Relocating the Active-Site Lysine in Rhodopsin: 2. Evolutionary Intermediates.

PubMed

Devine, Erin L; Theobald, Douglas L; Oprian, Daniel D

2016-08-30

The visual pigment rhodopsin is a G protein-coupled receptor that covalently binds its retinal chromophore via a Schiff base linkage to an active-site Lys residue in the seventh transmembrane helix. Although this residue is strictly conserved among all type II retinylidene proteins, we found previously that the active-site Lys in bovine rhodopsin (Lys296) can be moved to three other locations (G90K, T94K, S186K) while retaining the ability to form a pigment with retinal and to activate transducin in a light-dependent manner [ Devine et al. ( 2013 ) Proc. Natl. Acad. Sci. USA 110 , 13351 - 13355 ]. Because the active-site Lys is not functionally constrained to be in helix seven, it is possible that it could relocate within the protein, most likely via an evolutionary intermediate with two active-site Lys. Therefore, in this study we characterized potential evolutionary intermediates with two Lys in the active site. Four mutant rhodopsins were prepared in which the original Lys296 was left untouched and a second Lys residue was substituted for G90K, T94K, S186K, or F293K. All four constructs covalently bind 11-cis-retinal, form a pigment, and activate transducin in a light-dependent manner. These results demonstrate that rhodopsin can tolerate a second Lys in the retinal binding pocket and suggest that an evolutionary intermediate with two Lys could allow migration of the Schiff base Lys to a position other than the observed, highly conserved location in the seventh TM helix. From sequence-based searches, we identified two groups of natural opsins, insect UV cones and neuropsins, that contain Lys residues at two positions in their active sites and also have intriguing spectral similarities to the mutant rhodopsins studied here.

Structure-Activity Relationships of Constrained Phenylethylamine Ligands for the Serotonin 5-HT2 Receptors

PubMed Central

Isberg, Vignir; Paine, James; Leth-Petersen, Sebastian; Kristensen, Jesper L.; Gloriam, David E.

2013-01-01

Serotonergic ligands have proven effective drugs in the treatment of migraine, pain, obesity, and a wide range of psychiatric and neurological disorders. There is a clinical need for more highly 5-HT2 receptor subtype-selective ligands and the most attention has been given to the phenethylamine class. Conformationally constrained phenethylamine analogs have demonstrated that for optimal activity the free lone pair electrons of the 2-oxygen must be oriented syn and the 5-oxygen lone pairs anti relative to the ethylamine moiety. Also the ethyl linker has been constrained providing information about the bioactive conformation of the amine functionality. However, combined 1,2-constriction by cyclization has only been tested with one compound. Here, we present three new 1,2-cyclized phenylethylamines, 9–11, and describe their synthetic routes. Ligand docking in the 5-HT2B crystal structure showed that the 1,2-heterocyclized compounds can be accommodated in the binding site. Conformational analysis showed that 11 can only bind in a higher-energy conformation, which would explain its absent or low affinity. The amine and 2-oxygen interactions with D3.32 and S3.36, respectively, can form but shift the placement of the core scaffold. The constraints in 9–11 resulted in docking poses with the 4-bromine in closer vicinity to 5.46, which is polar only in the human 5-HT2A subtype, for which 9–11 have the lowest affinity. The new ligands, conformational analysis and docking expand the structure-activity relationships of constrained phenethylamines and contributes towards the development of 5-HT2 receptor subtype-selective ligands. PMID:24244317

Structure-activity relationships of constrained phenylethylamine ligands for the serotonin 5-HT2 receptors.

PubMed

Isberg, Vignir; Paine, James; Leth-Petersen, Sebastian; Kristensen, Jesper L; Gloriam, David E

2013-01-01

Serotonergic ligands have proven effective drugs in the treatment of migraine, pain, obesity, and a wide range of psychiatric and neurological disorders. There is a clinical need for more highly 5-HT2 receptor subtype-selective ligands and the most attention has been given to the phenethylamine class. Conformationally constrained phenethylamine analogs have demonstrated that for optimal activity the free lone pair electrons of the 2-oxygen must be oriented syn and the 5-oxygen lone pairs anti relative to the ethylamine moiety. Also the ethyl linker has been constrained providing information about the bioactive conformation of the amine functionality. However, combined 1,2-constriction by cyclization has only been tested with one compound. Here, we present three new 1,2-cyclized phenylethylamines, 9-11, and describe their synthetic routes. Ligand docking in the 5-HT2B crystal structure showed that the 1,2-heterocyclized compounds can be accommodated in the binding site. Conformational analysis showed that 11 can only bind in a higher-energy conformation, which would explain its absent or low affinity. The amine and 2-oxygen interactions with D3.32 and S3.36, respectively, can form but shift the placement of the core scaffold. The constraints in 9-11 resulted in docking poses with the 4-bromine in closer vicinity to 5.46, which is polar only in the human 5-HT2A subtype, for which 9-11 have the lowest affinity. The new ligands, conformational analysis and docking expand the structure-activity relationships of constrained phenethylamines and contributes towards the development of 5-HT2 receptor subtype-selective ligands.

Teen smoking cessation help via the Internet: a survey of search engines.

PubMed

Edwards, Christine C; Elliott, Sean P; Conway, Terry L; Woodruff, Susan I

2003-07-01

The objective of this study was to assess Web sites related to teen smoking cessation on the Internet. Seven Internet search engines were searched using the keywords teen quit smoking. The top 20 hits from each search engine were reviewed and categorized. The keywords teen quit smoking produced between 35 and 400,000 hits depending on the search engine. Of 140 potential hits, 62% were active, unique sites; 85% were listed by only one search engine; and 40% focused on cessation. Findings suggest that legitimate on-line smoking cessation help for teens is constrained by search engine choice and the amount of time teens spend looking through potential sites. Resource listings should be updated regularly. Smoking cessation Web sites need to be picked up on multiple search engine searches. Further evaluation of smoking cessation Web sites need to be conducted to identify the most effective help for teens.

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

PubMed Central

Naughton, Catherine; Avlonitis, Nicolaos; Corless, Samuel; Prendergast, James G.; Mati, Ioulia K.; Eijk, Paul P.; Cockroft, Scott L.; Bradley, Mark; Ylstra, Bauke; Gilbert, Nick

2013-01-01

DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes. PMID:23416946

Macrocyclic BACE inhibitors: Optimization of a micromolar hit to nanomolar leads.

PubMed

Huang, Yifang; Strobel, Eric D; Ho, Chih Y; Reynolds, Charles H; Conway, Kelly A; Piesvaux, Jennifer A; Brenneman, Douglas E; Yohrling, George J; Moore Arnold, H; Rosenthal, Daniel; Alexander, Richard S; Tounge, Brett A; Mercken, Marc; Vandermeeren, Marc; Parker, Michael H; Reitz, Allen B; Baxter, Ellen W

2010-05-15

We have identified macrocyclic inhibitors of the aspartic protease BACE, implicated in the etiology of Alzheimer's disease. An X-ray structure of screening hit 1 in the BACE active site revealed a hairpin conformation suggesting that constrained macrocyclic derivatives may also bind there. Several of the analogs we prepared were >100x more potent than 1, such as 7 (5 nM K(i)). Copyright 2010 Elsevier Ltd. All rights reserved.

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

PubMed Central

Isaac, R Stefan; Jiang, Fuguo; Doudna, Jennifer A; Lim, Wendell A; Narlikar, Geeta J; Almeida, Ricardo

2016-01-01

The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells, yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood. Here we investigate how the smallest unit of chromatin, a nucleosome, constrains the activity of the CRISPR-Cas9 system. We find that nucleosomes assembled on native DNA sequences are permissive to Cas9 action. However, the accessibility of nucleosomal DNA to Cas9 is variable over several orders of magnitude depending on dynamic properties of the DNA sequence and the distance of the PAM site from the nucleosome dyad. We further find that chromatin remodeling enzymes stimulate Cas9 activity on nucleosomal templates. Our findings imply that the spontaneous breathing of nucleosomal DNA together with the action of chromatin remodelers allow Cas9 to effectively act on chromatin in vivo. DOI: http://dx.doi.org/10.7554/eLife.13450.001 PMID:27130520

Vibration control of multiferroic fibrous composite plates using active constrained layer damping

NASA Astrophysics Data System (ADS)

Kattimani, S. C.; Ray, M. C.

2018-06-01

Geometrically nonlinear vibration control of fiber reinforced magneto-electro-elastic or multiferroic fibrous composite plates using active constrained layer damping treatment has been investigated. The piezoelectric (BaTiO3) fibers are embedded in the magnetostrictive (CoFe2O4) matrix forming magneto-electro-elastic or multiferroic smart composite. A three-dimensional finite element model of such fiber reinforced magneto-electro-elastic plates integrated with the active constrained layer damping patches is developed. Influence of electro-elastic, magneto-elastic and electromagnetic coupled fields on the vibration has been studied. The Golla-Hughes-McTavish method in time domain is employed for modeling a constrained viscoelastic layer of the active constrained layer damping treatment. The von Kármán type nonlinear strain-displacement relations are incorporated for developing a three-dimensional finite element model. Effect of fiber volume fraction, fiber orientation and boundary conditions on the control of geometrically nonlinear vibration of the fiber reinforced magneto-electro-elastic plates is investigated. The performance of the active constrained layer damping treatment due to the variation of piezoelectric fiber orientation angle in the 1-3 Piezoelectric constraining layer of the active constrained layer damping treatment has also been emphasized.

Molecular dynamics studies unravel role of conserved residues responsible for movement of ions into active site of DHBPS

NASA Astrophysics Data System (ADS)

Shinde, Ranajit Nivrutti; Karthikeyan, Subramanian; Singh, Balvinder

2017-01-01

3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg2+. Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg2+ is still elusive. Therefore, mechanistic role played by Mg2+ in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg2+ have shown entry of Mg2+ from bulk solvent into active site. Presence of Mg2+ in active site has constrained conformations of Ru5P and has reduced flexibility of loop-2. Formation of hydrogen bonds among Thr-108 and residues - Gly-109, Val-110, Ser-111, and Asp-114 are found to be critical for entry of Mg2+ into active site. Subsequent in silico mutations of residues, Thr-108 and Asp-114 have substantiated the importance of these interactions. Loop-4 of one monomer is being proposed to act as a “lid” covering the active site of other monomer. Further, the conserved nature of residues taking part in the transfer of Mg2+ suggests the same mechanism being present in DHBPS of other microorganisms. Thus, this study provides insights into the functioning of DHBPS that can be used for the designing of inhibitors.

Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All.

PubMed

Cummins, Peter L; Kannappan, Babu; Gready, Jill E

2018-01-01

The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is utilized by most photosynthetic organisms. Despite this central role, RuBisCO's efficiency surprisingly struggles, with both a very slow turnover rate to products and also impaired substrate specificity, features that have long been an enigma as it would be assumed that its efficiency was under strong evolutionary pressure. RuBisCO's substrate specificity is compromised as it catalyzes a side-fixation reaction with atmospheric oxygen; empirical kinetic results show a trend to tradeoff between relative specificity and low catalytic turnover rate. Although the dominant hypothesis has been that the active-site chemistry constrains the enzyme's evolution, a more recent study on RuBisCO stability and adaptability has implicated competing selection pressures. Elucidating these constraints is crucial for directing future research on improving photosynthesis, as the current literature casts doubt on the potential effectiveness of site-directed mutagenesis to improve RuBisCO's efficiency. Here we use regression analysis to quantify the relationships between kinetic parameters obtained from empirical data sets spanning a wide evolutionary range of RuBisCOs. Most significantly we found that the rate constant for dissociation of CO 2 from the enzyme complex was much higher than previous estimates and comparable with the corresponding catalytic rate constant. Observed trends between relative specificity and turnover rate can be expressed as the product of negative and positive correlation factors. This provides an explanation in simple kinetic terms of both the natural variation of relative specificity as well as that obtained by reported site-directed mutagenesis results. We demonstrate that the kinetic behaviour shows a lesser rather than more constrained RuBisCO, consistent with growing empirical evidence of higher variability in relative specificity. In summary our analysis supports an explanation for the origin of the tradeoff between specificity and turnover as due to competition between protein stability and activity, rather than constraints between rate constants imposed by the underlying chemistry. Our analysis suggests that simultaneous improvement in both specificity and turnover rate of RuBisCO is possible.

Sediment Contaminants and Infauna Associated with Recreational Boating Structures in a Multi-Use Marine Park.

PubMed

Sim, Vivian X Y; Dafforn, Katherine A; Simpson, Stuart L; Kelaher, Brendan P; Johnston, Emma L

2015-01-01

Multi-use marine parks achieve conservation through spatial management of activities. Zoning of marine parks in New South Wales, Australia, includes high conservation areas and special purpose zones (SPZ) where maritime activities are concentrated. Although such measures geographically constrain anthropogenic impacts, we have limited understanding of potential ecological effects. We assessed sediment communities and contaminants adjacent to boating infrastructure (boat ramps, jetties and a marina) in a SPZ from the Clyde Estuary in Batemans Marine Park. Metal concentrations and fines content were elevated at boating structures compared to reference sites. Species richness was higher at sites with boating structures, where capitellid polychaetes and nematodes dominated the communities. Changes associated with boating structures were localised and did not extend beyond breakwalls or to reference sites outside the SPZ. The study highlights the benefits of appropriate zoning in a multi-use marine park and the potential to minimise stress on pristine areas through the application of spatial management.

Sediment Contaminants and Infauna Associated with Recreational Boating Structures in a Multi-Use Marine Park

PubMed Central

Sim, Vivian X. Y.; Dafforn, Katherine A.; Simpson, Stuart L.; Kelaher, Brendan P.; Johnston, Emma L.

2015-01-01

Multi-use marine parks achieve conservation through spatial management of activities. Zoning of marine parks in New South Wales, Australia, includes high conservation areas and special purpose zones (SPZ) where maritime activities are concentrated. Although such measures geographically constrain anthropogenic impacts, we have limited understanding of potential ecological effects. We assessed sediment communities and contaminants adjacent to boating infrastructure (boat ramps, jetties and a marina) in a SPZ from the Clyde Estuary in Batemans Marine Park. Metal concentrations and fines content were elevated at boating structures compared to reference sites. Species richness was higher at sites with boating structures, where capitellid polychaetes and nematodes dominated the communities. Changes associated with boating structures were localised and did not extend beyond breakwalls or to reference sites outside the SPZ. The study highlights the benefits of appropriate zoning in a multi-use marine park and the potential to minimise stress on pristine areas through the application of spatial management. PMID:26086427

Fragments of a larger whole: retrieval cues constrain observed neural correlates of memory encoding.

PubMed

Otten, Leun J

2007-09-01

Laying down a new memory involves activity in a number of brain regions. Here, it is shown that the particular regions associated with successful encoding depend on the way in which memory is probed. Event-related functional magnetic resonance imaging signals were acquired while subjects performed an incidental encoding task on a series of visually presented words denoting objects. A recognition memory test using the Remember/Know procedure to separate responses based on recollection and familiarity followed 1 day later. Critically, half of the studied objects were cued with a corresponding spoken word, and half with a corresponding picture. Regardless of cue, activity in prefrontal and hippocampal regions predicted subsequent recollection of a word. Type of retrieval cue modulated activity in prefrontal, temporal, and parietal cortices. Words subsequently recognized on the basis of a sense of familiarity were at study also associated with differential activity in a number of brain regions, some of which were probe dependent. Thus, observed neural correlates of successful encoding are constrained by type of retrieval cue, and are only fragments of all encoding-related neural activity. Regions exhibiting cue-specific effects may be sites that support memory through the degree of overlap between the processes engaged during encoding and those engaged during retrieval.

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.

PubMed

Studer, Romain A; Christin, Pascal-Antoine; Williams, Mark A; Orengo, Christine A

2014-02-11

A well-known case of evolutionary adaptation is that of ribulose-1,5-bisphosphate carboxylase (RubisCO), the enzyme responsible for fixation of CO2 during photosynthesis. Although the majority of plants use the ancestral C3 photosynthetic pathway, many flowering plants have evolved a derived pathway named C4 photosynthesis. The latter concentrates CO2, and C4 RubisCOs consequently have lower specificity for, and faster turnover of, CO2. The C4 forms result from convergent evolution in multiple clades, with substitutions at a small number of sites under positive selection. To understand the physical constraints on these evolutionary changes, we reconstructed in silico ancestral sequences and 3D structures of RubisCO from a large group of related C3 and C4 species. We were able to precisely track their past evolutionary trajectories, identify mutations on each branch of the phylogeny, and evaluate their stability effect. We show that RubisCO evolution has been constrained by stability-activity tradeoffs similar in character to those previously identified in laboratory-based experiments. The C4 properties require a subset of several ancestral destabilizing mutations, which from their location in the structure are inferred to mainly be involved in enhancing conformational flexibility of the open-closed transition in the catalytic cycle. These mutations are near, but not in, the active site or at intersubunit interfaces. The C3 to C4 transition is preceded by a sustained period in which stability of the enzyme is increased, creating the capacity to accept the functionally necessary destabilizing mutations, and is immediately followed by compensatory mutations that restore global stability.

Present day crustal deformation of the Italian peninsula observed by permanent GPS stations

NASA Astrophysics Data System (ADS)

Devoti, Roberto; Esposito, Alessandra; Galvani, Alessandro; Pietrantonio, Grazia; Pisani, Anna Rita; Riguzzi, Federica; Sepe, Vincenzo

2010-05-01

Italian penisula is a crucial area in the Mediterranean region to understand the active deformation processes along Nubia-Eurasia plate boundary. We present the velocity and strain rate fields of the Italian area derived from continuous GPS observations of more than 300 sites in the time span 1998-2009. The GPS networks were installed and managed by different institutions and for different purposes; altogether they cover the whole country with a mean inter-site distance of about 50 km and provide a valuable source of data to map the present day kinematics of the region. The data processing is performed by BERNESE software ver. 5.0, adopting a distributed session approach, with more than 10 clusters, sharing common stations, each of them consisting of about 40 stations. Daily loosely constrained solutions are routinely produced for each cluster and then combined into a network daily loose solution. Subsequently daily solutions are transformed on the chosen reference frame and the constrained time series are fitted using the complete covariance matrix, simultaneously estimating site velocities together with annual signals and sporadic offsets at epochs of instrumental changes. In this work we provide an updated detailed picture of the horizontal and vertical kinematics (velocity maps) and deformation pattern (strain rate maps) of the Italian area. The results show several crustal domains characterized by different velocity rates and styles of deformation.

Controls on tree species stem transport and emission of methane from tropical peatlands

NASA Astrophysics Data System (ADS)

Van Haren, J. L. M.; Cadillo-Quiroz, H.

2016-12-01

Methane emissions from wetlands dominate the global budget and are most likely responsible for the annual variability in emissions. Methane is produced and consumed by microbial activity and then transported to the atmosphere. Plants have been shown to facilitate the transport of methane to significant amounts, but broad surveys across multiple sites have been lacking. We present data collected from multiple peatland and wetland sites south of Iquitos Peru and varzea sites from Santarem Brazil and compare our results to the limited literature of tree stem fluxes. The survey suggests that methane stem emissions might be conserved at the genera level, but not the family level. Large emitters exist in the Aracaceae, Euphorbiaceae, and Sapotaceae, however, other genera within the same families do not emit any methane. Certain genera are consistent pan-tropical methane emitters. The methane emission from the stems decreases generally with height, suggesting a diffusion constrained stem flux. Further constraints on the methane emissions from tree stems involve soil methane concentration and wood density, which is likely an indicator for stem conductivity. Diurnal cycles, flooding level and tree leaves appear to have less of an influence on the tree methane emissions though flooding can lead to a translocation of emissions up the stem to above the flooding level. Methane emissions and the plant transport pathways appear to be constrained at the genera level within wetlands.

Small constrained SP1-7 analogs bind to a unique site and promote anti-allodynic effects following systemic injection in mice.

PubMed

Jonsson, A; Fransson, R; Haramaki, Y; Skogh, A; Brolin, E; Watanabe, H; Nordvall, G; Hallberg, M; Sandström, A; Nyberg, F

2015-07-09

Previous results have shown that the substance P (SP) N-terminal fragment SP1-7 may attenuate hyperalgesia and produce anti-allodynia in animals using various experimental models for neuropathic pain. The heptapeptide was found to induce its effects through binding to and activating specific sites apart from any known neurokinin or opioid receptor. Furthermore, we have applied a medicinal chemistry program to develop lead compounds mimicking the effect of SP1-7. The present study was designed to evaluate the pharmacological effect of these compounds using the mouse spared nerve injury (SNI) model of chronic neuropathic pain. Also, as no comprehensive screen with the aim to identify the SP1-7 target has yet been performed we screened our lead compound H-Phe-Phe-NH2 toward a panel of drug targets. The extensive target screen, including 111 targets, did not reveal any hit for the binding site among a number of known receptors or enzymes involved in pain modulation. Our animal studies confirmed that SP1-7, but also synthetic analogs thereof, possesses anti-allodynic effects in the mouse SNI model of neuropathic pain. One of the lead compounds, a constrained H-Phe-Phe-NH2 analog, was shown to exhibit a significant anti-allodynic effect. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

A format for the interchange of scheduling models

NASA Technical Reports Server (NTRS)

Jaap, John P.; Davis, Elizabeth K.

