pathophysiological differences between positive and negative and their complex joint. Forming a set of typical core of symptoms, and some feature of a syndrome belonging to a specific pathophysiological mechanism, negative symptoms of schizophrenia emerge from old descriptions of clinical pictures, related to the overall look of madness, the heart of alienation, a central sign of early dementia, gradually more precisely describing the strange nature of the autistic withdrawal and schizophrenic apragmatism. At therapeutic era, negative symptoms have taken over the positive symptoms to establish an operational criteria whose importance lies in the progressive severity of this clinical type and in their contribution to therapeutic resistance. Despite the efforts of modern typological classifications, this work rehabilitates the old concept of "unitary psychosis" by defining a common symptomatic core to multiple clinical forms of psychosis, combining deficit of emotional expression and avolition, meaning a native psychopathology and a pathophysiology possibly in a common final way, and calling the arrival of new treatment strategies. Copyright © 2015 Elsevier Masson SAS. All rights reserved.
Enhanced SH3/Linker Interaction Overcomes Abl Kinase Activation by Gatekeeper and Myristic Acid Binding Pocket Mutations and Increases Sensitivity to Small Molecule Inhibitors*

PubMed Central

Panjarian, Shoghag; Iacob, Roxana E.; Chen, Shugui; Wales, Thomas E.; Engen, John R.; Smithgall, Thomas E.

2013-01-01

Multidomain kinases such as c-Src and c-Abl are regulated by complex allosteric interactions involving their noncatalytic SH3 and SH2 domains. Here we show that enhancing natural allosteric control of kinase activity by SH3/linker engagement has long-range suppressive effects on the kinase activity of the c-Abl core. Surprisingly, enhanced SH3/linker interaction also dramatically sensitized the Bcr-Abl tyrosine kinase associated with chronic myelogenous leukemia to small molecule inhibitors that target either the active site or the myristic acid binding pocket in the kinase domain C-lobe. Dynamics analyses using hydrogen exchange mass spectrometry revealed a remarkable allosteric network linking the SH3 domain, the myristic acid binding pocket, and the active site of the c-Abl core, providing a structural basis for the biological observations. These results suggest a rational strategy for enhanced drug targeting of Bcr-Abl and other multidomain kinase systems that use multiple small molecules to exploit natural mechanisms of kinase control. PMID:23303187
Coupled field-structural analysis of HGTR fuel brick using ABAQUS

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

Mohanty, S.; Jain, R.; Majumdar, S.

2012-07-01

High-temperature, gas-cooled reactors (HTGRs) are usually helium-gas cooled, with a graphite core that can operate at reactor outlet temperatures much higher than can conventional light water reactors. In HTGRs, graphite components moderate and reflect neutrons. During reactor operation, high temperature and high irradiation cause damage to the graphite crystal and grains and create other defects. This cumulative structural damage during the reactor lifetime leads to changes in graphite properties, which can alter the ability to support the designed loads. The aim of the present research is to develop a finite-element code using commercially available ABAQUS software for the structural integritymore » analysis of graphite core components under extreme temperature and irradiation conditions. In addition, the Reactor Geometry Generator tool-kit, developed at Argonne National Laboratory, is used to generate finite-element mesh for complex geometries such as fuel bricks with multiple pin holes and coolant flow channels. This paper presents the proposed concept and discusses results of stress analysis simulations of a fuel block with H-451 grade material properties. (authors)« less
Bacterial formate hydrogenlyase complex.

PubMed

McDowall, Jennifer S; Murphy, Bonnie J; Haumann, Michael; Palmer, Tracy; Armstrong, Fraser A; Sargent, Frank

2014-09-23

Under anaerobic conditions, Escherichia coli can carry out a mixed-acid fermentation that ultimately produces molecular hydrogen. The enzyme directly responsible for hydrogen production is the membrane-bound formate hydrogenlyase (FHL) complex, which links formate oxidation to proton reduction and has evolutionary links to Complex I, the NADH:quinone oxidoreductase. Although the genetics, maturation, and some biochemistry of FHL are understood, the protein complex has never been isolated in an intact form to allow biochemical analysis. In this work, genetic tools are reported that allow the facile isolation of FHL in a single chromatographic step. The core complex is shown to comprise HycE (a [NiFe] hydrogenase component termed Hyd-3), FdhF (the molybdenum-dependent formate dehydrogenase-H), and three iron-sulfur proteins: HycB, HycF, and HycG. A proportion of this core complex remains associated with HycC and HycD, which are polytopic integral membrane proteins believed to anchor the core complex to the cytoplasmic side of the membrane. As isolated, the FHL complex retains formate hydrogenlyase activity in vitro. Protein film electrochemistry experiments on Hyd-3 demonstrate that it has a unique ability among [NiFe] hydrogenases to catalyze production of H2 even at high partial pressures of H2. Understanding and harnessing the activity of the FHL complex is critical to advancing future biohydrogen research efforts.
Core Promoter Functions in the Regulation of Gene Expression of Drosophila Dorsal Target Genes*

PubMed Central

Zehavi, Yonathan; Kuznetsov, Olga; Ovadia-Shochat, Avital; Juven-Gershon, Tamar

2014-01-01

Developmental processes are highly dependent on transcriptional regulation by RNA polymerase II. The RNA polymerase II core promoter is the ultimate target of a multitude of transcription factors that control transcription initiation. Core promoters consist of core promoter motifs, e.g. the initiator, TATA box, and the downstream core promoter element (DPE), which confer specific properties to the core promoter. Here, we explored the importance of core promoter functions in the dorsal-ventral developmental gene regulatory network. This network includes multiple genes that are activated by different nuclear concentrations of Dorsal, an NFκB homolog transcription factor, along the dorsal-ventral axis. We show that over two-thirds of Dorsal target genes contain DPE sequence motifs, which is significantly higher than the proportion of DPE-containing promoters in Drosophila genes. We demonstrate that multiple Dorsal target genes are evolutionarily conserved and functionally dependent on the DPE. Furthermore, we have analyzed the activation of key Dorsal target genes by Dorsal, as well as by another Rel family transcription factor, Relish, and the dependence of their activation on the DPE motif. Using hybrid enhancer-promoter constructs in Drosophila cells and embryo extracts, we have demonstrated that the core promoter composition is an important determinant of transcriptional activity of Dorsal target genes. Taken together, our results provide evidence for the importance of core promoter composition in the regulation of Dorsal target genes. PMID:24634215
Particle Filter-Based Recursive Data Fusion With Sensor Indexing for Large Core Neutron Flux Estimation

NASA Astrophysics Data System (ADS)

Tamboli, Prakash Kumar; Duttagupta, Siddhartha P.; Roy, Kallol

2017-06-01

We introduce a sequential importance sampling particle filter (PF)-based multisensor multivariate nonlinear estimator for estimating the in-core neutron flux distribution for pressurized heavy water reactor core. Many critical applications such as reactor protection and control rely upon neutron flux information, and thus their reliability is of utmost importance. The point kinetic model based on neutron transport conveniently explains the dynamics of nuclear reactor. The neutron flux in the large core loosely coupled reactor is sensed by multiple sensors measuring point fluxes located at various locations inside the reactor core. The flux values are coupled to each other through diffusion equation. The coupling facilitates redundancy in the information. It is shown that multiple independent data about the localized flux can be fused together to enhance the estimation accuracy to a great extent. We also propose the sensor anomaly handling feature in multisensor PF to maintain the estimation process even when the sensor is faulty or generates data anomaly.
Crustal structure in the Elko-Carlin Region, Nevada, during Eocene gold mineralization: Ruby-East Humboldt metamorphic core complex as a guide to the deep crust

USGS Publications Warehouse

Howard, K.A.

2003-01-01

The deep crustal rocks exposed in the Ruby-East Humboldt metamorphic core complex, northeastern Nevada, provide a guide for reconstructing Eocene crustal structure ~50 km to the west near the Carlin trend of gold deposits. The deep crustal rocks, in the footwall of a west-dipping normal-sense shear system, may have underlain the Pinon and Adobe Ranges about 50 km to the west before Tertiary extension, close to or under part of the Carlin trend. Eocene lakes formed on the hanging wall of the fault system during an early phase of extension and may have been linked to a fluid reservoir for hydrothermal circulation. The magnitude and timing of Paleogene extension remain indistinct, but dikes and tilt axes in the upper crust indicate that spreading was east-west to northwest-southeast, perpendicular to a Paleozoic and Mesozoic orogen that the spreading overprinted. High geothermal gradients associated with Eocene or older crustal thinning may have contributed to hydrothermal circulation in the upper crust. Late Eocene eruptions, upper crustal dike intrusion, and gold mineralization approximately coincided temporally with deep intrusion of Eocene sills of granite and quartz diorite and shallower intrusion of the Harrison Pass pluton into the core-complex rocks. Stacked Mesozoic nappes of metamorphosed Paleozoic and Precambrian rocks in the core complex lay at least 13 to 20 km deep in Eocene time, on the basis of geobarometry studies. In the northern part of the complex, the presently exposed rocks had been even deeper in the late Mesozoic, to >30 km depths, before losing part of their cover by Eocene time. Nappes in the core plunge northward beneath the originally thicker Mesozoic tectonic cover in the north part of the core complex. Mesozoic nappes and tectonic wedging likely occupied the thickened midlevel crustal section between the deep crustal core-complex intrusions and nappes and the overlying upper crust. These structures, as well as the subsequent large-displacement Cenozoic extensional faulting and flow in the deep crust, would be expected to blur the expression of any regional structural roots that could correlate with mineral belts. Structural mismatch of the mineralized upper crust and the tectonically complex middle crust suggests that the Carlin trend relates not to subjacent deeply penetrating rooted structures but to favorable upper crustal host rocks aligned within a relatively coherent regional block of upper crust.
CdSe/AsS core-shell quantum dots: preparation and two-photon fluorescence.

PubMed

Wang, Junzhong; Lin, Ming; Yan, Yongli; Wang, Zhe; Ho, Paul C; Loh, Kian Ping

2009-08-19

Arsenic(II) sulfide (AsS)-coated CdSe core-shell nanocrystals can be prepared by a cluster-complex deposition approach under mild conditions. At 60 degrees C, growth of an AsS shell onto a CdSe nanocrystal can be realized through the crystallization of a cluster complex of AsS/butylamine in a mixed solvent of isopropanol/chloroform. The new, type I core-shell nanocrystal exhibits markedly enhanced one-photon fluorescence as well two-photon upconversion fluorescence. The nanocrystals can be used for infrared-excited upconversion cellular labeling.
Core Self-Evaluations as Causes of Satisfaction: The Mediating Role of Seeking Task Complexity

ERIC Educational Resources Information Center

Srivastava, Abhishek; Locke, Edwin A.; Judge, Timothy A.; Adams, John W.

2010-01-01

This study examined the mediating role of task complexity in the relationship between core self-evaluations (CSE) and satisfaction. In Study 1, eighty three undergraduate business students worked on a strategic decision-making simulation. The simulated environment enabled us to verify the temporal sequence of variables, use an objective measure of…
Submillimeter-wave Observations of Complex Organic Molecules in Southern Massive Star Forming Regions

NASA Astrophysics Data System (ADS)

Kamegai, Kazuhisa; Sakai, Takeshi; Sakai, Nami; Hirota, Tomoya; Yamamoto, Satoshi

2013-03-01

Submillimeter-wave observations of complex organic molecules toward southern massive star forming regions were carried out with ASTE 10m telescope. Methyl formate (HCOOCH3) and dimethyl ether (CH3OCH3) were detected in some molecular cloud cores with young protostars. Differences in chemical composition among neighboring cores were also found.
Towards a new common Greenland Ice Core Chronology for the last 5000 years

NASA Astrophysics Data System (ADS)

Winstrup, Mai; Olander Rasmussen, Sune; Møllesøe Vinther, Bo; Cook, Eliza; Svensson, Anders; McConnell, Joe; Steffensen, Jørgen Peder

2017-04-01

Since the development of the Greenland Ice Core Chronology 2005 (GICC05), it has been widely used as a reference chronology in paleoclimate research. However, recent research (Sigl et al, 2015) demonstrated that this timescale has small, but significant, issues over historical time. These discrepancies was found by counting annual layers in high-resolution chemistry records from the NEEM S1 shallow core, and confirmed by linking via 10Be marker horizons to the layer-counted WAIS Divide ice core, Antarctica, and accurately-dated tree-ring series. This work showed that a revision of GICC05 is required prior to 1250AD. We here refine and extend this work. Layer-counting in a single core will always involve some uncertainty, and we hence use data from multiple Greenland ice cores, for which high-resolution impurity records recently have been measured. These ice cores have been synchronized using volcanic marker horizons, and the layer-counting is performed automatically using the StratiCounter algorithm (Winstrup et al, 2012), while ensuring that the number of layers between volcanic horizons are the same in all cores. Based on this extended multiple-core data set, we are further able to extend the new Greenland timescale another few thousand years back in time. This will, among others, provide a new ice-core date for the catastrophic volcanic eruption ( 1600 BC) that destroyed the Greek Minoan culture, an important time marker in Greek history.
Characterization of subunit-specific interactions in a double-stranded RNA virus: Raman difference spectroscopy of the phi6 procapsid.

PubMed

Benevides, James M; Juuti, Jarmo T; Tuma, Roman; Bamford, Dennis H; Thomas, George J

2002-10-08

The icosahedral core of a double-stranded (ds) RNA virus hosts RNA-dependent polymerase activity and provides the molecular machinery for RNA packaging. The stringent requirements of dsRNA metabolism may explain the similarities observed in core architecture among a broad spectrum of dsRNA viruses, from the mammalian rotaviruses to the Pseudomonas bacteriophage phi6. Although the structure of the assembled core has been described in atomic detail for Reoviridae (blue tongue virus and reovirus), the molecular mechanism of assembly has not been characterized in terms of conformational changes and key interactions of protein constituents. In the present study, we address such questions through the application of Raman spectroscopy to an in vitro core assembly system--the procapsid of phi6. The phi6 procapsid, which comprises multiple copies of viral proteins P1 (copy number 120), P2 (12), P4 (72), and P7 (60), represents a precursor of the core that is devoid of RNA. Raman signatures of the procapsid, its purified recombinant core protein components, and purified sub-assemblies lacking either one or two of the protein components have been obtained and interpreted. The major procapsid protein (P1), which forms the skeletal frame of the core, is an elongated and monomeric molecule of high alpha-helical content. The fold of the core RNA polymerase (P2) is also mostly alpha-helical. On the other hand, the folds of both the procapsid accessory protein (P7) and RNA-packaging ATPase (P4) are of the alpha/beta type. Raman difference spectra show that conformational changes occur upon interaction of P1 with either P4 or P7 in the procapsid. These changes involve substantial ordering of the polypeptide backbone. Conversely, conformations of procapsid subunits are not significantly affected by interactions with P2. An assembly model is proposed in which P1 induces alpha-helix in P4 during formation of the nucleation complex. Subsequently, the partially disordered P7 subunit is folded within the context of the procapsid shell.
The structure of the core NuRD repression complex provides insights into its interaction with chromatin

PubMed Central

Millard, Christopher J; Varma, Niranjan; Saleh, Almutasem; Morris, Kyle; Watson, Peter J; Bottrill, Andrew R; Fairall, Louise; Smith, Corinne J; Schwabe, John WR

2016-01-01

The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin. DOI: http://dx.doi.org/10.7554/eLife.13941.001 PMID:27098840
The socio-genetics of a complex society: female gelada relatedness patterns mirror association patterns in a multilevel society.

PubMed

Snyder-Mackler, Noah; Alberts, Susan C; Bergman, Thore J

2014-12-01

Multilevel societies with fission-fusion dynamics--arguably the most complex animal societies--are defined by two or more nested levels of organization. The core of these societies are modular social units that regularly fission and fuse with one another. Despite convergent evolution in disparate taxa, we know strikingly little about how such societies form and how fitness benefits operate. Understanding the kinship structure of complex societies could inform us about the origins of the social structure as well as about the potential for individuals in these societies to accrue indirect fitness benefits. Here, we combined genetic and behavioural data on geladas (Theropithecus gelada), an Old World Monkey, to complete the most comprehensive socio-genetic analysis of a multilevel society to date. In geladas, individuals in the core social 'units', associate at different frequencies to form 'teams', 'bands' and, the largest aggregations, 'communities'. Units were composed of closely related females, and females remained with their close kin during permanent fissions of units. Interestingly, female-female relatedness also significantly predicted between-unit, between-team and between-band association patterns, while male-male relatedness did not. Thus, it is likely that the socio-genetic structure of gelada society results from females maintaining associations with their female relatives during successive unit fissions--possibly in an attempt to balance the direct and indirect fitness benefits of group living. Overall, the persistence of associations among related females across generations appears to drive the formation of higher levels of gelada society, suggesting that females seek kin for inclusive fitness benefits at multiple levels of gelada society. © 2014 John Wiley & Sons Ltd.
Tunable arbitrary unitary transformer based on multiple sections of multicore fibers with phase control.

PubMed

Zhou, Junhe; Wu, Jianjie; Hu, Qinsong

2018-02-05

In this paper, we propose a novel tunable unitary transformer, which can achieve arbitrary discrete unitary transforms. The unitary transformer is composed of multiple sections of multi-core fibers with closely aligned coupled cores. Phase shifters are inserted before and after the sections to control the phases of the waves in the cores. A simple algorithm is proposed to find the optimal phase setup for the phase shifters to realize the desired unitary transforms. The proposed device is fiber based and is particularly suitable for the mode division multiplexing systems. A tunable mode MUX/DEMUX for a three-mode fiber is designed based on the proposed structure.
[Impact of TDZ and NAA on adventitious bud induction and cluster bud multiplication in Tulipa edulis].

PubMed

Zhu, Li-Fang; Xu, Chao; Zhu, Zai-Biao; Yang, He-Tong; Guo, Qiao-Sheng; Xu, Hong-jian; Ma, Hong-Jian; Zhao, Gui-Hua

2014-08-01

To explore the method of explants directly induced bud and establish the tissue culture system of mutiple shoot by means of direct organogenesis, core bud and daughter bulbs (the top of bud stem expanded to form daughter bulb) of T. edulis were used as explants and treated with thidiazuron (TDZ) and 1-naphthlcetic acid (NAA). The results showed that the optimal medium for bud inducted form core bud and daughter bulb were MS + TDZ 2.0 mg x L(-1) + NAA 4.0 mg x L(-1) and MS +TDZ 2.0 mg x L(-1) + NAA 2.0 mg x L(-1) respectively, both of them had a bud induction rate of 72.92%, 79.22%. The optimal medium for cluster buds multiplication was MS + TDZ 0.2 mg x L(-1) + NAA 0.2 mg x L(-1), and proliferation coefficient was 2.23. After proliferation, cluster buds rooting occurred on MS medium with IBA 1.0 mg x L(-1) and the rooting rate was 52.6%, three to five seedlings in each plant. Using core bud and daughter bulb of T. edulis, the optimum medium for adventitious bud directly inducted from daughter bulb, core bud and cluster bud multiplication were screened out and the tissue culture system of multiple shoot by means of direct organogenesis was established.
Effective organizational control: implications for academic medicine.

PubMed

Wilkes, Michael S; Srinivasan, Malathi; Flamholtz, Eric

2005-11-01

This article provides a framework for understanding the nature, role, functioning, design, and effects of organizational oversight systems. Using a case study with elements recognizable to an academic audience, the authors explore how a dean of a fictitious School of Medicine might use organizational control structures to develop effective solutions to global disarray within the academic medical center. Organizational control systems are intended to help influence the behavior of people as members of a formal organization. They are necessary to motivate people toward organizational goals, to coordinate diverse efforts, and to provide feedback about problems. The authors present a model of control to make this process more visible within organizations. They explore the overlap among academic medical centers and large businesses-for instance, each is a billion-dollar enterprise with complex internal and external demands and multiple audiences. The authors identify and describe how to use the key components of an organization's control system: environment, culture, structure, and core control system. Elements of the core control system are identified, described, and explored. These closely articulating elements include planning, operations, measurement, evaluation, and feedback systems. Use of control portfolios is explored to achieve goal-outcome congruence. Additionally, the authors describe how the components of the control system can be used synergistically by academic leadership to create organizational change, congruent with larger organizational goals. The enterprise of medicine is quickly learning from the enterprise of business. Achieving goal-action congruence will better position academic medicine to meet its multiple missions.

Isotopic and trace element characteristics of an unusual refractory inclusion from Essebi

NASA Technical Reports Server (NTRS)

Deloule, E.; Kennedy, A. K.; Hutcheon, I. D.; Elgoresy, A.

1993-01-01

The isotopic and chemical properties of Ca-Al-rich inclusions (CAI) provide important clues to the early solar nebula environment. While the abundances of refractory major and trace elements are similar to those expected for high temperature condensates, the variety of textural, chemical, and isotopic signatures indicate most CAI experienced complex, multi-stage histories involving repeated episodes of condensation, evaporation, and metamorphism. Evidence of multiple processes is especially apparent in an unusual refractory inclusion from Essebi (URIE) described by El Goresy et al. The melilite (mel)-rich core of URIE contains polygonal framboids of spinel (sp) and hibonite (hb) or sp and fassaite (fas) and is surrounded by a rim sequence consisting of five layers. In contrast to rims on Allende, the mineralogy of the URIE rim layers becomes increasingly refractory from the core outwards, ending in a layer of spinel-Al2O3 solid solution + Sc-rich fassaite. The chemical and mineralogical features of URIE are inconsistent with crystallization from a homogeneous melt, and El Goresy et al. proposed a multi-step history involving condensation of sp + hb and aggregation into framboids, capture of framboids by a refractory silicate melt droplet, condensation of rim layers, and alteration of mel to calcite and feldspathoid. The PANURGE ion probe was used to investigate the isotopic and trace element characteristics of URIE to develop a more complete picture of the multiple processes leading to formation and metamorphism.
Programmable chemical controllers made from DNA.

PubMed

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2013-10-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.
Programmable chemical controllers made from DNA

NASA Astrophysics Data System (ADS)

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2013-10-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.
Cognition, dopamine and bioactive lipids in schizophrenia

PubMed Central

Condray, Ruth; Yao, Jeffrey K.

2011-01-01

Schizophrenia is a remarkably complex disorder with a multitude of behavioral and biological perturbations. Cognitive deficits are a core feature of this disorder, and involve abnormalities across multiple domains, including memory, attention, and perception. The complexity of this debilitating illness has led to a view that the key to unraveling its pathophysiology lies in deconstructing the clinically-defined syndrome into pathophysiologically distinct intermediate phenotypes. Accumulating evidence suggests that one of these intermediate phenotypes may involve phospholipid signaling abnormalities, particularly in relation to arachidonic acid (AA). Our data show relationships between levels of AA and performance on tests of cognition for schizophrenia patients, with defects in AA signaling associated with deficits in cognition. Moreover, dopamine may moderate these relationships between AA and cognition. Taken together, cognitive deficits, dopaminergic neurotransmission, and bioactive lipids have emerged as related features of schizophrenia. Existing treatment options for cognitive deficits in schizophrenia do not specifically target lipid-derived signaling pathways; understanding these processes could inform efforts to identify novel targets for treatment innovation. PMID:21196378
Programmable chemical controllers made from DNA

PubMed Central

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2014-01-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language', and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents. PMID:24077029
Experimental observations of a complex, supersonic nozzle concept

NASA Astrophysics Data System (ADS)

Magstadt, Andrew; Berry, Matthew; Glauser, Mark; Ruscher, Christopher; Gogineni, Sivaram; Kiel, Barry; Skytop Turbulence Labs, Syracuse University Team; Spectral Energies, LLC. Team; Air Force Research Laboratory Team

2015-11-01

A complex nozzle concept, which fuses multiple canonical flows together, has been experimentally investigated via pressure, schlieren and PIV in the anechoic chamber at Syracuse University. Motivated by future engine designs of high-performance aircraft, the rectangular, supersonic jet under investigation has a single plane of symmetry, an additional shear layer (referred to as a wall jet) and an aft deck representative of airframe integration. Operating near a Reynolds number of 3 ×106 , the nozzle architecture creates an intricate flow field comprised of high turbulence levels, shocks, shear & boundary layers, and powerful corner vortices. Current data suggest that the wall jet, which is an order of magnitude less energetic than the core, has significant control authority over the acoustic power through some non-linear process. As sound is a direct product of turbulence, experimental and analytical efforts further explore this interesting phenomenon associated with the turbulent flow. The authors acknowledge the funding source, a SBIR Phase II project with Spectral Energies, LLC. and AFRL turbine engine branch under the direction of Dr. Barry Kiel.
A 3D virtual reality simulator for training of minimally invasive surgery.