1994-01-01

In recent years a variety of space-activity schedulers have been developed within the aerospace community. Space-activity schedulers are characterized by their need to handle large numbers of activities which are time-window constrained and make high demands on many scarce resources, but are minimally constrained by predecessor/successor requirements or critical paths. Two needs to exchange data between these schedulers have materialized. First, there is significant interest in comparing and evaluating the different scheduling engines to ensure that the best technology is applied to each scheduling endeavor. Second, there is a developing requirement to divide a single scheduling task among different sites, each using a different scheduler. In fact, the scheduling task for International Space Station Alpha (ISSA) will be distributed among NASA centers and among the international partners. The format used to interchange scheduling data for ISSA will likely use a growth version of the format discussed in this paper. The model interchange format (or MIF, pronounced as one syllable) discussed in this paper is a robust solution to the need to interchange scheduling requirements for space activities. It is highly extensible, human-readable, and can be generated or edited with common text editors. It also serves well the need to support a 'benchmark' data case which can be delivered on any computer platform.

Molecular dynamics studies unravel role of conserved residues responsible for movement of ions into active site of DHBPS

PubMed Central

Shinde, Ranajit Nivrutti; Karthikeyan, Subramanian; Singh, Balvinder

2017-01-01

3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg2+. Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg2+ is still elusive. Therefore, mechanistic role played by Mg2+ in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg2+ have shown entry of Mg2+ from bulk solvent into active site. Presence of Mg2+ in active site has constrained conformations of Ru5P and has reduced flexibility of loop-2. Formation of hydrogen bonds among Thr-108 and residues - Gly-109, Val-110, Ser-111, and Asp-114 are found to be critical for entry of Mg2+ into active site. Subsequent in silico mutations of residues, Thr-108 and Asp-114 have substantiated the importance of these interactions. Loop-4 of one monomer is being proposed to act as a “lid” covering the active site of other monomer. Further, the conserved nature of residues taking part in the transfer of Mg2+ suggests the same mechanism being present in DHBPS of other microorganisms. Thus, this study provides insights into the functioning of DHBPS that can be used for the designing of inhibitors. PMID:28079168

Paleoseismic observations along the Langshan range-front fault, Hetao Basin, China: Tectonic and seismic implications

NASA Astrophysics Data System (ADS)

Dong, Shaopeng; Zhang, Peizhen; Zheng, Wenjun; Yu, Zhongyuan; Lei, Qiyun; Yang, Huili; Liu, Jinfeng; Gong, Huilin

2018-04-01

The Langshan range-front fault (LRF) is an active Holocene normal fault that borders Langshan Mountain and the Hetao Basin, northwest of the Ordos Plateau, China. In this study, paleoseismic trenching was undertaken at three sites (North-South): Dongshen village (TC1), Qingshan (TC2), and Wulanhashao (TC3). The paleoevents ED1, ED2, ED3 from TC1 were constrained to 6.0 ± 1.3, 9.6 ± 2.0, and 19.7 ± 4.2 ka, respectively. The single paleoevent (EQ1) from TC2 was constrained to about 6.7 ± 0.1 ka, and the paleoevents EW1, EW2, and EW3 from TC3 were constrained to 2.3 ± 0.4, 6.0 ± 1.0, and before 7.0 ka, respectively. With reference to previous research, the Holocene earthquake sequence of the LRF can be established as 2.30-2.43 (E1), 3.06-4.41 (E2), 6.71-6.80 (E3), 7.60-9.81 (E4), and 19.70 ± 4.20 (E5) ka BP. Events E1, E3, and E4 might have been caused by events with magnitudes of Mw 7.6-7.8 that ruptured the entire LRF. Event E2 might have been smaller magnitude, about M7.0, and ruptured only a portion of the fault. The vertical slip rate of the LRF at the Qingshan site is inferred as 0.9 or 1.4-1.6 mm/year in the last 6.8 ka. The slip rate at Wulanhashao is considered to have been close to, but not <0.66 mm/year since 15 ka BP. We deem the LRF is an unsegmented active fault. Although the possibility of missing events in Late Pleistocene can not be dismissed, we argue the Holocene paleoearthquake history is complete, indicating an average recurrence interval of 2500 years.

Effect of soil property uncertainties on permafrost thaw projections: A calibration-constrained analysis

DOE PAGES

Harp, Dylan R.; Atchley, Adam L.; Painter, Scott L.; ...

2016-02-11

Here, the effect of soil property uncertainties on permafrost thaw projections are studied using a three-phase subsurface thermal hydrology model and calibration-constrained uncertainty analysis. The Null-Space Monte Carlo method is used to identify soil hydrothermal parameter combinations that are consistent with borehole temperature measurements at the study site, the Barrow Environmental Observatory. Each parameter combination is then used in a forward projection of permafrost conditions for the 21more » $$^{st}$$ century (from calendar year 2006 to 2100) using atmospheric forcings from the Community Earth System Model (CESM) in the Representative Concentration Pathway (RCP) 8.5 greenhouse gas concentration trajectory. A 100-year projection allows for the evaluation of intra-annual uncertainty due to soil properties and the inter-annual variability due to year to year differences in CESM climate forcings. After calibrating to borehole temperature data at this well-characterized site, soil property uncertainties are still significant and result in significant intra-annual uncertainties in projected active layer thickness and annual thaw depth-duration even with a specified future climate. Intra-annual uncertainties in projected soil moisture content and Stefan number are small. A volume and time integrated Stefan number decreases significantly in the future climate, indicating that latent heat of phase change becomes more important than heat conduction in future climates. Out of 10 soil parameters, ALT, annual thaw depth-duration, and Stefan number are highly dependent on mineral soil porosity, while annual mean liquid saturation of the active layer is highly dependent on the mineral soil residual saturation and moderately dependent on peat residual saturation. By comparing the ensemble statistics to the spread of projected permafrost metrics using different climate models, we show that the effect of calibration-constrained uncertainty in soil properties, although significant, is less than that produced by structural climate model uncertainty for this location.« less

Effect of soil property uncertainties on permafrost thaw projections: A calibration-constrained analysis

DOE PAGES

Harp, D. R.; Atchley, A. L.; Painter, S. L.; ...

2015-06-29

The effect of soil property uncertainties on permafrost thaw projections are studied using a three-phase subsurface thermal hydrology model and calibration-constrained uncertainty analysis. The Null-Space Monte Carlo method is used to identify soil hydrothermal parameter combinations that are consistent with borehole temperature measurements at the study site, the Barrow Environmental Observatory. Each parameter combination is then used in a forward projection of permafrost conditions for the 21st century (from calendar year 2006 to 2100) using atmospheric forcings from the Community Earth System Model (CESM) in the Representative Concentration Pathway (RCP) 8.5 greenhouse gas concentration trajectory. A 100-year projection allows formore » the evaluation of intra-annual uncertainty due to soil properties and the inter-annual variability due to year to year differences in CESM climate forcings. After calibrating to borehole temperature data at this well-characterized site, soil property uncertainties are still significant and result in significant intra-annual uncertainties in projected active layer thickness and annual thaw depth-duration even with a specified future climate. Intra-annual uncertainties in projected soil moisture content and Stefan number are small. A volume and time integrated Stefan number decreases significantly in the future climate, indicating that latent heat of phase change becomes more important than heat conduction in future climates. Out of 10 soil parameters, ALT, annual thaw depth-duration, and Stefan number are highly dependent on mineral soil porosity, while annual mean liquid saturation of the active layer is highly dependent on the mineral soil residual saturation and moderately dependent on peat residual saturation. As a result, by comparing the ensemble statistics to the spread of projected permafrost metrics using different climate models, we show that the effect of calibration-constrained uncertainty in soil properties, although significant, is less than that produced by structural climate model uncertainty for this location.« less

Effect of soil property uncertainties on permafrost thaw projections: a calibration-constrained analysis

NASA Astrophysics Data System (ADS)

Harp, D. R.; Atchley, A. L.; Painter, S. L.; Coon, E. T.; Wilson, C. J.; Romanovsky, V. E.; Rowland, J. C.

2016-02-01

The effects of soil property uncertainties on permafrost thaw projections are studied using a three-phase subsurface thermal hydrology model and calibration-constrained uncertainty analysis. The null-space Monte Carlo method is used to identify soil hydrothermal parameter combinations that are consistent with borehole temperature measurements at the study site, the Barrow Environmental Observatory. Each parameter combination is then used in a forward projection of permafrost conditions for the 21st century (from calendar year 2006 to 2100) using atmospheric forcings from the Community Earth System Model (CESM) in the Representative Concentration Pathway (RCP) 8.5 greenhouse gas concentration trajectory. A 100-year projection allows for the evaluation of predictive uncertainty (due to soil property (parametric) uncertainty) and the inter-annual climate variability due to year to year differences in CESM climate forcings. After calibrating to measured borehole temperature data at this well-characterized site, soil property uncertainties are still significant and result in significant predictive uncertainties in projected active layer thickness and annual thaw depth-duration even with a specified future climate. Inter-annual climate variability in projected soil moisture content and Stefan number are small. A volume- and time-integrated Stefan number decreases significantly, indicating a shift in subsurface energy utilization in the future climate (latent heat of phase change becomes more important than heat conduction). Out of 10 soil parameters, ALT, annual thaw depth-duration, and Stefan number are highly dependent on mineral soil porosity, while annual mean liquid saturation of the active layer is highly dependent on the mineral soil residual saturation and moderately dependent on peat residual saturation. By comparing the ensemble statistics to the spread of projected permafrost metrics using different climate models, we quantify the relative magnitude of soil property uncertainty to another source of permafrost uncertainty, structural climate model uncertainty. We show that the effect of calibration-constrained uncertainty in soil properties, although significant, is less than that produced by structural climate model uncertainty for this location.

Effect of soil property uncertainties on permafrost thaw projections: a calibration-constrained analysis

NASA Astrophysics Data System (ADS)

Harp, D. R.; Atchley, A. L.; Painter, S. L.; Coon, E. T.; Wilson, C. J.; Romanovsky, V. E.; Rowland, J. C.

2015-06-01

The effect of soil property uncertainties on permafrost thaw projections are studied using a three-phase subsurface thermal hydrology model and calibration-constrained uncertainty analysis. The Null-Space Monte Carlo method is used to identify soil hydrothermal parameter combinations that are consistent with borehole temperature measurements at the study site, the Barrow Environmental Observatory. Each parameter combination is then used in a forward projection of permafrost conditions for the 21st century (from calendar year 2006 to 2100) using atmospheric forcings from the Community Earth System Model (CESM) in the Representative Concentration Pathway (RCP) 8.5 greenhouse gas concentration trajectory. A 100-year projection allows for the evaluation of intra-annual uncertainty due to soil properties and the inter-annual variability due to year to year differences in CESM climate forcings. After calibrating to borehole temperature data at this well-characterized site, soil property uncertainties are still significant and result in significant intra-annual uncertainties in projected active layer thickness and annual thaw depth-duration even with a specified future climate. Intra-annual uncertainties in projected soil moisture content and Stefan number are small. A volume and time integrated Stefan number decreases significantly in the future climate, indicating that latent heat of phase change becomes more important than heat conduction in future climates. Out of 10 soil parameters, ALT, annual thaw depth-duration, and Stefan number are highly dependent on mineral soil porosity, while annual mean liquid saturation of the active layer is highly dependent on the mineral soil residual saturation and moderately dependent on peat residual saturation. By comparing the ensemble statistics to the spread of projected permafrost metrics using different climate models, we show that the effect of calibration-constrained uncertainty in soil properties, although significant, is less than that produced by structural climate model uncertainty for this location.

Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking.

PubMed Central

Harris, M E; Kazantsev, A V; Chen, J L; Pace, N R

1997-01-01

Bacterial ribonuclease P (RNase P), an endonuclease involved in tRNA maturation, is a ribonucleoprotein containing a catalytic RNA. The secondary structure of this ribozyme is well-established, and a low-resolution model of the three-dimensional structure of the ribozyme-substrate complex has been proposed based on site-specific crosslinking and phylogenetic comparative data [Harris ME et al., 1994 EMBO J 13:3953-3963]. However, several substructures of that model were poorly constrained by the available data. In the present analysis, additional constraints between elements within the Escherichia coli RNase P RNA-pre-tRNA complex were determined by intra- and intermolecular crosslinking experiments. Circularly permuted RNase P RNAs were used to position an azidophenacyl photoactive crosslinking agent specifically at strategic sites within the ribozyme-substrate complex. Crosslink sites were mapped by primer extension and confirmed by analysis of the mobility of the crosslinked RNA lariats on denaturing acrylamide gels relative to circular and linear RNA standards. Crosslinked species generally retained significant catalytic activity, indicating that the results reflect the native ribozyme structure. The crosslinking results support the general configuration of the structure model and predicate new positions and orientations for helices that were previously poorly constrained by the data set. The expanded library of crosslinking constraints was used, together with secondary and tertiary structure identified by phylogenetic sequence comparisons, to refine significantly the model of RNase P RNA with bound substrate pre-tRNA. The crosslinking results and data from chemical-modification and mutational studies are discussed in the context of the current structural perspective on this ribozyme. PMID:9174092

The Lusi mud eruption dynamics: constraints from field data.

NASA Astrophysics Data System (ADS)

Mazzini, Adriano; Sciarra, Alessandra; Lupi, Matteo; Mauri, Guillaume; Karyono, Karyono; Husein, Alwi; Aquino, Ida; Ricco, Ciro; Obermann, Anne; Hadi, Soffian

2017-04-01

The Indonesian Lusi eruption has been spewing boiling water, gas, and sediments since the 29th of May 2006. Initially, numerous aligned eruptions sites appeared along the Watukosek fault system that was reactivated after the Yogyakarta earthquake occurring the 27th of May in the Java Island. Since its birth Lusi erupted with a pulsating behavior showing intermittent periods of stronger activity resulting in higher fluids and solid emissions intervals. Since 2010 two active vents are constantly active. We conducted detailed monitoring of such clastic geysering activity and this allowed us to distinguish four distinct phases that follow each other and that reoccur every 30 minutes: (1) regular bubbling activity (constant emission of water, mud breccia, and gas); (2) clastic geysering phase with intense bubbling (consisting in reduced vapor emission and more powerful diffused mud bursting); (3) clastic geysering with mud bursts and intense vapour discharge (typically dense plume that propagates up to 100 m in height); (4) quiescent phase marking the end of the geysering activity (basically no gas emissions or bursts observed). In order to better understand this pulsating behavior and to constrain the mechanisms controlling its activity, we designed a multidisciplinary monitoring of the eruption site combining the deployment of numerous instruments around the crater site. Processing of the collected data reveals the dynamic activity of Lusi's craters. Satellite images show that the location of these vents migrated along a NE-SW direction. This is subparallel to the direction of the Watukosek fault system that is the zone of (left) lateral deformation upon which Lusi developed in 2006. Coupling HR camera images with broadband and short period seismic stations allowed us to describe the seismic signal generated by clastic geysering and to constrain the depth of the source generating the signal. We measure a delay between the seismic (harmonic) record and the associated clastic geyser explosion of approximately 3 s. This, in agreement with previous studies, corresponds to a source located some tens of meters depth inside the conduits. We ascribe the harmonic seismic signal to rise of batches of H2O-CO2-CH4 fluids inside the conduit. Once they approach the water-vapour region the sudden pressure drop triggers flashing and the exsolution of the dissolved CO2 and CH4. In the last part of our study we verified whether the powerful clastic geysering (emitting jets up to 20 m high) may induce local deformation of the mud edifice. During the stronger geysering events we measure an increase and drop of gravity overtime that are related to change of mud density within the feeder conduit. We process continuous camera recordings with a video magnifying tool capable of enhancing small variations in the recorded images. Results highlight that major eruptive events are preceded by a deformation of the mud edifice surrounding the vents. Ongoing studies aim to verify if these events are also captured by the tiltmeter measurements. This study represents a step forward to better understand the activity that characterizes Lusi. Further studies will help to better constrain the reactions and dynamics ongoing inside the conduit.

Seismic velocity and crustal thickness inversions: Moon and Mars

NASA Astrophysics Data System (ADS)

Drilleau, Melanie; Blanchette-Guertin, Jean-François; Kawamura, Taichi; Lognonné, Philippe; Wieczorek, Mark

2017-04-01

We present results from new inversions of seismic data arrival times acquired by the Apollo active and passive experiments. Markov chain Monte Carlo inversions are used to constrain (i) 1-D lunar crustal and upper mantle velocity models and (ii) 3-D lateral crustal thickness models under the Apollo stations and the artificial and natural impact sites. A full 3-D model of the lunar crustal thickness is then obtained using the GRAIL gravimetric data, anchored by the crustal thicknesses under each Apollo station and impact site. To avoid the use of any seismic reference model, a Bayesian inversion technique is implemented. The advantage of such an approach is to obtain robust probability density functions of interior structure parameters governed by uncertainties on the seismic data arrival times. 1-D seismic velocities are parameterized using C1-Bézier curves, which allow the exploration of both smoothly varying models and first-order discontinuities. The parameters of the inversion include the seismic velocities of P and S waves as a function of depth, the thickness of the crust under each Apollo station and impact epicentre. The forward problem consists in a ray tracing method enabling both the relocation of the natural impact epicenters, and the computation of time corrections associated to the surface topography and the crustal thickness variations under the stations and impact sites. The results show geology-related differences between the different sites, which are due to contrasts in megaregolith thickness and to shallow subsurface composition and structure. Some of the finer structural elements might be difficult to constrain and might fall within the uncertainties of the dataset. However, we use the more precise LROC-located epicentral locations for the lunar modules and Saturn-IV upper stage artificial impacts, reducing some of the uncertainties observed in past studies. In the framework of the NASA InSight/SEIS mission to Mars, the method developed in this study will be used to constrain the Martian crustal thickness as soon as the first data will be available (late 2018). For Insight, impacts will be located by MRO data differential analysis, which provide a known location enabling the direct inversion of all differential travel times with respect to P arrival time. We have performed resolution tests to investigate to what extend impact events might help us to constrain the Martian crustal thickness. Due to the high flexibility of the Bayesian algorithm, the interior model will be refined each time a new event will be detected.

The Importance of Mars Samples in Constraining the Geological and Geophysical Processes on Mars and the Nature of its Crust, Mantle, and Core

NASA Astrophysics Data System (ADS)

iMOST Team; Herd, C. D. K.; Ammannito, E.; Anand, M.; Debaille, V.; Hallis, L. J.; McCubbin, F. M.; Schmitz, N.; Usui, T.; Weiss, B. P.; Altieri, F.; Amelin, Y.; Beaty, D. W.; Benning, L. G.; Bishop, J. L.; Borg, L. E.; Boucher, D.; Brucato, J. R.; Busemann, H.; Campbell, K. A.; Carrier, B. L.; Czaja, A. D.; Des Marais, D. J.; Dixon, M.; Ehlmann, B. L.; Farmer, J. D.; Fernandez-Remolar, D. C.; Fogarty, J.; Glavin, D. P.; Goreva, Y. S.; Grady, M. M.; Harrington, A. D.; Hausrath, E. M.; Horgan, B.; Humayun, M.; Kleine, T.; Kleinhenz, J.; Mangold, N.; Mackelprang, R.; Mayhew, L. E.; McCoy, J. T.; McLennan, S. M.; McSween, H. Y.; Moser, D. E.; Moynier, F.; Mustard, J. F.; Niles, P. B.; Ori, G. G.; Raulin, F.; Rettberg, P.; Rucker, M. A.; Sefton-Nash, E.; Sephton, M. A.; Shaheen, R.; Shuster, D. L.; Siljestrom, S.; Smith, C. L.; Spry, J. A.; Steele, A.; Swindle, T. D.; ten Kate, I. L.; Tosca, N. J.; Van Kranendonk, M. J.; Wadhwa, M.; Werner, S. C.; Westall, F.; Wheeler, R. M.; Zipfel, J.; Zorzano, M. P.

2018-04-01

We present the main sample types from any potential Mars Sample Return landing site that would be required to constrain the geological and geophysical processes on Mars, including the origin and nature of its crust, mantle, and core.

Unmasking tandem site interaction in human acetylcholinesterase. Substrate activation with a cationic acetanilide substrate.

PubMed

Johnson, Joseph L; Cusack, Bernadette; Davies, Matthew P; Fauq, Abdul; Rosenberry, Terrone L

2003-05-13

Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge, and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acyl enzyme intermediate is produced. A conformational interaction between the A- and P-sites has recently been found to modulate ligand affinities. We now demonstrate that this interaction is of functional importance by showing that the acetylation rate constant of a substrate bound to the A-site is increased by a factor a when a second molecule of substrate binds to the P-site. This demonstration became feasible through the introduction of a new acetanilide substrate analogue of acetylcholine, 3-(acetamido)-N,N,N-trimethylanilinium (ATMA), for which a = 4. This substrate has a low acetylation rate constant and equilibrates with the catalytic site, allowing a tractable algebraic solution to the rate equation for substrate hydrolysis. ATMA affinities for the A- and P-sites deduced from the kinetic analysis were confirmed by fluorescence titration with thioflavin T as a reporter ligand. Values of a >1 give rise to a hydrolysis profile called substrate activation, and the AChE site-specific mutant W86F, and to a lesser extent wild-type human AChE itself, showed substrate activation with acetylthiocholine as the substrate. Substrate activation was incorporated into a previous catalytic scheme for AChE in which a bound P-site ligand can also block product dissociation from the A-site, and two additional features of the AChE catalytic pathway were revealed. First, the ability of a bound P-site ligand to increase the substrate acetylation rate constant varied with the structure of the ligand: thioflavin T accelerated ATMA acetylation by a factor a(2) of 1.3, while propidium failed to accelerate. Second, catalytic rate constants in the initial intermediate formed during acylation (EAP, where EA is the acyl enzyme and P is the alcohol leaving group cleaved from the ester substrate) may be constrained such that the leaving group P must dissociate before hydrolytic deacylation can occur.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

PubMed

Suzuki, Harukazu; Forrest, Alistair R R; van Nimwegen, Erik; Daub, Carsten O; Balwierz, Piotr J; Irvine, Katharine M; Lassmann, Timo; Ravasi, Timothy; Hasegawa, Yuki; de Hoon, Michiel J L; Katayama, Shintaro; Schroder, Kate; Carninci, Piero; Tomaru, Yasuhiro; Kanamori-Katayama, Mutsumi; Kubosaki, Atsutaka; Akalin, Altuna; Ando, Yoshinari; Arner, Erik; Asada, Maki; Asahara, Hiroshi; Bailey, Timothy; Bajic, Vladimir B; Bauer, Denis; Beckhouse, Anthony G; Bertin, Nicolas; Björkegren, Johan; Brombacher, Frank; Bulger, Erika; Chalk, Alistair M; Chiba, Joe; Cloonan, Nicole; Dawe, Adam; Dostie, Josee; Engström, Pär G; Essack, Magbubah; Faulkner, Geoffrey J; Fink, J Lynn; Fredman, David; Fujimori, Ko; Furuno, Masaaki; Gojobori, Takashi; Gough, Julian; Grimmond, Sean M; Gustafsson, Mika; Hashimoto, Megumi; Hashimoto, Takehiro; Hatakeyama, Mariko; Heinzel, Susanne; Hide, Winston; Hofmann, Oliver; Hörnquist, Michael; Huminiecki, Lukasz; Ikeo, Kazuho; Imamoto, Naoko; Inoue, Satoshi; Inoue, Yusuke; Ishihara, Ryoko; Iwayanagi, Takao; Jacobsen, Anders; Kaur, Mandeep; Kawaji, Hideya; Kerr, Markus C; Kimura, Ryuichiro; Kimura, Syuhei; Kimura, Yasumasa; Kitano, Hiroaki; Koga, Hisashi; Kojima, Toshio; Kondo, Shinji; Konno, Takeshi; Krogh, Anders; Kruger, Adele; Kumar, Ajit; Lenhard, Boris; Lennartsson, Andreas; Lindow, Morten; Lizio, Marina; Macpherson, Cameron; Maeda, Norihiro; Maher, Christopher A; Maqungo, Monique; Mar, Jessica; Matigian, Nicholas A; Matsuda, Hideo; Mattick, John S; Meier, Stuart; Miyamoto, Sei; Miyamoto-Sato, Etsuko; Nakabayashi, Kazuhiko; Nakachi, Yutaka; Nakano, Mika; Nygaard, Sanne; Okayama, Toshitsugu; Okazaki, Yasushi; Okuda-Yabukami, Haruka; Orlando, Valerio; Otomo, Jun; Pachkov, Mikhail; Petrovsky, Nikolai; Plessy, Charles; Quackenbush, John; Radovanovic, Aleksandar; Rehli, Michael; Saito, Rintaro; Sandelin, Albin; Schmeier, Sebastian; Schönbach, Christian; Schwartz, Ariel S; Semple, Colin A; Sera, Miho; Severin, Jessica; Shirahige, Katsuhiko; Simons, Cas; St Laurent, George; Suzuki, Masanori; Suzuki, Takahiro; Sweet, Matthew J; Taft, Ryan J; Takeda, Shizu; Takenaka, Yoichi; Tan, Kai; Taylor, Martin S; Teasdale, Rohan D; Tegnér, Jesper; Teichmann, Sarah; Valen, Eivind; Wahlestedt, Claes; Waki, Kazunori; Waterhouse, Andrew; Wells, Christine A; Winther, Ole; Wu, Linda; Yamaguchi, Kazumi; Yanagawa, Hiroshi; Yasuda, Jun; Zavolan, Mihaela; Hume, David A; Arakawa, Takahiro; Fukuda, Shiro; Imamura, Kengo; Kai, Chikatoshi; Kaiho, Ai; Kawashima, Tsugumi; Kawazu, Chika; Kitazume, Yayoi; Kojima, Miki; Miura, Hisashi; Murakami, Kayoko; Murata, Mitsuyoshi; Ninomiya, Noriko; Nishiyori, Hiromi; Noma, Shohei; Ogawa, Chihiro; Sano, Takuma; Simon, Christophe; Tagami, Michihira; Takahashi, Yukari; Kawai, Jun; Hayashizaki, Yoshihide

2009-05-01

Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their time-dependent activities and target genes. Systematic siRNA knockdown of 52 transcription factors confirmed the roles of individual factors in the regulatory network. Our results indicate that cellular states are constrained by complex networks involving both positive and negative regulatory interactions among substantial numbers of transcription factors and that no single transcription factor is both necessary and sufficient to drive the differentiation process.

Seasonal and diel movements of white sturgeon in the lower columbia river

USGS Publications Warehouse

Parsley, M.J.; Popoff, N.D.; Van Der Leeuw, B. K.; Wright, C.D.

2008-01-01

Continuous monitoring of the movements and depths used by white sturgeon Acipenser transmontanus with acoustic telemetry technologies in the lower Columbia River provided information on diel and seasonal migrations, local movements, and site fidelity. White sturgeon moved to shallower water at night and showed greater activity, inferred from rates of movement, than during daytime. The extent of local movement within a season was variable among fish; some fish readily moved among habitats while the movements of others were more constrained. White sturgeon were absent from the study area (river kilometers 45-52) during winter and returned from upstream during the spring, confirming an upstream seasonal migration in the fall and downstream migration in spring. The return of individual fish and reoccupation of areas previously inhabited showed that some white sturgeon exhibit site fidelity. This work shows that studies seeking to characterize habitat for white sturgeon need to be cognizant of diel migrations and site fidelity. We urge caution in the use of limited fish location data to describe habitats if diel activities and fine-scale movements are not known.

Site-Specific Hydrogen Isotope Composition of Propane: Mass spectrometric methods, equilibrium temperature dependence, and kinetics of exchange

NASA Astrophysics Data System (ADS)

Xie, H.; Ponton, C.; Kitchen, N.; Lloyd, M. K.; Lawson, M.; Formolo, M. J.; Eiler, J. M.

2016-12-01

Intramolecular isotope ordering can constrain temperatures of synthesis, mechanisms of formation, and/or source substrates of organic compounds. Here we explore site-specific hydrogen isotope variations of propane. Statistical thermodynamic models predict that at equilibrium methylene hydrogen (-CH2-) in propane will be 10's of per mil higher in D/H ratio than methyl hydrogen (-CH3) at geologically relevant temperatures, and that this difference is highly temperature dependent ( 0.5-1 ‰/°C). Chemical-kinetic controls on site-specific D/H in propane could constrain the mechanisms, conditions and extents of propane synthesis or destruction. We have developed a method for measuring the difference in D/H ratio between methylene and methyl hydrogen in propane by gas source mass spectrometry. The data were measured using the Thermo Fisher Double Focusing Sector high resolution mass spectrometer (DFS), and involve comparison of the D/H ratios of molecular ion (C3H8+) and the ethyl fragmental ion (C2H5+). We demonstrate the accuracy and precision of this method through analysis of D-labeled and independently analyzed propanes. In the exchange experiments, propane was heated (100-200 oC) either alone or in the presence of D-enriched water (δD=1,1419 ‰ SMOW), with or without one of several potentially catalytic substrates for hours to weeks. Propane was found to exchange hydrogen with water vigorously at 200 °C in the presence of metal catalysts. In the presence of Ni catalyst, methylene hydrogen exchanges 2.5 times faster than methyl hydrogen. Hydrogen exchange in the presence of Pd catalyst is more effective and can equilibrate hydrogen isotope distribution on propane on the order of 7 days. Isotopic exchange in the presence of natural materials have also been tested, but is only measurable in the methylene group at 200 °C. High catalytic activity of Pd permits attainment of a bracketed, time-invariant equilibrium state that we use to calibrate the site-specific thermometer; these experiments also provide a reference frame for reporting mass spectrometric data. Differential H-exchange rates of the two molecular sites in propane could be a new tool to constrain thermal history of sub-surface propane. Our experimental and mass spectrometric approaches should be generalizable to other hydrocarbon compounds.

Workplace health and safety regulations: Impact of enforcement and consultation on workers' compensation claims rates in Washington State.

PubMed

Baggs, James; Silverstein, Barbara; Foley, Michael

2003-05-01

There has been considerable debate in the public policy arena about the appropriate mix of regulatory enforcement and consultation in achieving desired health and safety behavior across industries. Recently there has been a shift in federal policy toward voluntary approaches and constraining the scope of enforcement programs, although there is little evidence that this might improve health and safety outcomes. To address this, we examined changes in lost time workers compensation claims rates for Washington State employers who had (1) no OSHA State Plan (WISHA) activity, (2) enforcement, (3) consultation, and (4) both types of visits. Compensable claims rates, hours, and WISHA activity were determined for each employer account with a single business location that had payroll hours reported for every quarter from 1997-2000 and more than 10 employees. We used a generalized estimating equations (GEE) approach to Poisson regression to model the association between WISHA activity and claims rate controlling for other external factors. Controlling for previous claims rate and average size, claims rates for employers with WISHA enforcement activity declined 22.5% in fixed site industry SIC codes compared to 7% among employers with no WISHA activity (P < 0.05), and in non-fixed site SICs (e.g., construction) claims rates declined 12.8% for employers with enforcement activity compared to a 7.4% decline for those with no WISHA activity (P > 0.10). WISHA consultation activity was not associated with a greater decline in compensable claims rates (-2.3% for fixed sites and +3.5% for non-fixed sites). WISHA activity did not adversely affect worksite survivability through the study period. Enforcement inspections are significantly associated with decreasing compensable workers compensation claims rates especially for fixed site employers. We were unable to identify an association between consultation activities and decreasing claims rates. Copyright 2003 Wiley-Liss, Inc.

Mineralogical impact on long-term patterns of soil nitrogen and phosphorus enzyme activities

NASA Astrophysics Data System (ADS)

Mikutta, Robert; Turner, Stephanie; Meyer-Stüve, Sandra; Guggenberger, Georg; Dohrmann, Reiner; Schippers, Axel

2014-05-01

Soil chronosequences provide a unique opportunity to study microbial activity over time in mineralogical diverse soils of different ages. The main objective of this study was to test the effect of mineralogical properties, nutrient and organic matter availability over whole soil pro-files on the abundance and activity of the microbial communities. We focused on microbio-logical processes involved in nitrogen and phosphorus cycling at the 120,000-year Franz Josef soil chronosequence. Microbial abundances (microbial biomass and total cell counts) and enzyme activities (protease, urease, aminopeptidase, and phosphatase) were determined and related to nutrient contents and mineralogical soil properties. Both, microbial abundances and enzyme activities decreased with soil depth at all sites. In the organic layers, microbial biomass and the activities of N-hydrolyzing enzymes showed their maximum at the intermediate-aged sites, corresponding to a high aboveground biomass. In contrast, the phosphatase activity increased with site age. The activities of N-hydrolyzing enzymes were positively correlated with total carbon and nitrogen contents, whereas the phosphatase activity was negatively correlated with the phosphorus content. In the mineral soil, the enzyme activities were generally low, thus reflecting the presence of strongly sorbing minerals. Sub-strate-normalized enzyme activities correlated negatively to clay content as well as poorly crystalline Al and Fe oxyhydroxides, supporting the view that the evolution of reactive sec-ondary mineral phases alters the activity of the microbial communities by constraining sub-strate availability. Our data suggest a strong mineralogical influence on nutrient cycling par-ticularly in subsoil environments.

Assessing the responses of coastal cetaceans to the construction of offshore wind turbines.

PubMed

Thompson, Paul M; Lusseau, David; Barton, Tim; Simmons, Dave; Rusin, Jan; Bailey, Helen

2010-08-01

The expansion of offshore renewables has raised concerns over potential disturbance to coastal cetaceans. In this study, we used passive acoustic monitoring to assess whether cetaceans responded to pile-driving noise during the installation of two 5MW offshore wind turbines off NE Scotland in 2006. Monitoring was carried out at both the turbine site and a control site in 2005, 2006 and 2007. Harbour porpoises occurred regularly around the turbine site in all years, but there was some evidence that porpoises did respond to disturbance from installation activities. We use these findings to highlight how uncertainty over cetacean distribution and the scale of disturbance effects constrains opportunities for B-A-C-I studies. We explore alternative approaches to assessing the impact of offshore wind farm upon cetaceans, and make recommendations for the research and monitoring that will be required to underpin future developments. Copyright 2010 Elsevier Ltd. All rights reserved.

PPSITE - A New Method of Site Evaluation for Longleaf Pine: Model Development and User's Guide

Treesearch

Constance A. Harrington

1990-01-01

A model was developed to predict site index (base age 50 years) for longleaf pine (Pinus palustris Mill.). The model, named PPSITE, was based on soil characteristics, site location on the landscape, and land history. The model was constrained so that the relationship between site index and each soil-site variable was consistent with what was known...

Wind-Driven Erosion and Exposure Potential at Mars 2020 Rover Candidate-Landing Sites.

PubMed

Chojnacki, Matthew; Banks, Maria; Urso, Anna

2018-02-01

Aeolian processes have likely been the predominant geomorphic agent for most of Mars' history and have the potential to produce relatively young exposure ages for geologic units. Thus, identifying local evidence for aeolian erosion is highly relevant to the selection of landing sites for future missions, such as the Mars 2020 Rover mission that aims to explore astrobiologically relevant ancient environments. Here we investigate wind-driven activity at eight Mars 2020 candidate-landing sites to constrain erosion potential at these locations. To demonstrate our methods, we found that contemporary dune-derived abrasion rates were in agreement with rover-derived exhumation rates at Gale crater and could be employed elsewhere. The Holden crater candidate site was interpreted to have low contemporary erosion rates, based on the presence of a thick sand coverage of static ripples. Active ripples at the Eberswalde and southwest Melas sites may account for local erosion and the dearth of small craters. Moderate-flux regional dunes near Mawrth Vallis were deemed unrepresentative of the candidate site, which is interpreted to currently be experiencing low levels of erosion. The Nili Fossae site displayed the most unambiguous evidence for local sand transport and erosion, likely yielding relatively young exposure ages. The downselected Jezero crater and northeast Syrtis sites had high-flux neighboring dunes and exhibited substantial evidence for sediment pathways across their ellipses. Both sites had relatively high estimated abrasion rates, which would yield young exposure ages. The downselected Columbia Hills site lacked evidence for sand movement, and contemporary local erosion rates are estimated to be relatively low.

Wind-Driven Erosion and Exposure Potential at Mars 2020 Rover Candidate-Landing Sites

PubMed Central

Chojnacki, Matthew; Banks, Maria; Urso, Anna

2018-01-01

Aeolian processes have likely been the predominant geomorphic agent for most of Mars’ history and have the potential to produce relatively young exposure ages for geologic units. Thus, identifying local evidence for aeolian erosion is highly relevant to the selection of landing sites for future missions, such as the Mars 2020 Rover mission that aims to explore astrobiologically relevant ancient environments. Here we investigate wind-driven activity at eight Mars 2020 candidate-landing sites to constrain erosion potential at these locations. To demonstrate our methods, we found that contemporary dune-derived abrasion rates were in agreement with rover-derived exhumation rates at Gale crater and could be employed elsewhere. The Holden crater candidate site was interpreted to have low contemporary erosion rates, based on the presence of a thick sand coverage of static ripples. Active ripples at the Eberswalde and southwest Melas sites may account for local erosion and the dearth of small craters. Moderate-flux regional dunes near Mawrth Vallis were deemed unrepresentative of the candidate site, which is interpreted to currently be experiencing low levels of erosion. The Nili Fossae site displayed the most unambiguous evidence for local sand transport and erosion, likely yielding relatively young exposure ages. The downselected Jezero crater and northeast Syrtis sites had high-flux neighboring dunes and exhibited substantial evidence for sediment pathways across their ellipses. Both sites had relatively high estimated abrasion rates, which would yield young exposure ages. The downselected Columbia Hills site lacked evidence for sand movement, and contemporary local erosion rates are estimated to be relatively low. PMID:29568719

Wind-Driven Erosion and Exposure Potential at Mars 2020 Rover Candidate-Landing Sites

NASA Astrophysics Data System (ADS)

Chojnacki, Matthew; Banks, Maria; Urso, Anna

2018-02-01

Aeolian processes have likely been the predominant geomorphic agent for most of Mars' history and have the potential to produce relatively young exposure ages for geologic units. Thus, identifying local evidence for aeolian erosion is highly relevant to the selection of landing sites for future missions, such as the Mars 2020 Rover mission that aims to explore astrobiologically relevant ancient environments. Here we investigate wind-driven activity at eight Mars 2020 candidate-landing sites to constrain erosion potential at these locations. To demonstrate our methods, we found that contemporary dune-derived abrasion rates were in agreement with rover-derived exhumation rates at Gale crater and could be employed elsewhere. The Holden crater candidate site was interpreted to have low contemporary erosion rates, based on the presence of a thick sand coverage of static ripples. Active ripples at the Eberswalde and southwest Melas sites may account for local erosion and the dearth of small craters. Moderate-flux regional dunes near Mawrth Vallis were deemed unrepresentative of the candidate site, which is interpreted to currently be experiencing low levels of erosion. The Nili Fossae site displayed the most unambiguous evidence for local sand transport and erosion, likely yielding relatively young exposure ages. The downselected Jezero crater and northeast Syrtis sites had high-flux neighboring dunes and exhibited substantial evidence for sediment pathways across their ellipses. Both sites had relatively high estimated abrasion rates, which would yield young exposure ages. The downselected Columbia Hills site lacked evidence for sand movement, and contemporary local erosion rates are estimated to be relatively low.

Active constrained clustering by examining spectral Eigenvectors

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri L.; desJardins, Marie; Xu, Qianjun

2005-01-01

This work focuses on the active selection of pairwise constraints for spectral clustering. We develop and analyze a technique for Active Constrained Clustering by Examining Spectral eigenvectorS (ACCESS) derived from a similarity matrix.

Constraints on the Opening Rate of Bands on Europa

NASA Technical Reports Server (NTRS)

Stempel, M. M.; Barr, A. C.; Pappalardo, R. T.

2004-01-01

The opening rates of two bands on Europa, inferred to be sites of spreading of the icy lithosphere, are constrained based on a mid-ocean ridge analog model. Estimates of brittle-ductile transition depth combined with a conductive cooling model limit active band lifetimes to 0.24 - 35 Myr and strain rates of 8.1 x 10(exp -13) - 8.2 x 10(exp -15)/s. These values suggest tensile strengths for ice on Europa of 0.46 - 2.3 MPa, consistent with nonsynchronous rotation as the dominant driving mechanism for band opening.

An orthosteric inhibitor of the RAS-SOS interaction.

PubMed

Nickerson, Seth; Joy, Stephen T; Arora, Paramjit S; Bar-Sagi, Dafna

2013-01-01

Rat sarcoma (RAS) proteins are signaling nodes that transduce extracellular cues into precise alterations in cellular physiology by engaging effector pathways. RAS signaling thus regulates diverse cell processes including proliferation, migration, differentiation, and survival. Owing to this central role in governing mitogenic signals, RAS pathway components are often dysregulated in human diseases. Targeted therapy of RAS pathways has generally not been successful, largely because of the robust biochemistry of the targets and their multifaceted network of molecular regulators. The rate-limiting step of RAS activation is Son of Sevenless (SOS)-mediated nucleotide exchange involving a single evolutionarily conserved catalytic helix from SOS. Structure function data of this mechanism provided a strong platform to design an SOS-derived, helically constrained peptide mimic as an inhibitor of the RAS-SOS interaction. In this chapter, we review RAS-SOS signaling dynamics and present evidence supporting the novel paradigm of inhibiting their interaction as a therapeutic strategy. We then describe a method of generating helically constrained peptide mimics of protein surfaces, which we have employed to inhibit the RAS-SOS active site interaction. The biochemical and functional properties of this SOS mimic support the premise that inhibition of RAS-nucleotide exchange can effectively block RAS activation and downstream signaling. © 2013 Elsevier Inc. All rights reserved.