PubMed

Mi, Shao-Hua; Hou, Zeng-Gunag; Yang, Fan; Xie, Xiao-Liang; Bian, Gui-Bin

2014-01-01

For the last decade, remarkable progress has been made in the field of cardiovascular disease treatment. However, these complex medical procedures require a combination of rich experience and technical skills. In this paper, a 3D virtual reality simulator for core skills training in minimally invasive surgery is presented. The system can generate realistic 3D vascular models segmented from patient datasets, including a beating heart, and provide a real-time computation of force and force feedback module for surgical simulation. Instruments, such as a catheter or guide wire, are represented by a multi-body mass-spring model. In addition, a realistic user interface with multiple windows and real-time 3D views are developed. Moreover, the simulator is also provided with a human-machine interaction module that gives doctors the sense of touch during the surgery training, enables them to control the motion of a virtual catheter/guide wire inside a complex vascular model. Experimental results show that the simulator is suitable for minimally invasive surgery training.
Responsive polymer-based colloids for drug delivery and bioconversion

NASA Astrophysics Data System (ADS)

Kudina, Olena

Responsive polymer-based colloids (RPBC) are the colloidal structures containing responsive polymeric component which is able to adapt its physico-chemical properties to the environment by undergoing chemical and/or conformational changes. The goal of the dissertation is to develop and characterize several groups of RPBC with different morphological complexity and explore their potential in drug delivery and bioconversion. The role of RPBC morphology for these specific applications is discussed in details. Three groups of RPBC were fabricated: i. polymeric micelles; ii. mixed polymeric micelles; iii. hybrid polymer-inorganic particles. All fabricated RPBCs contain polymeric component in their structure. The dissertation investigates how the changes of the responsive polymeric component properties are reflected in morphologies of RPBC. The first group of RPBC, polymeric micelles, was formed by the self-assembly of amphiphilic invertible polymers (AIPs) synthesized in our group. AIPs self-assemble into invertible micellar assemblies (IMAs) in solvents of different polarity. In this work, IMAs ability to invert the structure as a response to the change in solvent polarity was demonstrated using 1H NMR spectroscopy and SANS. It was shown that the IMAs incorporate hydrophobic cargo either in the core or in the shell, depending on the chemical structure of cargo molecules. Following in vitro study demonstrates that loaded with drug (curcumin) IMAs are cytotoxic to osteosarcoma cells. Mixed polymeric micelles represent another, more complex, RPBC morphologies studied in the dissertation. Mixed micelles were fabricated from AIPs and amphiphilic oligomers synthesized from pyromellitic dianhydride, polyethylene glycol methyl ethers, and alkanols/cholesterol. The combination of selected AIP and oligomers based on cholesterol results in mixed micelles with an increased drug-loading capacity (from 10% w/w loaded curcumin in single component IMAs to 26%w/w in mixed micelles). Even more complex colloids are hybrid polymer-inorganic particles, the third RPBC group studied in dissertation. Material was designed as core--shell particles with superparamagnetic core engulfed by grafted polymer brushes. These particles were loaded with enzymes (cellulases), thus, are turned into enzymogels for cellulose bioconversion. The study demonstrates that such RPBCs can be used multiple times during hydrolysis and provide an about four-fold increase in glucose production in comparison to free enzymes.
Paleoenvironmental evolution based on benthic foraminifera biofacies of the Paraíba do Sul Deltaic Complex, eastern Brazil

NASA Astrophysics Data System (ADS)

Gasparini, Sarah Pereira; Vilela, Claudia Gutterres

2017-12-01

The paleoecology and distribution of benthic foraminiferal assemblages were analyzed in the core 2-MU-1-RJ well, drilled in the Paraíba do Sul Deltaic Complex, Rio de Janeiro (Brazil). An abundant assemblage was found in the upper portion of the well core, inferred to be pleistocenic deposits. The coastal dynamic was recognized from five biofacies based on clusters, the Planktonic/Benthic (P/B) ratios and indicator species distribution in the core. Several biofacies were identified along the core depending on the species dominance. From the bottom to the top of the core, the biofacies succession represents the environmental changes in the coastal area associated to sea-level oscillations. The biofacies ABP dominated by Ammonia parkinsoniana and Bolivina spp. and Pararotalia cananeiaensis represents an inner shelf environment; biofacies QP dominated by shelf miliolids species; biofacies PGH, dominated by P. cananeiaensis, Gavelinopsis praegeri, and Hanzawaia nitidula, represents the estuary complex with middle or outer shelf influence; biofacies QL represents hypersaline waters dominated by lagoonal miliolids; and biofacies HP characterized by Haynesina germanica and P. cananeiaensis is associated with paralic environments. Marine ingressions are recorded and those biofacies show the pleistocenic coastal hydrodinamic in the deltaic complex. The foraminiferal biofacies contribute with detailed information to sedimentary facies previously characterized in the study area by the reconstruction of paleoenvironment succession.
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions.

PubMed

Ko, Junsu; Park, Hahnbeom; Seok, Chaok

2012-08-10

Protein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. However, it is challenging to obtain structures more accurate than the single best templates by either combining information from multiple templates or by modeling regions that vary among templates or are not covered by any templates. We introduce GalaxyTBM, a new TBM method in which the more reliable core region is modeled first from multiple templates and less reliable, variable local regions, such as loops or termini, are then detected and re-modeled by an ab initio method. This TBM method is based on "Seok-server," which was tested in CASP9 and assessed to be amongst the top TBM servers. The accuracy of the initial core modeling is enhanced by focusing on more conserved regions in the multiple-template selection and multiple sequence alignment stages. Additional improvement is achieved by ab initio modeling of up to 3 unreliable local regions in the fixed framework of the core structure. Overall, GalaxyTBM reproduced the performance of Seok-server, with GalaxyTBM and Seok-server resulting in average GDT-TS of 68.1 and 68.4, respectively, when tested on 68 single-domain CASP9 TBM targets. For application to multi-domain proteins, GalaxyTBM must be combined with domain-splitting methods. Application of GalaxyTBM to CASP9 targets demonstrates that accurate protein structure prediction is possible by use of a multiple-template-based approach, and ab initio modeling of variable regions can further enhance the model quality.
The Formation of Glycine in Hot Cores: New Gas-grain Chemical Simulations of Star-forming Regions

NASA Astrophysics Data System (ADS)

Garrod, Robin

2012-07-01

Organic molecules of increasing complexity have been detected in the warm envelopes of star-forming cores, commonly referred to as "hot cores". Spectroscopic searches at mm/sub-mm wavelengths have uncovered both amines and carboxylic acids in these regions, as well as a range of other compounds including alcohols, ethers, esters, and nitriles. However, the simplest amino acid, glycine (NH2CH2COOH), has not yet been reliably detected in the ISM. There has been much interest in this molecule, due to its importance to the formation of proteins, and to life, while the positive identification of interstellar molecules of similar or greater complexity suggests that its existence in star-forming regions is plausible. I will present the results of recent models of hot-core chemistry that simulate the formation of both simple and complex molecules on the surfaces or within the ice mantles of dust grains. I will also present results from the first gas-grain astrochemical model to approach the question of amino-acid formation in hot cores. The formation of glycine in moderate abundance is found to be as efficient as that for similarly complex species, while its sublimation from the grains occurs at somewhat higher temperatures. However, simulated emission spectra based on the model results show that the degree of compactness of high-abundance regions, and the density and temperature profiles of the cores may be the key variables affecting the future detection of glycine, as well as other amino acids, and may explain its non-detection to date.
An assessment of butyltins and metals in sediment cores from the St. Thomas East End Reserves, USVI.

PubMed

Hartwell, S Ian; Apeti, Dennis A; Mason, Andrew L; Pait, Anthony S

2016-11-01

Tributyltin (TBT) concentrations near a marina complex in Benner Bay on St. Thomas, US Virgin Islands, were elevated relative to other areas in a larger study of the southeastern shore of the island. At the request of the USVI Coastal Zone Management Program, sediment cores and surface sediment samples were collected to better define the extent and history of TBT deposition in the vicinity of Benner Bay. The sediment cores were sectioned into 2-cm intervals and dated with 210 Pb and 137 Cs. The core sections and the surface samples were analyzed for butyltins and 16 elements. Deposition rates varied from 0.07-5.0 mm/year, and were highest in the marina complex. Core ages ranged from 54 to 200 years. The bottoms of the cores contained shell hash, but the top layers all consisted of much finer material. Surface concentrations of TBT exceeded 2000 ng Sn/g (dry weight) at two locations. At a depth of 8 cm TBT exceeded 8800 ng Sn/g in the marina complex sediment. Based on the ratio of tributyltin to total butyltins, it appears that the marina sediments are the source of contamination of the surrounding area. There is evidence that vessels from neighboring islands may also be a source of fresh TBT. Copper concentrations increase over time up to the present. Gradients of virtually all metals and metalloids extended away from the marina complex. NOAA sediment quality guidelines were exceeded for As, Pb, Cu, Zn, and Hg.
Separating Multiple Episodes of Partial Melting in Polyorogenic Crust: AN Example from the Haiyangsuo Complex, Northern Sulu Belt, Eastern China

NASA Astrophysics Data System (ADS)

Feng, P.; Wang, L.; Brown, M.; Wang, S.

2017-12-01

Determining the timing, mechanism and source of partial melts in polyorogenic crust is challenging. In the Sulu belt, the tectonic affinity of the Haiyangsuo (HYS) complex is controversial due to its polyphase metamorphic history. Here we use detailed field mapping, petrology, microstructural analysis and zircon geochronology to study thin stromatic leucosomes in host granite gneiss, and crosscutting leucogranite dykes to decipher the melting history. Zircon grains from both granite gneiss and thin leucosomes exhibit core-mantle-rim structures. Zircon cores yield protolith ages of 2.86-2.81 Ga, whereas the mantles and rims yield younger metamorphic/melt crystallization ages of ca. 1.82-1.80 Ga. The mantles are characterized by gray luminescence, flat HREE distribution patterns and relatively low Th/U ratios, indicating crystallization during granulite-facies metamorphism. Whereas rims show bright luminescence, steep HREE distribution patterns and higher Th/U ratios, suggesting they crystallized from melt. The mantles and rims have ɛHf (t) of -18.2 to -11.0. Using 176Lu/177Hf = 0.001, these data project back to the array of ɛHf (t) values for the zircon cores. This demonstrates that the thin leucosomes were derived from the gneiss without any mass input from a mantle source. These features are consistent with an origin of the HYS as part of the eastern margin of the NCC prior to juxtaposition with the Sulu belt. Zircons from the leucogranite dykes also show core-mantle-rim structure. Inherited cores yield concordant 206Pb/238U ages of 776-701 Ma consistent with the dominant age range for protoliths of the UHP metamorphic rocks in the Sulu belt. Zircon mantle and rim domains, which both contain multiphase solid inclusions (Kfs + Pl + Qz and Hem + Pl + Qz in mantles and Kfs + Pl + Qz + Bt in rims), yield melt crystallization ages of 226-217 and 169-156 Ma, respectively. High Sr, low Y and Yb contents, high Sr/Y ratios, and the range of ɛNd (t) values (-18.2- -15.0) and initial 87Sr/86Sr ratios (0.7106 - 0.7146) for the leucogranites are consistent with melting of thickened lower continental crust of the Sulu belt. We interpret the dykes to have been emplaced during post-collisional collapse of the orogenic root of this belt in the Middle-Upper Jurassic.
An expanding universe of circadian networks in higher plants.

PubMed

Pruneda-Paz, Jose L; Kay, Steve A

2010-05-01

Extensive circadian clock networks regulate almost every biological process in plants. Clock-controlled physiological responses are coupled with daily oscillations in environmental conditions resulting in enhanced fitness and growth vigor. Identification of core clock components and their associated molecular interactions has established the basic network architecture of plant clocks, which consists of multiple interlocked feedback loops. A hierarchical structure of transcriptional feedback overlaid with regulated protein turnover sets the pace of the clock and ultimately drives all clock-controlled processes. Although originally described as linear entities, increasing evidence suggests that many signaling pathways can act as both inputs and outputs within the overall network. Future studies will determine the molecular mechanisms involved in these complex regulatory loops. 2010 Elsevier Ltd. All rights reserved.
GPU accelerated study of heat transfer and fluid flow by lattice Boltzmann method on CUDA

NASA Astrophysics Data System (ADS)

Ren, Qinlong

Lattice Boltzmann method (LBM) has been developed as a powerful numerical approach to simulate the complex fluid flow and heat transfer phenomena during the past two decades. As a mesoscale method based on the kinetic theory, LBM has several advantages compared with traditional numerical methods such as physical representation of microscopic interactions, dealing with complex geometries and highly parallel nature. Lattice Boltzmann method has been applied to solve various fluid behaviors and heat transfer process like conjugate heat transfer, magnetic and electric field, diffusion and mixing process, chemical reactions, multiphase flow, phase change process, non-isothermal flow in porous medium, microfluidics, fluid-structure interactions in biological system and so on. In addition, as a non-body-conformal grid method, the immersed boundary method (IBM) could be applied to handle the complex or moving geometries in the domain. The immersed boundary method could be coupled with lattice Boltzmann method to study the heat transfer and fluid flow problems. Heat transfer and fluid flow are solved on Euler nodes by LBM while the complex solid geometries are captured by Lagrangian nodes using immersed boundary method. Parallel computing has been a popular topic for many decades to accelerate the computational speed in engineering and scientific fields. Today, almost all the laptop and desktop have central processing units (CPUs) with multiple cores which could be used for parallel computing. However, the cost of CPUs with hundreds of cores is still high which limits its capability of high performance computing on personal computer. Graphic processing units (GPU) is originally used for the computer video cards have been emerged as the most powerful high-performance workstation in recent years. Unlike the CPUs, the cost of GPU with thousands of cores is cheap. For example, the GPU (GeForce GTX TITAN) which is used in the current work has 2688 cores and the price is only 1,000 US dollars. The release of NVIDIA's CUDA architecture which includes both hardware and programming environment in 2007 makes GPU computing attractive. Due to its highly parallel nature, lattice Boltzmann method is successfully ported into GPU with a performance benefit during the recent years. In the current work, LBM CUDA code is developed for different fluid flow and heat transfer problems. In this dissertation, lattice Boltzmann method and immersed boundary method are used to study natural convection in an enclosure with an array of conduting obstacles, double-diffusive convection in a vertical cavity with Soret and Dufour effects, PCM melting process in a latent heat thermal energy storage system with internal fins, mixed convection in a lid-driven cavity with a sinusoidal cylinder, and AC electrothermal pumping in microfluidic systems on a CUDA computational platform. It is demonstrated that LBM is an efficient method to simulate complex heat transfer problems using GPU on CUDA.
An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

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

Hammel, Michal; Yu, Yaping; Radhakrishnan, Sarvan K.

DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). But, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcsmore » (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Our collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.« less
An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

DOE PAGES

Hammel, Michal; Yu, Yaping; Radhakrishnan, Sarvan K.; ...

2016-11-14

DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). But, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcsmore » (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Our collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.« less
Core-shell nanofibers of curcumin/cyclodextrin inclusion complex and polylactic acid: Enhanced water solubility and slow release of curcumin.

PubMed

Aytac, Zeynep; Uyar, Tamer

2017-02-25

Core-shell nanofibers were designed via electrospinning using inclusion complex (IC) of model hydrophobic drug (curcumin, CUR) with cyclodextrin (CD) in the core and polymer (polylactic acid, PLA) in the shell (cCUR/HPβCD-IC-sPLA-NF). CD-IC of CUR and HPβCD was formed at 1:2 molar ratio. The successful formation of core-shell nanofibers was revealed by TEM and CLSM images. cCUR/HPβCD-IC-sPLA-NF released CUR slowly but much more in total than PLA-CUR-NF at pH 1 and pH 7.4 due to the restriction of CUR in the core of nanofibers and solubility improvement shown in phase solubility diagram, respectively. Improved antioxidant activity of cCUR/HPβCD-IC-sPLA-NF in methanol:water (1:1) is related with the solubility enhancement achieved in water based system. The slow reaction of cCUR/HPβCD-IC-sPLA-NF in methanol is associated with the shell inhibiting the quick release of CUR. On the other hand, cCUR/HPβCD-IC-sPLA-NF exhibited slightly higher rate of antioxidant activity than PLA-CUR-NF in methanol:water (1:1) owing to the enhanced solubility. To conclude, slow release of CUR was achieved by core-shell nanofiber structure and inclusion complexation of CUR with HPβCD provides high solubility. Briefly, electrospinning of core-shell nanofibers with CD-IC core could offer slow release of drugs as well as solubility enhancement for hydrophobic drugs. Copyright © 2017 Elsevier B.V. All rights reserved.
Gold core/ceria shell-based redox active nanozyme mimicking the biological multienzyme complex phenomenon

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

Bhagat, Stuti; Srikanth Vallabani, N. V.; Shutthanandan, Vaithiyalingam

Catalytically active individual gold (Au) and cerium oxide (CeO2) nanoparticles are well known to exhibit specific enzyme-like activities, such as natural catalase, oxidase, superoxide dismutase, and peroxidase enzymes. These activities have been maneuvered to design several biological applications such as immunoassays, glucose detection, radiation and free radical protection and tissue engineering. A functional nanozyme depicting multienzyme like properties that functions as a synthetic super enzyme has eluded the researchers in the nanoscience community for past decade. In current report, we have designed a functional multienzyme in the form of Gold (core)-CeO2 (shell) nanoparticles (Au@CeO2 CSNPs) exhibiting excellent peroxidase, catalase andmore » superoxide dismutase enzyme-like activities that are controlled simply by tuning the pH. The reaction kinetic parameters reveal that the peroxidase-like activity of this core shell nanozyme is comparable to natural HRP enzyme. Unlike peroxidase-like activity exhibited by other nanomaterials, Au@CeO2 CSNPs showed decrease in hydroxyl radical formation, suggesting that the bio catalytic reactions are performed by efficient electron transfers. A significant enzyme-like activity of this core shell nanoparticle was conserved at extreme pH (2 – 11) and temperatures (up to 90 °C), clearly suggesting the superiority over natural enzymes. Further, the utility of peroxidase-like activity of this core shell nanoparticles was extended for the detection of glucose, which showed a linear range of detection between (100 µM – 1 mM). It is hypothesized that the proximity of the redox potentials of Au+/Au and Ce (III)/Ce (IV) may result in a redox couple promoting the multienzyme activity of core shell nanoparticles. Au@CeO2 CSNPs may open new directions for development of single platform sensors in multiple biosensing applications.« less
Raccoon spatial requirements and multi-scale habitat selection within an intensively managed central Appalachian forest

USGS Publications Warehouse

Owen, Sheldon F.; Berl, Jacob L.; Edwards, John W.; Ford, W. Mark; Wood, Petra Bohall

2015-01-01

We studied a raccoon (Procyon lotor) population within a managed central Appalachian hardwood forest in West Virginia to investigate the effects of intensive forest management on raccoon spatial requirements and habitat selection. Raccoon home-range (95% utilization distribution) and core-area (50% utilization distribution) size differed between sexes with males maintaining larger (2×) home ranges and core areas than females. Home-range and core-area size did not differ between seasons for either sex. We used compositional analysis to quantify raccoon selection of six different habitat types at multiple spatial scales. Raccoons selected riparian corridors (riparian management zones [RMZ]) and intact forests (> 70 y old) at the core-area spatial scale. RMZs likely were used by raccoons because they provided abundant denning resources (i.e., large-diameter trees) as well as access to water. Habitat composition associated with raccoon foraging locations indicated selection for intact forests, riparian areas, and regenerating harvest (stands <10 y old). Although raccoons were able to utilize multiple habitat types for foraging resources, a selection of intact forest and RMZs at multiple spatial scales indicates the need of mature forest (with large-diameter trees) for this species in managed forests in the central Appalachians.

Episodic growth of a Late Cretaceous and Paleogene intrusive complex of pegmatitic leucogranite, Ruby Mountains core complex, Nevada, USA

USGS Publications Warehouse

Howard, Keith A.; Wooden, J.L.; Barnes, C.G.; Premo, W.R.; Snoke, A.W.; Lee, S.-Y.

2011-01-01

Gneissic pegmatitic leucogranite forms a dominant component (>600 km3) of the midcrustal infrastructure of the Ruby Mountains–East Humboldt Range core complex (Nevada, USA), and was assembled and modified episodically into a batholithic volume by myriad small intrusions from ca. 92 to 29 Ma. This injection complex consists of deformed sheets and other bodies emplaced syntectonically into a stratigraphic framework of marble, calc-silicate rocks, quartzite, schist, and other granitoids. Bodies of pegmatitic granite coalesce around host-rock remnants, which preserve relict or ghost stratigraphy, thrusts, and fold nappes. Intrusion inflated but did not disrupt the host-rock structure. The pegmatitic granite increases proportionally downward from structurally high positions to the bottoms of 1-km-deep canyons where it constitutes 95%–100% of the rock. Zircon and monazite dated by U-Pb (sensitive high-resolution ion microprobe, SHRIMP) for this rock type cluster diffusely at ages near 92, 82(?), 69, 38, and 29 Ma, and indicate successive or rejuvenated igneous crystallization multiple times over long periods of the Late Cretaceous and the Paleogene. Initial partial melting of unexposed pelites may have generated granite forerunners, which were remobilized several times in partial melting events. Sources for the pegmatitic granite differed isotopically from sources of similar-aged interleaved equigranular granites. Dominant Late Cretaceous and fewer Paleogene ages recorded from some pegmatitic granite samples, and Paleogene-only ages from the two structurally deepest samples, together with varying zircon trace element contents, suggest several disparate ages of final emplacement or remobilization of various small bodies. Folded sills that merge with dikes that cut the same folds suggest that there may have been in situ partial remobilization. The pegmatitic granite intrusions represent prolonged and recurrent generation, assembly, and partial melting modification of a batholithic volume even while the regional tectonic environment varied dramatically from contractile thickening to extension and mafic underplating.
A Search for Starless Core Substructure in Ophiuchus

NASA Astrophysics Data System (ADS)

Kirk, Helen

2017-06-01

Density substructure is expected in evolved starless cores: a single peak to form a protostar, or multiple peaks from fragmentation. Searches for this substructure have had mixed success. In an ALMA survey of Ophiuchus, we find two starless cores with signs of substructure, consistent with simulation predictions. A similar survey in Chameleon (Dunham et al. 2016) had no detections, despite expecting at least two. Our results suggest that Chamleon may lack a more evolved starless cores. Future ALMA observations will better trace the influence of environment on core substructure formation.
CoreTSAR: Core Task-Size Adapting Runtime

DOE PAGES

Scogland, Thomas R. W.; Feng, Wu-chun; Rountree, Barry; ...

2014-10-27

Heterogeneity continues to increase at all levels of computing, with the rise of accelerators such as GPUs, FPGAs, and other co-processors into everything from desktops to supercomputers. As a consequence, efficiently managing such disparate resources has become increasingly complex. CoreTSAR seeks to reduce this complexity by adaptively worksharing parallel-loop regions across compute resources without requiring any transformation of the code within the loop. Lastly, our results show performance improvements of up to three-fold over a current state-of-the-art heterogeneous task scheduler as well as linear performance scaling from a single GPU to four GPUs for many codes. In addition, CoreTSAR demonstratesmore » a robust ability to adapt to both a variety of workloads and underlying system configurations.« less
Uphill energy transfer in photosystem I from Chlamydomonas reinhardtii. Time-resolved fluorescence measurements at 77 K.

PubMed

Giera, Wojciech; Szewczyk, Sebastian; McConnell, Michael D; Redding, Kevin E; van Grondelle, Rienk; Gibasiewicz, Krzysztof

2018-04-04

Energetic properties of chlorophylls in photosynthetic complexes are strongly modulated by their interaction with the protein matrix and by inter-pigment coupling. This spectral tuning is especially striking in photosystem I (PSI) complexes that contain low-energy chlorophylls emitting above 700 nm. Such low-energy chlorophylls have been observed in cyanobacterial PSI, algal and plant PSI-LHCI complexes, and individual light-harvesting complex I (LHCI) proteins. However, there has been no direct evidence of their presence in algal PSI core complexes lacking LHCI. In order to determine the lowest-energy states of chlorophylls and their dynamics in algal PSI antenna systems, we performed time-resolved fluorescence measurements at 77 K for PSI core and PSI-LHCI complexes isolated from the green alga Chlamydomonas reinhardtii. The pool of low-energy chlorophylls observed in PSI cores is generally smaller and less red-shifted than that observed in PSI-LHCI complexes. Excitation energy equilibration between bulk and low-energy chlorophylls in the PSI-LHCI complexes at 77 K leads to population of excited states that are less red-shifted (by ~ 12 nm) than at room temperature. On the other hand, analysis of the detection wavelength dependence of the effective trapping time of bulk excitations in the PSI core at 77 K provided evidence for an energy threshold at ~ 675 nm, above which trapping slows down. Based on these observations, we postulate that excitation energy transfer from bulk to low-energy chlorophylls and from bulk to reaction center chlorophylls are thermally activated uphill processes that likely occur via higher excitonic states of energy accepting chlorophylls.
Synthesis and characterization of Na(Gd0.5Lu0.5)F4: Nd3+,a core-shell free multifunctional contrast agent.

PubMed

Mimun, L Christopher; Ajithkumar, G; Rightsell, Chris; Langloss, Brian W; Therien, Michael J; Sardar, Dhiraj K

2017-02-25

Compared to conventional core-shell structures, core-shell free nanoparticles with multiple functionalities offer several advantages such as minimal synthetic complexity and low production cost. In this paper, we present the synthesis and characterization of Nd 3+ doped Na(Gd 0.5 Lu 0.5 )F 4 as a core-shell free nanoparticle system with three functionalities. Nanocrystals with 20 nm diameter, high crystallinity and a narrow particle size distributions were synthesized by the solvothermal method and characterized by various analytical techniques to understand their phase and morphology. Fluorescence characteristics under near infrared (NIR) excitation at 808 nm as well as X-ray excitation were studied to explore their potential in NIR optical and X-ray imaging. At 1.0 mol% Nd concentration, we observed a quantum yield of 25% at 1064 nm emission with 13 W/cm 2 excitation power density which is sufficiently enough for imaging applications. Under 130 kVp (5 mA) power of X-ray excitation, Nd 3+ doped Na(Gd 0.5 Lu 0.5 )F 4 shows the characteristic emission bands of Gd 3+ and Nd 3+ with the strongest emission peak at 1064 nm due to Nd 3+ . Furthermore, magnetization measurements show that the nanocrystals are paramagnetic in nature with a calculated magnetic moment per particle of ~570 μB at 2T. These preliminary results support the suitability of the present nanophosphor as a multimodal contrast agent with three imaging features viz. optical, magnetic and X-ray.
How a submarine returns to periscope depth: analysing complex socio-technical systems using Cognitive Work Analysis.