The promise and peril of intensive-site-based ecological research: insights from the Hubbard Brook ecosystem study

Treesearch

Timothy J. Fahey; Pamela H. Templer; Bruce T. Anderson; John J. Battles; John L. Campbell; Charles T. Driscoll; Anthony R. Fusco; Mark B. Green; Karim-Aly S. Kassam; Nicholas L. Rodenhouse; Lindsey Rustad; Paul G. Schaberg; Matthew A. Vadeboncoeur

2015-01-01

Ecological research is increasingly concentrated at particular locations or sites. This trend reflects a variety of advantages of intensive, site-based research, but also raises important questions about the nature of such spatially delimited research: how well does site based research represent broader areas, and does it constrain scientific discovery? We provide an...

SITE CHARACTERIZATION TO SUPPORT DEVELOPMENT OF CONCEPTUAL SITE MODELS AND TRANSPORT MODELS FOR MONITORING CONTAMINANTS IN GROUND WATER

EPA Science Inventory

The development of conceptual and predictive models is an important tool to guide site characterization in support of monitoring contaminants in ground water. The accuracy of predictive models is limited by the adequacy of the input data and the assumptions made to constrain mod...

One- and two-objective approaches to an area-constrained habitat reserve site selection problem

Treesearch

Stephanie Snyder; Charles ReVelle; Robert Haight

2004-01-01

We compare several ways to model a habitat reserve site selection problem in which an upper bound on the total area of the selected sites is included. The models are cast as optimization coverage models drawn from the location science literature. Classic covering problems typically include a constraint on the number of sites that can be selected. If potential reserve...

Methyl Transfer by Substrate Signaling from a Knotted Protein Fold

PubMed Central

Christian, Thomas; Sakaguchi, Reiko; Perlinska, Agata P.; Lahoud, Georges; Ito, Takuhiro; Taylor, Erika A.; Yokoyama, Shigeyuki; Sulkowska, Joanna I.; Hou, Ya-Ming

2017-01-01

Proteins with knotted configurations are restricted in conformational space relative to unknotted proteins. Little is known if knotted proteins have sufficient dynamics to communicate between spatially separated substrate-binding sites. In bacteria, TrmD is a methyl transferase that uses a knotted protein fold to catalyze methyl transfer from S-adenosyl methionine (AdoMet) to G37-tRNA. The product m1G37-tRNA is essential for life as a determinant to maintain protein synthesis reading-frame. Using an integrated approach of structure, kinetic, and computational analysis, we show here that the structurally constrained TrmD knot is required for its catalytic activity. Unexpectedly, the TrmD knot has complex internal movements that respond to AdoMet binding and signaling. Most of the signaling propagates the free energy of AdoMet binding to stabilize tRNA binding and to assemble the active site. This work demonstrates new principles of knots as an organized structure that captures the free energies of substrate binding to facilitate catalysis. PMID:27571175

Optocontrol of glutamate receptor activity by single side-chain photoisomerization

PubMed Central

Klippenstein, Viktoria; Hoppmann, Christian; Ye, Shixin; Wang, Lei; Paoletti, Pierre

2017-01-01

Engineering light-sensitivity into proteins has wide ranging applications in molecular studies and neuroscience. Commonly used tethered photoswitchable ligands, however, require solvent-accessible protein labeling, face structural constrains, and are bulky. Here, we designed a set of optocontrollable NMDA receptors by directly incorporating single photoswitchable amino acids (PSAAs) providing genetic encodability, reversibility, and site tolerance. We identified several positions within the multi-domain receptor endowing robust photomodulation. PSAA photoisomerization at the GluN1 clamshell hinge is sufficient to control glycine sensitivity and activation efficacy. Strikingly, in the pore domain, flipping of a M3 residue within a conserved transmembrane cavity impacts both gating and permeation properties. Our study demonstrates the first detection of molecular rearrangements in real-time due to the reversible light-switching of single amino acid side-chains, adding a dynamic dimension to protein site-directed mutagenesis. This novel approach to interrogate neuronal protein function has general applicability in the fast expanding field of optopharmacology. DOI: http://dx.doi.org/10.7554/eLife.25808.001 PMID:28534738

Active site remodeling switches HIV specificity of antiretroviral TRIMCyp

PubMed Central

Price, Amanda J; Marzetta, Flavia; Lammers, Michael; Ylinen, Laura M J; Schaller, Torsten; Wilson, Sam J; Towers, Greg J; James, Leo C

2011-01-01

TRIMCyps are primate antiretroviral proteins that potently inhibit HIV replication. Here we describe how rhesus macaque TRIMCyp (RhTC) has evolved to target and restrict HIV-2. We show that the ancestral cyclophilin A (CypA) domain of RhTC targets HIV-2 capsid with weak affinity, which is strongly increased in RhTC by two mutations (D66N and R69H) at the expense of HIV-1 binding. These mutations disrupt a constraining intramolecular interaction in CypA, triggering the complete restructuring (>16 Å) of an active site loop. This new configuration discriminates between divergent HIV-1 and HIV-2 loop conformations mediated by capsid residue 88. Viral sensitivity to RhTC restriction can be conferred or abolished by mutating position 88. Furthermore, position 88 determines the susceptibility of naturally occurring HIV-1 sequences to restriction. Our results reveal the complex molecular, structural and thermodynamic changes that underlie the ongoing evolutionary race between virus and host. PMID:19767750

Impact of dissolution on the sedimentary record of the Paleocene-Eocene thermal maximum

NASA Astrophysics Data System (ADS)

Bralower, Timothy J.; Kelly, D. Clay; Gibbs, Samantha; Farley, Kenneth; Eccles, Laurie; Lindemann, T. Logan; Smith, Gregory J.

2014-09-01

The input of massive amounts of carbon to the atmosphere and ocean at the Paleocene-Eocene Thermal Maximum (PETM; ˜55.53 Ma) resulted in pervasive carbonate dissolution at the seafloor. At many sites this dissolution also penetrated into the underlying sediment column. The magnitude of dissolution at and below the seafloor, a process known as chemical erosion, and its effect on the stratigraphy of the PETM, are notoriously difficult to constrain. Here, we illuminate the impact of dissolution by analyzing the complete spectrum of sedimentological grain sizes across the PETM at three deep-sea sites characterized by a range of bottom water dissolution intensity. We show that the grain size spectrum provides a measure of the sediment fraction lost during dissolution. We compare these data with dissolution and other proxy records, electron micrograph observations of samples and lithology. The complete data set indicates that the two sites with slower carbonate accumulation, and less active bioturbation, are characterized by significant chemical erosion. At the third site, higher carbonate accumulation rates, more active bioturbation, and possibly winnowing have limited the impacts of dissolution. However, grain size data suggest that bioturbation and winnowing were not sufficiently intense to diminish the fidelity of isotopic and microfossil assemblage records.

Hydrothermal Alteration of Open Fractures in Prospective Geothermal Drill Cores, Akutan Island, Alaska

NASA Astrophysics Data System (ADS)

Kent, T.

2011-12-01

The goal of this study is to constrain the most recent thermal alteration of two drill cores (HSB2/HSB4) from the Island of Akutan in the Aleutian Islands of Alaska. These cores are characterized by identifying mineralogy using x-ray diffraction spectra, energy dispersive spectroscopy with a scanning electron microscope and optical mineralogy. This is then compared with the coincident thermal data gathered on site in order to help constrain the most recent thermal activity of this dynamic resource. Using multiple temperature diagnostic minerals and their paragenesis, a relative thermal history is produced of expansive propylitic alteration. When combined with the wireline temperature gradients of the cores a model of downward migration emerges. Shallow occurrences of high temperature minerals that lie above the boiling point to depth curve indicate higher hydrostatic pressures in the past which can be attributed to a combination of glacial effects, including a significant amount of glacial erosion that is recognized due to a lack of significant clay cap to the geothermal resource.

Oxidation of ethane to ethanol by N2O in a metal-organic framework with coordinatively unsaturated iron(II) sites.

PubMed

Xiao, Dianne J; Bloch, Eric D; Mason, Jarad A; Queen, Wendy L; Hudson, Matthew R; Planas, Nora; Borycz, Joshua; Dzubak, Allison L; Verma, Pragya; Lee, Kyuho; Bonino, Francesca; Crocellà, Valentina; Yano, Junko; Bordiga, Silvia; Truhlar, Donald G; Gagliardi, Laura; Brown, Craig M; Long, Jeffrey R

2014-07-01

Enzymatic haem and non-haem high-valent iron-oxo species are known to activate strong C-H bonds, yet duplicating this reactivity in a synthetic system remains a formidable challenge. Although instability of the terminal iron-oxo moiety is perhaps the foremost obstacle, steric and electronic factors also limit the activity of previously reported mononuclear iron(IV)-oxo compounds. In particular, although nature's non-haem iron(IV)-oxo compounds possess high-spin S = 2 ground states, this electronic configuration has proved difficult to achieve in a molecular species. These challenges may be mitigated within metal-organic frameworks that feature site-isolated iron centres in a constrained, weak-field ligand environment. Here, we show that the metal-organic framework Fe2(dobdc) (dobdc(4-) = 2,5-dioxido-1,4-benzenedicarboxylate) and its magnesium-diluted analogue, Fe0.1Mg1.9(dobdc), are able to activate the C-H bonds of ethane and convert it into ethanol and acetaldehyde using nitrous oxide as the terminal oxidant. Electronic structure calculations indicate that the active oxidant is likely to be a high-spin S = 2 iron(IV)-oxo species.

Developing Age Models to Utilize High Arctic Coastal Sediments for Paleoclimate Research: Results from the Colville Delta and Simpson Lagoon, Alaska

NASA Astrophysics Data System (ADS)

Miller, A. J.; Allison, M. A.; Bianchi, T. S.; Marcantonio, F.

2012-12-01

Sediment cores collected from Simpson Lagoon on the inner Beaufort Sea shelf adjacent to the Colville River delta, AK are being utilized to develop new, high-resolution (sub-decadal scale) archives of the 0-3,000 year Arctic paleoclimate record necessary to assess natural and anthropogenic climate variability. An imperative first step for developing a new paleoclimate archive is to establish methodologies for constraining the age-depth relationship. Naturally occurring and bomb-produced radioisotopes have been utilized in sediments to constrain downcore variability of accumulation rates on 100-103 y timescales, but this methodology is complicated by low activities of many of these tracers at high latitudes. The present study utilizes the combination of a (1) multi-tracer approach and a (2) tailored measurement strategy to overcome this limitation. 210Pb and 137Cs analyses were conducted on the fine (<32μm) sediment fraction to maximize measurable activity and to minimize radioisotope activity variability resulting from changes in grain size: 137Cs geochronologies proved more reliable in this setting and revealed mm/y sediment accumulation in the lagoon. To corroborate the 137Cs results, 239,240Pu activities were analyzed for selected sites using ICP-MS which has ultra-low detection limits, and yielded accumulation rates that matched the Cs geochronology. Age model development for the remainder of the core lengths (>~100 y in age) were completed using radiocarbon dating of benthic foraminifera tests, which proved the only datable in situ carbon available in this sediment archive. These dates have been used to constrain the ages of acoustic reflectors in CHIRP subbottom seismic records collected from the lagoon. Using this age control, spatial patterns of lagoonal sediment accumulation over the last ~3 ky were derived from the CHIRP data. Two depocenters are identified and validate combining age-dated coring with high-resolution seismic profiling to identify areas of the highest temporal resolution for Arctic paleoclimate research in coastal sediments.

Determining Size Distribution at the Phoenix Landing Site

NASA Astrophysics Data System (ADS)

Mason, E. L.; Lemmon, M. T.

2016-12-01

Dust aerosols play a crucial role in determining atmospheric radiative heating on Mars through absorption and scattering of sunlight. How dust scatters and absorbs light is dependent on size, shape, composition, and quantity. Optical properties of the dust have been well constrained in the visible and near infrared wavelengths using various methods [Wolff et al. 2009, Lemmon et al. 2004]. In addition, the dust is nonspherical, and irregular shapes have shown to work well in determining effective particle size [Pollack et al. 1977]. Variance of the size distribution is less constrained but constitutes an important parameter in fully describing the dust. The Phoenix Lander's Surface Stereo Imager performed several cross-sky brightness surveys to determine the size distribution and scattering properties of dust in the wavelength range of 400 to 1000 nm. In combination with a single-layer radiative transfer model, these surveys can be used to help constrain variance of the size distribution. We will present a discussion of seasonal size distribution as it pertains to the Phoenix landing site.

Study participants incentives, compensation and reimbursement in resource-constrained settings.

PubMed

Mduluza, Takafira; Midzi, Nicholas; Duruza, Donold; Ndebele, Paul

2013-01-01

Controversies still exists within the research fraternity on the form and level of incentives, compensation and reimbursement to study participants in resource-constrained settings. While most research activities contribute significantly to advancement of mankind, little has been considered in rewarding directly the research participants from resource-constrained areas. A study was conducted in Zimbabwe to investigate views and expectations of various stakeholders on study participation incentives, compensation and reimbursement issues. Data was collected using various methods including a survey of about 1,008 parents/guardians of school children participating in various immunological cohort studies and parasitology surveys. Community advisory boards (CABs) at 9 of the sites were also consulted. Further, information was gathered during discussions held at a basic research ethics training workshop. The workshop had 45 participants that including 40 seasoned Zimbabwean researchers and 5 international research collaborators. About 90% (907) of the study participants and guardians expected compensation of reasonable value, in view of the researchers' value and comparison to other sites regardless of economic status of the community. During discussion with researchers at a basic ethics training workshop, about 80% (32) believed that decisions on level of compensation should be determined by the local research ethics committees. While, the few international research collaborators were of the opinion that compensation should be in accordance with local guidelines, and incentives should be in line with funding. Both the CAB members and study participants expressed that there should be a clear distinction between study incentive and compensation accorded to individual and community expectations on benefits from studies. However, CABs expressed that their suggestions on incentives and compensation are often moderated by the regulatory authorities who cite fear of unknown concerns. Overall, both personal and community benefits need to be considered collectively in future studies to be conducted in resource-constrained communities. There is projected fear that recruitment in future may be a challenge, now that almost every community, has somehow been reached and participated in some form of studies. A major concern on reimbursement, compensation or incentives should be internationally pegged regardless of different economic status of the individuals or communities where the study is to be conducted.

The Apollo 16 regolith - A petrographically-constrained chemical mixing model

NASA Technical Reports Server (NTRS)

Kempa, M. J.; Papike, J. J.; White, C.

1980-01-01

A mixing model for Apollo 16 regolith samples has been developed, which differs from other A-16 mixing models in that it is both petrographically constrained and statistically sound. The model was developed using three components representative of rock types present at the A-16 site, plus a representative mare basalt. A linear least-squares fitting program employing the chi-squared test and sum of components was used to determine goodness of fit. Results for surface soils indicate that either there are no significant differences between Cayley and Descartes material at the A-16 site or, if differences do exist, they have been obscured by meteoritic reworking and mixing of the lithologies.

SITE CHARACTERIZATION TO SUPPORT MODEL DEVELOPMENT FOR CONTAMINANTS IN GROUND WATER

EPA Science Inventory

The development of conceptual and predictive models is an important tool to guide site characterization in support of monitoring contaminants in ground water. The accuracy of predictive models is limited by the adequacy of the input data and the assumptions made to constrain mod...

Big maggots dig deeper: size-dependent larval dispersal in flies.

PubMed

Davis, Jeremy M; Coogan, Laura E; Papaj, Daniel R

2015-09-01

The ability of individual animals to select habitats optimal for development and survival can be constrained by the costs of moving through the environment. Animals that seek overwintering sites underground, for example, may be constrained by the energy required to burrow into the soil. We conducted field and laboratory studies to determine the relationship between individual size and overwintering site selection in the tephritid flies, Rhagoletis juglandis and Rhagoletis suavis. We also explored the effect of site selection on pupal mortality, parasitism, and the ability to emerge from overwintering sites after eclosion. In both species, and in both lab and field tests, larger pupae were found at deeper soil depths. In addition, marginally non-significant trends indicated pupae in deeper sites were 48% more likely to survive the overwintering period. Finally, larger individuals were more likely to eclose and emerge from the soil at a given depth, but flies in deep overwintering sites were less likely to emerge from those sites than flies in shallow sites. Our data indicate that overwintering site selection represents a trade-off between avoiding predators and parasites that occur at shallow sites, and the energetic and mortality costs of burrowing to, overwintering in, and emerging from, deeper sites. The size-dependent overwintering site selection demonstrated here has implications for population dynamics and pest control strategies. Some fly control measures, such as the introduction of parasites or predators, will be mitigated when the deepest and least accessible overwintering pupae represent a disproportionately large amount of the population's reproductive capacity.

The rotation of Iberia during the Aptian and the opening of the Bay of Biscay

NASA Astrophysics Data System (ADS)

Gong, Z.; Langereis, C. G.; Mullender, T. A. T.

2008-08-01

The Cretaceous rotation of the Iberian plate in a geodynamical active setting between Africa and Europe is contemporaneous with the opening of the northern Atlantic Ocean, and provides fundamental, temporal and kinematical constraints on the evolution of the Bay of Biscay and the Pyrenees. Here, we report new paleomagnetic data from 50 sites (1109 drilled cores) from marine sediments of the Cretaceous Organyà Basin in the southern Pyrenees, to constrain the timing and magnitude of the rotation of Iberia. Berriasian to Barremian directions in exclusively limestone lithology are remagnetised, in agreement with previous Organyà Basin studies. The Aptian to Cenomanian marls and limestones in the Organyà Basin, however, provide primary magnetisations asserted by rock magnetic experiments and positive fold tests. Our results constrain the rotation of Iberia to be finished just before the Albian. Paleomagnetic data cannot well constrain the onset of the rotation, but sea-floor anomaly studies restrict the onset of the rotation to anomaly M0, or the Barremian-Aptian boundary. This implies that the entire rotation of Iberia happened in one single phase, and is confined to the Aptian. This is in contrast to earlier studies that suggested a two-phase rotation of Iberia, but we argue that the large errors in published ages are not in disagreement with our results. In summary, we constrain the ∼ 35° rotation of Iberia to the Aptian period which implies a rotation rate of 2.7-5.1°/Myr, depending on the (controversial) duration of the Aptian.

Glucose and lactate as metabolic constraints on presynaptic transmission at an excitatory synapse.

PubMed

Lucas, Sarah J; Michel, Christophe B; Marra, Vincenzo; Smalley, Joshua L; Hennig, Matthias H; Graham, Bruce P; Forsythe, Ian D

2018-05-01

Synapses have high energy demands which increase during intense activity. We show that presynaptic terminals can utilise extracellular glucose or lactate to generate energy to maintain synaptic transmission. Reducing energy substrates induces a metabolic stress: presynaptic ATP depletion impaired synaptic transmission through a reduction in the number of functional synaptic vesicle release sites and a slowing of vesicle pool replenishment, without a consistent change in release probability. Metabolic function is compromised in many pathological conditions (e.g. stroke, traumatic brain injury and neurodegeneration). Knowledge of how synaptic transmission is constrained by metabolic stress, especially during intense brain activity, will provide insights to improve cognition following pathological insults. The synapse has high energy demands, which increase during intense activity. Presynaptic ATP production depends on substrate availability and usage will increase during activity, which in turn could influence transmitter release and information transmission. We investigated transmitter release at the mouse calyx of Held synapse using glucose or lactate (10, 1 or 0 mm) as the extracellular substrates while inducing metabolic stress. High-frequency stimulation (HFS) and recovery paradigms evoked trains of EPSCs monitored under voltage-clamp. Whilst postsynaptic intracellular ATP was stabilised by diffusion from the patch pipette, depletion of glucose increased EPSC depression during HFS and impaired subsequent recovery. Computational modelling of these data demonstrated a reduction in the number of functional release sites and slowed vesicle pool replenishment during metabolic stress, with little change in release probability. Directly depleting presynaptic terminal ATP impaired transmitter release in an analogous manner to glucose depletion. In the absence of glucose, presynaptic terminal metabolism could utilise lactate from the aCSF and this was blocked by inhibition of monocarboxylate transporters (MCTs). MCT inhibitors significantly suppressed transmission in low glucose, implying that lactate is a presynaptic substrate. Additionally, block of glycogenolysis accelerated synaptic transmission failure in the absence of extracellular glucose, consistent with supplemental supply of lactate by local astrocytes. We conclude that both glucose and lactate support presynaptic metabolism and that limited availability, exacerbated by high-intensity firing, constrains presynaptic ATP, impeding transmission through a reduction in functional presynaptic release sites as vesicle recycling slows when ATP levels are low. © 2018 The Authors. The Journal of Physiology © 2018 The Physiological Society.

Active/Passive Control of Sound Radiation from Panels using Constrained Layer Damping

NASA Technical Reports Server (NTRS)

Gibbs, Gary P.; Cabell, Randolph H.

2003-01-01

A hybrid passive/active noise control system utilizing constrained layer damping and model predictive feedback control is presented. This system is used to control the sound radiation of panels due to broadband disturbances. To facilitate the hybrid system design, a methodology for placement of constrained layer damping which targets selected modes based on their relative radiated sound power is developed. The placement methodology is utilized to determine two constrained layer damping configurations for experimental evaluation of a hybrid system. The first configuration targets the (4,1) panel mode which is not controllable by the piezoelectric control actuator, and the (2,3) and (5,2) panel modes. The second configuration targets the (1,1) and (3,1) modes. The experimental results demonstrate the improved reduction of radiated sound power using the hybrid passive/active control system as compared to the active control system alone.

High probability neurotransmitter release sites represent an energy efficient design

PubMed Central

Lu, Zhongmin; Chouhan, Amit K.; Borycz, Jolanta A.; Lu, Zhiyuan; Rossano, Adam J; Brain, Keith L.; Zhou, You; Meinertzhagen, Ian A.; Macleod, Gregory T.

2016-01-01

Nerve terminals contain multiple sites specialized for the release of neurotransmitters. Release usually occurs with low probability, a design thought to confer many advantages. High probability release sites are not uncommon but their advantages are not well understood. Here we test the hypothesis that high probability release sites represent an energy efficient design. We examined release site probabilities and energy efficiency at the terminals of two glutamatergic motor neurons synapsing on the same muscle fiber in Drosophila larvae. Through electrophysiological and ultrastructural measurements we calculated release site probabilities to differ considerably between terminals (0.33 vs. 0.11). We estimated the energy required to release and recycle glutamate from the same measurements. The energy required to remove calcium and sodium ions subsequent to nerve excitation was estimated through microfluorimetric and morphological measurements. We calculated energy efficiency as the number of glutamate molecules released per ATP molecule hydrolyzed, and high probability release site terminals were found to be more efficient (0.13 vs. 0.06). Our analytical model indicates that energy efficiency is optimal (~0.15) at high release site probabilities (~0.76). As limitations in energy supply constrain neural function, high probability release sites might ameliorate such constraints by demanding less energy. Energy efficiency can be viewed as one aspect of nerve terminal function, in balance with others, because high efficiency terminals depress significantly during episodic bursts of activity. PMID:27593375

Source Spectra and Site Response for Two Indonesian Earthquakes: the Tasikmalaya and Kerinci Events of 2009

NASA Astrophysics Data System (ADS)

Gunawan, I.; Cummins, P. R.; Ghasemi, H.; Suhardjono, S.

2012-12-01

Indonesia is very prone to natural disasters, especially earthquakes, due to its location in a tectonically active region. In September-October 2009 alone, intraslab and crustal earthquakes caused the deaths of thousands of people, severe infrastructure destruction and considerable economic loss. Thus, both intraslab and crustal earthquakes are important sources of earthquake hazard in Indonesia. Analysis of response spectra for these intraslab and crustal earthquakes are needed to yield more detail about earthquake properties. For both types of earthquakes, we have analysed available Indonesian seismic waveform data to constrain source and path parameters - i.e., low frequency spectral level, Q, and corner frequency - at reference stations that appear to be little influenced by site response.. We have considered these analyses for the main shocks as well as several aftershocks. We obtain corner frequencies that are reasonably consistent with the constant stress drop hypothesis. Using these results, we consider using them to extract information about site response form other stations form the Indonesian strong motion network that appear to be strongly affected by site response. Such site response data, as well as earthquake source parameters, are important for assessing earthquake hazard in Indonesia.

PM2.5 source apportionment in a French urban coastal site under steelworks emission influences using constrained non-negative matrix factorization receptor model.

PubMed

Kfoury, Adib; Ledoux, Frédéric; Roche, Cloé; Delmaire, Gilles; Roussel, Gilles; Courcot, Dominique

2016-02-01

The constrained weighted-non-negative matrix factorization (CW-NMF) hybrid receptor model was applied to study the influence of steelmaking activities on PM2.5 (particulate matter with equivalent aerodynamic diameter less than 2.5 μm) composition in Dunkerque, Northern France. Semi-diurnal PM2.5 samples were collected using a high volume sampler in winter 2010 and spring 2011 and were analyzed for trace metals, water-soluble ions, and total carbon using inductively coupled plasma--atomic emission spectrometry (ICP-AES), ICP--mass spectrometry (ICP-MS), ionic chromatography and micro elemental carbon analyzer. The elemental composition shows that NO3(-), SO4(2-), NH4(+) and total carbon are the main PM2.5 constituents. Trace metals data were interpreted using concentration roses and both influences of integrated steelworks and electric steel plant were evidenced. The distinction between the two sources is made possible by the use Zn/Fe and Zn/Mn diagnostic ratios. Moreover Rb/Cr, Pb/Cr and Cu/Cd combination ratio are proposed to distinguish the ISW-sintering stack from the ISW-fugitive emissions. The a priori knowledge on the influencing source was introduced in the CW-NMF to guide the calculation. Eleven source profiles with various contributions were identified: 8 are characteristics of coastal urban background site profiles and 3 are related to the steelmaking activities. Between them, secondary nitrates, secondary sulfates and combustion profiles give the highest contributions and account for 93% of the PM2.5 concentration. The steelwork facilities contribute in about 2% of the total PM2.5 concentration and appear to be the main source of Cr, Cu, Fe, Mn, Zn. Copyright © 2015. Published by Elsevier B.V.

Sedimentation of oil-derived material to the seabed is an unrecognized fate for oil derived from natural seepage.

NASA Astrophysics Data System (ADS)

Joye, S. B.

2016-02-01

The fate of oil derived from natural seepage in the marine environment is poorly constrained. In the aftermath of the 2010 BP/Macondo oil well blowout, sedimentation of oil-containing material to the seafloor was an important fate for discharged oil. Though the amount of oil accounted for by sedimentation processes remains poorly constrained, sedimentation is now considered an important fate of oil during large open water spills that generate extensive surface slicks. In the Gulf of Mexico, vigorous natural oil seeps generate extensive, sometimes thick, surface slicks. In the case of highly active seeps, these surface oil slicks persist at the sea surface over the seep site a majority of the time. We investigated the fate of oil released through natural seepage and the potential for the sedimentation of surface-slick derived oil at two vigorous hydrocarbon seeps in the Gulf of Mexico, Green Canyon block 600 and block 767. Hydrocarbon analyses were performed on samples collected from oil vents at the seafloor, in surface slicks, and in sediments cores apparently containing sedimented oil. Sediment cores collected from both of these active seep sites away from known oil vents contained distinct (1-3 cm thick) layers that were brown in coloration and which displayed distinct sedimentology compared to deeper strata. The oil fingerprint was also different, suggesting this material was not the result of weathering during transit through the sediment column. Available data suggest that sedimentation of weathered oil also occurs at vigorous natural seeps. Detailed studies of the weathered oil sedimentation process at natural seeps will help reveal the mechanisms driving this phenomena and are important for understanding the fate of oil released during accidental discharges and spills.

CH4 emission estimates from an active landfill site inferred from a combined approach of CFD modelling and in situ FTIR measurements

NASA Astrophysics Data System (ADS)

Sonderfeld, Hannah; Boesch, Hartmut; Jeanjean, Antoine P. R.; Riddick, Stuart N.; Allen, Grant; Ars, Sebastien; Davies, Stewart; Harris, Neil; Humpage, Neil; Leigh, Roland; Pitt, Joseph

2017-04-01

Globally, the waste sector contributes to nearly a fifth of anthropogenic methane (CH4) emitted to the atmosphere and is the second largest source of methane in the UK. In recent years great improvements to reduce those emissions have been achieved by installation of methane recovery systems at landfill sites and subsequently methane emissions reported in national emission inventories have been reduced. Nevertheless, methane emissions of landfills remain uncertain and quantification of emission fluxes is essential to verify reported emission inventories and to monitor changes in emissions. We are presenting data from the deployment of an in situ FTIR (Fourier Transform Infrared Spectrometer, Ecotech) for continuous and simultaneous sampling of CO2, CH4, N2O and CO with high time resolution of the order of minutes. During a two week field campaign at an operational landfill site in Eastern England in August 2014, measurements were taken within a radius of 320 m of the uncovered and active area of the landfill, which was still filled with new incoming waste. We have applied a computation fluid dynamics (CFD) model, constrained with local wind measurements and a detailed topographic map of the landfill site, to the in situ concentration data to calculate CH4 fluxes of the active site. A mean daytime flux of 0.83 mg m-2 s-1 (53.26 kg h-1) was calculated for the area of the active site. An additional source area was identified and incorporated into the CFD model, which resulted in higher total methane emissions of 75.97 kg h-1 for the combined emission areas. Our method of combining a CFD model to in situ data, in medium proximity of the source area, allows to distinguish between different emission areas and thereby provide more detailed information compared to bulk emission approaches.

Rubisco mutagenesis provides new insight into limitations on photosynthesis and growth in Synechocystis PCC6803

PubMed Central

Marcus, Yehouda; Altman-Gueta, Hagit; Wolff, Yael; Gurevitz, Michael

2011-01-01

Orthophosphate (Pi) stimulates the activation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) while paradoxically inhibiting its catalysis. Of three Pi-binding sites, the roles of the 5P- and latch sites have been documented, whereas that of the 1P-site remained unclear. Conserved residues at the 1P-site of Rubisco from the cyanobacterium Synechocystis PCC6803 were substituted and the kinetic properties of the enzyme derivatives and effects on cell photosynthesis and growth were examined. While Pi-stimulated Rubisco activation diminished for enzyme mutants T65A/S and G404A, inhibition of catalysis by Pi remained unchanged. Together with previous studies, the results suggest that all three Pi-binding sites are involved in stimulation of Rubisco activation, whereas only the 5P-site is involved in inhibition of catalysis. While all the mutations reduced the catalytic turnover of Rubisco (Kcat) between 6- and 20-fold, the photosynthesis and growth rates under saturating irradiance and inorganic carbon (Ci) concentrations were only reduced 40–50% (in the T65A/S mutants) or not at all (G404A mutant). Analysis of the mutant cells revealed a 3-fold increase in Rubisco content that partially compensated for the reduced Kcat so that the carboxylation rate per chlorophyll was one-third of that in the wild type. Correlation between the kinetic properties of Rubisco and the photosynthetic rate (Pmax) under saturating irradiance and Ci concentrations indicate that a >60% reduction in Kcat can be tolerated before Pmax in Synechocystsis PCC6803 is affected. These results indicate that the limitation of Rubisco activity on the rate of photosynthesis in Synechocystis is low. Determination of Calvin cycle metabolites revealed that unlike in higher plants, cyanobacterial photosynthesis is constrained by phosphoglycerate reduction probably due to limitation of ATP or NADPH. PMID:21551078

Diazotrophic Community Structure and Function in Two Successional Stages of Biological Soil Crusts from the Colorado Plateau and Chihuahuan Desert

USGS Publications Warehouse

Yeager, C.M.; Kornosky, J.L.; Housman, D.C.; Grote, E.E.; Belnap, J.; Kuske, C.R.

2004-01-01

The objective of this study was to characterize the community structure and activity of N2-fixing microorganisms in mature and poorly developed biological soil crusts from both the Colorado Plateau and Chihuahuan Desert. Nitrogenase activity was approximately 10 and 2.5 times higher in mature crusts than in poorly developed crusts at the Colorado Plateau site and Chihuahuan Desert site, respectively. Analysis of nifH sequences by clone sequencing and the terminal restriction fragment length polymorphism technique indicated that the crust diazotrophic community was 80 to 90% heterocystous cyanobacteria most closely related to Nostoc spp. and that the composition of N2-fixing species did not vary significantly between the poorly developed and mature crusts at either site. In contrast, the abundance of nifH sequences was approximately 7.5 times greater (per microgram of total DNA) in mature crusts than in poorly developed crusts at a given site as measured by quantitative PCR. 16S rRNA gene clone sequencing and microscopic analysis of the cyanobacterial community within both crust types demonstrated a transition from a Microcoleus vaginatus-dominated, poorly developed crust to mature crusts harboring a greater percentage of Nostoc and Scytonema spp. We hypothesize that ecological factors, such as soil instability and water stress, may constrain the growth of N2-fixing microorganisms at our study sites and that the transition to a mature, nitrogen-producing crust initially requires bioengineering of the surface microenvironment by Microcoleus vaginatus.

The making of the minibody: an engineered beta-protein for the display of conformationally constrained peptides.

PubMed

Tramontano, A; Bianchi, E; Venturini, S; Martin, F; Pessi, A; Sollazzo, M

1994-03-01

Conformationally constraining selectable peptides onto a suitable scaffold that enables their conformation to be predicted or readily determined by experimental techniques would considerably boost the drug discovery process by reducing the gap between the discovery of a peptide lead and the design of a peptidomimetic with a more desirable pharmacological profile. With this in mind, we designed the minibody, a 61-residue beta-protein aimed at retaining some desirable features of immunoglobulin variable domains, such as tolerance to sequence variability in selected regions of the protein and predictability of the main chain conformation of the same regions, based on the 'canonical structures' model. To test the ability of the minibody scaffold to support functional sites we also designed a metal binding version of the protein by suitably choosing the sequences of its loops. The minibody was produced both by chemical synthesis and expression in E. coli and characterized by size exclusion chromatography, UV CD (circular dichroism) spectroscopy and metal binding activity. All our data supported the model, but a more detailed structural characterization of the molecule was impaired by its low solubility. We were able to overcome this problem both by further mutagenesis of the framework and by addition of a solubilizing motif. The minibody is being used to select constrained human IL-6 peptidic ligands from a library displayed on the surface of the f1 bacteriophage.

How Rules Shape Experience

ERIC Educational Resources Information Center

Emo, Kenneth

2008-01-01

Rules guide and constrain participants' actions as they participate in any educational activity. This ethnographically driven case study examines how organizational rules--the implicit and explicit regulations that constrain actions and interactions--influence children to use science in the experiential educational activity of raising 4-H market…

State-of-stress in magmatic rift zones: Predicting the role of surface and subsurface topography

NASA Astrophysics Data System (ADS)

Oliva, S. J. C.; Ebinger, C.; Rivalta, E.; Williams, C. A.

2017-12-01

Continental rift zones are segmented along their length by large fault systems that form in response to extensional stresses. Volcanoes and crustal magma chambers cause fundamental changes to the density structure, load the plates, and alter the state-of-stress within the crust, which then dictates fracture orientation. In this study, we develop geodynamic models scaled to a < 7 My rift sector in the Eastern rift, East Africa where geophysical imaging provides tight constraints on subsurface structure, petrologic and thermodynamic studies constrain material densities, and seismicity and structural analyses constrain active and time-averaged kinematics. This area is an ideal test area because a 60º stress rotation is observed in time-averaged fault and magma intrusion, and in local seismicity, and because this was the site of a large volume dike intrusion and seismic sequence in 2007. We use physics-based 2D and 3D models (analytical and finite elements) constrained by data from active rift zones to quantify the effects of loading on state-of-stress. By modeling varying geometric arrangements, and density contrasts of topographic and subsurface loads, and with reasonable regional extensional forces, the resulting state-of-stress reveals the favored orientation for new intrusions. Although our models are generalized, they allow us to evaluate whether a magmatic system (surface and subsurface) can explain the observed stress rotation, and enable new intrusions, new faults, or fault reactivation with orientations oblique to the main border faults. Our results will improve our understanding of the different factors at play in these extensional regimes, as well as contribute to a better assessment of the hazards in the area.

Relictual amphibians and old-growth forest

Treesearch

H.H. Welsh

1990-01-01

Terrestrial and aquatic herpetofauna were sampled by pitfall traps, time-constrained searches, and areaconstrained searches (stream sites only) over a three-year period to examine the importance of forest age to amphibians and reptiles. Fifty-four terrestrial and 39 aquatic sites in Douglas-fir-dominated, mixed evergreen forests were located in southwestern Oregon and...

Changes in deep-sea carbonate-hosted microbial communities associated with high and low methane flux

NASA Astrophysics Data System (ADS)

Case, D. H.; Steele, J. A.; Chadwick, G.; Mendoza, G. F.; Levin, L. A.; Orphan, V. J.

2012-12-01

Methane seeps on continental shelves are rich in authigenic carbonates built of methane-derived carbon. These authigenic carbonates are home to micro- and macroscopic communities whose compositions are thus far poorly constrained but are known to broadly depend on local methane flux. The formation of authigenic carbonates is itself a result of microbial metabolic activity, as associations of anaerobic methane oxidizing archaea (ANME) and sulfate reducing bacteria (SRB) in the sediment subsurface increase both dissolved inorganic carbon (DIC) and alkalinity in pore waters. This 1:1 increase in DIC and alkalinity promotes the precipitation of authigenic carbonates. In this study, we performed in situ manipulations to test the response of micro- and macrofaunal communities to a change in methane flux. Methane-derived authigenic carbonates from two locations at Hydrate Ridge, OR, USA (depth range 595-604 mbsl), were transplanted from "active" cold seep sites (high methane flux) to "inactive" background sites (low methane flux), and vise versa, for one year. Community diversity surveys using T-RFLP and 16S rRNA clone libraries revealed how both bacterial and archaeal assemblages respond to this change in local environment, specifically demonstrating reproducible shifts in different ANME groups (ANME-1 vs. ANME-2). Animal assemblage composition also shifted during transplantation; gastropod representation increased (relative to control rocks) when substrates were moved from inactive to active sites and polychaete, crustacean and echinoderm representation increased when substrates were moved from active to inactive sites. Combined with organic and inorganic carbon δ13C measurements and mineralogy, this unique in situ experiment demonstrates that authigenic carbonates are viable habitats, hosting microbial and macrofaunal communities capable of responding to changes in external environment over relatively short time periods.

Need for multiscale planning for conservation of urban bats.

PubMed

Gallo, Travis; Lehrer, Elizabeth W; Fidino, Mason; Kilgour, R Julia; Wolff, Patrick J; Magle, Seth B

2017-11-10

For over a century there have been continual efforts to incorporate nature into urban planning. These efforts (i.e., urban reconciliation) aim to manage and create habitats that support biodiversity within cities. Given that species select habitat at different spatial scales, understanding the scale at which urban species respond to their environment is critical to the success of urban reconciliation efforts. We assessed species-habitat relationships for common bat species at 50-m, 500-m, and 1 km spatial scales in the Chicago (U.S.A.) metropolitan area and predicted bat activity across the greater Chicago region. Habitat characteristics across all measured scales were important predictors of silver-haired bat (Lasionycteris noctivagans) and eastern red bat (Lasiurus borealis) activity, and big brown bat (Eptesicus fuscus) activity was significantly lower at urban sites relative to rural sites. Open vegetation had a negative effect on silver-haired bat activity at the 50-m scale but a positive effect at the 500-m scale, indicating potential shifts in the relative importance of some habitat characteristics at different scales. These results demonstrate that localized effects may be constrained by broader spatial patterns. Our findings highlight the importance of considering scale in urban reconciliation efforts and our landscape predictions provide information that can help prioritize urban conservation work. © 2017 Society for Conservation Biology.

8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors

PubMed Central

2016-01-01

We report the discovery of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site; incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 54j and 54k which demonstrate equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and, for 54k, inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay. PMID:26741168

Refining the Subseafloor Circulation Model of the Middle Valley Hydrothermal System Using Fluid Geochemistry

NASA Astrophysics Data System (ADS)

Inderbitzen, K. E.; Wheat, C. G.; Baker, P. A.; Fisher, A. T.

2014-12-01

Currently, fluid circulation patterns and the evolution of rock/fluid compositions as circulation occurs in subseafloor hydrothermal systems are poorly constrained. Sedimented spreading centers provide a unique opportunity to study subsurface flow because sediment acts as an insulating blanket that traps heat from the cooling magma body and limits: (a) potential flow paths for seawater to recharge the aquifer in permeable upper basaltic basement and (b) points of altered fluid egress. This also allows for a range of thermal and geochemical gradients to exist near the sediment-water interface. Models of fluid circulation patterns in this type of hydrologic setting have been generated (eg. Stein and Fisher, 2001); however fluid chemistry datasets have not previously been used to test the model's viability. We address this issue by integrating the existing circulation model with fluid compositional data collected from sediment pore waters and high temperature hydrothermal vents located in Middle Valley on the Juan de Fuca Ridge. Middle Valley hosts a variety of hydrologic regimes: including areas of fluid recharge (Site 855), active venting (Site 858/1036; Dead Dog vent field), recent venting (Site 856/1035; Bent Hill Massive Sulfide deposit) and a section of heavily sedimented basement located between recharge and discharge sites (Site 857). We will present new results based on thermal and geochemical data from the area of active venting (Sites 858 and 1036), that was collected during Ocean Drilling Program Legs 139 and 169 and a subsequent heat flow/gravity coring effort. These results illuminate fine scale controls on secondary recharge and fluid flow within the sediment section at Site 858/1036. The current status of high temperature vents in this area (based on observations made in July, 2014) will also be outlined.