PubMed

Stanton, Neville A; Bessell, Kevin

2014-01-01

This paper presents the application of Cognitive Work Analysis to the description of the functions, situations, activities, decisions, strategies, and competencies of a Trafalgar class submarine when performing the function of returning to periscope depth. All five phases of Cognitive Work Analysis are presented, namely: Work Domain Analysis, Control Task Analysis, Strategies Analysis, Social Organisation and Cooperation Analysis, and Worker Competencies Analysis. Complex socio-technical systems are difficult to analyse but Cognitive Work Analysis offers an integrated way of analysing complex systems with the core of functional means-ends analysis underlying all of the other representations. The joined-up analysis offers a coherent framework for understanding how socio-technical systems work. Data were collected through observation and interviews at different sites across the UK. The resultant representations present a statement of how the work domain and current activities are configured in this complex socio-technical system. This is intended to provide a baseline, from which all future conceptions of the domain may be compared. The strength of the analysis is in the multiple representations from which the constraints acting on the work may be analysed. Future research needs to challenge the assumptions behind these constraints in order to develop new ways of working. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.
Tributyltin (TBT) inhibition of oligomycin-sensitive Mg-ATPase activity in mussel mitochondria.

PubMed

Pagliarani, Alessandra; Bandiera, Patrizia; Ventrella, Vittoria; Trombetti, Fabiana; Pirini, Maurizio; Nesci, Salvatore; Borgatti, Anna Rosa

2008-06-01

Tributyltin (TBT), one of the most toxic lipophilic aquatic pollutants, can be efficiently incorporated from sea water and sediments by filter-feeding molluscs. As far as we are aware TBT effects on the mitochondrial oligomycin-sensitive Mg-ATPase, the enzymatic core of energy production and a known target of TBT toxicity in mammals, have not been yet investigated in molluscs; thus the hydrolytic capability of the mitochondrial complex in the presence of micromolar concentrations of TBT was assayed in the mussel Mytilus galloprovincialis. Gill and mantle ATPase activities were progressively depressed by increasing TBT doses up to a maximal inhibition (82% in the gills and 74% in the mantle) at 0.62 microM TBT. Non-cooperative inhibition kinetics (n(H) approximately -1) and a non-competitive mechanism with respect to ATP substrate were pointed out. The mitochondrial Mg-ATPase susceptivity to TBT in the marine mussel was consistent with the formation of a TBT-Mg-ATPase complex, apparently more stable in the gills than in the mantle. The complex shape of the dose-response curve and the partial release of Mg-ATPase inhibition within the 0.6-34.4 microM TBT range suggest multiple interactions of TBT with the enzyme complex putatively related to its molecular mechanism of toxicity.
Middle region of FancM interacts with Mhf and Rmi1 in silkworms, a species lacking the Fanconi anaemia (FA) core complex.

PubMed

Sugahara, R; Mon, H; Lee, J M; Kusakabe, T

2014-04-01

The Fanconi anaemia (FA) pathway is responsible for interstrand crosslink (ICL) repair. Among the FA core complex components, FANCM is believed to act as a damage sensor for the ICL-blocked replication fork and also as a molecular platform for FA core complex assembly and interaction with Bloom's syndrome (BS) complex that is thought to play an important role in the processing of DNA structures such as stalled replication forks. In the present study, we found that in silkworms, Bombyx mori, a species lacking the major FA core complex components (FANCA, B, C, E, F, and G), FancM is required for FancD2 monoubiquitination and cell proliferation in the presence of mitomycin C (MMC). Silkworm FancM (BmFancM) was phosphorylated in the middle regions, and the modification was associated with its subcellular localization. In addition, BmFancM interacted with Mhf1, a histone-fold protein, and Rmi1, a subunit of the BS complex, in the different regions. The interaction region containing at least these two protein-binding domains played an essential role in FancM-dependent resistance to MMC. Our results suggest that BmFancM also acts as a platform for recruitment of both the FA protein and the BS protein, although the silkworm genome seems to lose FAAP24, a FancM-binding partner protein in mammals. © 2013 The Royal Entomological Society.
Continuations of the nonlinear Schrödinger equation beyond the singularity

NASA Astrophysics Data System (ADS)

Fibich, G.; Klein, M.

2011-07-01

We present four continuations of the critical nonlinear Schrödinger equation (NLS) beyond the singularity: (1) a sub-threshold power continuation, (2) a shrinking-hole continuation for ring-type solutions, (3) a vanishing nonlinear-damping continuation and (4) a complex Ginzburg-Landau (CGL) continuation. Using asymptotic analysis, we explicitly calculate the limiting solutions beyond the singularity. These calculations show that for generic initial data that lead to a loglog collapse, the sub-threshold power limit is a Bourgain-Wang solution, both before and after the singularity, and the vanishing nonlinear-damping and CGL limits are a loglog solution before the singularity, and have an infinite-velocity expanding core after the singularity. Our results suggest that all NLS continuations share the universal feature that after the singularity time Tc, the phase of the singular core is only determined up to multiplication by eiθ. As a result, interactions between post-collapse beams (filaments) become chaotic. We also show that when the continuation model leads to a point singularity and preserves the NLS invariance under the transformation t → -t and ψ → ψ*, the singular core of the weak solution is symmetric with respect to Tc. Therefore, the sub-threshold power and the shrinking-hole continuations are symmetric with respect to Tc, but continuations which are based on perturbations of the NLS equation are generically asymmetric.
Pluripotency gene network dynamics: System views from parametric analysis.

PubMed

Akberdin, Ilya R; Omelyanchuk, Nadezda A; Fadeev, Stanislav I; Leskova, Natalya E; Oschepkova, Evgeniya A; Kazantsev, Fedor V; Matushkin, Yury G; Afonnikov, Dmitry A; Kolchanov, Nikolay A

2018-01-01

Multiple experimental data demonstrated that the core gene network orchestrating self-renewal and differentiation of mouse embryonic stem cells involves activity of Oct4, Sox2 and Nanog genes by means of a number of positive feedback loops among them. However, recent studies indicated that the architecture of the core gene network should also incorporate negative Nanog autoregulation and might not include positive feedbacks from Nanog to Oct4 and Sox2. Thorough parametric analysis of the mathematical model based on this revisited core regulatory circuit identified that there are substantial changes in model dynamics occurred depending on the strength of Oct4 and Sox2 activation and molecular complexity of Nanog autorepression. The analysis showed the existence of four dynamical domains with different numbers of stable and unstable steady states. We hypothesize that these domains can constitute the checkpoints in a developmental progression from naïve to primed pluripotency and vice versa. During this transition, parametric conditions exist, which generate an oscillatory behavior of the system explaining heterogeneity in expression of pluripotent and differentiation factors in serum ESC cultures. Eventually, simulations showed that addition of positive feedbacks from Nanog to Oct4 and Sox2 leads mainly to increase of the parametric space for the naïve ESC state, in which pluripotency factors are strongly expressed while differentiation ones are repressed.
Hydrodynamic metamaterials: Microfabricated arrays to steer, refract, and focus streams of biomaterials

PubMed Central

Morton, Keith J.; Loutherback, Kevin; Inglis, David W.; Tsui, Ophelia K.; Sturm, James C.; Chou, Stephen Y.; Austin, Robert H.

2008-01-01

We show that it is possible to direct particles entrained in a fluid along trajectories much like rays of light in classical optics. A microstructured, asymmetric post array forms the core hydrodynamic element and is used as a building block to construct microfluidic metamaterials and to demonstrate refractive, focusing, and dispersive pathways for flowing beads and cells. The core element is based on the concept of deterministic lateral displacement where particles choose different paths through the asymmetric array based on their size: Particles larger than a critical size are displaced laterally at each row by a post and move along the asymmetric axis at an angle to the flow, while smaller particles move along streamline paths. We create compound elements with complex particle handling modes by tiling this core element using multiple transformation operations; we show that particle trajectories can be bent at an interface between two elements and that particles can be focused into hydrodynamic jets by using a single inlet port. Although particles propagate through these elements in a way that strongly resembles light rays propagating through optical elements, there are unique differences in the paths of our particles as compared with photons. The unusual aspects of these modular, microfluidic metamaterials form a rich design toolkit for mixing, separating, and analyzing cells and functional beads on-chip. PMID:18495920
"What--me worry?" "Why so serious?": a personal view on the Fukushima nuclear reactor accidents.

PubMed

Gallucci, Raymond

2012-09-01

Infrequently, it seems that a significant accident precursor or, worse, an actual accident, involving a commercial nuclear power reactor occurs to remind us of the need to reexamine the safety of this important electrical power technology from a risk perspective. Twenty-five years since the major core damage accident at Chernobyl in the Ukraine, the Fukushima reactor complex in Japan experienced multiple core damages as a result of an earthquake-induced tsunami beyond either the earthquake or tsunami design basis for the site. Although the tsunami itself killed tens of thousands of people and left the area devastated and virtually uninhabitable, much concern still arose from the potential radioactive releases from the damaged reactors, even though there was little population left in the area to be affected. As a lifelong probabilistic safety analyst in nuclear engineering, even I must admit to a recurrence of the doubt regarding nuclear power safety after Fukushima that I had experienced after Three Mile Island and Chernobyl. This article is my attempt to "recover" my personal perspective on acceptable risk by examining both the domestic and worldwide history of commercial nuclear power plant accidents and attempting to quantify the risk in terms of the frequency of core damage that one might glean from a review of operational history. © 2012 Society for Risk Analysis.
CCR4-Not Complex Subunit Not2 Plays Critical Roles in Vegetative Growth, Conidiation and Virulence in Watermelon Fusarium Wilt Pathogen Fusarium oxysporum f. sp. niveum

PubMed Central

Dai, Yi; Cao, Zhongye; Huang, Lihong; Liu, Shixia; Shen, Zhihui; Wang, Yuyan; Wang, Hui; Zhang, Huijuan; Li, Dayong; Song, Fengming

2016-01-01

CCR4-Not complex is a multifunctional regulator that plays important roles in multiple cellular processes in eukaryotes. In the present study, the biological function of FonNot2, a core subunit of the CCR4-Not complex, was explored in Fusarium oxysporum f. sp. niveum (Fon), the causal agent of watermelon wilt disease. FonNot2 was expressed at higher levels in conidia and germinating conidia and during infection in Fon-inoculated watermelon roots than in mycelia. Targeted disruption of FonNot2 resulted in retarded vegetative growth, reduced conidia production, abnormal conidial morphology, and reduced virulence on watermelon. Scanning electron microscopy observation of infection behaviors and qRT-PCR analysis of in planta fungal growth revealed that the ΔFonNot2 mutant was defective in the ability to penetrate watermelon roots and showed reduced fungal biomass in root and stem of the inoculated plants. Phenotypic and biochemical analyses indicated that the ΔFonNot2 mutant displayed hypersensitivity to cell wall perturbing agents (e.g., Congo Red and Calcofluor White) and oxidative stress (e.g., H2O2 and paraquat), decreased fusaric acid content, and reduced reactive oxygen species (ROS) production during spore germination. Our data demonstrate that FonNot2 plays critical roles in regulating vegetable growth, conidiogenesis and conidia morphology, and virulence on watermelon via modulating cell wall integrity, oxidative stress response, ROS production and FA biosynthesis through the regulation of transcription of genes involved in multiple pathways. PMID:27695445
Conformational changes accompany activation of reovirus RNA-dependent RNA transcription

PubMed Central

Mendez, Israel I.; Weiner, Scott G.; She, Yi-Min; Yeager, Mark; Coombs, Kevin M.

2009-01-01

Many critical biologic processes involve dynamic interactions between proteins and nucleic acids. Such dynamic processes are often difficult to delineate by conventional static methods. For example, while a variety of nucleic acid polymerase structures have been determined at atomic resolution, the details of how some multi-protein transcriptase complexes actively produce mRNA, as well as conformational changes associated with activation of such complexes, remain poorly understood. The mammalian reovirus innermost capsid (core) manifests all enzymatic activities necessary to produce mRNA from each of the 10 encased double-stranded RNA genes. We used rapid freezing and electron cryo-microscopy to trap and visualize transcriptionally active reovirus core particles and compared them to inactive core images. Rod-like density centered within actively transcribing core spike channels was attributed to exiting nascent mRNA. Comparative radial density plots of active and inactive core particles identified several structural changes in both internal and external regions of the icosahedral core capsid. Inactive and transcriptionally active cores were partially digested with trypsin and identities of initial tryptic peptides determined by mass spectrometry. Differentially-digested peptides, which also suggest transcription-associated conformational changes, were placed within the known 3-dimensional structures of major core proteins. PMID:18321727
Thermal Modeling of the Injection of Standard and Thermally Insulated Cored Wire

NASA Astrophysics Data System (ADS)

Castro-Cedeno, E.-I.; Jardy, A.; Carré, A.; Gerardin, S.; Bellot, J. P.

2017-12-01

Cored wire injection is a widespread method used to perform alloying additions during ferrous and non-ferrous liquid metal treatment. The wire consists of a metal casing that is tightly wrapped around a core of material; the casing delays the release of the material as the wire is immersed into the melt. This method of addition presents advantages such as higher repeatability and yield of cored material with respect to bulk additions. Experimental and numerical work has been performed by several authors on the subject of alloy additions, spherical and cylindrical geometries being mainly considered. Surprisingly this has not been the case for cored wire, where the reported experimental or numerical studies are scarce. This work presents a 1-D finite volume numerical model aimed for the simulation of the thermal phenomena which occurs when the wire is injected into a liquid metal bath. It is currently being used as a design tool for the conception of new types of cored wire. A parametric study on the effect of injection velocity and steel casing thickness for an Al cored wire immersed into a steel melt at 1863 K (1590 °C) is presented. The standard single casing wire is further compared against a wire with multiple casings. Numerical results show that over a certain range of injection velocities, the core contents' release is delayed in the multiple casing when compared to a single casing wire.
Management of non-traumatic avascular necrosis of the femoral head-a comparative analysis of the outcome of multiple small diameter drilling and core decompression with fibular grafting.

PubMed

Mohanty, S P; Singh, K A; Kundangar, R; Shankar, V

2017-04-01

The purpose of this study was to compare the clinical and radiological outcomes of multiple small diameter drilling and core decompression with fibular strut grafting in the management of non-traumatic avascular necrosis (AVN) of the femoral head. Outcomes of patients with AVN treated by multiple small diameter drilling (group 1) were compared retrospectively with patients treated by core decompression and fibular grafting (group 2). Harris hip score (HHS) was used to assess the clinical status pre- and postoperatively. Modified Ficat and Arlet classification was used to assess the radiological stage pre- and postoperatively. Forty-six patients (68 hips) were included in this study. Group 1 consisted of 33 hips, and group 2 consisted of 35 hips. In stages I and IIB, there was no statistically significant difference in the final HHS between the two groups. However, in stages IIA and III, hips in group 2 had a better final HHS (P < 0.05). In terms of radiographic progression, there was no statistical difference between hips in stages I, IIA and stage IIB. However, in stage III, hips belonging to group 2 had better results (P < 0.05). Kaplan-Meier survivorship analysis showed better outcome in group 2 in stage III (P < 0.05). Hips with AVN in the precollapse stage can be salvaged by core decompression with or without fibular grafting. Multiple small diameter drilling is relatively simple and carries less morbidity and hence preferred in stages I and II. However, in stage III disease, core decompression with fibular strut grafting gives better results.
High temperature fiber sensor using the interference effect within a suspended core microstructured optical fiber

NASA Astrophysics Data System (ADS)

Nguyen, Linh V.; Warren-Smith, Stephen C.; Ebendorff-Heidepriem, Heike; Monro, Tanya M.

2016-04-01

We report a high temperature fiber sensor based on the multimode interference effect within a suspended core microstructured optical fiber (SCF). By splicing a short section of SCF with a lead-in single-mode fiber (SMF), the sensor head was formed. A complex interference pattern was obtained in the reflection spectrum as the result of the multiple excited modes in the SCF. The complexity of the interference indicates that there are more than two dominantly excited modes in the SCF, as resolved by Fast Fourier Transform (FFT) analysis of the interference. The proposed sensor was subjected to temperature variation from 20°C to 1100°C. The fringe of the filtered spectrum red-shifted linearly with respect to temperature varying between 20°C and 1100°C, with similar temperature sensitivity for increasing and decreasing temperature. Phase monitoring was used for an extended temperature experiment (80 hours) in which the sensor was subjected to several different temperature variation conditions namely (i) step-wise increase/decrease with 100°C steps between 20°C and 1100°C, (ii) dwelling overnight at 400°C, (iii) free fall from 1100°C to 132°C, and (iv) continuous increase of temperature from 132°C to 1100°C. Our approach serves as a simple and cost-effective alternative to the better-known high temperature fiber sensors such as the fiber Bragg grating (FBG) in sapphire fibers or regenerated FBG in photosensitive optical fibers.
Structure of an intermediate conformer of the spindle checkpoint protein Mad2

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

Hara, Mayuko; Özkan, Engin; Sun, Hongbin

2015-08-24

The spindle checkpoint senses unattached kinetochores during prometaphase and inhibits the anaphase-promoting complex or cyclosome (APC/C), thus ensuring accurate chromosome segregation. The checkpoint protein mitotic arrest deficient 2 (Mad2) is an unusual protein with multiple folded states. Mad2 adopts the closed conformation (C-Mad2) in a Mad1–Mad2 core complex. In mitosis, kinetochore-bound Mad1–C-Mad2 recruits latent, open Mad2 (O-Mad2) from the cytosol and converts it to an intermediate conformer (I-Mad2), which can then bind and inhibit the APC/C activator cell division cycle 20 (Cdc20) as C-Mad2. In this paper, we report the crystal structure and NMR analysis of I-Mad2 bound to C-Mad2.more » Although I-Mad2 retains the O-Mad2 fold in crystal and in solution, its core structural elements undergo discernible rigid-body movements and more closely resemble C-Mad2. Residues exhibiting methyl chemical shift changes in I-Mad2 form a contiguous, interior network that connects its C-Mad2–binding site to the conformationally malleable C-terminal region. Mutations of residues at the I-Mad2–C-Mad2 interface hinder I-Mad2 formation and impede the structural transition of Mad2. Finally, our study provides insight into the conformational activation of Mad2 and establishes the basis of allosteric communication between two distal sites in Mad2.« less
The Data Transfer Kit: A geometric rendezvous-based tool for multiphysics data transfer

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

Slattery, S. R.; Wilson, P. P. H.; Pawlowski, R. P.

2013-07-01

The Data Transfer Kit (DTK) is a software library designed to provide parallel data transfer services for arbitrary physics components based on the concept of geometric rendezvous. The rendezvous algorithm provides a means to geometrically correlate two geometric domains that may be arbitrarily decomposed in a parallel simulation. By repartitioning both domains such that they have the same geometric domain on each parallel process, efficient and load balanced search operations and data transfer can be performed at a desirable algorithmic time complexity with low communication overhead relative to other types of mapping algorithms. With the increased development efforts in multiphysicsmore » simulation and other multiple mesh and geometry problems, generating parallel topology maps for transferring fields and other data between geometric domains is a common operation. The algorithms used to generate parallel topology maps based on the concept of geometric rendezvous as implemented in DTK are described with an example using a conjugate heat transfer calculation and thermal coupling with a neutronics code. In addition, we provide the results of initial scaling studies performed on the Jaguar Cray XK6 system at Oak Ridge National Laboratory for a worse-case-scenario problem in terms of algorithmic complexity that shows good scaling on 0(1 x 104) cores for topology map generation and excellent scaling on 0(1 x 105) cores for the data transfer operation with meshes of O(1 x 109) elements. (authors)« less
GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores.

PubMed

Chikkagoudar, Satish; Wang, Kai; Li, Mingyao

2011-05-26

Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1) the interaction of SNPs within it in parallel, and 2) the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/.

What Factors Influence States' Capacity to Report Children's Health Care Quality Measures? A Multiple-Case Study.

PubMed

Christensen, Anna L; Petersen, Dana M; Burton, Rachel A; Forsberg, Vanessa C; Devers, Kelly J

2017-01-01

Objectives The objective of this study was to describe factors that influence the ability of state Medicaid agencies to report the Centers for Medicare & Medicaid Services' (CMS) core set of children's health care quality measures (Child Core Set). Methods We conducted a multiple-case study of four high-performing states participating in the Children's Health Insurance Program Reauthorization Act (CHIPRA) Quality Demonstration Grant Program: Illinois, Maine, Pennsylvania, and Oregon. Cases were purposively selected for their diverse measurement approaches and used data from 2010 to 2015, including 154 interviews, semiannual grant progress reports, and annual public reports on Child Core Set measures. We followed Yin's multiple-case study methodology to describe how and why each state increased the number of measures reported to CMS. Results All four states increased the number of Child Core Set measures reported to CMS during the grant period. Each took a different approach to reporting, depending on the available technical, organizational, and behavioral inputs in the state. Reporting capacity was influenced by a state's Medicaid data availability, ability to link to other state data systems, past experience with quality measurement, staff time and technical expertise, and demand for the measures. These factors were enhanced by CHIPRA Quality Demonstration grant funding and other federal capacity building activities, as hypothesized in our conceptual framework. These and other states have made progress reporting the Child Core Set since 2010. Conclusion With financial support and investment in state data systems and organizational factors, states can overcome challenges to reporting most of the Child Core Set measures.
GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

PubMed Central

2011-01-01

Background Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Findings Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1) the interaction of SNPs within it in parallel, and 2) the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. Conclusions GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/. PMID:21615923
Evidence for a Role of VIPP1 in the Structural Organization of the Photosynthetic Apparatus in Chlamydomonas[W][OA

PubMed Central

Nordhues, André; Schöttler, Mark Aurel; Unger, Ann-Katrin; Geimer, Stefan; Schönfelder, Stephanie; Schmollinger, Stefan; Rütgers, Mark; Finazzi, Giovanni; Soppa, Barbara; Sommer, Frederik; Mühlhaus, Timo; Roach, Thomas; Krieger-Liszkay, Anja; Lokstein, Heiko; Crespo, José Luis; Schroda, Michael

2012-01-01

The vesicle-inducing protein in plastids (VIPP1) was suggested to play a role in thylakoid membrane formation via membrane vesicles. As this functional assignment is under debate, we investigated the function of VIPP1 in Chlamydomonas reinhardtii. Using immunofluorescence, we localized VIPP1 to distinct spots within the chloroplast. In VIPP1-RNA interference/artificial microRNA cells, we consistently observed aberrant, prolamellar body-like structures at the origin of multiple thylakoid membrane layers, which appear to coincide with the immunofluorescent VIPP1 spots and suggest a defect in thylakoid membrane biogenesis. Accordingly, using quantitative shotgun proteomics, we found that unstressed vipp1 mutant cells accumulate 14 to 20% less photosystems, cytochrome b6f complex, and ATP synthase but 30% more light-harvesting complex II than control cells, while complex assembly, thylakoid membrane ultrastructure, and bulk lipid composition appeared unaltered. Photosystems in vipp1 mutants are sensitive to high light, which coincides with a lowered midpoint potential of the QA/QA− redox couple and increased thermosensitivity of photosystem II (PSII), suggesting structural defects in PSII. Moreover, swollen thylakoids, despite reduced membrane energization, in vipp1 mutants grown on ammonium suggest defects in the supermolecular organization of thylakoid membrane complexes. Overall, our data suggest a role of VIPP1 in the biogenesis/assembly of thylakoid membrane core complexes, most likely by supplying structural lipids. PMID:22307852
Treatment for residual stones using flexible ureteroscopy and holmium laser lithotripsy after the management of complex calculi with single-tract percutaneous nephrolithotomy.