Phosphorylated Nuclear Receptor CAR Forms a Homodimer To Repress Its Constitutive Activity for Ligand Activation

PubMed Central

Shizu, Ryota; Osabe, Makoto; Perera, Lalith; Moore, Rick; Sueyoshi, Tatsuya

2017-01-01

ABSTRACT The nuclear receptor CAR (NR1I3) regulates hepatic drug and energy metabolism as well as cell fate. Its activation can be a critical factor in drug-induced toxicity and the development of diseases, including diabetes and tumors. CAR inactivates its constitutive activity by phosphorylation at threonine 38. Utilizing receptor for protein kinase 1 (RACK1) as the regulatory subunit, protein phosphatase 2A (PP2A) dephosphorylates threonine 38 to activate CAR. Here we demonstrate that CAR undergoes homodimer-monomer conversion to regulate this dephosphorylation. By coexpression of two differently tagged CAR proteins in Huh-7 cells, mouse primary hepatocytes, and mouse livers, coimmunoprecipitation and two-dimensional gel electrophoresis revealed that CAR can form a homodimer in a configuration in which the PP2A/RACK1 binding site is buried within its dimer interface. Epidermal growth factor (EGF) was found to stimulate CAR homodimerization, thus constraining CAR in its inactive form. The agonistic ligand CITCO binds directly to the CAR homodimer and dissociates phosphorylated CAR into its monomers, exposing the PP2A/RACK1 binding site for dephosphorylation. Phenobarbital, which is not a CAR ligand, binds the EGF receptor, reversing the EGF signal to monomerize CAR for its indirect activation. Thus, the homodimer-monomer conversion is the underlying molecular mechanism that regulates CAR activation, by placing phosphorylated threonine 38 as the common target for both direct and indirect activation of CAR. PMID:28265001

Picosecond-Resolved Fluorescent Probes at Functionally Distinct Tryptophans within a Thermophilic Alcohol Dehydrogenase: Relationship of Temperature-Dependent Changes in Fluorescence to Catalysis

PubMed Central

2015-01-01

Two single-tryptophan variants were generated in a thermophilic alcohol dehydrogenase with the goal of correlating temperature-dependent changes in local fluorescence with the previously demonstrated catalytic break at ca. 30 °C (Kohen et al., Nature1999, 399, 496). One tryptophan variant, W87in, resides at the active site within van der Waals contact of bound alcohol substrate; the other variant, W167in, is a remote-site surface reporter located >25 Å from the active site. Picosecond-resolved fluorescence measurements were used to analyze fluorescence lifetimes, time-dependent Stokes shifts, and the extent of collisional quenching at Trp87 and Trp167 as a function of temperature. A subnanosecond fluorescence decay rate constant has been detected for W87in that is ascribed to the proximity of the active site Zn2+ and shows a break in behavior at 30 °C. For the remainder of the reported lifetime measurements, there is no detectable break between 10 and 50 °C, in contrast with previously reported hydrogen/deuterium exchange experiments that revealed a temperature-dependent break analogous to catalysis (Liang et al., Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9556). We conclude that the motions that lead to the rigidification of ht-ADH below 30 °C are likely to be dominated by global processes slower than the picosecond to nanosecond motions measured herein. In the case of collisional quenching of fluorescence by acrylamide, W87in and W167in behave in a similar manner that resembles free tryptophan in water. Stokes shift measurements, by contrast, show distinctive behaviors in which the active-site tryptophan relaxation is highly temperature-dependent, whereas the solvent-exposed tryptophan’s dynamics are temperature-independent. These data are concluded to reflect a significantly constrained environment surrounding the active site Trp87 that both increases the magnitude of the Stokes shift and its temperature-dependence. The results are discussed in the context of spatially distinct differences in enthalpic barriers for protein conformational sampling that may be related to catalysis. PMID:24892947

Thermal Imaging of the Waccasassa Bay Preserve: Image Acquisition and Processing

USGS Publications Warehouse

Raabe, Ellen A.; Bialkowska-Jelinska, Elzbieta

2010-01-01

Thermal infrared (TIR) imagery was acquired along coastal Levy County, Florida, in March 2009 with the goal of identifying groundwater-discharge locations in Waccasassa Bay Preserve State Park (WBPSP). Groundwater discharge is thermally distinct in winter when Floridan aquifer temperature, 71-72 degrees F, contrasts with the surrounding cold surface waters. Calibrated imagery was analyzed to assess temperature anomalies and related thermal traces. The influence of warm Gulf water and image artifacts on small features was successfully constrained by image evaluation in three separate zones: Creeks, Bay, and Gulf. Four levels of significant water-temperature anomalies were identified, and 488 sites of interest were mapped. Among the sites identified, at least 80 were determined to be associated with image artifacts and human activity, such as excavation pits and the Florida Barge Canal. Sites of interest were evaluated for geographic concentration and isolation. High site densities, indicating interconnectivity and prevailing flow, were located at Corrigan Reef, No. 4 Channel, Winzy Creek, Cow Creek, Withlacoochee River, and at excavation sites. In other areas, low to moderate site density indicates the presence of independent vents and unique flow paths. A directional distribution assessment of natural seep features produced a northwest trend closely matching the strike direction of regional faults. Naturally occurring seeps were located in karst ponds and tidal creeks, and several submerged sites were detected in Waccasassa River and Bay, representing the first documentation of submarine vents in the Waccasassa region. Drought conditions throughout the region placed constraints on positive feature identification. Low discharge or displacement by landward movement of saltwater may have reduced or reversed flow during this season. Approximately two-thirds of seep locations in the overlap between 2009 and 2005 TIR night imagery were positively re-identified in 2009. These results indicate a 33 percent chance of feature omission in the 2009 imagery. This assessment of seep location and distribution contributes to an understanding of the underlying geology, the role of fault and fracture patterns, and the presence of both interconnected and constrained flow paths in the region. The maps and evaluations will enhance Park management efforts, interpretation of Park resources, and increase understanding of the combined effects of land and water use on the coastal lowlands, estuarine habitats, and natural resources of WBPSP.

Modelling and Vibration Control of Beams with Partially Debonded Active Constrained Layer Damping Patch

NASA Astrophysics Data System (ADS)

SUN, D.; TONG, L.

2002-05-01

A detailed model for the beams with partially debonded active constraining damping (ACLD) treatment is presented. In this model, the transverse displacement of the constraining layer is considered to be non-identical to that of the host structure. In the perfect bonding region, the viscoelastic core is modelled to carry both peel and shear stresses, while in the debonding area, it is assumed that no peel and shear stresses be transferred between the host beam and the constraining layer. The adhesive layer between the piezoelectric sensor and the host beam is also considered in this model. In active control, the positive position feedback control is employed to control the first mode of the beam. Based on this model, the incompatibility of the transverse displacements of the active constraining layer and the host beam is investigated. The passive and active damping behaviors of the ACLD patch with different thicknesses, locations and lengths are examined. Moreover, the effects of debonding of the damping layer on both passive and active control are examined via a simulation example. The results show that the incompatibility of the transverse displacements is remarkable in the regions near the ends of the ACLD patch especially for the high order vibration modes. It is found that a thinner damping layer may lead to larger shear strain and consequently results in a larger passive and active damping. In addition to the thickness of the damping layer, its length and location are also key factors to the hybrid control. The numerical results unveil that edge debonding can lead to a reduction of both passive and active damping, and the hybrid damping may be more sensitive to the debonding of the damping layer than the passive damping.

Informing Carbon Dynamics in the Community Land Model with Observations from Across Timescales

NASA Astrophysics Data System (ADS)

Fox, A. M.; Hoar, T. J.

2014-12-01

Correct simulation of carbon dynamics in Earth System Models is required to accurately predict both short and long-term land carbon-cycle climate and concentration feedbacks. As new model structures and parameterizations of increasing complexity are introduced there is an ever present need for data to inform these developments, either indirectly through benchmarking activities, or directly through model-data fusion techniques. Here we briefly describe a very rich source of data that will come from the National Ecological Observatory Network (NEON), a continental-scale facility that will collect freely available biogeochemical and biophysical data from 60 sites representative of a full range of ecosystems across the USA over 30 years. Relevant data at each site include a full suite of micrometeorology measurements, profiles of CO2 and H2O vapor isotopes, soil temperature, moisture and CO2 flux, fine root images, and plot-based NPP, leaf area and litterfall estimates. This is accompanied by Lidar and hyperspectral derived biomass, leaf area and canopy chemistry at < 1m resolution of 100s km2. Critically, these observations are well calibrated and highly standardized across sites allowing comparisons, whilst plot and site selection has been designed to optimize representativeness and spatial scaling opportunities. To illustrate the potential utility of these data in constraining models, we show the range of Community Land Model (CLM) output at NEON site locations, and in model-space look at a number of different functional responses that characterize the model in space and time and could be tested with data. These observations can be used most directly through a data assimilation (DA) system and we demonstrate how we have developed support for CLM within the Data Assimilation Research Testbed (DART) that uses ensemble techniques for state estimation. Using an observing system experiment, we investigate how infrequent observations of carbon stocks constrain model dynamics and how these observations types can be used with more frequently available flux and leaf area index observations. We demonstrate the use of the latter with real Ameriflux and MODIS data.

Application of Crunch-Flow Routines to Constrain Present and Past Carbon Fluxes at Gas-Hydrate Bearing Sites

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

Torres, Marta

2014-01-31

In November 2012, Oregon State University initiated the project entitled: Application of Crunch-Flow routines to constrain present and past carbon fluxes at gas-hydrate bearing sites. Within this project we developed Crunch-Flow based modeling modules that include important biogeochemical processes that need to be considered in gas hydrate environments. Our modules were applied to quantify carbon cycling in present and past systems, using data collected during several DOE-supported drilling expeditions, which include the Cascadia margin in US, Ulleung Basin in South Korea, and several sites drilled offshore India on the Bay of Bengal and Andaman Sea. Specifically, we completed modeling effortsmore » that: 1) Reproduce the compositional and isotopic profiles observed at the eight drilled sites in the Ulleung Basin that constrain and contrast the carbon cycling pathways at chimney (high methane flux) and non-chimney sites (low methane, advective systems); 2) Simulate the Ba record in the sediments to quantify the past dynamics of methane flux in the southern Hydrate Ridge, Cascadia margin; and 3) Provide quantitative estimates of the thickness of individual mass transport deposits (MTDs), time elapsed after the MTD event, rate of sulfate reduction in the MTD, and time required to reach a new steady state at several sites drilled in the Krishna-Godavari (K-G) Basin off India. In addition we developed a hybrid model scheme by coupling a home-made MATLAB code with CrunchFlow to address the methane transport and chloride enrichment at the Ulleung Basins chimney sites, and contributed the modeling component to a study focusing on pore-scale controls on gas hydrate distribution in sediments from the Andaman Sea. These efforts resulted in two manuscripts currently under review, and contributed the modeling component of another pare, also under review. Lessons learned from these efforts are the basis of a mini-workshop to be held at Oregon State University (Feb 2014) to instruct graduate students (OSU and UW) as well as DOE staff from the NETL lab in Albany on the use of Crunch Flow for geochemical applications.« less

Innovative Field Methods for Characterizing the Hydraulic Properties of a Complex Fractured Rock Aquifer (Ploemeur, Brittany)

NASA Astrophysics Data System (ADS)

Bour, O.; Le Borgne, T.; Longuevergne, L.; Lavenant, N.; Jimenez-Martinez, J.; De Dreuzy, J. R.; Schuite, J.; Boudin, F.; Labasque, T.; Aquilina, L.

2014-12-01

Characterizing the hydraulic properties of heterogeneous and complex aquifers often requires field scale investigations at multiple space and time scales to better constrain hydraulic property estimates. Here, we present and discuss results from the site of Ploemeur (Brittany, France) where complementary hydrological and geophysical approaches have been combined to characterize the hydrogeological functioning of this highly fractured crystalline rock aquifer. In particular, we show how cross-borehole flowmeter tests, pumping tests and frequency domain analysis of groundwater levels allow quantifying the hydraulic properties of the aquifer at different scales. In complement, we used groundwater temperature as an excellent tracer for characterizing groundwater flow. At the site scale, measurements of ground surface deformation through long-base tiltmeters provide robust estimates of aquifer storage and allow identifying the active structures where groundwater pressure changes occur, including those acting during recharge process. Finally, a numerical model of the site that combines hydraulic data and groundwater ages confirms the geometry of this complex aquifer and the consistency of the different datasets. The Ploemeur site, which has been used for water supply at a rate of about 106 m3 per year since 1991, belongs to the French network of hydrogeological sites H+ and is currently used for monitoring groundwater changes and testing innovative field methods.

Constrained Total Energy Expenditure and Metabolic Adaptation to Physical Activity in Adult Humans.

PubMed

Pontzer, Herman; Durazo-Arvizu, Ramon; Dugas, Lara R; Plange-Rhule, Jacob; Bovet, Pascal; Forrester, Terrence E; Lambert, Estelle V; Cooper, Richard S; Schoeller, Dale A; Luke, Amy

2016-02-08

Current obesity prevention strategies recommend increasing daily physical activity, assuming that increased activity will lead to corresponding increases in total energy expenditure and prevent or reverse energy imbalance and weight gain [1-3]. Such Additive total energy expenditure models are supported by exercise intervention and accelerometry studies reporting positive correlations between physical activity and total energy expenditure [4] but are challenged by ecological studies in humans and other species showing that more active populations do not have higher total energy expenditure [5-8]. Here we tested a Constrained total energy expenditure model, in which total energy expenditure increases with physical activity at low activity levels but plateaus at higher activity levels as the body adapts to maintain total energy expenditure within a narrow range. We compared total energy expenditure, measured using doubly labeled water, against physical activity, measured using accelerometry, for a large (n = 332) sample of adults living in five populations [9]. After adjusting for body size and composition, total energy expenditure was positively correlated with physical activity, but the relationship was markedly stronger over the lower range of physical activity. For subjects in the upper range of physical activity, total energy expenditure plateaued, supporting a Constrained total energy expenditure model. Body fat percentage and activity intensity appear to modulate the metabolic response to physical activity. Models of energy balance employed in public health [1-3] should be revised to better reflect the constrained nature of total energy expenditure and the complex effects of physical activity on metabolic physiology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Uncertainty analysis of depth predictions from seismic reflection data using Bayesian statistics

NASA Astrophysics Data System (ADS)

Michelioudakis, Dimitrios G.; Hobbs, Richard W.; Caiado, Camila C. S.

2018-03-01

Estimating the depths of target horizons from seismic reflection data is an important task in exploration geophysics. To constrain these depths we need a reliable and accurate velocity model. Here, we build an optimum 2D seismic reflection data processing flow focused on pre - stack deghosting filters and velocity model building and apply Bayesian methods, including Gaussian process emulation and Bayesian History Matching (BHM), to estimate the uncertainties of the depths of key horizons near the borehole DSDP-258 located in the Mentelle Basin, south west of Australia, and compare the results with the drilled core from that well. Following this strategy, the tie between the modelled and observed depths from DSDP-258 core was in accordance with the ± 2σ posterior credibility intervals and predictions for depths to key horizons were made for the two new drill sites, adjacent the existing borehole of the area. The probabilistic analysis allowed us to generate multiple realizations of pre-stack depth migrated images, these can be directly used to better constrain interpretation and identify potential risk at drill sites. The method will be applied to constrain the drilling targets for the upcoming International Ocean Discovery Program (IODP), leg 369.

Uncertainty analysis of depth predictions from seismic reflection data using Bayesian statistics

NASA Astrophysics Data System (ADS)

Michelioudakis, Dimitrios G.; Hobbs, Richard W.; Caiado, Camila C. S.

2018-06-01

Estimating the depths of target horizons from seismic reflection data is an important task in exploration geophysics. To constrain these depths we need a reliable and accurate velocity model. Here, we build an optimum 2-D seismic reflection data processing flow focused on pre-stack deghosting filters and velocity model building and apply Bayesian methods, including Gaussian process emulation and Bayesian History Matching, to estimate the uncertainties of the depths of key horizons near the Deep Sea Drilling Project (DSDP) borehole 258 (DSDP-258) located in the Mentelle Basin, southwest of Australia, and compare the results with the drilled core from that well. Following this strategy, the tie between the modelled and observed depths from DSDP-258 core was in accordance with the ±2σ posterior credibility intervals and predictions for depths to key horizons were made for the two new drill sites, adjacent to the existing borehole of the area. The probabilistic analysis allowed us to generate multiple realizations of pre-stack depth migrated images, these can be directly used to better constrain interpretation and identify potential risk at drill sites. The method will be applied to constrain the drilling targets for the upcoming International Ocean Discovery Program, leg 369.

Constrained spectral clustering under a local proximity structure assumption

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri; Xu, Qianjun; des Jardins, Marie

2005-01-01

This work focuses on incorporating pairwise constraints into a spectral clustering algorithm. A new constrained spectral clustering method is proposed, as well as an active constraint acquisition technique and a heuristic for parameter selection. We demonstrate that our constrained spectral clustering method, CSC, works well when the data exhibits what we term local proximity structure.

Tephrochronology of Bed II, Olduvai Gorge, Tanzania, and placement of the Oldowan-Acheulean transition.

PubMed

McHenry, Lindsay J; Stanistreet, Ian G

2018-04-12

Tuffaceous marker beds, derived from volcanic products from the Ngorongoro Volcanic Highlands, help define a stratigraphic framework for the world-renowned fossil and stone tool record exposed at Olduvai Gorge, Tanzania. However, previous efforts to constrain this tuff record, especially for Olduvai Bed II, have been limited because of erosion, contamination, reworking, and the alteration of volcanic glass under saline-alkaline conditions. This paper applies previously defined geochemical and mineralogical "fingerprints" for several major Bed II marker tuffs, based on glass (where available) and phenocrysts more resistant to alteration (feldspar, hornblende, augite, and titanomagnetite), to tuffs from stratigraphic sections in the Olduvai Junction Area, including previously and recently excavated Acheulean and Oldowan sites (HWK EE (Locality (Loc) 42), EF-HR (Loc 12a), FLK (Loc 45), and MNK (Loc 88)). The Middle Bed II Bird Print Tuff (BPT) is found to be more compositionally variable than previously reported but is still valuable as a stratigraphic marker over short distances. The confirmation of blocks of Tuff IID in conglomerate helps constrain Upper Bed II stratigraphy at sites where in-situ tuffs are absent. This paper also compiles the results of published geochronological research, providing stratigraphic context and updating previously reported dates using a consistent 40 Ar/ 39 Ar reference standard age. The results of this work support the following paleoanthropologically relevant conclusions: 1) the early Acheulean site EF-HR (Loc 12a) is situated above the level of Hay's Tuff IIC, and thus sits in Upper rather than Middle Bed II, (2) the HWK EE (Loc 42) Oldowan site is constrained between Tuff IIA and Tuff IIB, just above the boundary between Lower and Middle Bed II, and 3) the Acheulean site at FLK W most likely lies within the Middle Augitic Sandstone, above Tuff IIB, similar to the placements by Leakey and Hay for the earliest Acheulean at Olduvai. Copyright © 2018 Elsevier Ltd. All rights reserved.

Chromosome dynamics in the yeast interphase nucleus.

PubMed

Heun, P; Laroche, T; Shimada, K; Furrer, P; Gasser, S M

2001-12-07

Little is known about the dynamics of chromosomes in interphase nuclei. By tagging four chromosomal regions with a green fluorescent protein fusion to lac repressor, we monitored the movement and subnuclear position of specific sites in the yeast genome, sampling at short time intervals. We found that early and late origins of replication are highly mobile in G1 phase, frequently moving at or faster than 0.5 micrometers/10 seconds, in an energy-dependent fashion. The rapid diffusive movement of chromatin detected in G1 becomes constrained in S phase through a mechanism dependent on active DNA replication. In contrast, telomeres and centromeres provide replication-independent constraint on chromatin movement in both G1 and S phases.

Using InSAR to Observe Sinkhole Activity in Central Florida

NASA Astrophysics Data System (ADS)

Oliver-Cabrera, T.; Wdowinski, S.; Kruse, S.; Kiflu, H. G.

2017-12-01

Sinkhole collapse in Florida is a major geologic hazard, threatening human life and causing substantial damage to property. Detecting sinkhole deformation before a collapse is an important but difficult task; most techniques used to monitor sinkholes are spatially constrained to relatively small areas (tens to hundred meters). To overcome this limitation, we use Interferometric Synthetic Aperture Radar (InSAR), which is a very useful technique for detecting localized deformation while covering vast areas. InSAR results show localized deformation at several houses and commercial buildings in different locations along the study sites. We use a subsurface imaging technique, ground penetrating radar, to verify sinkhole existence beneath the observed deforming areas.

More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature

PubMed Central

Ladunga, Istvan

2007-01-01

Highly accurate knockdown functional analyses based on RNA interference (RNAi) require the possible most complete hydrolysis of the targeted mRNA while avoiding the degradation of untargeted genes (off-target effects). This in turn requires significant improvements to target selection for two reasons. First, the average silencing activity of randomly selected siRNAs is as low as 62%. Second, applying more than five different siRNAs may lead to saturation of the RNA-induced silencing complex (RISC) and to the degradation of untargeted genes. Therefore, selecting a small number of highly active siRNAs is critical for maximizing knockdown and minimizing off-target effects. To satisfy these needs, a publicly available and transparent machine learning tool is presented that ranks all possible siRNAs for each targeted gene. Support vector machines (SVMs) with polynomial kernels and constrained optimization models select and utilize the most predictive effective combinations from 572 sequence, thermodynamic, accessibility and self-hairpin features over 2200 published siRNAs. This tool reaches an accuracy of 92.3% in cross-validation experiments. We fully present the underlying biophysical signature that involves free energy, accessibility and dinucleotide characteristics. We show that while complete silencing is possible at certain structured target sites, accessibility information improves the prediction of the 90% active siRNA target sites. Fast siRNA activity predictions can be performed on our web server at . PMID:17169992

Increasing subterranean mobilization of organic contaminants and petroleum by aqueous thermal oxidation

DOEpatents

Leif, Roald N.; Knauss, Kevin G.; Newmark, Robin L.; Aines, Roger D.; Eaker, Craig

2002-01-01

In situ hydrous pyrolysis/partial oxidation of organics at the site of the organics constrained in an subsurface reservoir produces surfactants that can form an oil/water emulsion that is effectively removed from an underground formation. The removal of the oil/water emulsions is particularly useful in several applications, e.g., soil contaminant remediation and enhanced oil recovery operations. A portion of the constrained organics react in heated reservoir water with injected steam containing dissolved oxygen gas at ambient reservoir conditions to produce such surfactants.

Photometric Properties of Soils at the Mars Phoenix Landing Site: Preliminary Analysis from CRISM EPF Data

NASA Astrophysics Data System (ADS)

Cull, S. C.; Arvidson, R. E.; Seelos, F.; Wolff, M. J.

2010-03-01

Using data from CRISM's Emission Phase Function observations, we attempt to constrain Phoenix soil scattering properties, including soil grain size, single-scattering albedo, and surface phase function.

Investigation of the Roles of Allosteric Domain Arginine, Aspartate, and Glutamate Residues of Rhizobium etli Pyruvate Carboxylase in Relation to Its Activation by Acetyl CoA.

PubMed

Sirithanakorn, Chaiyos; Jitrapakdee, Sarawut; Attwood, Paul V

2016-08-02

The mechanism of allosteric activation of pyruvate carboxylase by acetyl CoA is not fully understood. Here we have examined the roles of residues near the acetyl CoA binding site in the allosteric activation of Rhizobium etli pyruvate carboxylase using site-directed mutagenesis. Arg429 was found to be especially important for acetyl CoA binding as substitution with serine resulted in a 100-fold increase in the Ka of acetyl CoA activation and a large decrease in the cooperativity of this activation. Asp420 and Arg424, which do not make direct contact with bound acetyl CoA, were nonetheless found to affect acetyl CoA binding when mutated, probably through changed interactions with another acetyl CoA binding residue, Arg427. Thermodynamic activation parameters for the pyruvate carboxylation reaction were determined from modified Arrhenius plots and showed that acetyl CoA acts to decrease the activation free energy of the reaction by both increasing the activation entropy and decreasing the activation enthalpy. Most importantly, mutations of Asp420, Arg424, and Arg429 enhanced the activity of the enzyme in the absence of acetyl CoA. A main focus of this work was the detailed investigation of how this increase in activity occurred in the R424S mutant. This mutation decreased the activation enthalpy of the pyruvate carboxylation reaction by an amount consistent with removal of a single hydrogen bond. It is postulated that Arg424 forms a hydrogen bonding interaction with another residue that stabilizes the asymmetrical conformation of the R. etli pyruvate carboxylase tetramer, constraining its interconversion to the symmetrical conformer that is required for catalysis.

USE OF ENVIRONMENTAL ISOTOPES TO DIFFERENTIATE WATER SOURCES AND CONSTRAIN THE WATER BUDGET AT THE SULPHUR BANK MERCURY MINE, CLEAR LAKE, CALIFORNIA

EPA Science Inventory

The Sulphur Bank Mercury Mine (SBMM) is a 65 ha site located on the eastern shore of the Oaks Arm of Clear Lake, Lake County, California. Between 1864 and 1957, SBMM was the site of underground and open pit mining operations for S and Hg, coinciding with past and present hot spr...

Physical Conditions Associated with Widespread Seafloor Methane Discharge on the Northern US Atlantic Margin

NASA Astrophysics Data System (ADS)

Skarke, A. D.; Ruppel, C. D.; Brothers, D. S.

2014-12-01

Recent analysis of water column backscatter data and remotely operated vehicle (ROV) video imagery collected by NOAA Ship Okeanos Explorer between 2011 and 2013 revealed methane discharge from the seafloor at over 570 gas seep locations along the northern US Atlantic margin. To the best of our knowledge, such large-scale seepage has not previously been observed on a passive margin outside the Arctic or not spatially associated with a petroleum basin. This seepage has implications for the global carbon cycle, ocean chemistry (e.g., acidification), and in some cases, the climate system. Using data collected by Okeanos Explorer and NOAA's Deep Discoverer ROV, we combine water column backscatter data with video imagery and seafloor backscatter data to estimate gas flux and constrain the geoacoustic properties of the seabed at methane discharge sites. The total methane flux from the northern US Atlantic margin seeps is conservatively estimated at ~15-90 Mg y-1, based on observations of gas bubble volume, discharge rates, and discharge points per site. However, fewer than 1% of the identified seep sites have been inspected with a ROV, and this estimate is likely to be revised upward as the characteristics of the seeps are further constrained. Another important observation to emerge from our analysis is the lack of spatial correlation between seep sites and the ~5000 pockmarks mapped on the northern part of the US Atlantic margin. In this region, pockmarks, which are often easily identified by geophysical imaging of the seafloor, should not be considered potential target sites for finding undiscovered areas of seepage. Conversely, discrete patches of elevated relative seafloor acoustic backscatter amplitude do appear to be correlated with the spatial distribution of methane seeps, implying anomalous seafloor characteristic at seep loci. This finding is consistent with ROV video observations of authigenic carbonate outcrops and extensive chemosynthetic bivalve communities at seep sites, which create a seafloor substrate with higher acoustic impedance. This result suggests that seafloor acoustic reflectivity data, which are far more commonly collected and archived than water column backscatter data, might be used diagnostically to identify and constrain the distribution of seafloor locations of methane discharge.

Climate-induced landslide reactivation at the edge of the Most Basin (Czech Republic) - progress towards better landslide prediction

NASA Astrophysics Data System (ADS)

Burda, J.; Hartvich, F.; Valenta, J.; Smítka, V.; Rybář, J.

2013-02-01

The catastrophic landslide at Eisenberg in North Bohemia was reactivated during January 2011. This study integrates a range of geoscientific evidence in order to constrain the spatial and temporal development of this reactivation. It has investigated long-term geodetic measurements to assess the morphological development of the site over the last two decades. There is evidence to suggest that, over this period, the site had been subjected to progressive deformation caused by the collapse of an old mine gallery. However, climatic data show that the reactivation itself was triggered by a dramatic rise in the water table induced by rapid snowmelt during a period of winter warming. Furthermore, geomorphological mapping has been used to characterise the morphology of the reactivated landslide and geophysical profiling has been used to analyse its internal structure. The results show that fissures are continuing to develop above the reactivated landslide scarp while highly saturated stiff-fissured claystones provide an incipient slide plane. The application of laser scanning has shown minimal evidence for ongoing landslide activity. It is, however, clear that future landslide events will occur here due to the favourable lithological, structural, and geotechnical conditions. Finally, we propose that future landslide activity at the site may be predicted by the height of water table as this defines theoretical pore pressure at the depth of the shear plane.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem.

PubMed

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-03-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem

PubMed Central

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-01-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models. PMID:26925871

Glomerular and Mitral-Granule Cell Microcircuits Coordinate Temporal and Spatial Information Processing in the Olfactory Bulb.

PubMed

Cavarretta, Francesco; Marasco, Addolorata; Hines, Michael L; Shepherd, Gordon M; Migliore, Michele

2016-01-01

The olfactory bulb processes inputs from olfactory receptor neurons (ORNs) through two levels: the glomerular layer at the site of input, and the granule cell level at the site of output to the olfactory cortex. The sequence of action of these two levels has not yet been examined. We analyze this issue using a novel computational framework that is scaled up, in three-dimensions (3D), with realistic representations of the interactions between layers, activated by simulated natural odors, and constrained by experimental and theoretical analyses. We suggest that the postulated functions of glomerular circuits have as their primary role transforming a complex and disorganized input into a contrast-enhanced and normalized representation, but cannot provide for synchronization of the distributed glomerular outputs. By contrast, at the granule cell layer, the dendrodendritic interactions mediate temporal decorrelation, which we show is dependent on the preceding contrast enhancement by the glomerular layer. The results provide the first insights into the successive operations in the olfactory bulb, and demonstrate the significance of the modular organization around glomeruli. This layered organization is especially important for natural odor inputs, because they activate many overlapping glomeruli.

Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity

PubMed Central

Zandvakili, Arya; Campbell, Ian; Weirauch, Matthew T.

2018-01-01

Cells use thousands of regulatory sequences to recruit transcription factors (TFs) and produce specific transcriptional outcomes. Since TFs bind degenerate DNA sequences, discriminating functional TF binding sites (TFBSs) from background sequences represents a significant challenge. Here, we show that a Drosophila regulatory element that activates Epidermal Growth Factor signaling requires overlapping, low-affinity TFBSs for competing TFs (Pax2 and Senseless) to ensure cell- and segment-specific activity. Testing available TF binding models for Pax2 and Senseless, however, revealed variable accuracy in predicting such low-affinity TFBSs. To better define parameters that increase accuracy, we developed a method that systematically selects subsets of TFBSs based on predicted affinity to generate hundreds of position-weight matrices (PWMs). Counterintuitively, we found that degenerate PWMs produced from datasets depleted of high-affinity sequences were more accurate in identifying both low- and high-affinity TFBSs for the Pax2 and Senseless TFs. Taken together, these findings reveal how TFBS arrangement can be constrained by competition rather than cooperativity and that degenerate models of TF binding preferences can improve identification of biologically relevant low affinity TFBSs. PMID:29617378

Highly conformationally constrained halogenated 6-spiroepoxypenicillins as probes for the bioactive side-chain conformation of benzylpenicillin

NASA Astrophysics Data System (ADS)

Shute, Richard E.; Jackson, David E.; Bycroft, Barrie W.

1989-06-01

The halogenated 6-spiroepoxypenicillins are a series of novel semisynthetic β-lactam compounds with highly conformationally restricted side chains incorporating an epoxide. Their biological activity profiles depend crucially on the configuration at position C-3 of that epoxide. In derivatives with aromatic-containing side chains, e.g., anilide, the 3 R-compounds possess notable Gram-positive antibacterial activity and potent β-lactamase inhibitory properties. The comparable 3S-compounds are antibacterially inactive, but retain β-lactamase inhibitory activity. Using the molecular simulation programs COSMIC and ASTRAL, we attempted to map a putative, lipophilic accessory binding site on the PBPs that must interact with the side-chain aromatic residue. Comparative computer-assisted modelling of the 3 R, and 3 S-anilides, along with benzylpenicillin, indicated that the available conformational space at room temperature for the side chains of the 3 R and the 3 S-anilides was mutually exclusive. The conformational space for the more flexible benzylpenicillin could accommodate the side chains of both the constrained penicillin derivatives. By a combination of van der Waals surface calculations and a pharmacophoric distance approach, closely coincident conformers of the 3 R-anilide and benzylpenicillin were identified. These conformers must be related to the antibacterial, `bioactive' conformer for the classical β-lactam antibiotics. From these proposed bioactive conformations, a model for the binding of benzylpenicillin to the PBPs relating the three-dimensional arrangement of a putative lipophilic S2-subsite, specific for the side-chain aromatic moiety, and the 3 α-carboxylate functionality is presented.

An International Symposium and Exhibition on Active Materials and Adaptive Structures.

DTIC Science & Technology

1991-11-08

into Tubular Composite Structures Using Embedded Constraining Layers 232 S. Sattinger, Z. Sanjana, Westinghouse Science and Technology Center...struts, constrained layers , and tuned mass dampers. The most effective damping treatment was selected for each mode depending on its modal...paper) the passive damping component* in the structure will be deserth^ These »dude constrained layer viscoelastic struts« viscous DStrlJi . .^ of

Diffusion of a Concentrated Lattice Gas in a Regular Comb Structure

NASA Astrophysics Data System (ADS)

Garcia, Paul; Wentworth, Christopher

2008-10-01

Understanding diffusion in constrained geometries is of interest in a variety of contexts as varied as mass transport in disordered solids, such as a percolation cluster, or intercellular transport of water molecules in biological tissue. In this investigation we explore diffusion in a very simple constrained geometry: a comb-like structure involving a one-dimensional backbone of lattice sites with regularly spaced teeth of fixed length. The model considered assumes a fixed concentration of diffusing particles can hop to nearest-neighbor sites only, and they do not interact with each other except that double occupancy is not allowed. The system is simulated using a Monte Carlo simulation procedure. The mean-square displacement of a tagged particle is calculated from the simulation as a function of time. The simulation shows normal diffusive behavior after a period of anomalous diffusion that increases as the tooth size increases.

Finite-density effects in the Fredrickson-Andersen and Kob-Andersen kinetically-constrained models

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

Teomy, Eial, E-mail: eialteom@post.tau.ac.il; Shokef, Yair, E-mail: shokef@tau.ac.il

2014-08-14

We calculate the corrections to the thermodynamic limit of the critical density for jamming in the Kob-Andersen and Fredrickson-Andersen kinetically-constrained models, and find them to be finite-density corrections, and not finite-size corrections. We do this by introducing a new numerical algorithm, which requires negligible computer memory since contrary to alternative approaches, it generates at each point only the necessary data. The algorithm starts from a single unfrozen site and at each step randomly generates the neighbors of the unfrozen region and checks whether they are frozen or not. Our results correspond to systems of size greater than 10{sup 7} ×more » 10{sup 7}, much larger than any simulated before, and are consistent with the rigorous bounds on the asymptotic corrections. We also find that the average number of sites that seed a critical droplet is greater than 1.« less

Initiation and slow propagation of epileptiform activity from ventral to dorsal medial entorhinal cortex is constrained by an inhibitory gradient.

PubMed

Ridler, Thomas; Matthews, Peter; Phillips, Keith G; Randall, Andrew D; Brown, Jonathan T

2018-06-01

The medial entorhinal cortex (mEC) has an important role in initiation and propagation of seizure activity. Several anatomical relationships exist in neurophysiological properties of mEC neurons; however, in the context of hyperexcitability, previous studies often considered it as a homogeneous structure. Using multi-site extracellular recording techniques, ictal-like activity was observed along the dorso-ventral axis of the mEC in vitro in response to various ictogenic stimuli. This originated predominantly from ventral areas, spreading to dorsal mEC with a surprisingly slow velocity. Modulation of inhibitory tone was capable of changing the slope of ictal initiation, suggesting seizure propagation behaviours are highly dependent on levels of GABAergic function in this region. A distinct disinhibition model also showed, in the absence of inhibition, a prevalence for interictal-like initiation in ventral mEC, reflecting the intrinsic differences in mEC neurons. These findings suggest the ventral mEC is more prone to hyperexcitable discharge than the dorsal mEC, which may be relevant under pathological conditions. The medial entorhinal cortex (mEC) has an important role in the generation and propagation of seizure activity. The organization of the mEC is such that a number of dorso-ventral relationships exist in neurophysiological properties of neurons. These range from intrinsic and synaptic properties to density of inhibitory connectivity. We examined the influence of these gradients on generation and propagation of epileptiform activity in the mEC. Using a 16-shank silicon probe array to record along the dorso-ventral axis of the mEC in vitro, we found 4-aminopyridine application produces ictal-like activity originating predominantly in ventral areas. This activity spreads to dorsal mEC at a surprisingly slow velocity (138 μm s -1 ), while cross-site interictal-like activity appeared relatively synchronous. We propose that ictal propagation is constrained by differential levels of GABAergic control since increasing (diazepam) or decreasing (Ro19-4603) GABA A receptor activation, respectively, reduced or increased the slope of ictal initiation. The observation that ictal activity is predominately generated in ventral mEC was replicated using a separate 0-Mg 2+ model of epileptiform activity in vitro. By using a distinct disinhibition model (co-application of kainate and picrotoxin) we show that additional physiological features (for example intrinsic properties of mEC neurons) still produce a prevalence for interictal-like initiation in ventral mEC. These findings suggest that the ventral mEC is more likely to initiate hyperexcitable discharges than the dorsal mEC, and that seizure propagation is highly dependent on levels of GABAergic expression across the mEC. © 2018 The Authors. The Journal of Physiology © 2018 The Physiological Society.

A constitutively activating mutation alters the dynamics and energetics of a key conformational change in a ligand-free G protein-coupled receptor.

PubMed

Tsukamoto, Hisao; Farrens, David L

2013-09-27

G protein-coupled receptors (GPCRs) undergo dynamic transitions between active and inactive conformations. Usually, these conversions are triggered when the receptor detects an external signal, but some so-called constitutively activating mutations, or CAMs, induce a GPCR to bind and activate G proteins in the absence of external stimulation, in ways still not fully understood. Here, we investigated how a CAM alters the structure of a GPCR and the dynamics involved as the receptor transitions between different conformations. Our approach used site-directed fluorescence labeling (SDFL) spectroscopy to compare opsin, the ligand-free form of the GPCR rhodopsin, with opsin containing the CAM M257Y, focusing specifically on key movements that occur in the sixth transmembrane helix (TM6) during GPCR activation. The site-directed fluorescence labeling data indicate opsin is constrained to an inactive conformation both in detergent micelles and lipid membranes, but when it contains the M257Y CAM, opsin is more dynamic and can interact with a G protein mimetic. Further study of these receptors using tryptophan-induced quenching (TrIQ) methods indicates that in detergent, the CAM significantly increases the population of receptors in the active state, but not in lipids. Subsequent Arrhenius analysis of the TrIQ data suggests that, both in detergent and lipids, the CAM lowers the energy barrier for TM6 movement, a key transition required for conversion between the inactive and active conformations. Together, these data suggest that the lowered energy barrier is a primary effect of the CAM on the receptor dynamics and energetics.

Tilt and strain deformation induced by hydrologically active natural fractures: application to the tiltmeters installed in Sainte-Croix-aux-Mines observatory (France)

NASA Astrophysics Data System (ADS)

Longuevergne, Laurent; Florsch, Nicolas; Boudin, Frédéric; Oudin, Ludovic; Camerlynck, Christian

2009-08-01

We investigate the deformation induced by water pressure variations in hydrologically active natural fractures, and recorded by tiltmeters and strainmeters. The deformation associated with a single fracture is derived using finite-element modelling (FEM). A range in fracture geometries is explored, first to highlight the sensitivity of each geometrical parameter to the deformation, and secondly to allow transfer to observation sites. Water level variations in the fracture are then derived from a hydrological model, driven by observed rainfall, and calibrated on fracture water flow measurements. The modelling results are explicitly applied to constrain the local hydrological contribution to observations with the 100-m-long hydrostatic tiltmeter installed at Sainte-Croix-aux-Mines (France). Our study shows that well-founded physical modelling of local hydrological effect allows a substantial correction of records in observatories.

Tighter Ligand Binding Can Compensate for Impaired Stability of an RNA-Binding Protein.

PubMed

Wallis, Christopher P; Richman, Tara R; Filipovska, Aleksandra; Rackham, Oliver

2018-06-15

It has been widely shown that ligand-binding residues, by virtue of their orientation, charge, and solvent exposure, often have a net destabilizing effect on proteins that is offset by stability conferring residues elsewhere in the protein. This structure-function trade-off can constrain possible adaptive evolutionary changes of function and may hamper protein engineering efforts to design proteins with new functions. Here, we present evidence from a large randomized mutant library screen that, in the case of PUF RNA-binding proteins, this structural relationship may be inverted and that active-site mutations that increase protein activity are also able to compensate for impaired stability. We show that certain mutations in RNA-protein binding residues are not necessarily destabilizing and that increased ligand-binding can rescue an insoluble, unstable PUF protein. We hypothesize that these mutations restabilize the protein via thermodynamic coupling of protein folding and RNA binding.

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

Bond-Lamberty, Benjamin; Bolton, Harvey; Fansler, Sarah J.