PubMed

Chen, L; Sha, M-L; Li, D; Zhuo, J; Jiang, C-Y; Zhu, Y-P; Xia, S-J; Lu, J; Shao, Y

2017-04-01

This study validated the effectiveness and safety of the treatment for residual stones using flexible ureteroscopy (fURS) and holmium laser (0.6-1.2 J, 20-30 Hz) lithotripsy via a fiber with a 200-μm core diameter and 0.22 numerical aperture (NA) after the management of complex calculi with single-tract percutaneous nephrolithotomy (PCNL). Between January 2014 and June 2016, 27 consecutive patients with complex calculi underwent fURS and holmium laser lithotripsy after a planned single-tract PCNL. Among the 27 patients with complex calculi, 9 had full staghorn calculi, 7 had partial staghorn calculi, and 11 had multiple calculi. After the first single-tract PCNL session, the mean stone size and mean stone surface area were 18.0 ± 10.7 mm and 181.9 ± 172.2 mm 2 , respectively. Treatment for residual stones with fURS and holmium laser lithotripsy was successfully completed and was performed without intraoperative complications. The mean operative time of the fURS procedure was 69.1 ± 23.6 min, and the mean hospital stay was 5.3 ± 2.4 days. The mean decrease in the hemoglobin level was 7.3 ± 6.5 g/l. After the fURS procedure, the overall stone-free rate was 88.9%. The overall postoperative complication rate was 14.8% (Clavien grade I 11.1%; Clavien grade II 3.7%). The current approach tested here combines the advantages of both PCNL and fURS and effectively manages complex calculi with a high stone-free rate (SFR) (88.9%). This approach also reduced the number of treatment sessions, the number of percutaneous access tracts, and the blood loss and potential morbidity associated with multiple tracts.
Strike-slip linked core complexes: A new kinematic model of basement rock exhumation in a crustal-scale fault system

NASA Astrophysics Data System (ADS)

Meyer, Sven Erik; Passchier, Cees; Abu-Alam, Tamer; Stüwe, Kurt

2014-05-01

Metamorphic core complexes usually develop as extensional features during continental crustal thinning, such as the Basin and Range and the Aegean Terrane. The Najd fault system in Saudi Arabia is a 2000 km-long and 400 km-wide complex network of crustal-scale strike-slip shear zones in a Neoproterozoic collision zone. Locally, the anastomosing shear zones lead to exhumation of lower crustal segments and represent a new kinematic model for the development of core complexes. We report on two such structures: the Qazaz complex in Saudi Arabia and the Hafafit complex in Egypt. The 15 km-wide Qazaz complex is a triangular dome of gently dipping mylonitic foliations within the 140 km-long sinistral strike-slip Qazaz mylonite zone. The gneissic dome consists of high-grade rocks, surrounded by low-grade metasediments and metavolcanics. The main SE-trending strike-slip Qazaz shear zone splits southwards into two branches around the gneiss dome: the western branch is continuous with the shallow dipping mylonites of the dome core, without overprinting, and changes by more than 90 degrees from a NS-trending strike-slip zone to an EW-trending 40 degree south-dipping detachment that bounds the gneiss dome to the south. The eastern SE-trending sinistral strike-slip shear zone branch is slightly younger and transects the central dome fabrics. The gneiss dome appears to have formed along a jog in the strike-slip shear zone during 40 km of horizontal strike-slip motion, which caused local exhumation of lower crustal rocks by 25 km along the detachment. The eastern shear zone branch formed later during exhumation, transacted the gneiss dome and offset the two parts by another 70 km. The Hafafit core complex in Egypt is of similar shape and size to the Qazaz structure, but forms the northern termination of a sinistral strike-slip zone that is at least 100 km in length. This zone may continue into Saudi Arabia as the Ajjaj shear zone for another 100 km. The NW trending strike slip mylonite zone grades into a gently N-dipping detachment to the west which accommodated strike slip by exhumation of high-grade lower crustal rocks. The Qazaz and the Hafafit Domes are similar, mirror-image structures with small differences in the accommodating shear zones. It is likely that these types of strike-slip related oblique core complexes are common in the Arabian Nubian shield, and possibly elsewhere.
We Don't Live in a Multiple-Choice World: Inquiry and the Common Core

ERIC Educational Resources Information Center

Jaeger, Paige

2012-01-01

The Common Core raises the bar for states struggling to decide what should be taught or tested. As low-performing schools strive to improve instruction, the blueprint has been defined. The Common Core defines the curriculum in enough detail and specifies ways to teach that content creatively and innovatively, to produce graduates who are problem…
The Correlation Entropy as a Measure of the Complexity of High-Lying Single-Particle Modes

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

Stoyanov, Chavdar; Zelevinsky, Vladimir; Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824-1321

Highly-excited single-particle states in nuclei are coupled with the excitations of a more complex character, first of all with collective phonon-like modes of the core. In the framework of the quasiparticle-phonon model we consider the structure of resulting complex configurations using the 1k17/2 orbital in 209Pb as an example. The eigenstates of the model carry significant degree of complexity that can be quantified with the aid of correlational invariant entropy. With artificially enhanced particle-core coupling, the system undergoes the doubling phase transition with the quasiparticle strength concentrated in two repelling peaks.
Complex organic molecules and star formation

NASA Astrophysics Data System (ADS)

Bacmann, A.; Faure, A.

2014-12-01

Star forming regions are characterised by the presence of a wealth of chemical species. For the past two to three decades, ever more complex organic species have been detected in the hot cores of protostars. The evolution of these molecules in the course of the star forming process is still uncertain, but it is likely that they are partially incorporated into protoplanetary disks and then into planetesimals and the small bodies of planetary systems. The complex organic molecules seen in star forming regions are particularly interesting since they probably make up building blocks for prebiotic chemistry. Recently we showed that these species were also present in the cold gas in prestellar cores, which represent the very first stages of star formation. These detections question the models which were until now accepted to account for the presence of complex organic molecules in star forming regions. In this article, we shortly review our current understanding of complex organic molecule formation in the early stages of star formation, in hot and cold cores alike and present new results on the formation of their likely precursor radicals.
Operational Issues: What Science in Available?

NASA Technical Reports Server (NTRS)

Rosekind, Mark R.; Neri, David F.

1997-01-01

Flight/duty/rest considerations involve two highly complex factors: the diverse demands of aviation operations and human physiology (especially sleep and circadian rhythms). Several core operational issues related to fatigue have been identified, such as minimum rest requirements, duty length, flight time considerations, crossing multiple time zones, and night flying. Operations also can involve on-call reserve status and callout, delays due to unforeseen circumstances (e.g., weather, mechanical), and on-demand flights. Over 40 years of scientific research is now available to apply to these complex issues of flight/duty/rest requirements. This research involves controlled 'laboratory studies, simulations, and data collected during regular flight operations. When flight/duty/rest requirements are determined they are typically based on a variety of considerations, such as operational demand, safety, economic, etc. Rarely has the available, state-of-the-art science been a consideration along with these other factors when determining flight/duty/rest requirements. While the complexity of the operational demand and human physiology precludes an absolute solution, there is an opportunity to take full advantage of the current scientific data. Incorporating these data in a rational operational manner into flight/duty/rest requirements can improve flight crew performance, alertness, and ultimately, aviation safety.
Drosophila Brahma complex remodels nucleosome organizations in multiple aspects.

PubMed

Shi, Jiejun; Zheng, Meizhu; Ye, Youqiong; Li, Min; Chen, Xiaolong; Hu, Xinjie; Sun, Jin; Zhang, Xiaobai; Jiang, Cizhong

2014-09-01

ATP-dependent chromatin remodeling complexes regulate nucleosome organizations. In Drosophila, gene Brm encodes the core Brahma complex, the ATPase subunit of SWI/SNF class of chromatin remodelers. Its role in modulating the nucleosome landscape in vivo is unclear. In this study, we knocked down Brm in Drosophila third instar larvae to explore the changes in nucleosome profiles and global gene transcription. The results show that Brm knockdown leads to nucleosome occupancy changes throughout the entire genome with a bias in occupancy decrease. In contrast, the knockdown has limited impacts on nucleosome position shift. The knockdown also alters another important physical property of nucleosome positioning, fuzziness. Nucleosome position shift, gain or loss and fuzziness changes are all enriched in promoter regions. Nucleosome arrays around the 5' ends of genes are reorganized in five patterns as a result of Brm knockdown. Intriguingly, the concomitant changes in the genes adjacent to the Brahma-dependent remodeling regions have important roles in development and morphogenesis. Further analyses reveal abundance of AT-rich motifs for transcription factors in the remodeling regions. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Simulation Based Optimization of Complex Monolithic Composite Structures Using Cellular Core Technology

NASA Astrophysics Data System (ADS)

Hickmott, Curtis W.

Cellular core tooling is a new technology which has the capability to manufacture complex integrated monolithic composite structures. This novel tooling method utilizes thermoplastic cellular cores as inner tooling. The semi-rigid nature of the cellular cores makes them convenient for lay-up, and under autoclave temperature and pressure they soften and expand providing uniform compaction on all surfaces including internal features such as ribs and spar tubes. This process has the capability of developing fully optimized aerospace structures by reducing or eliminating assembly using fasteners or bonded joints. The technology is studied in the context of evaluating its capabilities, advantages, and limitations in developing high quality structures. The complex nature of these parts has led to development of a model using the Finite Element Analysis (FEA) software Abaqus and the plug-in COMPRO Common Component Architecture (CCA) provided by Convergent Manufacturing Technologies. This model utilizes a "virtual autoclave" technique to simulate temperature profiles, resin flow paths, and ultimately deformation from residual stress. A model has been developed simulating the temperature profile during curing of composite parts made with the cellular core technology. While modeling of composites has been performed in the past, this project will look to take this existing knowledge and apply it to this new manufacturing method capable of building more complex parts and develop a model designed specifically for building large, complex components with a high degree of accuracy. The model development has been carried out in conjunction with experimental validation. A double box beam structure was chosen for analysis to determine the effects of the technology on internal ribs and joints. Double box beams were manufactured and sectioned into T-joints for characterization. Mechanical behavior of T-joints was performed using the T-joint pull-off test and compared to traditional tooling methods. Components made with the cellular core tooling method showed an improved strength at the joints. It is expected that this knowledge will help optimize the processing of complex, integrated structures and benefit applications in aerospace where lighter, structurally efficient components would be advantageous.
Theoretical Models of Protostellar Binary and Multiple Systems with AMR Simulations

NASA Astrophysics Data System (ADS)

Matsumoto, Tomoaki; Tokuda, Kazuki; Onishi, Toshikazu; Inutsuka, Shu-ichiro; Saigo, Kazuya; Takakuwa, Shigehisa

2017-05-01

We present theoretical models for protostellar binary and multiple systems based on the high-resolution numerical simulation with an adaptive mesh refinement (AMR) code, SFUMATO. The recent ALMA observations have revealed early phases of the binary and multiple star formation with high spatial resolutions. These observations should be compared with theoretical models with high spatial resolutions. We present two theoretical models for (1) a high density molecular cloud core, MC27/L1521F, and (2) a protobinary system, L1551 NE. For the model for MC27, we performed numerical simulations for gravitational collapse of a turbulent cloud core. The cloud core exhibits fragmentation during the collapse, and dynamical interaction between the fragments produces an arc-like structure, which is one of the prominent structures observed by ALMA. For the model for L1551 NE, we performed numerical simulations of gas accretion onto protobinary. The simulations exhibit asymmetry of a circumbinary disk. Such asymmetry has been also observed by ALMA in the circumbinary disk of L1551 NE.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Yang; Glover, Karen; Su, Minfei

BECN1 (Beclin 1), a highly conserved eukaryotic protein, is a key regulator of autophagy, a cellular homeostasis pathway, and also participates in vacuolar protein sorting, endocytic trafficking, and apoptosis. BECN1 is important for embryonic development, the innate immune response, tumor suppression, and protection against neurodegenerative disorders, diabetes, and heart disease. BECN1 mediates autophagy as a core component of the class III phosphatidylinositol 3-kinase complexes. However, the exact mechanism by which it regulates the activity of these complexes, or mediates its other diverse functions is unclear. BECN1 interacts with several diverse protein partners, perhaps serving as a scaffold or interaction hubmore » for autophagy. Based on extensive structural, biophysical and bioinformatics analyses, BECN1 consists of an intrinsically disordered region (IDR), which includes a BH3 homology domain (BH3D); a flexible helical domain (FHD); a coiled-coil domain (CCD); and a β-α-repeated autophagy-specific domain (BARAD). Each of these BECN1 domains mediates multiple diverse interactions that involve concomitant conformational changes. Thus, BECN1 conformational flexibility likely plays a key role in facilitating diverse protein interactions. Further, BECN1 conformation and interactions are also modulated by numerous post-translational modifications. A better structure-based understanding of the interplay between different BECN1 conformational and binding states, and the impact of post-translational modifications will be essential to elucidating the mechanism of its multiple biological roles.« less
Magnetically encoded luminescent composite nanoparticles through layer-by-layer self-assembly.

PubMed

Song, Erqun; Han, Weiye; Xu, Hongyan; Jiang, Yunfei; Cheng, Dan; Song, Yang; Swihart, Mark T

2014-11-03

Sensitive and rapid detection of multiple analytes and the collection of components from complex samples are important in fields ranging from bioassays/chemical assays, clinical diagnosis, to environmental monitoring. A convenient strategy for creating magnetically encoded luminescent CdTe@SiO2 @n Fe3 O4 composite nanoparticles, by using a layer-by-layer self-assembly approach based on electrostatic interactions, is described. Silica-coated CdTe quantum dots (CdTe@SiO2 ) serve as core templates for the deposition of alternating layers of Fe3 O4 magnetic nanoparticles and poly(dimethyldiallyl ammonium chloride), to construct CdTe@SiO2 @n Fe3 O4 (n=1, 2, 3, …︁) composite nanoparticles with a defined number (n) of Fe3 O4 layers. Composite nanoparticles were characterized by zeta-potential analysis, fluorescence spectroscopy, vibrating sample magnetometry, and transmission electron microscopy, which showed that the CdTe@SiO2 @n Fe3 O4 composite nanoparticles exhibited excellent luminescence properties coupled with well-defined magnetic responses. To demonstrate the utility of these magnetically encoded nanoparticles for near-simultaneous detection and separation of multiple components from complex samples, three different fluorescently labeled IgG proteins, as model targets, were identified and collected from a mixture by using the CdTe@SiO2 @n Fe3 O4 nanoparticles. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Cadmium-sulfide crystallites in Cd-. gamma. -glutamyl peptide complexes from Lycopersicon and Daucus

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

Reese, R.N.; Winge, D.R.

1989-04-01

Hydroponically-grown tomato plants (Lycopersicon esculentum P. Mill. cv stone) and suspension-cultured carrot cells (Daucus carota L.) exposed to 100 {mu}M cadmium salts produced metal-{gamma}-glutamyl peptide complexes containing acid labile sulfur. The properties of the complexes resemble the Cd-{gamma}-glutamyl complexes from Schizosaccharomyces pombe and Candida glabrata, known to contain a CdS crystallite core. The crystallite core is stabilized by a coating of peptides of the general structure ({gamma}-Glu-Cys){sub n}-Gly. The Cd-peptide complexes contain predominantly peptides of n{sub 2}, n{sub 3}, n{sub 4} and n{sub 3}desGly. Zn-peptide complexes were also isolated from carrot cultures grown in MS medium supplemented with 2 mMmore » Zn and cysteine. Results of preliminary characterization of these complexes are consistent with the presence of a colloidal particle similar to that of the Cd-complexes.« less
Online track detection in triggerless mode for INO

NASA Astrophysics Data System (ADS)

Jain, A.; Padmini, S.; Joseph, A. N.; Mahesh, P.; Preetha, N.; Behere, A.; Sikder, S. S.; Majumder, G.; Behera, S. P.

2018-03-01

The India based Neutrino Observatory (INO) is a proposed particle physics research project to study the atmospheric neutrinos. INO-Iron Calorimeter (ICAL) will consist of 28,800 detectors having 3.6 million electronic channels expected to activate with 100 Hz single rate, producing data at a rate of 3 GBps. Data collected contains a few real hits generated by muon tracks and the remaining noise-induced spurious hits. Estimated reduction factor after filtering out data of interest from generated data is of the order of 103. This makes trigger generation critical for efficient data collection and storage. Trigger is generated by detecting coincidence across multiple channels satisfying trigger criteria, within a small window of 200 ns in the trigger region. As the probability of neutrino interaction is very low, track detection algorithm has to be efficient and fast enough to process 5 × 106 events-candidates/s without introducing significant dead time, so that not even a single neutrino event is missed out. A hardware based trigger system is presently proposed for on-line track detection considering stringent timing requirements. Though the trigger system can be designed with scalability, a lot of hardware devices and interconnections make it a complex and expensive solution with limited flexibility. A software based track detection approach working on the hit information offers an elegant solution with possibility of varying trigger criteria for selecting various potentially interesting physics events. An event selection approach for an alternative triggerless readout scheme has been developed. The algorithm is mathematically simple, robust and parallelizable. It has been validated by detecting simulated muon events for energies of the range of 1 GeV-10 GeV with 100% efficiency at a processing rate of 60 μs/event on a 16 core machine. The algorithm and result of a proof-of-concept for its faster implementation over multiple cores is presented. The paper also discusses about harnessing the computing capabilities of multi-core computing farm, thereby optimizing number of nodes required for the proposed system.
Emission Characteristics of InGaN/GaN Core-Shell Nanorods Embedded in a 3D Light-Emitting Diode.

PubMed

Jung, Byung Oh; Bae, Si-Young; Lee, Seunga; Kim, Sang Yun; Lee, Jeong Yong; Honda, Yoshio; Amano, Hiroshi

2016-12-01

We report the selective-area growth of a gallium nitride (GaN)-nanorod-based InGaN/GaN multiple-quantum-well (MQW) core-shell structure embedded in a three-dimensional (3D) light-emitting diode (LED) grown by metalorganic chemical vapor deposition (MOCVD) and its optical analysis. High-resolution transmission electron microscopy (HR-TEM) observation revealed the high quality of the GaN nanorods and the position dependence of the structural properties of the InGaN/GaN MQWs on multiple facets. The excitation and temperature dependences of photoluminescence (PL) revealed the m-plane emission behaviors of the InGaN/GaN core-shell nanorods. The electroluminescence (EL) of the InGaN/GaN core-shell-nanorod-embedded 3D LED changed color from green to blue with increasing injection current. This phenomenon was mainly due to the energy gradient and deep localization of the indium in the selectively grown InGaN/GaN core-shell MQWs on the 3D architecture.
Atg6/UVRAG/Vps34-Containing Lipid Kinase Complex Is Required for Receptor Downregulation through Endolysosomal Degradation and Epithelial Polarity during Drosophila Wing Development

PubMed Central

Szatmári, Zsuzsanna; Sass, Miklós

2014-01-01

Atg6 (Beclin 1 in mammals) is a core component of the Vps34 PI3K (III) complex, which promotes multiple vesicle trafficking pathways. Atg6 and Vps34 form two distinct PI3K (III) complexes in yeast and mammalian cells, either with Atg14 or with UVRAG. The functions of these two complexes are not entirely clear, as both Atg14 and UVRAG have been suggested to regulate both endocytosis and autophagy. In this study, we performed a microscopic analysis of UVRAG, Atg14, or Atg6 loss-of-function cells in the developing Drosophila wing. Both autophagy and endocytosis are seriously impaired and defective endolysosomes accumulate upon loss of Atg6. We show that Atg6 is required for the downregulation of Notch and Wingless signaling pathways; thus it is essential for normal wing development. Moreover, the loss of Atg6 impairs cell polarity. Atg14 depletion results in autophagy defects with no effect on endocytosis or cell polarity, while the silencing of UVRAG phenocopies all but the autophagy defect of Atg6 depleted cells. Thus, our results indicate that the UVRAG-containing PI3K (III) complex is required for receptor downregulation through endolysosomal degradation and for the establishment of proper cell polarity in the developing wing, while the Atg14-containing complex is involved in autophagosome formation. PMID:25006588
COMPREHENSIVE ASSESSMENT OF COMPLEX TECHNOLOGIES: INTEGRATING VARIOUS ASPECTS IN HEALTH TECHNOLOGY ASSESSMENT.

PubMed

Lysdahl, Kristin Bakke; Mozygemba, Kati; Burns, Jacob; Brönneke, Jan Benedikt; Chilcott, James B; Ward, Sue; Hofmann, Bjørn

2017-01-01

Despite recent development of health technology assessment (HTA) methods, there are still methodological gaps for the assessment of complex health technologies. The INTEGRATE-HTA guidance for effectiveness, economic, ethical, socio-cultural, and legal aspects, deals with challenges when assessing complex technologies, such as heterogeneous study designs, multiple stakeholder perspectives, and unpredictable outcomes. The objective of this article is to outline this guidance and describe the added value of integrating these assessment aspects. Different methods were used to develop the various parts of the guidance, but all draw on existing, published knowledge and were supported by stakeholder involvement. The guidance was modified after application in a case study and in response to feedback from internal and external reviewers. The guidance consists of five parts, addressing five core aspects of HTA, all presenting stepwise approaches based on the assessment of complexity, context, and stakeholder involvement. The guidance on effectiveness, health economics and ethics aspects focus on helping users choose appropriate, or further develop, existing methods. The recommendations are based on existing methods' applicability for dealing with problems arising with complex interventions. The guidance offers new frameworks to identify socio-cultural and legal issues, along with overviews of relevant methods and sources. The INTEGRATE-HTA guidance outlines a wide range of methods and facilitates appropriate choices among them. The guidance enables understanding of how complexity matters for HTA and brings together assessments from disciplines, such as epidemiology, economics, ethics, law, and social theory. This indicates relevance for a broad range of technologies.
Ethical analysis in HTA of complex health interventions.

PubMed

Lysdahl, Kristin Bakke; Oortwijn, Wija; van der Wilt, Gert Jan; Refolo, Pietro; Sacchini, Dario; Mozygemba, Kati; Gerhardus, Ansgar; Brereton, Louise; Hofmann, Bjørn

2016-03-22

In the field of health technology assessment (HTA), there are several approaches that can be used for ethical analysis. However, there is a scarcity of literature that critically evaluates and compares the strength and weaknesses of these approaches when they are applied in practice. In this paper, we analyse the applicability of some selected approaches for addressing ethical issues in HTA in the field of complex health interventions. Complex health interventions have been the focus of methodological attention in HTA. However, the potential methodological challenges for ethical analysis are as yet unknown. Six of the most frequently described and applied ethical approaches in HTA were critically assessed against a set of five characteristics of complex health interventions: multiple and changing perspectives, indeterminate phenomena, uncertain causality, unpredictable outcomes, and ethical complexity. The assessments are based on literature and the authors' experiences of developing, applying and assessing the approaches. The Interactive, participatory HTA approach is by its nature and flexibility, applicable across most complexity characteristics. Wide Reflective Equilibrium is also flexible and its openness to different perspectives makes it better suited for complex health interventions than more rigid conventional approaches, such as Principlism and Casuistry. Approaches developed for HTA purposes are fairly applicable for complex health interventions, which one could expect because they include various ethical perspectives, such as the HTA Core Model® and the Socratic approach. This study shows how the applicability for addressing ethical issues in HTA of complex health interventions differs between the selected ethical approaches. Knowledge about these differences may be helpful when choosing and applying an approach for ethical analyses in HTA. We believe that the study contributes to increasing awareness and interest of the ethical aspects of complex health interventions in general.

Preparation, characterization and luminescence properties of core-shell ternary terbium composites SiO2(600)@Tb(MABA-Si)•L

NASA Astrophysics Data System (ADS)

Ma, Yang-Yang; Li, Wen-Xian; Zheng, Yu-Shan; Bao, Jin-Rong; Li, Yi-Lian; Feng, Li-Na; Yang, Kui-Suo; Qiao, Yan; Wu, An-Ping

2018-03-01

Two novel core-shell structure ternary terbium composites SiO2(600)@Tb(MABA-Si)·L(L:dipy/phen) nanometre luminescence materials were prepared by ternary terbium complexes Tb(MABA-Si)·L2·(ClO4)3·2H2O shell grafted onto the surface of SiO2 microspheres. And corresponding ternary terbium complexes were synthesized using (CONH(CH2)3Si(OCH2CH3)3)2 (denoted as MABA-Si) as first ligand and L as second ligand coordinated with terbium perchlorate. The as-synthesized products were characterized by means of IR spectra, 1HNMR, element analysis, molar conductivity, SEM and TEM. It was found that the first ligand MABA-Si of terbium ternary complex hydrolysed to generate the Si-OH and the Si-OH condensate with the Si-OH on the surface of SiO2 microspheres; then ligand MABA-Si grafted onto the surface of SiO2 microspheres. The diameter of SiO2 core of SiO2(600)@Tb(MABA-Si)·L was approximately 600 nm. Interestingly, the luminescence properties demonstrate that the two core-shell structure ternary terbium composites SiO2(600)Tb(MABA-Si)·L(dipy/phen) exhibit strong emission intensities, which are 2.49 and 3.35 times higher than that of the corresponding complexes Tb(MABA-Si)·L2·(ClO4)3·2H2O, respectively. Luminescence decay curves show that core-shell structure ternary terbium composites have longer lifetime. Excellent luminescence properties enable the core-shell materials to have potential applications in medicine, industry, luminescent fibres and various biomaterials fields.
Preparation, characterization and luminescence properties of core-shell ternary terbium composites SiO2(600)@Tb(MABA-Si)•L.

PubMed

Ma, Yang-Yang; Li, Wen-Xian; Zheng, Yu-Shan; Bao, Jin-Rong; Li, Yi-Lian; Feng, Li-Na; Yang, Kui-Suo; Qiao, Yan; Wu, An-Ping

2018-03-01

Two novel core-shell structure ternary terbium composites SiO 2(600) @Tb(MABA-Si)·L(L:dipy/phen) nanometre luminescence materials were prepared by ternary terbium complexes Tb(MABA-Si)·L 2 ·(ClO 4 ) 3 ·2H 2 O shell grafted onto the surface of SiO 2 microspheres. And corresponding ternary terbium complexes were synthesized using (CONH(CH 2 ) 3 Si(OCH 2 CH 3 ) 3 ) 2 (denoted as MABA-Si) as first ligand and L as second ligand coordinated with terbium perchlorate. The as-synthesized products were characterized by means of IR spectra, 1 HNMR, element analysis, molar conductivity, SEM and TEM. It was found that the first ligand MABA-Si of terbium ternary complex hydrolysed to generate the Si-OH and the Si-OH condensate with the Si-OH on the surface of SiO 2 microspheres; then ligand MABA-Si grafted onto the surface of SiO 2 microspheres. The diameter of SiO 2 core of SiO 2(600) @Tb(MABA-Si)·L was approximately 600 nm. Interestingly, the luminescence properties demonstrate that the two core-shell structure ternary terbium composites SiO 2(600) Tb(MABA-Si)·L(dipy/phen) exhibit strong emission intensities, which are 2.49 and 3.35 times higher than that of the corresponding complexes Tb(MABA-Si)·L 2 ·(ClO 4 ) 3 ·2H 2 O, respectively. Luminescence decay curves show that core-shell structure ternary terbium composites have longer lifetime. Excellent luminescence properties enable the core-shell materials to have potential applications in medicine, industry, luminescent fibres and various biomaterials fields.
Interfacial charge separation and recombination in InP and quasi-type II InP/CdS core/shell quantum dot-molecular acceptor complexes.

PubMed

Wu, Kaifeng; Song, Nianhui; Liu, Zheng; Zhu, Haiming; Rodríguez-Córdoba, William; Lian, Tianquan

2013-08-15

Recent studies of group II-VI colloidal semiconductor heterostuctures, such as CdSe/CdS core/shell quantum dots (QDs) or dot-in-rod nanorods, show that type II and quasi-type II band alignment can facilitate electron transfer and slow down charge recombination in QD-molecular electron acceptor complexes. To explore the general applicability of this wave function engineering approach for controlling charge transfer properties, we investigate exciton relaxation and dissociation dynamics in InP (a group III-V semiconductor) and InP/CdS core/shell (a heterostructure beween group III-V and II-VI semiconductors) QDs by transient absorption spectroscopy. We show that InP/CdS QDs exhibit a quasi-type II band alignment with the 1S electron delocalized throughout the core and shell and the 1S hole confined in the InP core. In InP-methylviologen (MV(2+)) complexes, excitons in the QD can be dissociated by ultrafast electron transfer to MV(2+) from the 1S electron level (with an average time constant of 11.4 ps) as well as 1P and higher electron levels (with a time constant of 0.39 ps), which is followed by charge recombination to regenerate the complex in its ground state (with an average time constant of 47.1 ns). In comparison, InP/CdS-MV(2+) complexes show similar ultrafast charge separation and 5-fold slower charge recombination rates, consistent with the quasi-type II band alignment in these heterostructures. This result demonstrates that wave function engineering in nanoheterostructures of group III-V and II-VI semiconductors provides a promising approach for optimizing their light harvesting and charge separation for solar energy conversion applications.
Identification of a Functional, CRM-1-Dependent Nuclear Export Signal in Hepatitis C Virus Core Protein

PubMed Central

Cerutti, Andrea; Maillard, Patrick; Minisini, Rosalba; Vidalain, Pierre-Olivier; Roohvand, Farzin; Pecheur, Eve-Isabelle; Pirisi, Mario; Budkowska, Agata

2011-01-01

Hepatitis C virus (HCV) infection is a major cause of chronic liver disease worldwide. HCV core protein is involved in nucleocapsid formation, but it also interacts with multiple cytoplasmic and nuclear molecules and plays a crucial role in the development of liver disease and hepatocarcinogenesis. The core protein is found mostly in the cytoplasm during HCV infection, but also in the nucleus in patients with hepatocarcinoma and in core-transgenic mice. HCV core contains nuclear localization signals (NLS), but no nuclear export signal (NES) has yet been identified. We show here that the aa(109–133) region directs the translocation of core from the nucleus to the cytoplasm by the CRM-1-mediated nuclear export pathway. Mutagenesis of the three hydrophobic residues (L119, I123 and L126) in the identified NES or in the sequence encoding the mature core aa(1–173) significantly enhanced the nuclear localisation of the corresponding proteins in transfected Huh7 cells. Both the NES and the adjacent hydrophobic sequence in domain II of core were required to maintain the core protein or its fragments in the cytoplasmic compartment. Electron microscopy studies of the JFH1 replication model demonstrated that core was translocated into the nucleus a few minutes after the virus entered the cell. The blockade of nucleocytoplasmic export by leptomycin B treatment early in infection led to the detection of core protein in the nucleus by confocal microscopy and coincided with a decrease in virus replication. Our data suggest that the functional NLS and NES direct HCV core protein shuttling between the cytoplasmic and nuclear compartments, with at least some core protein transported to the nucleus. These new properties of HCV core may be essential for virus multiplication and interaction with nuclear molecules, influence cell signaling and the pathogenesis of HCV infection. PMID:22039426
Architecture of the RNA polymerase II-Mediator core initiation complex.

PubMed

Plaschka, C; Larivière, L; Wenzeck, L; Seizl, M; Hemann, M; Tegunov, D; Petrotchenko, E V; Borchers, C H; Baumeister, W; Herzog, F; Villa, E; Cramer, P

2015-02-19

The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.
Protein kinases responsible for the phosphorylation of the nuclear egress core complex of human cytomegalovirus.

PubMed

Sonntag, Eric; Milbradt, Jens; Svrlanska, Adriana; Strojan, Hanife; Häge, Sigrun; Kraut, Alexandra; Hesse, Anne-Marie; Amin, Bushra; Sonnewald, Uwe; Couté, Yohann; Marschall, Manfred

2017-10-01

Nuclear egress of herpesvirus capsids is mediated by a multi-component nuclear egress complex (NEC) assembled by a heterodimer of two essential viral core egress proteins. In the case of human cytomegalovirus (HCMV), this core NEC is defined by the interaction between the membrane-anchored pUL50 and its nuclear cofactor, pUL53. NEC protein phosphorylation is considered to be an important regulatory step, so this study focused on the respective role of viral and cellular protein kinases. Multiply phosphorylated pUL50 varieties were detected by Western blot and Phos-tag analyses as resulting from both viral and cellular kinase activities. In vitro kinase analyses demonstrated that pUL50 is a substrate of both PKCα and CDK1, while pUL53 can also be moderately phosphorylated by CDK1. The use of kinase inhibitors further illustrated the importance of distinct kinases for core NEC phosphorylation. Importantly, mass spectrometry-based proteomic analyses identified five major and nine minor sites of pUL50 phosphorylation. The functional relevance of core NEC phosphorylation was confirmed by various experimental settings, including kinase knock-down/knock-out and confocal imaging, in which it was found that (i) HCMV core NEC proteins are not phosphorylated solely by viral pUL97, but also by cellular kinases; (ii) both PKC and CDK1 phosphorylation are detectable for pUL50; (iii) no impact of PKC phosphorylation on NEC functionality has been identified so far; (iv) nonetheless, CDK1-specific phosphorylation appears to be required for functional core NEC interaction. In summary, our findings provide the first evidence that the HCMV core NEC is phosphorylated by cellular kinases, and that the complex pattern of NEC phosphorylation has functional relevance.
Core to College Evaluation: Exploring the Use of Multiple Measures for Placement into College-Level Courses. Seeking Alternatives or Improvements to the Use of a Single Standardized Test

ERIC Educational Resources Information Center

Bracco, Kathy Reeves; Dadgar, Mina; Austin, Kim; Klarin, Becca; Broek, Marie; Finkelstein, Neal; Mundry, Susan; Bugler, Dan

2014-01-01

"Core to College: Preparing Students for College Readiness and Success" is a three-year initiative. The initiative's mission is to "facilitate greater coordination between K-12 and postsecondary education systems around implementation of the Common Core State Standards (CCSS) and aligned assessments." Its aim is to foster…
Sparkle model for AM1 calculation of lanthanide complexes: improved parameters for europium.

PubMed

Rocha, Gerd B; Freire, Ricardo O; Da Costa, Nivan B; De Sá, Gilberto F; Simas, Alfredo M

2004-04-05

In the present work, we sought to improve our sparkle model for the calculation of lanthanide complexes, SMLC,in various ways: (i) inclusion of the europium atomic mass, (ii) reparametrization of the model within AM1 from a new response function including all distances of the coordination polyhedron for tris(acetylacetonate)(1,10-phenanthroline) europium(III), (iii) implementation of the model in the software package MOPAC93r2, and (iv) inclusion of spherical Gaussian functions in the expression which computes the core-core repulsion energy. The parametrization results indicate that SMLC II is superior to the previous version of the model because Gaussian functions proved essential if one requires a better description of the geometries of the complexes. In order to validate our parametrization, we carried out calculations on 96 europium(III) complexes, selected from Cambridge Structural Database 2003, and compared our predicted ground state geometries with the experimental ones. Our results show that this new parametrization of the SMLC model, with the inclusion of spherical Gaussian functions in the core-core repulsion energy, is better capable of predicting the Eu-ligand distances than the previous version. The unsigned mean error for all interatomic distances Eu-L, in all 96 complexes, which, for the original SMLC is 0.3564 A, is lowered to 0.1993 A when the model was parametrized with the inclusion of two Gaussian functions. Our results also indicate that this model is more applicable to europium complexes with beta-diketone ligands. As such, we conclude that this improved model can be considered a powerful tool for the study of lanthanide complexes and their applications, such as the modeling of light conversion molecular devices.
Multistep Oxidation of Diethynyl Oligophenylamine-Bridged Diruthenium and Diiron Complexes.

PubMed

Zhang, Jing; Guo, Shen-Zhen; Dong, Yu-Bao; Rao, Li; Yin, Jun; Yu, Guang-Ao; Hartl, František; Liu, Sheng Hua

2017-01-17

Homo-dinuclear nonlinear complexes [{M(dppe)Cp*} 2 {μ-(-C≡C) 2 X}] (dppe = 1,2-bis(diphenylphosphino)ethane; Cp* = η 5 -C 5 Me 5 ; X = triphenylamine (TPA), M = Ru (1a) and Fe (1b); X = N,N,N',N'-tetraphenylphenylene-1,4-diamine (TPPD), M = Ru (2a)) were prepared and characterized by 1 H, 13 C, and 31 P NMR spectroscopy and single-crystal X-ray diffraction (1a, 2a). Attempts to prepare the diiron analogue of 2a were not successful. Experimental data obtained from cyclic voltammetry, square wave voltammetry, UV-vis-NIR (NIR = near-infrared) spectro-electrochemistry, and very informative IR spectro-electrochemistry in the C≡C stretching region, combined with density functional theory calculations, afford to make an emphasizing assessment of the close association between the metal-ethynyl termini and the oligophenylamine bridge core as well as their respective involvement in sequential one-electron oxidations of these complexes. The anodic behavior of the homo-bimetallic complexes depends strongly both on the metal center and the length of the oligophenylamine bridge core. The poorly separated first two oxidations of diiron complex 1b are localized on the electronically nearly independent Fe termini. In contrast, diruthenium complex 1a exhibits a significantly delocalized character and a marked electronic communication between the ruthenium centers through the diethynyl-TPA bridge. The ruthenium-ethynyl halves in 2a, separated by the doubly extended and more flexible TPPD bridge core, show a lower degree of electronic coupling, resulting in close-lying first two anodic waves and the NIR electronic absorption of [2a] + with an indistinctive intervalence charge transfer character. Finally, the third anodic waves in the voltammetric responses of the homo-bimetallic complexes are associated with the concurrent exclusive oxidation of the TPA or TPPD bridge cores.
Bcs1p can rescue a large and productive cytochrome bc(1) complex assembly intermediate in the inner membrane of yeast mitochondria.

PubMed

Conte, Laura; Trumpower, Bernard L; Zara, Vincenzo

2011-01-01

The yeast cytochrome bc(1) complex, a component of the mitochondrial respiratory chain, is composed of ten distinct protein subunits. In the assembly of the bc(1) complex, some ancillary proteins, such as the chaperone Bcs1p, are actively involved. The deletion of the nuclear gene encoding this chaperone caused the arrest of the bc(1) assembly and the formation of a functionally inactive bc(1) core structure of about 500-kDa. This immature bc(1) core structure could represent, on the one hand, a true assembly intermediate or, on the other hand, a degradation product and/or an incorrect product of assembly. The experiments here reported show that the gradual expression of Bcs1p in the yeast strain lacking this protein was progressively able to rescue the bc(1) core structure leading to the formation of the functional homodimeric bc(1) complex. Following Bcs1p expression, the mature bc(1) complex was also progressively converted into two supercomplexes with the cytochrome c oxidase complex. The capability of restoring the bc(1) complex and the supercomplexes was also possessed by the mutated yeast R81C Bcsp1. Notably, in the human ortholog BCS1L, the corresponding point mutation (R45C) was instead the cause of a severe bc(1) complex deficiency. Differently from the yeast R81C Bcs1p, two other mutated Bcs1p's (K192P and F401I) were unable to recover the bc(1) core structure in yeast. This study identifies for the first time a productive assembly intermediate of the yeast bc(1) complex and gives new insights into the molecular mechanisms involved in the last steps of bc(1) assembly. Copyright Â© 2010 Elsevier B.V. All rights reserved.
Large scale magmatic event, magnetic anomalies and ore exploration in northern Norway

NASA Astrophysics Data System (ADS)

Pastore, Z.; Church, N. S.; ter Maat, G. W.; Michels, A.; McEnroe, S. A.; Fichler, C.; Larsen, R. B.

2016-12-01

More than 17000 km3of igneous melts intruded into the deep crust at ca. 560-580 Ma and formed the Seiland Igneous Province (SIP), the largest complex of mafic and ultramafic intrusions in northern Fennoscandia. The original emplacement of the SIP is matter of current discussion. The SIP is now located within the Kalak Nappe Complex (KNC), a part of the Middle Allochthon of the North Norwegian Caledonides. The province is believed to represent a cross section of the deep plumbing system of a large igneous province and it is known for its layered intrusions sharing geological features with large ore-forming exploration provinces. In this study we investigate one of the four major ultramafic complexes of the province, the Reinfjord Complex. This was emplaced during three magmatic events in a time span of 4 Ma, and consists in a cylindrically zoned complex with a slightly younger dunite core (Central Series) surrounded by wehrlite and lherzolite dominated series (Upper and Lower Layered Series). Sulphides are present throughout the complex, and an electromagnetic survey identified a Ni-Cu-and a PGE reef deposit within the dunite, 100 meters below the surface. This discovery increased the ore potential of the complex and subsequently 4 deep drill cores were made. High-resolution magnetic helicopter survey was later followed up with ground magnetic and gravity surveys. Extensive sampling of surface rocks and drill cores were made to measure the rock-magnetic and physical properties of the samples and to explore the subsurface structure of the complex. Here, we developed a magnetic model for the Reinfjord complex integrating petrophysical data from both oriented surface samples and from the deep drill cores, with the new ground magnetic, and helicopter data (SkyTEM survey). A 3D model of the geometry of the ultramafic intrusion is presented and a refinement of the geological interpretation of the Reinfjord ultramafic intrusion.
Complex Inner Core of the Earth

NASA Astrophysics Data System (ADS)

Tkalcic, H.; Pachhai, S.; Tanaka, S.; Mattesini, M.; Stephenson, J.

2015-12-01

Recent studies have revealed an increasingly complex structure of the Earth's inner core (IC) in properties such as seismic velocity, attenuation, anisotropy, and differential rotation. In addition, the inner core boundary (ICB) has proven to be more complex than just a dividing boundary between the liquid outer core and the solid IC. On one hand, these advancements have been achieved due to the availability of new data. On the other hand, this is due to better computational facilities, the introduction of new mathematical techniques to this field of study, and a multidisciplinary approach. Through first principles treatment of global seismological differential travel time data, it is possible to acquire a complex mineralogical structure of the IC, consisting of at least three different phases of iron. This has the potential to unify seismological observations and interpretation of IC anisotropy with mineral physics and recent geodynamical scenarios suggesting a predominant degree 1 structure in the IC, although a new complexity emerges from recent attenuation and isotropic velocity studies. A number of studies have recently shown lateral variability of these properties in the uppermost IC, to an increasingly more complex extent than a simple harmonic degree 1. While large earthquakes recorded on individual stations constrain established ray-path corridors through the IC, large arrays provide an unprecedented and overwhelming number of deep Earth-sensitive data. For example, the most complete collection of empirical travel time curves of core phases, from simultaneous recordings of a distant individual earthquake on hundreds of stations is now within reach. Similarly, we can recover hundreds of simultaneous observations of PKiKP and PcP waves from more proximate earthquakes. Traditionally, these have been used to study the sharpness of the ICB by a far more modest number of data points in the time domain. A new study of these observations in the frequency domain reveals the existence of small-scale topography at the ICB and puts invaluable constraints on the process of solidification and melting of the IC in the eastern hemisphere.
Identification of protein W, the elusive sixth subunit of the Rhodopseudomonas palustris reaction center-light harvesting 1 core complex.

PubMed

Jackson, Philip J; Hitchcock, Andrew; Swainsbury, David J K; Qian, Pu; Martin, Elizabeth C; Farmer, David A; Dickman, Mark J; Canniffe, Daniel P; Hunter, C Neil

2018-02-01

The X-ray crystal structure of the Rhodopseudomonas (Rps.) palustris reaction center-light harvesting 1 (RC-LH1) core complex revealed the presence of a sixth protein component, variably referred to in the literature as helix W, subunit W or protein W. The position of this protein prevents closure of the LH1 ring, possibly to allow diffusion of ubiquinone/ubiquinol between the RC and the cytochrome bc 1 complex in analogous fashion to the well-studied PufX protein from Rhodobacter sphaeroides. The identity and function of helix W have remained unknown for over 13years; here we use a combination of biochemistry, mass spectrometry, molecular genetics and electron microscopy to identify this protein as RPA4402 in Rps. palustris CGA009. Protein W shares key conserved sequence features with PufX homologs, and although a deletion mutant was able to grow under photosynthetic conditions with no discernible phenotype, we show that a tagged version of protein W pulls down the RC-LH1 complex. Protein W is not encoded in the photosynthesis gene cluster and our data indicate that only approximately 10% of wild-type Rps. palustris core complexes contain this non-essential subunit; functional and evolutionary consequences of this observation are discussed. The ability to purify uniform RC-LH1 and RC-LH1-protein W preparations will also be beneficial for future structural studies of these bacterial core complexes. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.
Two-stage Uplift of Granite-Gneiss-Migmatite Complex (GGMC) of Çataldaǧ Core Complex (Western Anatolia, Turkey): the role of detachment faults on uplift processes

NASA Astrophysics Data System (ADS)

Kamaci, Omer; Altunkaynak, Safak

2016-04-01

The most recently identified core complex of western Anatolia (Turkey), the Çataldaǧ Core Complex (ÇCC) consists of a granite-gneiss-migmatite complex (GGMC) representing deep crustal rocks of NW Turkey and a shallow level granodioritic body (ÇG: Çataldaǧ granodiorite). The GGMC is Latest Eocene-Early Oligocene and ÇG is Early Miocene in age, and both were exhumed in the footwall of the Çataldaǧ Detachment Fault Zone (ÇDFZ) in the Early Miocene. On the basis of correlation of age data and the closure temperatures of zircon, monazite, muscovite, biotite and K-feldspar, the T-time history of GGMC reveals that GGMC has experienced at least two stages of cooling and uplift, from 33.8 to 30.1 Ma and 21.3 to 20.7 Ma. In stage I, from 33.8 to 30.1 Ma, the cooling rate of GGMC was relatively slow (35°C/my) however cooling rate increase dramatically to ≥500°C/my in stage II between 21.3 and 20.7 Ma. T-time history also indicate that GGMC was elevated to the final location in at least 8-13 My according to the monazite and zircon and mica ages obtained from the same rock. Rapid slab rollback at the Hellenic trench at ca. 23 Ma may have increased extension rates leading to the development of detachment faults (i.e. ÇDFZ), core complexes and associated syn-extensional granitoids in Western Anatolia and the Aegean extensional province.
a Prestellar Core 3MM Line Survey: Molecular Complexity in L183

NASA Astrophysics Data System (ADS)

Lattanzi, Valerio; Bizzocchi, Luca; Caselli, Paola

2017-06-01

Cold dark clouds represent a very unique environment to test our knowledge of the chemical and physical evolution of the structures that ultimately led to life. Starless cores, such as L183, are indeed the first phase of the star formation process and the nursery of chemical complexity. In this work we present the detection of several large astronomical molecules in the prestellar core L183, as a result of a 3mm single-pointing survey performed with the IRAM 30m antenna. The abundances of the observed species will be then compared to those found in similar environments, highlighting correspondences and uniquenesses of the different sources.
The Cohesion Protein SOLO Associates with SMC1 and Is Required for Synapsis, Recombination, Homolog Bias and Cohesion and Pairing of Centromeres in Drosophila Meiosis

PubMed Central

Yan, Rihui; McKee, Bruce D.

2013-01-01

Cohesion between sister chromatids is mediated by cohesin and is essential for proper meiotic segregation of both sister chromatids and homologs. solo encodes a Drosophila meiosis-specific cohesion protein with no apparent sequence homology to cohesins that is required in male meiosis for centromere cohesion, proper orientation of sister centromeres and centromere enrichment of the cohesin subunit SMC1. In this study, we show that solo is involved in multiple aspects of meiosis in female Drosophila. Null mutations in solo caused the following phenotypes: 1) high frequencies of homolog and sister chromatid nondisjunction (NDJ) and sharply reduced frequencies of homolog exchange; 2) reduced transmission of a ring-X chromosome, an indicator of elevated frequencies of sister chromatid exchange (SCE); 3) premature loss of centromere pairing and cohesion during prophase I, as indicated by elevated foci counts of the centromere protein CID; 4) instability of the lateral elements (LE)s and central regions of synaptonemal complexes (SCs), as indicated by fragmented and spotty staining of the chromosome core/LE component SMC1 and the transverse filament protein C(3)G, respectively, at all stages of pachytene. SOLO and SMC1 are both enriched on centromeres throughout prophase I, co-align along the lateral elements of SCs and reciprocally co-immunoprecipitate from ovarian protein extracts. Our studies demonstrate that SOLO is closely associated with meiotic cohesin and required both for enrichment of cohesin on centromeres and stable assembly of cohesin into chromosome cores. These events underlie and are required for stable cohesion of centromeres, synapsis of homologous chromosomes, and a recombination mechanism that suppresses SCE to preferentially generate homolog crossovers (homolog bias). We propose that SOLO is a subunit of a specialized meiotic cohesin complex that mediates both centromeric and axial arm cohesion and promotes homolog bias as a component of chromosome cores. PMID:23874232
The cohesion protein SOLO associates with SMC1 and is required for synapsis, recombination, homolog bias and cohesion and pairing of centromeres in Drosophila Meiosis.

PubMed

Yan, Rihui; McKee, Bruce D

2013-01-01

Cohesion between sister chromatids is mediated by cohesin and is essential for proper meiotic segregation of both sister chromatids and homologs. solo encodes a Drosophila meiosis-specific cohesion protein with no apparent sequence homology to cohesins that is required in male meiosis for centromere cohesion, proper orientation of sister centromeres and centromere enrichment of the cohesin subunit SMC1. In this study, we show that solo is involved in multiple aspects of meiosis in female Drosophila. Null mutations in solo caused the following phenotypes: 1) high frequencies of homolog and sister chromatid nondisjunction (NDJ) and sharply reduced frequencies of homolog exchange; 2) reduced transmission of a ring-X chromosome, an indicator of elevated frequencies of sister chromatid exchange (SCE); 3) premature loss of centromere pairing and cohesion during prophase I, as indicated by elevated foci counts of the centromere protein CID; 4) instability of the lateral elements (LE)s and central regions of synaptonemal complexes (SCs), as indicated by fragmented and spotty staining of the chromosome core/LE component SMC1 and the transverse filament protein C(3)G, respectively, at all stages of pachytene. SOLO and SMC1 are both enriched on centromeres throughout prophase I, co-align along the lateral elements of SCs and reciprocally co-immunoprecipitate from ovarian protein extracts. Our studies demonstrate that SOLO is closely associated with meiotic cohesin and required both for enrichment of cohesin on centromeres and stable assembly of cohesin into chromosome cores. These events underlie and are required for stable cohesion of centromeres, synapsis of homologous chromosomes, and a recombination mechanism that suppresses SCE to preferentially generate homolog crossovers (homolog bias). We propose that SOLO is a subunit of a specialized meiotic cohesin complex that mediates both centromeric and axial arm cohesion and promotes homolog bias as a component of chromosome cores.
Two sides of the same coin: TFIIH complexes in transcription and DNA repair.

PubMed

Zhovmer, Alexander; Oksenych, Valentyn; Coin, Frédéric

2010-04-13

TFIIH is organized into a seven-subunit core associated with a three-subunit Cdk-activating kinase (CAK) module. TFIIH has roles in both transcription initiation and DNA repair. During the last 15 years, several studies have been conducted to identify the composition of the TFIIH complex involved in DNA repair. Recently, a new technique combining chromatin immunoprecipitation and western blotting resolved the hidden nature of the TFIIH complex participating in DNA repair. Following the recruitment of TFIIH to the damaged site, the CAK module is released from the core TFIIH, and the core subsequently associates with DNA repair factors. The release of the CAK is specifically driven by the recruitment of the DNA repair factor XPA and is required to promote the incision/excision of the damaged DNA. Once the DNA lesions have been repaired, the CAK module returns to the core TFIIH on the chromatin, together with the release of the repair factors. These data highlight the dynamic composition of a fundamental cellular factor that adapts its subunit composition to the cell needs.
Interindividual differences in cognitive flexibility: influence of gray matter volume, functional connectivity and trait impulsivity

PubMed Central

Langner, Robert; Cieslik, Edna C.; Rottschy, Claudia; Eickhoff, Simon B.

2016-01-01

Cognitive flexibility, a core aspect of executive functioning, is required for the speeded shifting between different tasks and sets. Using an interindividual differences approach, we examined whether cognitive flexibility, as assessed by the Delis–Kaplan card-sorting test, is associated with gray matter volume (GMV) and functional connectivity (FC) of regions of a core network of multiple cognitive demands as well as with different facets of trait impulsivity. The core multiple-demand network was derived from three large-scale neuroimaging meta-analyses and only included regions that showed consistent associations with sustained attention, working memory as well as inhibitory control. We tested to what extent self-reported impulsivity as well as GMV and resting-state FC in this core network predicted cognitive flexibility independently and incrementally. Our analyses revealed that card-sorting performance correlated positively with GMV of the right anterior insula, FC between bilateral anterior insula and midcingulate cortex/supplementary motor area as well as the impulsivity dimension “Premeditation.” Importantly, GMV, FC and impulsivity together accounted for more variance of card-sorting performance than every parameter alone. Our results therefore indicate that various factors contribute individually to cognitive flexibility, underlining the need to search across multiple modalities when aiming to unveil the mechanisms behind executive functioning. PMID:24878823
Design and characterization of 16-mode PANDA polarization-maintaining few-mode ring-core fiber for spatial division multiplexing

NASA Astrophysics Data System (ADS)

Cao, Yuan; Zhao, Yongli; Yu, Xiaosong; Han, Jiawei; Zhang, Jie

2017-11-01

A PANDA polarization-maintaining few-mode ring-core fiber (PM-FM-RCF) structure with two air holes around the ring core is proposed. The relative mode multiplicity factor (RMMF) is defined to evaluate the spatial efficiency of the designed PM-FM-RCF. The performance analysis and comparison of the proposed PANDA PM-FM-RCFs considering three different types of step-index profiles are detailed. Through modal characteristic analysis and numerical simulation, the PM-FM-RCF with a lower refractive index difference (Δnoi=1.5%) between the ring core and the inner central circle can support up to 16 polarization modes with large RMMF at C-band, which shows the optimum modal properties compared with the PM-FM-RCF with higher Δnoi. All the supported polarization modes are effectively separated from their adjacent polarization modes with effective refractive index differences (Δn) larger than 10-4, which also show relatively small chromatic dispersion (-20 to 25 ps/nm/km), low attenuation (<1.4 dB/km), and small bending radius (˜8 mm) over the C-band. The designed PM-FM-RCF can be compatible with standard single-mode fibers and applied in multiple-input multiple-output-free spatial division multiplexing optical networks for short-reach optical interconnection.

Performance comparison of a fiber optic communication system based on optical OFDM and an optical OFDM-MIMO with Alamouti code by using numerical simulations

NASA Astrophysics Data System (ADS)

Serpa-Imbett, C. M.; Marín-Alfonso, J.; Gómez-Santamaría, C.; Betancur-Agudelo, L.; Amaya-Fernández, F.

2013-12-01

Space division multiplexing in multicore fibers is one of the most promise technologies in order to support transmissions of next-generation peta-to-exaflop-scale supercomputers and mega data centers, owing to advantages in terms of costs and space saving of the new optical fibers with multiple cores. Additionally, multicore fibers allow photonic signal processing in optical communication systems, taking advantage of the mode coupling phenomena. In this work, we numerically have simulated an optical MIMO-OFDM (multiple-input multiple-output orthogonal frequency division multiplexing) by using the coded Alamouti to be transmitted through a twin-core fiber with low coupling. Furthermore, an optical OFDM is transmitted through a core of a singlemode fiber, using pilot-aided channel estimation. We compare the transmission performance in the twin-core fiber and in the singlemode fiber taking into account numerical results of the bit-error rate, considering linear propagation, and Gaussian noise through an optical fiber link. We carry out an optical fiber transmission of OFDM frames using 8 PSK and 16 QAM, with bit rates values of 130 Gb/s and 170 Gb/s, respectively. We obtain a penalty around 4 dB for the 8 PSK transmissions, after 100 km of linear fiber optic propagation for both singlemode and twin core fiber. We obtain a penalty around 6 dB for the 16 QAM transmissions, with linear propagation after 100 km of optical fiber. The transmission in a two-core fiber by using Alamouti coded OFDM-MIMO exhibits a better performance, offering a good alternative in the mitigation of fiber impairments, allowing to expand Alamouti coded in multichannel systems spatially multiplexed in multicore fibers.
Field Performance of Three-Phase Amorphous Metal Core Distribution Transformers at Pearl Harbor, Hawaii

DTIC Science & Technology

1990-08-01

transformer core, such as loose or fractured core laminations . A sound level meter with an A- weighting frequency network was used for the...loaded on flatbed trucks as shown in Figure 2 and permanently installed at various sites throughout the Pearl Harbor complex. Figure 3 shows the final
High temperature superconducting composite conductor and method for manufacturing the same

DOEpatents

Holesinger, Terry G.; Bingert, John F.

2002-01-01

A high temperature superconducting composite conductor is provided including a high temperature superconducting material surrounded by a noble metal layer, the high temperature superconducting composite conductor characterized as having a fill factor of greater than about 40. Additionally, the conductor can be further characterized as containing multiple cores of high temperature superconducting material surrounded by a noble metal layer, said multiple cores characterized as having substantially uniform geometry in the cross-sectional dimensions. Processes of forming such a high temperature superconducting composite conductor are also provided.
Strong scattering of short-period seismic waves by the core-mantle boundary and the P-diffracted wave

NASA Astrophysics Data System (ADS)

Bataille, Klaus; Lund, Fernando

We interpret the long-tail-in-time (up to 3 minutes) decay of short-period Pdiff as being due to multiple scattering within D″, which, for this purpose, is assumed to be an heterogeneous region with a low velocity zone just next to the core-mantle boundary. A simple multiple scattering theory, generalized for a two-dimensional spherical geometry, provides good agreement with observations for values of the scattering and attenuation coefficients (η) of about 10-3 km-1.
The Ultramafic Complex of Reinfjord: from the Magnetic Petrology to the Interpretation of the Magnetic Anomalies

NASA Astrophysics Data System (ADS)

Pastore, Zeudia; McEnroe, Suzanne; Church, Nathan; Fichler, Christine; ter Maat, Geertje W.; Fumagalli, Patrizia; Oda, Hirokuni; Larsen, Rune B.

2017-04-01

A 3D model of the geometry of the Reinfjord complex integrating geological and petrophysical data with high resolution aeromagnetic, ground magnetic and gravity data is developed. The Reinfjord ultramafic complex in northern Norway is one of the major ultramafic complexes of the Neoproterozoic Seiland Igneous Province (SIP). This province, now embedded in the Caledonian orogen, was emplaced deep in the crust (30 km of depth) and is believed to represent a section of the deep plumbing system of a large igneous province. The Reinfjord complex consists of three magmatic series formed during multiple recharging events resulting in the formation of a cylindrically zoned complex with a slightly younger dunite core surrounded by wehrlite and lherzolite units. Gabbros and gneiss form the host rock. The ultramafic complex has several distinct magnetic anomalies which do not match the mapped lithological boundaries, but are correlated with changes in magnetic susceptibilities. In particular, the deviating densities and magnetic susceptibilities at the northern side of the complex are interpreted to be due to serpentinization. Detailed studies of magnetic anomalies and magnetic properties of samples can provide a powerful tool for mapping petrological changes. Samples can have wide range of magnetic properties depending on composition, amount of ferromagnetic minerals, grain sizes and microstructures. Later geological processes such as serpentinization can alter this signal. Therefore a micro-scale study of magnetic anomalies at the thin section scale was carried out to understand better the link between the magnetic petrology and the magnetic anomalies. Serpentinization can significantly enhance the magnetic properties and therefore change the nature of the magnetic anomaly. The detailed gravity and magnetic model here presented shows the subsurface structure of the ultramafic complex refining the geological interpretation of the magnetic sources within it, and the local effects of serpentinization.
Cadmium-sulfide crystallites in Cd-(. gamma. EC) sub n G peptide complexes from tomato. [Lycopersicon esculentum

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

Reese, R.N.; White, C.A.; Winge, D.R.

Hydroponically grown tomato plants (Lycopersicon esculentum P. Mill cv Golden Boy) exposed to 100 micromolar cadmium sulfate produced metal-({gamma}EC){sub n}G peptide complexes containing acid-labile sulfur. The properties of the complexes resemble those of the cadmium-({gamma}EC){sub n}G peptide complexes from Schizo-saccharomyces pombe and Candida glabrata known to contain a cadmium sulfide crystallite core. The crystallite is stabilized by a sheath of peptides of general structure ({gamma}Glu-Cys){sub n}-Gly. The cadmium-peptide complexes of tomato contained predominantly peptides of n{sub 3}, n{sub 4}, and n{sub 5}. Spectroscopic analyses indicated that the tomato cadmium-sulfide-peptide complex contained CdS crystallite core particles smaller than 2.0 nanometers inmore » diameter.« less
Development of recent chronologies and evaluation of temporal variations in Pb fluxes and sources in lake sediment and peat cores in a remote, highly radiogenic environment, Cairngorm Mountains, Scottish Highlands

NASA Astrophysics Data System (ADS)

Farmer, John G.; MacKenzie, Angus B.; Graham, Margaret C.; Macgregor, Kenneth; Kirika, Alexander

2015-05-01

The use of stable Pb isotope analyses in conjunction with recent (210Pb and anthropogenic radionuclide) chronologies has become a well-established method for evaluating historical trends in depositional fluxes and sources of atmospherically deposited Pb using archival records in lake sediment or peat cores. Such studies rely upon (i) simple radioactive disequilibrium between unsupported 210Pb and longer-lived members of the 238U decay series and (ii) well-defined values for the isotopic composition of contaminant Pb and indigenous Pb in the study area. However, areas of high natural radioactivity can present challenging environments for such studies, with potential complications arising from more complex disequilibria in the 238U decay series and the occurrence, at local or regional level, of anomalous, ill-defined stable isotope ratios due to the presence of elevated levels of radiogenic Pb. Results are presented here for a study of a sediment core from a freshwater lake, Loch Einich, in the high natural radioactivity area of the Cairngorm Mountains of Scotland. 238U decay series disequilibria revealed recent diagenetic re-deposition of both U and 226Ra, the latter resulting in a requirement to use a modified calculation to derive a 210Pb chronology for the core. Confidence in the chronology was provided by good agreement with the independent 241Am chronology, but the 137Cs distribution was affected by significant post-depositional mobility in the organic-rich sediment. The systematics of variations in 230Th, 232Th and stable Pb isotope ratio distributions were used to establish the indigenous Pb characteristics of the sediment. The relatively high radiogenic content of the indigenous Pb resulted in complications in source apportionment, in particular during the 20th century, with multiple natural and anthropogenic sources precluding the use of a simple binary mixing model. Consequently, 206Pb/207Pb ratios in Scottish moss samples from an archive collection were used to provide the input term for atmospheric deposition in order to establish historical trends in indigenous and anthropogenic Pb fluxes. A test of the accuracy of the derived Pb fluxes was provided by analysis of a core from a nearby blanket peat deposit, Great Moss. Independent atmospheric and basal inputs gave a complex distribution of 210Pb in the peat, but this did not affect calculation of a 210Pb chronology. Once again, the 210Pb chronology was supported by the 241Am distribution. Temporal trends in anthropogenic Pb deposition derived for the Loch Einich sediment core were in generally good agreement with those for the Great Moss peat core, other peat cores and some other lake sediment cores from northern Scotland, providing confidence in the use of the archive moss data to characterise atmospheric deposition. However, sustained input of Pb to Loch Einich sediment at relatively high levels in the late 20th century, after the regional decline in atmospheric Pb deposition, suggested that catchment-derived Pb is now a significant component of the depositional flux for Loch Einich.
Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach.

PubMed

Perez-Acle, Tomas; Fuenzalida, Ignacio; Martin, Alberto J M; Santibañez, Rodrigo; Avaria, Rodrigo; Bernardin, Alejandro; Bustos, Alvaro M; Garrido, Daniel; Dushoff, Jonathan; Liu, James H

2018-03-29

Computational simulation is a widely employed methodology to study the dynamic behavior of complex systems. Although common approaches are based either on ordinary differential equations or stochastic differential equations, these techniques make several assumptions which, when it comes to biological processes, could often lead to unrealistic models. Among others, model approaches based on differential equations entangle kinetics and causality, failing when complexity increases, separating knowledge from models, and assuming that the average behavior of the population encompasses any individual deviation. To overcome these limitations, simulations based on the Stochastic Simulation Algorithm (SSA) appear as a suitable approach to model complex biological systems. In this work, we review three different models executed in PISKaS: a rule-based framework to produce multiscale stochastic simulations of complex systems. These models span multiple time and spatial scales ranging from gene regulation up to Game Theory. In the first example, we describe a model of the core regulatory network of gene expression in Escherichia coli highlighting the continuous model improvement capacities of PISKaS. The second example describes a hypothetical outbreak of the Ebola virus occurring in a compartmentalized environment resembling cities and highways. Finally, in the last example, we illustrate a stochastic model for the prisoner's dilemma; a common approach from social sciences describing complex interactions involving trust within human populations. As whole, these models demonstrate the capabilities of PISKaS providing fertile scenarios where to explore the dynamics of complex systems. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
Multiple core computer processor with globally-accessible local memories

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

Shalf, John; Donofrio, David; Oliker, Leonid

A multi-core computer processor including a plurality of processor cores interconnected in a Network-on-Chip (NoC) architecture, a plurality of caches, each of the plurality of caches being associated with one and only one of the plurality of processor cores, and a plurality of memories, each of the plurality of memories being associated with a different set of at least one of the plurality of processor cores and each of the plurality of memories being configured to be visible in a global memory address space such that the plurality of memories are visible to two or more of the plurality ofmore » processor cores.« less
Electrogram fractionation in murine HL-1 atrial monolayer model.

PubMed

Umapathy, Karthikeyan; Masse, Stephane; Kolodziejska, Karolina; Veenhuyzen, George D; Chauhan, Vijay S; Husain, Mansoor; Farid, Talha; Downar, Eugene; Sevaptsidis, Elias; Nanthakumar, Kumaraswamy

2008-07-01

Complex fractionated atrial electrograms have been suggested as important targets for catheter ablation of atrial fibrillation. The etiology and the mechanism of these signals have not been completely elucidated because of limitations of interpretation of these signals in relation to simultaneously acquired signals in the neighboring atrial tissue. This study sought to study the origin of electrogram fractionation under the conditions of rotor formation and wave fragmentation, using atrial monolayer preparations. We performed optical mapping of 45 atrial monolayer preparations using a complementary metal oxide semiconductor (CMOS) Brainvision Ultima camera system (SciMedia-Brainvision, Tokyo, Japan). We observed stable rotors in 32 of the 45 recordings. The derived bipolar electrograms did not show complex fractionation at the core of the rotor in any of the 32 recordings. We were also able to show that 2 bipolar electrodes placed adjacent to the core of a stable rotor in a zone where there is no wave break will record electrical activity for the majority of the rotor's cycle length. In 13 of the 45 recordings, wave break or wave collision events were present. Of these, 8 of 13 recordings showed complex fractionation. In 19 of the 27, simulation of meandering rotors also showed complex fractionation. Complex fractionated electrograms can be recorded at sites of migrating rotors and wave break. No fractionation occurs at the core of a stable rotor. Electrograms that span the rotor cycle length and alternate between 2 bipoles that straddle the core can identify site of a stable rotor.
Simulation and performance evaluation of fiber optic sensor for detection of hepatic malignancies in human liver tissues

NASA Astrophysics Data System (ADS)

Sharma, Anuj K.; Gupta, Jyoti; Basu, Rikmantra

2018-01-01

A fiber optic sensor is proposed for the identification of healthy and cancerous liver tissues through determination of their corresponding refractive index values. Existing experimental results describing variation of complex refractive index of liver tissues in near infrared (NIR) spectral region are considered for theoretical calculations. The intensity interrogation method with chalcogenide fiber is considered. The sensor's performance is closely analyzed in terms of its sensitivity at multiple operating wavelengths falling in NIR region. Operating at shorter NIR wavelengths leads to greater sensitivity. The effect of design parameters (sensing region length and fiber core diameter), different launching conditions, and fiber glass materials on sensor's performance is examined. The proposed sensor has the potential to provide high sensitivity of liver tissue detection.
In Situ Trace Element Analysis of an Allende Type B1 CAI: EK-459-5-1

NASA Technical Reports Server (NTRS)

Jeffcoat, C. R.; Kerekgyarto, A.; Lapen, T. J.; Andreasen, R.; Righter, M.; Ross, D. K.

2014-01-01

Variations in refractory major and trace element composition of calcium, aluminum-rich inclusions (CAIs) provide constraints on physical and chemical conditions and processes in the earliest stages of the Solar System. Previous work indicates that CAIs have experienced complex histories involving, in many cases, multiple episodes of condensation, evaporation, and partial melting. We have analyzed major and trace element abundances in two core to rim transects of the melilite mantle as well as interior major phases of a Type B1 CAI (EK-459-5-1) from Allende by electron probe micro-analyzer (EPMA) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to investigate the behavior of key trace elements with a primary focus on the REEs Tm and Yb.
Roles of chromatin insulator proteins in higher-order chromatin organization and transcription regulation

PubMed Central

Vogelmann, Jutta; Valeri, Alessandro; Guillou, Emmanuelle; Cuvier, Olivier; Nollmann, Marcelo

2013-01-01

Eukaryotic chromosomes are condensed into several hierarchical levels of complexity: DNA is wrapped around core histones to form nucleosomes, nucleosomes form a higher-order structure called chromatin, and chromatin is subsequently compartmentalized in part by the combination of multiple specific or unspecific long-range contacts. The conformation of chromatin at these three levels greatly influences DNA metabolism and transcription. One class of chromatin regulatory proteins called insulator factors may organize chromatin both locally, by setting up barriers between heterochromatin and euchromatin, and globally by establishing platforms for long-range interactions. Here, we review recent data revealing a global role of insulator proteins in the regulation of transcription through the formation of clusters of long-range interactions that impact different levels of chromatin organization. PMID:21983085
Sumoylation promotes optimal APC/C Activation and Timely Anaphase.

PubMed

Lee, Christine C; Li, Bing; Yu, Hongtao; Matunis, Michael J

2018-03-08

The Anaphase Promoting Complex/Cyclosome (APC/C) is a ubiquitin E3 ligase that functions as the gatekeeper to mitotic exit. APC/C activity is controlled by an interplay of multiple pathways during mitosis, including the spindle assembly checkpoint (SAC), that are not yet fully understood. Here, we show that sumoylation of the APC4 subunit of the APC/C peaks during mitosis and is critical for timely APC/C activation and anaphase onset. We have also identified a functionally important SUMO interacting motif in the cullin-homology domain of APC2 located near the APC4 sumoylation sites and APC/C catalytic core. Our findings provide evidence of an important regulatory role for SUMO modification and binding in affecting APC/C activation and mitotic exit. © 2018, Lee et al.
Blue straggler formation at core collapse

NASA Astrophysics Data System (ADS)

Banerjee, Sambaran

Among the most striking feature of blue straggler stars (BSS) in globular clusters is the presence of multiple sequences of BSSs in the colour-magnitude diagrams (CMDs) of several globular clusters. It is often envisaged that such a multiple BSS sequence would arise due a recent core collapse of the host cluster, triggering a number of stellar collisions and binary mass transfers simultaneously over a brief episode of time. Here we examine this scenario using direct N-body computations of moderately-massive star clusters (of order 104 {M⊙). As a preliminary attempt, these models are initiated with ≈8-10 Gyr old stellar population and King profiles of high concentrations, being ``tuned'' to undergo core collapse quickly. BSSs are indeed found to form in a ``burst'' at the onset of the core collapse and several of such BS-bursts occur during the post-core-collapse phase. In those models that include a few percent primordial binaries, both collisional and binary BSSs form after the onset of the (near) core-collapse. However, there is as such no clear discrimination between the two types of BSSs in the corresponding computed CMDs. We note that this may be due to the less number of BSSs formed in these less massive models than that in actual globular clusters.
Description of core samples returned by Apollo 12

NASA Technical Reports Server (NTRS)

Lindsay, J. F.; Fryxell, R.

1971-01-01

Three core samples were collected by the Apollo 12 astronauts. Two are single cores, one of which (sample 12026) was collected close to the lunar module during the first extravehicular activity period and is 19.3 centimeters long. The second core (sample 12027) was collected at Sharp Crater during the second extravehicular activity period and is 17.4 centimeters long. The third sample is a double core (samples 12025 and 12028), which was collected near Halo Crater during the second extravehicular activity period. Unlike the other cores, the double-drive-tube core sample has complex layering with at least 10 clearly defined stratigraphic units. This core sample is approximately 41 centimeters long.
EVOLUTION OF MAGNETIC FIELD AND ENERGY IN A MAJOR ERUPTIVE ACTIVE REGION BASED ON SDO/HMI OBSERVATION

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

Sun Xudong; Hoeksema, J. Todd; Liu, Yang

We report the evolution of the magnetic field and its energy in NOAA active region 11158 over five days based on a vector magnetogram series from the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamic Observatory (SDO). Fast flux emergence and strong shearing motion led to a quadrupolar sunspot complex that produced several major eruptions, including the first X-class flare of Solar Cycle 24. Extrapolated nonlinear force-free coronal fields show substantial electric current and free energy increase during early flux emergence near a low-lying sigmoidal filament with a sheared kilogauss field in the filament channel. The computed magneticmore » free energy reaches a maximum of {approx}2.6 Multiplication-Sign 10{sup 32} erg, about 50% of which is stored below 6 Mm. It decreases by {approx}0.3 Multiplication-Sign 10{sup 32} erg within 1 hr of the X-class flare, which is likely an underestimation of the actual energy loss. During the flare, the photospheric field changed rapidly: the horizontal field was enhanced by 28% in the core region, becoming more inclined and more parallel to the polarity inversion line. Such change is consistent with the conjectured coronal field 'implosion' and is supported by the coronal loop retraction observed by the Atmospheric Imaging Assembly (AIA). The extrapolated field becomes more 'compact' after the flare, with shorter loops in the core region, probably because of reconnection. The coronal field becomes slightly more sheared in the lowest layer, relaxes faster with height, and is overall less energetic.« less
Coupling of radiofrequency with magnetic nanoparticles treatment as an alternative physical antibacterial strategy against multiple drug resistant bacteria

NASA Astrophysics Data System (ADS)

Chaurasia, Akhilesh K.; Thorat, Nanasaheb D.; Tandon, Anshula; Kim, Jin-Hahn; Park, Sung Ha; Kim, Kyeong Kyu

2016-09-01

Antibiotic resistant bacteria not only affect human health and but also threatens the safety in hospitals and among communities. However, the emergence of drug resistant bacteria is inevitable due to evolutionary selection as a consequence of indiscriminate antibiotic usage. Therefore, it is necessary to develop a novel strategy by which pathogenic bacteria can be eliminated without triggering resistance. We propose a novel magnetic nanoparticle-based physical treatment against pathogenic bacteria, which blocks biofilm formation and kills bacteria. In this approach, multiple drug resistant Staphylococcus aureus USA300 and uropathogenic Escherichia coli CFT073 are trapped to the positively charged magnetic core-shell nanoparticles (MCSNPs) by electrostatic interaction. All the trapped bacteria can be completely killed within 30 min owing to the loss of membrane potential and dysfunction of membrane-associated complexes when exposed to the radiofrequency current. These results indicate that MCSNP-based physical treatment can be an alternative antibacterial strategy without leading to antibiotic resistance, and can be used for many purposes including environmental and therapeutic applications.
A Multi-organisational Approach to Service Delivery

NASA Astrophysics Data System (ADS)

Purchase, Valerie; Mills, John; Parry, Glenn

Who is involved in delivering a service? There has been growing recognition in a wide variety of contexts that service is increasingly being delivered by multi-rather than single-organisational entities. Such recognition is evident not only in our experience but in a number of areas of literature including strategy development, core competence analysis, operations and supply chain management, and is reflected in and further facilitated by ICT developments. Customers have always been involved in some degree in the process of value delivery and such involvement is increasing to include complex co-creation of value. Such interactions are challenging when they involve individual customers, however, this becomes ever more challenging when the 'customer' is another organisation or when there are multiple 'customers'. Within this chapter we will consider some of the key drivers for a multi-organisational approach to service delivery; examine the ways in which the parties involved in service co-creation have expanded to include multiple service providers and customers; and finally, identify some of the challenges created by a multi-organisational approach to service delivery.
A heuristic approach using multiple criteria for environmentally benign 3PLs selection

NASA Astrophysics Data System (ADS)

Kongar, Elif

2005-11-01

Maintaining competitiveness in an environment where price and quality differences between competing products are disappearing depends on the company's ability to reduce costs and supply time. Timely responses to rapidly changing market conditions require an efficient Supply Chain Management (SCM). Outsourcing logistics to third-party logistics service providers (3PLs) is one commonly used way of increasing the efficiency of logistics operations, while creating a more "core competency focused" business environment. However, this alone may not be sufficient. Due to recent environmental regulations and growing public awareness regarding environmental issues, 3PLs need to be not only efficient but also environmentally benign to maintain companies' competitiveness. Even though an efficient and environmentally benign combination of 3PLs can theoretically be obtained using exhaustive search algorithms, heuristics approaches to the selection process may be superior in terms of the computational complexity. In this paper, a hybrid approach that combines a multiple criteria Genetic Algorithm (GA) with Linear Physical Weighting Algorithm (LPPW) to be used in efficient and environmentally benign 3PLs is proposed. A numerical example is also provided to illustrate the method and the analyses.

Self and identity in women with symptoms of borderline personality: A qualitative study.

PubMed

Agnew, Gillian; Shannon, Ciarán; Ryan, Tina; Storey, Lesley; McDonnell, Catherine

2016-01-01

Identity disturbance has been suggested to be a core feature of borderline personality disorder (BPD). However, there is little known about the identity of individuals with symptoms of BPD from the participant's perspective. This study availed of in-depth lightly structured life story interviews with five female participants. Thematic analysis was utilized to derive three themes of identity: connection, distance between us, and hurt and healing. Results provided support for multiple and flexible conceptualizations of identity in comparison to the idea of a unitary self/identity. Results also suggested that participants were able to establish differing connections to others ranging from disconnection to intimacy and care. Participants reported that their identities were impacted upon by historical and current family/relationship dysfunction, but life stories also illustrated the positive impact of healing relationship experiences. Findings provide support for psychological theories that consider a multiple and relational self/identity and the empowerment of healthy aspects of the self in BPD recovery. Studies that assess the association between insight and change may further our knowledge into this complex population.
Self and identity in women with symptoms of borderline personality: A qualitative study

PubMed Central

Agnew, Gillian; Shannon, Ciarán; Ryan, Tina; Storey, Lesley

2016-01-01

Identity disturbance has been suggested to be a core feature of borderline personality disorder (BPD). However, there is little known about the identity of individuals with symptoms of BPD from the participant's perspective. This study availed of in-depth lightly structured life story interviews with five female participants. Thematic analysis was utilized to derive three themes of identity: connection, distance between us, and hurt and healing. Results provided support for multiple and flexible conceptualizations of identity in comparison to the idea of a unitary self/identity. Results also suggested that participants were able to establish differing connections to others ranging from disconnection to intimacy and care. Participants reported that their identities were impacted upon by historical and current family/relationship dysfunction, but life stories also illustrated the positive impact of healing relationship experiences. Findings provide support for psychological theories that consider a multiple and relational self/identity and the empowerment of healthy aspects of the self in BPD recovery. Studies that assess the association between insight and change may further our knowledge into this complex population. PMID:27015876
Coupling of radiofrequency with magnetic nanoparticles treatment as an alternative physical antibacterial strategy against multiple drug resistant bacteria

PubMed Central

Chaurasia, Akhilesh K.; Thorat, Nanasaheb D.; Tandon, Anshula; Kim, Jin-Hahn; Park, Sung Ha; Kim, Kyeong Kyu

2016-01-01

Antibiotic resistant bacteria not only affect human health and but also threatens the safety in hospitals and among communities. However, the emergence of drug resistant bacteria is inevitable due to evolutionary selection as a consequence of indiscriminate antibiotic usage. Therefore, it is necessary to develop a novel strategy by which pathogenic bacteria can be eliminated without triggering resistance. We propose a novel magnetic nanoparticle-based physical treatment against pathogenic bacteria, which blocks biofilm formation and kills bacteria. In this approach, multiple drug resistant Staphylococcus aureus USA300 and uropathogenic Escherichia coli CFT073 are trapped to the positively charged magnetic core-shell nanoparticles (MCSNPs) by electrostatic interaction. All the trapped bacteria can be completely killed within 30 min owing to the loss of membrane potential and dysfunction of membrane-associated complexes when exposed to the radiofrequency current. These results indicate that MCSNP-based physical treatment can be an alternative antibacterial strategy without leading to antibiotic resistance, and can be used for many purposes including environmental and therapeutic applications. PMID:27670157
Building a functional multiple intelligences theory to advance educational neuroscience.

PubMed

Cerruti, Carlo

2013-01-01

A key goal of educational neuroscience is to conduct constrained experimental research that is theory-driven and yet also clearly related to educators' complex set of questions and concerns. However, the fields of education, cognitive psychology, and neuroscience use different levels of description to characterize human ability. An important advance in research in educational neuroscience would be the identification of a cognitive and neurocognitive framework at a level of description relatively intuitive to educators. I argue that the theory of multiple intelligences (MI; Gardner, 1983), a conception of the mind that motivated a past generation of teachers, may provide such an opportunity. I criticize MI for doing little to clarify for teachers a core misunderstanding, specifically that MI was only an anatomical map of the mind but not a functional theory that detailed how the mind actually processes information. In an attempt to build a "functional MI" theory, I integrate into MI basic principles of cognitive and neural functioning, namely interregional neural facilitation and inhibition. In so doing I hope to forge a path toward constrained experimental research that bears upon teachers' concerns about teaching and learning.
Single-molecule fluorescence measurements reveal the reaction mechanisms of the core RISC, composed of human Argonaute 2 and a guide RNA.

PubMed

Jo, Myung Hyun; Song, Ji-Joon; Hohng, Sungchul

2015-12-01

In eukaryotes, small RNAs play important roles in both gene regulation and resistance to viral infection. Argonaute proteins have been identified as a key component of the effector complexes of various RNA-silencing pathways, but the mechanistic roles of Argonaute proteins in these pathways are not clearly understood. To address this question, we performed single-molecule fluorescence experiments using an RNA-induced silencing complex (core-RISC) composed of a small RNA and human Argonaute 2. We found that target binding of core-RISC starts at the seed region of the guide RNA. After target binding, four distinct reactions followed: target cleavage, transient binding, stable binding, and Argonaute unloading. Target cleavage required extensive sequence complementarity and accelerated core-RISC dissociation for recycling. In contrast, the stable binding of core-RISC to target RNAs required seed-match only, suggesting a potential explanation for the seed-match rule of microRNA (miRNA) target selection.
High numerical aperture multimode fibers for prime focus use

NASA Astrophysics Data System (ADS)

Zhang, Kaiyuan; Zheng, Jessica R.; Saunders, Will

2016-07-01

Modern telescopes typically have prime focus speeds too fast for direct use with standard numerical aperture (NA=0.22+/-0.02) silica-cored fibers. Specifically, the current design for the proposed Maunakea Spectroscopic Explorer (MSE) telescope is f/2, requiring fibers with NA>0.25. Micro foreoptics can be used to slow the beam, as used on the prime focus spectrograph (PFS) on Subaru, but this adds cost and complexity, and increases losses. An attractive alternative is offered by high NA pure silica-cored fibers, which can be used directly at f/2, and which are now available from multiple vendors. We present throughput and focal ratio degradation measurements on two samples of these high NA fibers. It is found that the measured attenuation losses are comparable with the best available standard NA fibers. The fibers were also tested for focal ratio degradation, and the fiber from CeramOptec was found to have acceptable FRD, representng additional collimator losses 1%. The near field performance of the high NA fiber is also investigated and these high NA fibers exhibit very good scrambling performance; we saw no evidence for significant output near-field variations for varying input beam angles or position in a 50m fiber.
Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity

NASA Astrophysics Data System (ADS)

Harper, Bryan; Thomas, Dennis; Chikkagoudar, Satish; Baker, Nathan; Tang, Kaizhi; Heredia-Langner, Alejandro; Lins, Roberto; Harper, Stacey

2015-06-01

The integration of rapid assays, large datasets, informatics, and modeling can overcome current barriers in understanding nanomaterial structure-toxicity relationships by providing a weight-of-the-evidence mechanism to generate hazard rankings for nanomaterials. Here, we present the use of a rapid, low-cost assay to perform screening-level toxicity evaluations of nanomaterials in vivo. Calculated EZ Metric scores, a combined measure of morbidity and mortality in developing embryonic zebrafish, were established at realistic exposure levels and used to develop a hazard ranking of diverse nanomaterial toxicity. Hazard ranking and clustering analysis of 68 diverse nanomaterials revealed distinct patterns of toxicity related to both the core composition and outermost surface chemistry of nanomaterials. The resulting clusters guided the development of a surface chemistry-based model of gold nanoparticle toxicity. Our findings suggest that risk assessments based on the size and core composition of nanomaterials alone may be wholly inappropriate, especially when considering complex engineered nanomaterials. Research should continue to focus on methodologies for determining nanomaterial hazard based on multiple sub-lethal responses following realistic, low-dose exposures, thus increasing the availability of quantitative measures of nanomaterial hazard to support the development of nanoparticle structure-activity relationships.
Light-Harvesting Antenna System from the Phototrophic Bacterium Roseiflexus castenholzii

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

Collins, Aaron M.; Qian, Pu; Tang, Qun

Photosynthetic organisms have evolved diverse light-harvesting complexes to harness light of various qualities and intensities. Photosynthetic bacteria can have (bacterio)chlorophyll Q y antenna absorption bands ranging from ~650 to ~1100 nm. This broad range of wavelengths has allowed many organisms to thrive in unique light environments. Roseiflexus castenholzii is a niche-adapted, filamentous anoxygenic phototroph (FAP) that lacks chlorosomes, the dominant antenna found in most green bacteria, and here we describe the purification of a full complement of photosynthetic complexes: the light-harvesting (LH) antenna, reaction center (RC), and core complex (RC-LH). By high-performance liquid chromatography separation of bacteriochlorophyll and bacteriopheophytin pigmentsmore » extracted from the core complex and the RC, the number of subunits that comprise the antenna was determined to be 15 ± 1. Resonance Raman spectroscopy of the carbonyl stretching region displayed modes indicating that 3C-acetyl groups of BChl a are all involved in molecular interactions probably similar to those found in LH1 complexes from purple photosynthetic bacteria. Finally, two-dimensional projections of negatively stained core complexes and the LH antenna revealed a closed, slightly elliptical LH ring with an average diameter of 130 ± 10 Å surrounding a single RC that lacks an H-subunit but is associated with a tetraheme c-type cytochrome.« less
A neutral branched platinum-acetylide complex possessing a tetraphenylethylene core: preparation of a luminescent organometallic gelator and its unexpected spectroscopic behaviour during sol-to-gel transition.

PubMed

Ren, Yuan-Yuan; Wu, Nai-Wei; Huang, Junhai; Xu, Zheng; Sun, Dan-Dan; Wang, Cui-Hong; Xu, Lin

2015-10-21

A neutral branched platinum-acetylide complex TPA possessing a tetraphenylethylene core was successfully prepared, which was found to form luminescent organometallic gels in ethyl acetate. Stimulated by temperature or F(-), the reversible gel-sol transition was realized. More interestingly, TPA exhibited an unexpected blue shift of the emission during the sol-to-gel transition.
Oscillatory erosion and transport flume with superimposed unidirectional flow

DOEpatents

Jepsen, Richard A.; Roberts, Jesse D.

2004-01-20

A method and apparatus for measuring erosion rates of sediments and at high shear stresses due to complex wave action with, or without, a superimposed unidirectional current. Water is forced in a channel past an exposed sediment core sample, which erodes sediments when a critical shear stress has been exceeded. The height of the core sample is adjusted during testing so that the sediment surface remains level with the bottom of the channel as the sediments erode. Complex wave action is simulated by driving tandom piston/cylinder mechanisms with computer-controlled stepper motors. Unidirectional flow, forced by a head difference between two open tanks attached to each end of the channel, may be superimposed on to the complex wave action. Sediment traps may be used to collect bedload sediments. The total erosion rate equals the change in height of the sediment core sample divided by a fixed period of time.
Simulating Valence-to-Core X-ray Emission Spectroscopy of Transition Metal Complexes with Time-Dependent Density Functional Theory.

PubMed

Zhang, Yu; Mukamel, Shaul; Khalil, Munira; Govind, Niranjan

2015-12-08

Valence-to-core (VtC) X-ray emission spectroscopy (XES) has emerged as a powerful technique for the structural characterization of complex organometallic compounds in realistic environments. Since the spectrum represents electronic transitions from the ligand molecular orbitals to the core holes of the metal centers, the approach is more chemically sensitive to the metal-ligand bonding character compared with conventional X-ray absorption techniques. In this paper we study how linear-response time-dependent density functional theory (LR-TDDFT) can be harnessed to simulate K-edge VtC X-ray emission spectra reliably. LR-TDDFT allows one to go beyond the single-particle picture that has been extensively used to simulate VtC-XES. We consider seven low- and high-spin model complexes involving chromium, manganese, and iron transition metal centers. Our results are in good agreement with experiment.
A current review of core decompression in the treatment of osteonecrosis of the femoral head.

PubMed

Pierce, Todd P; Jauregui, Julio J; Elmallah, Randa K; Lavernia, Carlos J; Mont, Michael A; Nace, James

2015-09-01

The review describes the following: (1) how traditional core decompression is performed, (2) adjunctive treatments, (3) multiple percutaneous drilling technique, and (4) the overall outcomes of these procedures. Core decompression has optimal outcomes when used in the earliest, precollapse disease stages. More recent studies have reported excellent outcomes with percutaneous drilling. Furthermore, adjunct treatment methods combining core decompression with growth factors, bone morphogenic proteins, stem cells, and bone grafting have demonstrated positive results; however, larger randomized trial is needed to evaluate their overall efficacy.
WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexes.

PubMed

Jia, Da; Gomez, Timothy S; Metlagel, Zoltan; Umetani, Junko; Otwinowski, Zbyszek; Rosen, Michael K; Billadeau, Daniel D

2010-06-08

We recently showed that the Wiskott-Aldrich syndrome protein (WASP) family member, WASH, localizes to endosomal subdomains and regulates endocytic vesicle scission in an Arp2/3-dependent manner. Mechanisms regulating WASH activity are unknown. Here we show that WASH functions in cells within a 500 kDa core complex containing Strumpellin, FAM21, KIAA1033 (SWIP), and CCDC53. Although recombinant WASH is constitutively active toward the Arp2/3 complex, the reconstituted core assembly is inhibited, suggesting that it functions in cells to regulate actin dynamics through WASH. FAM21 interacts directly with CAPZ and inhibits its actin-capping activity. Four of the five core components show distant (approximately 15% amino acid sequence identify) but significant structural homology to components of a complex that negatively regulates the WASP family member, WAVE. Moreover, biochemical and electron microscopic analyses show that the WASH and WAVE complexes are structurally similar. Thus, these two distantly related WASP family members are controlled by analogous structurally related mechanisms. Strumpellin is mutated in the human disease hereditary spastic paraplegia, and its link to WASH suggests that misregulation of actin dynamics on endosomes may play a role in this disorder.
A STRIPAK complex mediates axonal transport of autophagosomes and dense core vesicles through PP2A regulation

PubMed Central

Neufeld, Thomas P.

2017-01-01

Autophagy plays an essential role in the cellular homeostasis of neurons, facilitating the clearance of cellular debris. This clearance process is orchestrated through the assembly, transport, and fusion of autophagosomes with lysosomes for degradation. The motor protein dynein drives autophagosome motility from distal sites of assembly to sites of lysosomal fusion. In this study, we identify the scaffold protein CKA (connector of kinase to AP-1) as essential for autophagosome transport in neurons. Together with other core components of the striatin-interacting phosphatase and kinase (STRIPAK) complex, we show that CKA associates with dynein and directly binds Atg8a, an autophagosomal protein. CKA is a regulatory subunit of PP2A, a component of the STRIPAK complex. We propose that the STRIPAK complex modulates dynein activity. Consistent with this hypothesis, we provide evidence that CKA facilitates axonal transport of dense core vesicles and autophagosomes in a PP2A-dependent fashion. In addition, CKA-deficient flies exhibit PP2A-dependent motor coordination defects. CKA function within the STRIPAK complex is crucial to prevent transport defects that may contribute to neurodegeneration. PMID:28100687
A miniature electronic nose system based on an MWNT-polymer microsensor array and a low-power signal-processing chip.

PubMed

Chiu, Shih-Wen; Wu, Hsiang-Chiu; Chou, Ting-I; Chen, Hsin; Tang, Kea-Tiong

2014-06-01

This article introduces a power-efficient, miniature electronic nose (e-nose) system. The e-nose system primarily comprises two self-developed chips, a multiple-walled carbon nanotube (MWNT)-polymer based microsensor array, and a low-power signal-processing chip. The microsensor array was fabricated on a silicon wafer by using standard photolithography technology. The microsensor array comprised eight interdigitated electrodes surrounded by SU-8 "walls," which restrained the material-solvent liquid in a defined area of 650 × 760 μm(2). To achieve a reliable sensor-manufacturing process, we used a two-layer deposition method, coating the MWNTs and polymer film as the first and second layers, respectively. The low-power signal-processing chip included array data acquisition circuits and a signal-processing core. The MWNT-polymer microsensor array can directly connect with array data acquisition circuits, which comprise sensor interface circuitry and an analog-to-digital converter; the signal-processing core consists of memory and a microprocessor. The core executes the program, classifying the odor data received from the array data acquisition circuits. The low-power signal-processing chip was designed and fabricated using the Taiwan Semiconductor Manufacturing Company 0.18-μm 1P6M standard complementary metal oxide semiconductor process. The chip consumes only 1.05 mW of power at supply voltages of 1 and 1.8 V for the array data acquisition circuits and the signal-processing core, respectively. The miniature e-nose system, which used a microsensor array, a low-power signal-processing chip, and an embedded k-nearest-neighbor-based pattern recognition algorithm, was developed as a prototype that successfully recognized the complex odors of tincture, sorghum wine, sake, whisky, and vodka.
Nuclear reactor

DOEpatents

Wade, Elman E.

1979-01-01

A nuclear reactor including two rotatable plugs and a positive top core holddown structure. The top core holddown structure is divided into two parts: a small core cover, and a large core cover. The small core cover, and the upper internals associated therewith, are attached to the small rotating plug, and the large core cover, with its associated upper internals, is attached to the large rotating plug. By so splitting the core holddown structures, under-the-plug refueling is accomplished without the necessity of enlarging the reactor pressure vessel to provide a storage space for the core holddown structure during refueling. Additionally, the small and large rotating plugs, and their associated core covers, are arranged such that the separation of the two core covers to permit rotation is accomplished without the installation of complex lifting mechanisms.
Vps15 is required for stress induced and developmentally triggered autophagy and salivary gland protein secretion in Drosophila.

PubMed

Anding, A L; Baehrecke, E H

2015-03-01

Autophagy is a catabolic process used to deliver cellular material to the lysosome for degradation. The core Vps34/class III phosphatidylinositol 3-kinase (PI3K) complex, consisting of Atg6, Vps15, and Vps34, is highly conserved throughout evolution, critical for recruiting autophagy-related proteins to the preautophagosomal structure and for other vesicular trafficking processes, including vacuolar protein sorting. Atg6 and Vps34 have been well characterized, but the Vps15 kinase remains poorly characterized with most studies focusing on nutrient deprivation-induced autophagy. Here, we investigate the function of Vps15 in different cellular contexts and find that it is necessary for both stress-induced and developmentally programmed autophagy in various tissues in Drosophila melanogaster. Vps15 is required for autophagy that is induced by multiple forms of stress, including nutrient deprivation, hypoxia, and oxidative stress. Furthermore, autophagy that is triggered by physiological stimuli during development in the fat body, intestine, and salivary gland also require the function of Vps15. In addition, we show that Vps15 is necessary for efficient salivary gland protein secretion. These data illustrate the broad importance of Vps15 in multiple forms of autophagy in different animal cells, and also highlight the pleiotropic function of this kinase in multiple vesicle-trafficking pathways.
Exploiting the anti-HIV 6-desfluoroquinolones to design multiple ligands.

PubMed

Sancineto, Luca; Iraci, Nunzio; Barreca, Maria Letizia; Massari, Serena; Manfroni, Giuseppe; Corazza, Gianmarco; Cecchetti, Violetta; Marcello, Alessandro; Daelemans, Dirk; Pannecouque, Christophe; Tabarrini, Oriana

2014-09-01

It is getting clearer that many drugs effective in different therapeutic areas act on multiple rather than single targets. The application of polypharmacology concepts might have numerous advantages especially for disease such as HIV/AIDS, where the rapid emergence of resistance requires a complex combination of more than one drug. In this paper, we have designed three hybrid molecules combining WM5, a quinolone derivative we previously identified as HIV Tat-mediated transcription (TMT) inhibitor, with the tricyclic core of nevirapine and BILR 355BS (BILR) non-nucleoside reverse transcriptase inhibitors (NNRTIs) to investigate whether it could be possible to obtain molecules acting on both transcription steps of the HIV replicative cycle. One among the three designed multiple ligands, reached this goal. Indeed, compound 1 inhibited both TMT and reverse transcriptase (RT) activity. Unexpectedly, while the anti-TMT activity exerted by compound 1 resulted into a selective inhibition of HIV-1 reactivation from latently infected OM10.1 cells, the anti-RT properties shown by all of the synthesized compounds did not translate into an anti-HIV activity in acutely infected cells. Thus, we have herein produced the proof of concept that the design of dual TMT-RT inhibitors is indeed possible, but optimization efforts are needed to obtain more potent derivatives. Copyright © 2014 Elsevier Ltd. All rights reserved.
Automated statistical matching of multiple tephra records exemplified using five long maar sequences younger than 75 ka, Auckland, New Zealand

NASA Astrophysics Data System (ADS)

Green, Rebecca M.; Bebbington, Mark S.; Cronin, Shane J.; Jones, Geoff

2014-09-01

Detailed tephrochronologies are built to underpin probabilistic volcanic hazard forecasting, and to understand the dynamics and history of diverse geomorphic, climatic, soil-forming and environmental processes. Complicating factors include highly variable tephra distribution over time; difficulty in correlating tephras from site to site based on physical and chemical properties; and uncertain age determinations. Multiple sites permit construction of more accurate composite tephra records, but correctly merging individual site records by recognizing common events and site-specific gaps is complex. We present an automated procedure for matching tephra sequences between multiple deposition sites using stochastic local optimization techniques. If individual tephra age determinations are not significantly different between sites, they are matched and a more precise age is assigned. Known stratigraphy and mineralogical or geochemical compositions are used to constrain tephra matches. We apply this method to match tephra records from five long sediment cores (≤ 75 cal ka BP) in Auckland, New Zealand. Sediments at these sites preserve basaltic tephras from local eruptions of the Auckland Volcanic Field as well as distal rhyolitic and andesitic tephras from Okataina, Taupo, Egmont, Tongariro, and Tuhua (Mayor Island) volcanic centers. The new correlated record compiled is statistically more likely than previously published arrangements from this area.
The synaptinemal complex in Rhoeo spathacea.

PubMed

McQuade, H A; Wells, B

1975-03-01

The synaptinemal complex in meiocytes of Rhoeo spathacea is described. Unpaired zygotene chromosomes do not exhibit well defined axial cores under the ordinary fixations of electron microscopy and appear diffuse. However, the axial core is defined by ethanolic phosphotungstic acid (PTA) although it does not respond to uranyl-EDTA-lead. Thus the core appears to contain histone but not RNA and presents a condition which is modified later in pairing when lateral elements of the synaptinemal complex respond positively to both tests. The total number of attachments of synaptinemal complexes to the nuclear envelope was determined in several nuclei from serial sections. Eleven of the twelve possible attachments were found in one nucleus. It thus seems certain that all must be so attached. In the same manner all chromosomes can be seen to have an attachment to a chromocentre. Chromocentres are often very large and compound in that two kinds of heterochromatin can be distinguished. These states of chromatin within the chromocentre are considered to be a function of the degree of condensation. Segments of synaptinemal complexes are distributed randomly through sections of pachytene nuclei and long uncoiled segments of complexes are frequently found in or near the centres of median nuclear sections. Synaptinemal complexes are also found in chromocentres. Our findings suggest that on completion of pairing, which begins distally, homologous chromosomes in Rhoeo are paired throughout their entire lengths, rather than in small terminal segments only.

Architecture of the Yeast RNA Polymerase II Open Complex and Regulation of Activity by TFIIF

PubMed Central

Fishburn, James

2012-01-01

To investigate the function and architecture of the open complex state of RNA polymerase II (Pol II), Saccharomyces cerevisiae minimal open complexes were assembled by using a series of heteroduplex HIS4 promoters, TATA binding protein (TBP), TFIIB, and Pol II. The yeast system demonstrates great flexibility in the position of active open complexes, spanning 30 to 80 bp downstream from TATA, consistent with the transcription start site scanning behavior of yeast Pol II. TFIIF unexpectedly modulates the activity of the open complexes, either repressing or stimulating initiation. The response to TFIIF was dependent on the sequence of the template strand within the single-stranded bubble. Mutations in the TFIIB reader and linker region, which were inactive on duplex DNA, were suppressed by the heteroduplex templates, showing that a major function of the TFIIB reader and linker is in the initiation or stabilization of single-stranded DNA. Probing of the architecture of the minimal open complexes with TFIIB-FeBABE [TFIIB–p-bromoacetamidobenzyl–EDTA-iron(III)] derivatives showed that the TFIIB core domain is surprisingly positioned away from Pol II, and the addition of TFIIF repositions the TFIIB core domain to the Pol II wall domain. Together, our results show an unexpected architecture of minimal open complexes and the regulation of activity by TFIIF and the TFIIB core domain. PMID:22025674
Improving the SMM and luminescence properties of lanthanide complexes with LnO9 cores in the presence of ZnII: an emissive Zn2Dy single ion magnet.

PubMed

Fondo, Matilde; Corredoira-Vázquez, Julio; Herrera-Lanzós, Antía; García-Deibe, Ana M; Sanmartín-Matalobos, Jesús; Herrera, Juan Manuel; Colacio, Enrique; Nuñez, Cristina

2017-12-12

Mononuclear complexes of stoichiometry [Ln(H 3 L)(H 2 O)(NO 3 )](NO 3 ) 2 (Ln = Tb, 1; Dy, 2, Er, 3), which crystallise with different solvates, and the heterotrinuclear compound [Zn 2 Dy(L)(NO 3 ) 3 (OH)] (4) can be obtained with the same H 3 L compartmental ligand. The single X-ray crystal structure of the mononuclear complexes shows a LnO 9 core with a muffin-like disposition while the geometry of the DyO 9 core in 4 seems to be closer to spherical capped square antiprism. The analysis of the magnetic properties of all the complexes demonstrates that the mononuclear lanthanide compounds do not show slow relaxation of the magnetization, even when the samples are diluted with a diamagnetic matrix and subjected to a dc applied field of 1000 Oe. Nevertheless, the heterotrinuclear dysprosium complex 4·3H 2 O is a field-induced single ion magnet, with an estimated U eff barrier of 59 K. The luminescence characterisation of all the metal complexes in methanol solution at 298 K also shows a notable increase in the fluorescence emission of the heterotrinuclear complex with respect to the mononuclear ones, in such a way that 4 can be defined as a fluorescent single ion magnet.
New insights on multiplicity and clustering in Taurus.

NASA Astrophysics Data System (ADS)

Joncour, Isabelle; Duchene, Gaspard; Moraux, Estelle; Mundy, Lee

2018-01-01

Multiplicity and clustering of young stars are critical clues to constraint star formation process. The Taurus molecular complex is the archetype of a quiescent star forming region that may retain primeval signature of star formation.Using statistical and clustering tools such as nearest neighbor statistics, correlation functions and the density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm, this work reveals new spatial substructures in Taurus.We have identified unexpected ultra wide pairs (UWPs) candidates of high order multiplicity in Taurus in the 5-60 kAU separation range (Joncour et al 2017), beyond the separation assessed for wide pairs (Kraus & Hillenbrand 2009).Our work reveals 20 local stellar substructures, the Nested Elementary Structures (NESTs). These NESTs contain nearly half the stars of Taurus and 75% of the Class 0/I objects probing that they are the preferred sites of star formation (Joncour et al, sub.). The NESTs size ranges from few kAU up to 80 kAU making a length scale bridge between wide pairs and loose group (few hundreds kAU, Kirk & Myers, 2011). The NESTs mass ranges from 0.5-10 solar mass. The balance between Class I, II and III in NESTs suggests that they may be ordered as an evolutionary temporal scheme, some of them got infertile, while other shelter stars in infancy.The UWPs and the NESTs may be pristine imprints of their spatial configuration at birth. The UWPs population may result from a cascade fragmentation scenario of the natal molecular core. They could be the older counterparts, to the 0.5 Myr prestellar cores/Class 0 multiple objects observed at radio/millimeter wavelengths (Tobin et al 2010, 2016) and the precursors of the large number of UWPs (10–100 kAU) recently identified in older moving groups (Floriano-Alonso et al, 2015 ; Elliot et al 2016). The NESTs may result from the gravitational collapse of a gas clump that fragments to give a tight collection of stars within few millions years.This project has been partly supported by the StarFormMapper project funded by the European Union's Horizon 2020 Research and Innovation Action (RIA) program under grant agreement number 687528.
Empathetic, Critical Integrations of Multiple Perspectives: A Core Practice for Language Teacher Education?

ERIC Educational Resources Information Center

Daniel, Shannon M.

2015-01-01

In this self-study, the author reflects on her implementation of empathetic, critical integrations of multiple perspectives (ECI), which she designed to afford preservice teachers the opportunity to discuss and collectively reflect upon the oft-diverging multiple perspectives, values, and practices they experience during their practicum (Daniel,…
When complexity science meets implementation science: a theoretical and empirical analysis of systems change.

PubMed

Braithwaite, Jeffrey; Churruca, Kate; Long, Janet C; Ellis, Louise A; Herkes, Jessica

2018-04-30

Implementation science has a core aim - to get evidence into practice. Early in the evidence-based medicine movement, this task was construed in linear terms, wherein the knowledge pipeline moved from evidence created in the laboratory through to clinical trials and, finally, via new tests, drugs, equipment, or procedures, into clinical practice. We now know that this straight-line thinking was naïve at best, and little more than an idealization, with multiple fractures appearing in the pipeline. The knowledge pipeline derives from a mechanistic and linear approach to science, which, while delivering huge advances in medicine over the last two centuries, is limited in its application to complex social systems such as healthcare. Instead, complexity science, a theoretical approach to understanding interconnections among agents and how they give rise to emergent, dynamic, systems-level behaviors, represents an increasingly useful conceptual framework for change. Herein, we discuss what implementation science can learn from complexity science, and tease out some of the properties of healthcare systems that enable or constrain the goals we have for better, more effective, more evidence-based care. Two Australian examples, one largely top-down, predicated on applying new standards across the country, and the other largely bottom-up, adopting medical emergency teams in over 200 hospitals, provide empirical support for a complexity-informed approach to implementation. The key lessons are that change can be stimulated in many ways, but a triggering mechanism is needed, such as legislation or widespread stakeholder agreement; that feedback loops are crucial to continue change momentum; that extended sweeps of time are involved, typically much longer than believed at the outset; and that taking a systems-informed, complexity approach, having regard for existing networks and socio-technical characteristics, is beneficial. Construing healthcare as a complex adaptive system implies that getting evidence into routine practice through a step-by-step model is not feasible. Complexity science forces us to consider the dynamic properties of systems and the varying characteristics that are deeply enmeshed in social practices, whilst indicating that multiple forces, variables, and influences must be factored into any change process, and that unpredictability and uncertainty are normal properties of multi-part, intricate systems.
Heterobimetallic porphyrin complexes displaying triple dynamics: coupled metal motions controlled by constitutional evolution.

PubMed

Le Gac, Stéphane; Fusaro, Luca; Roisnel, Thierry; Boitrel, Bernard

2014-05-07

A bis-strap porphyrin ligand (1), with an overhanging carboxylic acid group on each side of the macrocycle, has been investigated toward the formation of dynamic libraries of bimetallic complexes with Hg(II), Cd(II), and Pb(II). Highly heteroselective metalation processes occurred in the presence of Pb(II), with Hg(II) or Cd(II) bound out-of-plane to the N-core and "PbOAc" bound to a carboxylate group of a strap on the opposite side. The resulting complexes, 1(Hg)·PbOAc and 1(Cd)·PbOAc, display three levels of dynamics. The first is strap-level (interactional dynamics), where the PbOAc moiety swings between the left and right side of the strap owing to a second sphere of coordination with lateral amide functions. The second is ligand-level (motional dynamics), where 1(Hg)·PbOAc and 1(Cd)·PbOAc exist as two degenerate states in equilibrium controlled by a chemical effector (AcO(-)). The process corresponds to a double translocation of the metal ions according to an intramolecular migration of Hg(II) or Cd(II) through the N-core, oscillating between the two equivalent overhanging carbonyl groups, coupled to an intermolecular pathway for PbOAc exchanging between the two equivalent overhanging carboxylate groups (N-core(up) ⇆ N-core(down) coupled to strap(down) ⇆ strap(up), i.e., coupled motion #1 in the abstract graphic). The third is library-level (constitutional dynamics), where a dynamic constitutional evolution of the system was achieved by the successive addition of two chemical effectors (DMAP and then AcO(-)). It allowed shifting equilibrium forward and backward between 1(Hg)·PbOAc and the corresponding homobimetallic complexes 1(Hg2)·DMAP and 1(Pb)·PbOAc. The latter displays a different ligand-level dynamics, in the form of an intraligand coupled migration of the Pb(II) ions (N-core(up) ⇆ strap(up) coupled to strap(down) ⇆ N-core(down), i.e., coupled motion #2 in the abstract graphic). In addition, the neutral "bridged" complexes 1HgPb and 1CdPb, with the metal ions on opposite sides both bound to the N-core and to a carboxylate of a strap, were structurally characterized. These results establish an unprecedented approach in supramolecular coordination chemistry, by considering the reversible interaction of a metal ion with the porphyrin N-core as a new source of self-organization processes. This work should provide new inspirations for the design of innovative adaptative materials and devices.
A Two-Step Approach to Uncertainty Quantification of Core Simulators

DOE PAGES

Yankov, Artem; Collins, Benjamin; Klein, Markus; ...

2012-01-01

For the multiple sources of error introduced into the standard computational regime for simulating reactor cores, rigorous uncertainty analysis methods are available primarily to quantify the effects of cross section uncertainties. Two methods for propagating cross section uncertainties through core simulators are the XSUSA statistical approach and the “two-step” method. The XSUSA approach, which is based on the SUSA code package, is fundamentally a stochastic sampling method. Alternatively, the two-step method utilizes generalized perturbation theory in the first step and stochastic sampling in the second step. The consistency of these two methods in quantifying uncertainties in the multiplication factor andmore » in the core power distribution was examined in the framework of phase I-3 of the OECD Uncertainty Analysis in Modeling benchmark. With the Three Mile Island Unit 1 core as a base model for analysis, the XSUSA and two-step methods were applied with certain limitations, and the results were compared to those produced by other stochastic sampling-based codes. Based on the uncertainty analysis results, conclusions were drawn as to the method that is currently more viable for computing uncertainties in burnup and transient calculations.« less
Structural and magnetic characterization of three tetranuclear Cu(II) complexes with face-sharing-dicubane/double-open-cubane like core framework

NASA Astrophysics Data System (ADS)

Paul, Aparup; Bertolasi, Valerio; Figuerola, Albert; Manna, Subal Chandra

2017-05-01

Three novel tetranuclear copper(II) complexes namely [Cu4(L1)4]•2(dmf) (1), [Cu4(L1)4] (2) and [Cu4(L2)2(HL2)2(H2O)2]•2(ClO4)·6(H2O) (3) (H2L1, (E)-2-((1-hydroxybutan-2-ylimino)methyl)phenol; H2L2, (E)-2-((1-hydroxybutan-2-ylimino)methyl)-6-methoxyphenol)) were synthesized from the self-assembly of copper(II) perchlorate and the tridentate Schiff base ligands. The structural determination reveals that complex 1 crystallizes in the monoclinic system with space group C2/c, whereas both the complexes 2 and 3 crystallize in the triclinic system with space group P-1. Complexes 1 and 2 possess face-sharing dicubane core, on the other hand complex 3 has double open cubane core structure. The copper(II) ions in the cubane core are in distorted square planar geometries, and weak π…π and C-H…π interactions lead to formation of a 2D supramolecular architecture for complexes 1 and 2. At room temperature complexes 1, 2 and 3, exhibit fluorescence with a quantum yield (Φs) of 0.47, 0.49 and 0.38, respectively. Variable temperature magnetic susceptibility measurements in the range 2-300 K indicate an overall weak antiferromagnetic exchange coupling in all complexes. The PHI program was used to study their magnetic behaviour. In agreement with their face-sharing dicubane structure, a Hamiltonian of the type H =- J1(S1S2+S1S2'+S1'S2+S1'S2') - J2S1S1', where S1 = S1' = S2 = S2' = SCu =1/2, was used for studying complexes 1 and 2. Simulations performed suggest magnetic exchange constants with values close to J1 =-20 cm-1 and J2 =0 cm-1 for these complexes. On the other hand, the spin Hamiltonian H =- J1(S1S4+S2S3) - J2(S1S3+S2S4) - J3S1S2, where S1 = S2 = S3 = S4 = SCu =1/2, was used to study the magnetic behaviour of the double open cubane core of complex 3 and a good agreement between the experimental and simulated results was found by using the parameters g1 = g2 =2.20, g3 = g4 =2.18, J1 =-36 cm-1, J2 =-44 cm-1 and J3 =0 cm-1.
Paleoseismic events inferred from marine seismogenic turbidites of the eastern Nankai Trough

NASA Astrophysics Data System (ADS)

Okutsu, N.; Ashi, J.; Omura, A.; Yamaguchi, A.; Suganuma, Y.; Kanamatsu, T.; Murayama, M.

2016-12-01

Paleoseismology using marine seismogenic turbidites is a developing field especially in subduction margins. However, very fine-grained turbidites are difficult to distinguish from hemipelagic mud. The primary focus of this study is to understand the characteristics of the muddy turbidites. The second focus is to discuss the muddy turbidites distributions and their ages from a longer sediment core, and understand the paleoseismic records of eastern Nankai Trough, Japan. The samples used in this study include multiple cores and a piston core which were collected from the sedimentary basin southwest off Kii Peninsula during the R/V Shinsei Maru KS-14-8 cruise. The sampling site is located at the ENE-WSW elongated basin between the accretionary prism and the forearc basin off Kumano without terrestrial sediment supply. The basin exhibits a terminal basin that captures all sediments supplied from outside. From the multiple core samples, the Cs-137 and Pb- 210 concentration distribution indicates that the muddy sediment layer in the upper 17 cm was formed from the 2004 off the Kii Peninsula earthquake. Visual observation and X-ray CT scans were conducted alongside other measurements for anisotropy of magnetic susceptibility (AMS), paleomagnetism, rock magnetism, electrical resistivity, and X-ray fluorescence core scanning (XRF). Muddy seismogenic turbidites associated with the 2004 off the Kii Peninsula earthquake have thick homogeneous clay layer above the silty lamination. The magnetic susceptibility decreases upwards in the lamination. This specific feature is thought to have formed as the muddy turbiditity current slowly decelerated and slowly settled down the slope. From the results of XRF core scanning, Ca and Fe have a peak at basement of turbidites, and decrease upwards. Ca is thought to correspond to amount of the foraminiferas. In piston core, we observed the same sedimentary and magnetic characteristics as the multiple cores. Based on stratigraphic information from volcanic ash and radiocarbon age of the foraminifera, intercalation pattern of muddy turbidite layers almost consistent with the known past earthquake recurrence times in the Nankai subduction margin. Reversed age recognized beneath the thick turbidite layer suggests reworking of landslide deposits probably due to the strong shaking.
Challenges Regarding IP Core Functional Reliability

NASA Technical Reports Server (NTRS)

Berg, Melanie D.; LaBel, Kenneth A.

2017-01-01

For many years, intellectual property (IP) cores have been incorporated into field programmable gate array (FPGA) and application specific integrated circuit (ASIC) design flows. However, the usage of large complex IP cores were limited within products that required a high level of reliability. This is no longer the case. IP core insertion has become mainstream including their use in highly reliable products. Due to limited visibility and control, challenges exist when using IP cores and subsequently compromise product reliability. We discuss challenges and suggest potential solutions to critical application IP insertion.
High-Speed Computation of the Kleene Star in Max-Plus Algebraic System Using a Cell Broadband Engine

NASA Astrophysics Data System (ADS)

Goto, Hiroyuki

This research addresses a high-speed computation method for the Kleene star of the weighted adjacency matrix in a max-plus algebraic system. We focus on systems whose precedence constraints are represented by a directed acyclic graph and implement it on a Cell Broadband Engine™ (CBE) processor. Since the resulting matrix gives the longest travel times between two adjacent nodes, it is often utilized in scheduling problem solvers for a class of discrete event systems. This research, in particular, attempts to achieve a speedup by using two approaches: parallelization and SIMDization (Single Instruction, Multiple Data), both of which can be accomplished by a CBE processor. The former refers to a parallel computation using multiple cores, while the latter is a method whereby multiple elements are computed by a single instruction. Using the implementation on a Sony PlayStation 3™ equipped with a CBE processor, we found that the SIMDization is effective regardless of the system's size and the number of processor cores used. We also found that the scalability of using multiple cores is remarkable especially for systems with a large number of nodes. In a numerical experiment where the number of nodes is 2000, we achieved a speedup of 20 times compared with the method without the above techniques.
Experimental demonstration of high spectral efficient 4 × 4 MIMO SCMA-OFDM/OQAM radio over multi-core fiber system.

PubMed

Liu, Chang; Deng, Lei; He, Jiale; Li, Di; Fu, Songnian; Tang, Ming; Cheng, Mengfan; Liu, Deming

2017-07-24

In this paper, 4 × 4 multiple-input multiple-output (MIMO) radio over 7-core fiber system based on sparse code multiple access (SCMA) and OFDM/OQAM techniques is proposed. No cyclic prefix (CP) is required by properly designing the prototype filters in OFDM/OQAM modulator, and non-orthogonally overlaid codewords by using SCMA is help to serve more users simultaneously under the condition of using equal number of time and frequency resources compared with OFDMA, resulting in the increase of spectral efficiency (SE) and system capacity. In our experiment, 11.04 Gb/s 4 × 4 MIMO SCMA-OFDM/OQAM signal is successfully transmitted over 20 km 7-core fiber and 0.4 m air distance in both uplink and downlink. As a comparison, 6.681 Gb/s traditional MIMO-OFDM signal with the same occupied bandwidth has been evaluated for both uplink and downlink transmission. The experimental results show that SE could be increased by 65.2% with no bit error rate (BER) performance degradation compared with the traditional MIMO-OFDM technique.
Dynamics of Photosystem II and Its Light Harvesting System in Response to Light Changes in the Halotolerant Alga Dunaliella salina1

PubMed Central

Pick, Uri; Gounaris, Kleoniki; Barber, James

1987-01-01

A photosystem two (PSII) core complex consisting of five major polypeptides (47, 40, 32, 30, and 10 kilodaltons) and a light harvesting chlorophyll a/b complex (LHC-2) have been isolated from the halotolerant alga Dunaliella salina. The chlorophyll and polypeptide composition of both complexes were compared in illuminated and dark-adapted cultures. Dark adaptation is accompanied by a decrease in the chlorophyll a to chlorophyll b (Chl a/Chl b) ratio of intact thylakoids without any change in total chlorophyll. These changes occur with a half-time of 3 hours and are reversed upon reillumination. Analyses of PSII enriched membrane fragments suggest that the decrease in the Chl a/Chl b is due partly to an increase in the Chl b content of LHC-2 and partly to changes in the relative levels of the two complexes. Apparently during dark adaptation there is: (a) a net synthesis of chlorophyll b, (b) removal of PSII core complexes resulting in a 2-fold drop in the PSII cores to LHC-2 chlorophyll ratio. These changes should dramatically increase the light harvesting capacity of the remaining PSII reaction centers. Presumably this adjustment of antenna size and composition is a physiological mechanism necessary for responding to shade conditions. Also detected, using 32P, are light-induced phosphorylation of the LHC-2 (consistent with the ability to undergo State transitions) and of the 40 and 30 kilodalton subunits of the PSII core complex. These observations indicate that additional mechanisms may also exist to help optimize the interception of quanta during rapid changes in illumination conditions. Images Fig. 4 PMID:16665656
FANCG promotes formation of a newly identified protein complex containing BRCA2, FANCD2 and XRCC3.

PubMed

Wilson, J B; Yamamoto, K; Marriott, A S; Hussain, S; Sung, P; Hoatlin, M E; Mathew, C G; Takata, M; Thompson, L H; Kupfer, G M; Jones, N J

2008-06-12

Fanconi anemia (FA) is a human disorder characterized by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. Thirteen complementation groups and genes are identified, including BRCA2, which is defective in the FA-D1 group. Eight of the FA proteins, including FANCG, participate in a nuclear core complex that is required for the monoubiquitylation of FANCD2 and FANCI. FANCD2, like FANCD1/BRCA2, is not part of the core complex, and we previously showed direct BRCA2-FANCD2 interaction using yeast two-hybrid analysis. We now show in human and hamster cells that expression of FANCG protein, but not the other core complex proteins, is required for co-precipitation of BRCA2 and FANCD2. We also show that phosphorylation of FANCG serine 7 is required for its co-precipitation with BRCA2, XRCC3 and FANCD2, as well as the direct interaction of BRCA2-FANCD2. These results argue that FANCG has a role independent of the FA core complex, and we propose that phosphorylation of serine 7 is the signalling event required for forming a discrete complex comprising FANCD1/BRCA2-FANCD2-FANCG-XRCC3 (D1-D2-G-X3). Cells that fail to express either phospho-Ser7-FANCG, or full length BRCA2 protein, lack the interactions amongst the four component proteins. A role for D1-D2-G-X3 in homologous recombination repair (HRR) is supported by our finding that FANCG and the RAD51-paralog XRCC3 are epistatic for sensitivity to DNA crosslinking compounds in DT40 chicken cells. Our findings further define the intricate interface between FANC and HRR proteins in maintaining chromosome stability.
Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin

PubMed Central

Bochyńska, Agnieszka; Lüscher-Firzlaff, Juliane

2018-01-01

Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. Here we discuss recent findings that try to elucidate the important question of how KMT2 complexes are recruited to specific sites on chromatin. This is embedded into short overviews of the biological functions of KMT2 complexes and the consequences of H3K4 methylation. PMID:29498679
Presupernova Evolution of Differentially Rotating Massive Stars Including Magnetic Fields

NASA Astrophysics Data System (ADS)

Heger, A.; Woosley, S. E.; Spruit, H. C.

2005-06-01

As a massive star evolves through multiple stages of nuclear burning on its way to becoming a supernova, a complex, differentially rotating structure is set up. Angular momentum is transported by a variety of classic instabilities and also by magnetic torques from fields generated by the differential rotation. We present the first stellar evolution calculations to follow the evolution of rotating massive stars including, at least approximately, all these effects, magnetic and nonmagnetic, from the zero-age main sequence until the onset of iron-core collapse. The evolution and action of the magnetic fields is as described by Spruit in 2002, and a range of uncertain parameters is explored. In general, we find that magnetic torques decrease the final rotation rate of the collapsing iron core by about a factor of 30-50 when compared with the nonmagnetic counterparts. Angular momentum in that part of the presupernova star destined to become a neutron star is an increasing function of main-sequence mass. That is, pulsars derived from more massive stars rotate faster and rotation plays a more important role in the star's explosion. The final angular momentum of the core has been determined-to within a factor of 2-by the time the star ignites carbon burning. For the lighter stars studied, around 15 Msolar, we predict pulsar periods at birth near 15 ms, though a factor of 2 range is easily tolerated by the uncertainties. Several mechanisms for additional braking in a young neutron star, especially by fallback, are explored.
Hollow-core fiber sensing technique for pipeline leak detection

NASA Astrophysics Data System (ADS)

Challener, W. A.; Kasten, Matthias A.; Karp, Jason; Choudhury, Niloy

2018-02-01

Recently there has been increased interest on the part of federal and state regulators to detect and quantify emissions of methane, an important greenhouse gas, from various parts of the oil and gas infrastructure including well pads and pipelines. Pressure and/or flow anomalies are typically used to detect leaks along natural gas pipelines, but are generally very insensitive and subject to false alarms. We have developed a system to detect and localize methane leaks along gas pipelines that is an order of magnitude more sensitive by combining tunable diode laser spectroscopy (TDLAS) with conventional sensor tube technology. This technique can potentially localize leaks along pipelines up to 100 km lengths with an accuracy of +/-50 m or less. A sensor tube buried along the pipeline with a gas-permeable membrane collects leaking gas during a soak period. The leak plume within the tube is then carried to the nearest sensor node along the tube in a purge cycle. The time-to-detection is used to determine leak location. Multiple sensor nodes are situated along the pipeline to minimize the time to detection, and each node is composed of a short segment of hollow core fiber (HCF) into which leaking gas is transported quickly through a small pressure differential. The HCF sensing node is spliced to standard telecom solid core fiber which transports the laser light for spectroscopy to a remote interrogator. The interrogator is multiplexed across the sensor nodes to minimize equipment cost and complexity.
Transient climate simulations of the deglaciation 21-9 thousand years before present (version 1) - PMIP4 Core experiment design and boundary conditions

NASA Astrophysics Data System (ADS)

Ivanovic, Ruza F.; Gregoire, Lauren J.; Kageyama, Masa; Roche, Didier M.; Valdes, Paul J.; Burke, Andrea; Drummond, Rosemarie; Peltier, W. Richard; Tarasov, Lev

2016-07-01

The last deglaciation, which marked the transition between the last glacial and present interglacial periods, was punctuated by a series of rapid (centennial and decadal) climate changes. Numerical climate models are useful for investigating mechanisms that underpin the climate change events, especially now that some of the complex models can be run for multiple millennia. We have set up a Paleoclimate Modelling Intercomparison Project (PMIP) working group to coordinate efforts to run transient simulations of the last deglaciation, and to facilitate the dissemination of expertise between modellers and those engaged with reconstructing the climate of the last 21 000 years. Here, we present the design of a coordinated Core experiment over the period 21-9 thousand years before present (ka) with time-varying orbital forcing, greenhouse gases, ice sheets and other geographical changes. A choice of two ice sheet reconstructions is given, and we make recommendations for prescribing ice meltwater (or not) in the Core experiment. Additional focussed simulations will also be coordinated on an ad hoc basis by the working group, for example to investigate more thoroughly the effect of ice meltwater on climate system evolution, and to examine the uncertainty in other forcings. Some of these focussed simulations will target shorter durations around specific events in order to understand them in more detail and allow for the more computationally expensive models to take part.
Locality Aware Concurrent Start for Stencil Applications

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

Shrestha, Sunil; Gao, Guang R.; Manzano Franco, Joseph B.

Stencil computations are at the heart of many physical simulations used in scientific codes. Thus, there exists a plethora of optimization efforts for this family of computations. Among these techniques, tiling techniques that allow concurrent start have proven to be very efficient in providing better performance for these critical kernels. Nevertheless, with many core designs being the norm, these optimization techniques might not be able to fully exploit locality (both spatial and temporal) on multiple levels of the memory hierarchy without compromising parallelism. It is no longer true that the machine can be seen as a homogeneous collection of nodesmore » with caches, main memory and an interconnect network. New architectural designs exhibit complex grouping of nodes, cores, threads, caches and memory connected by an ever evolving network-on-chip design. These new designs may benefit greatly from carefully crafted schedules and groupings that encourage parallel actors (i.e. threads, cores or nodes) to be aware of the computational history of other actors in close proximity. In this paper, we provide an efficient tiling technique that allows hierarchical concurrent start for memory hierarchy aware tile groups. Each execution schedule and tile shape exploit the available parallelism, load balance and locality present in the given applications. We demonstrate our technique on the Intel Xeon Phi architecture with selected and representative stencil kernels. We show improvement ranging from 5.58% to 31.17% over existing state-of-the-art techniques.« less
Consensus between Pipelines in Structural Brain Networks

PubMed Central

Parker, Christopher S.; Deligianni, Fani; Cardoso, M. Jorge; Daga, Pankaj; Modat, Marc; Dayan, Michael; Clark, Chris A.

2014-01-01

Structural brain networks may be reconstructed from diffusion MRI tractography data and have great potential to further our understanding of the topological organisation of brain structure in health and disease. Network reconstruction is complex and involves a series of processesing methods including anatomical parcellation, registration, fiber orientation estimation and whole-brain fiber tractography. Methodological choices at each stage can affect the anatomical accuracy and graph theoretical properties of the reconstructed networks, meaning applying different combinations in a network reconstruction pipeline may produce substantially different networks. Furthermore, the choice of which connections are considered important is unclear. In this study, we assessed the similarity between structural networks obtained using two independent state-of-the-art reconstruction pipelines. We aimed to quantify network similarity and identify the core connections emerging most robustly in both pipelines. Similarity of network connections was compared between pipelines employing different atlases by merging parcels to a common and equivalent node scale. We found a high agreement between the networks across a range of fiber density thresholds. In addition, we identified a robust core of highly connected regions coinciding with a peak in similarity across network density thresholds, and replicated these results with atlases at different node scales. The binary network properties of these core connections were similar between pipelines but showed some differences in atlases across node scales. This study demonstrates the utility of applying multiple structural network reconstrution pipelines to diffusion data in order to identify the most important connections for further study. PMID:25356977

Some links on this page may take you to non-federal websites. Their policies may differ from this site.