The effects of climate change on soil organic matter—its structure, microbial community, carbon storage, and respiration response—remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampledmore » the original 1994 soil transplants and controls, measuring CO 2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5 °C monthly maximum air temperature, +50 mm yr -1precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. Lastly, these results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.« less

Development of a minimal saponin vaccine adjuvant based on QS-21

NASA Astrophysics Data System (ADS)

Fernández-Tejada, Alberto; Chea, Eric K.; George, Constantine; Pillarsetty, Nagavarakishore; Gardner, Jeffrey R.; Livingston, Philip O.; Ragupathi, Govind; Lewis, Jason S.; Tan, Derek S.; Gin, David Y.

2014-07-01

Adjuvants are materials added to vaccines to enhance the immunological response to an antigen. QS-21 is a natural product adjuvant under investigation in numerous vaccine clinical trials, but its use is constrained by scarcity, toxicity, instability and an enigmatic molecular mechanism of action. Herein we describe the development of a minimal QS-21 analogue that decouples adjuvant activity from toxicity and provides a powerful platform for mechanistic investigations. We found that the entire branched trisaccharide domain of QS-21 is dispensable for adjuvant activity and that the C4-aldehyde substituent, previously proposed to bind covalently to an unknown cellular target, is also not required. Biodistribution studies revealed that active adjuvants were retained preferentially at the injection site and the nearest draining lymph nodes compared with the attenuated variants. Overall, these studies have yielded critical insights into saponin structure-function relationships, provided practical synthetic access to non-toxic adjuvants, and established a platform for detailed mechanistic studies.

Development of a minimal saponin vaccine adjuvant based on QS-21

PubMed Central

Fernández-Tejada, Alberto; Chea, Eric K.; George, Constantine; Pillarsetty, NagaVaraKishore; Gardner, Jeffrey R.; Livingston, Philip O.; Ragupathi, Govind; Lewis, Jason S.; Tan, Derek S.; Gin, David Y.

2014-01-01

Adjuvants are materials added to vaccines to enhance the immunological response to an antigen. QS-21 is a natural product adjuvant under investigation in numerous vaccine clinical trials, but its use is constrained by scarcity, toxicity, instability, and an enigmatic molecular mechanism of action. Herein, we describe the development of a minimal QS-21 analogue that decouples adjuvant activity from toxicity and provides a powerful platform for mechanistic investigations. We found that the entire branched trisaccharide domain of QS-21 is dispensable for adjuvant activity and that the C4-aldehyde substituent, previously proposed to bind covalently to an unknown cellular target, is also not required. Biodistribution studies revealed that active adjuvants were retained at the injection site and nearest draining lymph nodes preferentially compared to attenuated variants. Overall, these studies have yielded critical insights into saponin structure–function relationships, provided practical synthetic access to non-toxic adjuvants, and established a platform for detailed mechanistic studies. PMID:24950335

Conformationally Constrained Analogues of Diacylglycerol. 29. Cells Sort Diacylglycerol-Lactone Chemical Zip Codes to Produce Diverse and Selective Biological Activities

PubMed Central

Duan, Dehui; Sigano, Dina M.; Kelley, James A.; Lai, Christopher C.; Lewin, Nancy E.; Kedei, Noemi; Peach, Megan L.; Lee, Jeewoo; Abeyweera, Thushara P.; Rotenberg, Susan A.; Kim, Hee; Kim, Young Ho; Kazzouli, Saïd El; Chung, Jae-Uk; Young, Howard A.; Young, Matthew R.; Baker, Alyson; Colburn, Nancy H.; Haimovitz-Friedman, Adriana; Truman, Jean-Philip; Parrish, Damon A.; Deschamps, Jeffrey R.; Perry, Nicholas A.; Surawski, Robert J.; Blumberg, Peter M.; Marquez, Victor E.

2008-01-01

Diacylglycerol-lactone (DAG-lactone) libraries generated by a solid-phase approach using IRORI technology produced a variety of unique biological activities. Subtle differences in chemical diversity in two areas of the molecule, the combination of which generates what we have termed “chemical zip codes”, are able to transform a relatively small chemical space into a larger universe of biological activities, as membrane-containing organelles within the cell appear to be able to decode these “chemical zip codes”. It is postulated that after binding to protein kinase C (PKC) isozymes or other non-kinase target proteins that contain diacylglycerol responsive, membrane interacting domains (C1 domains), the resulting complexes are directed to diverse intracellular sites where different sets of substrates are accessed. Multiple cellular bioassays show that DAG-lactones, which bind in vitro to PKCα to varying degrees, expand their biological repertoire into a larger domain, eliciting distinct cellular responses. PMID:18698758

Late Quaternary cooling rate constrained by multiple IRSL thermochronometers of potassium feldspars for granites from Kongur Shan, Chinese Pamir

NASA Astrophysics Data System (ADS)

Qin, Jintang; Chen, Jie; Valla, Pierre; Herman, Frédéric

2015-04-01

The Kongur Shan (East Pamir), located at the northwestern Tibetan Plateau, is one of the most active orogens on Earth, where both tectonic processes along major active faults and climatic forcing (extensive glaciers coverage) are contributing to the regional landscape evolution. The exhumation rates since late Miocene was constrained to be ~6.5 - 4.2 mm/yr. However, it is still debated whether the exhumation rate accelerated since the Quaternary, of which the climate was featured by the cyclic glaciations with periods of 100 ka and 40 ka. In this study, we tried to employ luminescence thermochronology, which is a still in developing method, to resolve the impact of glacial cycles on exhumation rate. Our study site is located ~10 km to the east of the active Kongur normal fault, along the major valley of Gez river. We sampled three granite rocks from a sub-horizontal tunnel across the granite massif; one was from the entrance of the tunnel, and other two samples were from inside of the tunnel, where the measured ambient temperature is as high as 60-70 ° C. The distances of these samples are within 2 km. Four types of IRSL signals extracted from potassium feldspars (K-feldspars) were measured for each individual sample, and the results of isothermal decay experiments indicated these signals were of different thermal stabilities. Therefore, they may serve as four thermochronometers with different closure temperature. We employ these multiple thermochronometers together for each single sample to constrain their cooling rates. Our preliminary results, which are based on the simplified luminescence model of K-feldspars, suggest that the averaged cooling rate of the last 200 ka is as high as 1.4 oC/ka, which corresponds to an exhumation rate of ~ 2.3 to 0.9 cm/yr with the geothermal gradient assumed to be 60 to 150 oC/km. It seems to imply that the glacial cycles during the Quaternary substantially accelerated the exhumation rate of granite massif of Kongur Shan.

Nuclear Magnetic Resonance Observations of Octahedral Aluminum in Forsterite, Clinoenstatite and Periclase.

NASA Astrophysics Data System (ADS)

McCarty, R. J.; Stebbins, J. F.

2015-12-01

This research seeks to constrain the crystallographic site preferences of aluminum in forsterite, clinoenstatite and periclase, mantle minerals in which this element is only found at low concentrations. Improved site preference information will help constrain thermodynamic descriptions of the substitution mechanisms, making them more useful to geobarometric and geothermometric techniques. Using high field magic angle spinning nuclear magnetic resonance (NMR) and electron probe microanalysis (EPMA), we constrain the site preferences of minor and trace amounts (2000 to 400 mol ppm) of aluminum in extremely pure synthetic forsterite, clinoenstatite and periclase. The primary challenge of this research is determining how much of each of the aluminum species observed by NMR in the bulk sample (abundances and coordinations) resides in the major synthesized mineral. In our samples, the aluminum partitions between small amounts (often <1%) of impurity phases with high aluminum concentrations, such as glass and accessory crystals, and the major, intended phase with low aluminum concentrations. We use EPMA composition maps to locate scarce impurity phases and EPMA point analyses to determine the aluminum concentrations in both the intended major phase and in the impurity phases. Long NMR acquisitions (several days) and careful subtraction of rotor background signals (present in even 'low-Al' zirconia rotor materials) are required to obtain adequate signal-to-noise ratios at such low concentrations. Ordered octahedral aluminum has been identified in forsterite, clinoenstatite, and periclase. Disordered 4, 5 and 6 coordinated aluminum species have also been observed, but it is still unclear if the disordered species are in the major mineral phases, the impurity phases or both.

Progenitor Masses for Every Nearby Historic Core-Collapse Supernova

NASA Astrophysics Data System (ADS)

Williams, Benjamin

2016-10-01

Some of the most energetic explosions in the Universe are the core-collapse supernovae (CCSNe) that arise from the death of massive stars. They herald the birth of neutron stars and black holes, are prodigious emitters of neutrinos and gravitational waves, influence galactic hydrodynamics, trigger further star formation, and are a major site for nucleosynthesis, yet even the most basic elements of CCSN theory are poorly constrained by observations. Specifically, there are too few observations to constrain the progenitor mass distribution and fewer observations still to constrain the mapping between progenitor mass and explosion type (e.g. IIP IIL, IIb, Ib/c, etc.). Combining previous measurements with 9 proposed HST pointings covering 13 historic CCSNe, we plan to obtain progenitor mass measurements for all cataloged historic CCSNe within 8 Mpc, optimizing observational mass constraints for CCSN theory.

Spatial Patterns of Greenhouse Gases Across an Urbanization Gradient in a Suburban River Network

NASA Astrophysics Data System (ADS)

Robison, A.; Balch, E.; Wollheim, W. M.

2017-12-01

River networks are important components of the global carbon cycle, processing significant quantities of terrestrial carbon and are most often sources of greenhouse gases (GHGs) to the atmosphere. While recent investigations have begun to incorporate aquatic systems into continental carbon budgets, our understanding of what drives the variability in space and time of these dynamics is poorly constrained. Meanwhile, urban areas continue to expand rapidly across the globe, with wide ranging effects on aquatic systems. A better understanding of the effect of human activities on aquatic carbon and GHG dynamics at both local and global scales is needed. We address the question: How does urbanization affect GHG dynamics in river networks? To address this question, we conducted a synoptic survey of 45 sites in a suburban river network in New England (Ipswich River, MA), analyzing samples for physical and chemical characteristics, including dissolved GHGs, carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Sampling sites were selected across an urbanization gradient (1.4-90% developed) and included headwater streams, major tributaries, the basin mouth, and additional sites along the main stem. Initial results indicate dissolved N2O concentration in headwater streams is related to catchment development, while CO2 and CH4 are not correlated to land use generally. CO2 and CH4 signals from urban areas are likely modified by fluvial wetlands that are abundant along larger tributaries and the mainstem. Developed watersheds are inherently altered and heterogeneous landscapes. To fully quantify the role of urbanized waters in the larger carbon cycle, GHG dynamics must be considered at the river network scale. The work presented here begins this process, allowing for an examination of the interaction between land use and GHG concentrations. Additional analyses will focus on further constraining GHG patterns across the river network, and modeling gas transport through and flux out of the system. This relationship should also be examined across time and under varying flow conditions.

Baseline studies to select the most sound and sensitive sites to install continuous monitoring per sismo-geochemical networks. The case history of the Norcia-Amatrice-Spoleto seismic sequences (2016-2017)

NASA Astrophysics Data System (ADS)

Quattrocchi, F.; Gallo, F.

2017-12-01

The paper review methodologically and historically - in the frame of seismo-geochemical studies in Italy and abroad to select the most "sensitive" sites along active faults, mostly where structural geology is not able to discover "blind" faults or complex fault crossing systems, with maximum fluids-faults interaction. The paper is highlighting the "site specific" case histories and processes helping in networks design, gathered in occasion of strong-moderate earthquakes, gas-burst or groundwater evolution in geothermal-hydrocarbons field during EU projects (i.e., Geochemical Seismic Zonation, 3F-Faults-Fractures-Fluids Corinth). Some concepts are highlighted based on gather experimental data in 25 years: - if the network is in soil gas is necessary a preliminary study on groundwater too, to understand the sectors of shallow aquifers, as "buffer" bodies, more prone to be oversaturated by geogas from depth; a preliminary grid should consider both the CO2-CH4-Rn fluxes, all gas concentrations and isotopes analyses (TDIC, CH4 CO2 , rare gas) case by case described here, mostly where the regional faults are crossing each other and where a carrier gas is acting i.e., CO2. It is very un-correct to install mono-parametric stations, i.e. only Radon to understand the real WRI processes. - if the network is in groundwater is very important a preliminary study before, during and after seismic sequences, to realize where the maximum anomalies (i.e., anomalous animal behavior, temperature increasing, geochemical anomalies, new gas relase) are and will be envisaged, as found for the Umbria-Marche border (the Colfiorito 1997-1998 and the 2016-2017 Norcia-Amatrice seismic sequences), where a deep pore-pressure dominated situation could be constrained by seismo-geochemistry, along "still silent" close fault segments too. if the network is in groundwater is very important a geochemical multidisciplinary approach to constrain the segment length and relative maximum magnitude.

Parental Perceptions of the Social Environment Are Inversely Related to Constraint of Adolescents’ Neighborhood Physical Activity

PubMed Central

Kepper, Maura; Broyles, Stephanie; Scribner, Richard; Tseng, Tung-Sung; Zabaleta, Jovanny; Griffiths, Lauren; Sothern, Melinda

2016-01-01

Background: The current study examined relationships between the neighborhood social environment (parental perceived collective efficacy (PCE)), constrained behaviors (e.g., avoidance or defensive behaviors) and adolescent offspring neighborhood physical activity in low- versus high-incivility neighborhoods. Methods: Adolescents (n = 71; 11–18 years (14.2, SD ± 1.6); male = 37 (52%); non-white = 24 (33.8%); low-income = 20 (29%); overweight/obese = 40 (56%)) and their parents/guardians enrolled in the Molecular and Social Determinants of Obesity in Developing Youth study were included in the current study. Questionnaires measured parents’/guardians’ PCE, constrained outdoor play practices and offspring neighborhood physical activity. Systematic social observation performed at the parcel-level using Google Street View assessed neighborhood incivilities. t-tests and chi-square tests determined differences by incivilities. Multilevel regression models examined relationships between PCE and: (1) constrained behaviors; and (2) neighborhood physical activity. The Hayes (2013) macro determined the mediating role of constrained behaviors. Results: Parents who had higher PCE reported lower levels of avoidance (p = 0.04) and defensive (p = 0.05) behaviors. However, demographic variables (i.e., gender, race and annual household income) limited these results. The direct relationship between PCE and parent-reported neighborhood physical activity was statistically significant in high-incivility neighborhoods only. Neither avoidance nor defensive behavior mediated the relationship between PCE and neighborhood physical activity. Conclusions: PCE influences parenting behaviors related to youth physical activity. Community-based programs that seek to facilitate social cohesion and control may be needed to increase adolescents’ physical activity. PMID:28009839

Carbon Isotope Biogeochemistry of Methane from Anoxic Sediments

NASA Technical Reports Server (NTRS)

Blair, Neal E.

1993-01-01

The isotopic composition of naturally occurring methane was used to constrain the tropospheric budget of that radiatively active gas. Numerous studies have shown that the isotopic composition is not constant, even for a specific source, and may vary temporally and spatially. The objective was to develop a process-level model that reproduced the seasonal variations in the C-13/C-12 composition of methane observed at the coastal site, Cape Lookout Bight, NC. Details of the mass balance are provided. Experiments and models designed to determine what factors incluence C-13/C-12 ratio of dissolved CO2 are reported. All the factors described were combined in a model that faithfully reproduces the seasonal C-13/C-12 variations observed at Cape Lookout. The model is described.

Observations of Bromine Chloride (BrCl) at an Arctic Coastal Site

NASA Astrophysics Data System (ADS)

McNamara, S. M.; Garner, N.; Wang, S.; Raso, A. R. W.; Thanekar, S.; Fuentes, J. D.; Shepson, P. B.; Pratt, K.

2017-12-01

Chlorine and bromine chemistry in the Arctic boundary layer have significant impacts on tropospheric ozone depletion and the fates of atmospheric pollutants such as methane, a greenhouse gas, and mercury. However, there is sparse understanding of halogen production and removal pathways due to a lack of observations. Here, we report chemical ionization mass spectrometry measurements of bromine chloride (BrCl) observed at Utqiaġvik (Barrow), AK during March-May 2016. Over the course of the three-month study, two distinct BrCl diurnal trends were identified, and production mechanisms were explored using 0-dimensional modeling, constrained by a suite of reactive halogen measurements. The findings in this work highlight coupled chlorine and bromine chemistry, as well as halogen activation pathways in the Arctic.

Free energy landscape of electrocatalytic CO2 reduction to CO on aqueous FeN4 center embedded graphene studied by ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sheng, Tian; Sun, Shi-Gang

2017-11-01

Experiments have found that the porphyrin-like FeN4 site in Fe-N-C materials is highly efficient for the electrochemical reduction of CO2 into CO. In this work, we investigated the reduction mechanisms on FeN4 embedded graphene layer catalyst with some explicit water molecules by combining the constrained ab initio molecular dynamics simulations and thermodynamic integrations. The reaction free energy and electron transfer in each elementary step were identified. The initial CO2 activation was identified to go through the first electron transfer to form adsorbed CO2- anion and the CO desorption was the rate limiting step in the overall catalytic cycle.

Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.

PubMed Central

Hermann, T; Auffinger, P; Scott, W G; Westhof, E

1997-01-01

In the presence of magnesium ions, cleavage by the hammerhead ribozyme RNA at a specific residue leads to 2'3'-cyclic phosphate and 5'-OH extremities. In the cleavage reaction an activated ribose 2'-hydroxyl group attacks its attached 3'-phosphate. Molecular dynamics simulations of the crystal structure of the hammerhead ribozyme, obtained after flash-freezing of crystals under conditions where the ribozyme is active, provide evidence that a mu-bridging OH-ion is located between two Mg2+ions close to the cleavable phosphate. Constrained simulations show further that a flip from the C3'- endo to the C2'- endo conformation of the ribose at the cleavable phosphate brings the 2'-hydroxyl in proximity to both the attacked phosphorous atom and the mu-bridging OH-ion. Thus, the simulations lead to a detailed new insight into the mechanism of hammerhead ribozyme cleavage where a mu-hydroxo bridged magnesium cluster, located on the deep groove side, provides an OH-ion that is able to activate the 2'-hydroxyl nucleophile after a minor and localized conformational change in the RNA. PMID:9254698

An unusual mode of failure of a tripolar constrained acetabular liner: a case report.

PubMed

Banks, Louisa N; McElwain, John P

2010-04-01

Dislocation after primary total hip arthroplasty (THA) is the most commonly encountered complication and is unpleasant for both the patient and the surgeon. Constrained acetabular components can be used to treat or prevent instability after primary total hip arthroplasty. We present the case of a 42-year-old female with a BMI of 41. At 18 months post-primary THA the patient underwent further revision hip surgery after numerous (more than 20) dislocations. She had a tripolar Trident acetabular cup (Stryker-Howmedica-Osteonics, Rutherford, New Jersey) inserted. Shortly afterwards the unusual mode of failure of the constrained acetabular liner was noted from radiographs in that the inner liner had dissociated from the outer. The reinforcing ring remained intact and in place. We believe that the patient's weight, combined with poor abductor musculature caused excessive demand on the device leading to failure at this interface when the patient flexed forward. Constrained acetabular components are useful implants to treat instability but have been shown to have up to 42% long-term failure rates with problems such as dissociated inserts, dissociated constraining rings and dissociated femoral rings being sited. Sometimes they may be the only option left in difficult cases such as illustrated here, but still unfortunately have the capacity to fail in unusual ways.

Competitive learning with pairwise constraints.

PubMed

Covões, Thiago F; Hruschka, Eduardo R; Ghosh, Joydeep

2013-01-01

Constrained clustering has been an active research topic since the last decade. Most studies focus on batch-mode algorithms. This brief introduces two algorithms for on-line constrained learning, named on-line linear constrained vector quantization error (O-LCVQE) and constrained rival penalized competitive learning (C-RPCL). The former is a variant of the LCVQE algorithm for on-line settings, whereas the latter is an adaptation of the (on-line) RPCL algorithm to deal with constrained clustering. The accuracy results--in terms of the normalized mutual information (NMI)--from experiments with nine datasets show that the partitions induced by O-LCVQE are competitive with those found by the (batch-mode) LCVQE. Compared with this formidable baseline algorithm, it is surprising that C-RPCL can provide better partitions (in terms of the NMI) for most of the datasets. Also, experiments on a large dataset show that on-line algorithms for constrained clustering can significantly reduce the computational time.

The Elizabeth Lake paleoseismic site: Rupture pattern constraints for the past ~800 years for the Mojave section of the south-central San Andreas Fault

USGS Publications Warehouse

Bemis, Sean; Scharer, Katherine M.; Dolan, James F.; Rhodes, Ed

2016-01-01

The southern San Andreas Fault in California has hosted two historic surface-rupturing earthquakes, the ~M7 1812 Wrightwood earthquake and the ~M7.9 1857 Fort Tejon earthquake (e.g., Sieh, 1978; Jacoby et al., 1988). Numerous paleoseismic studies have established chronologies of historic and prehistoric earthquakes at sites along the full length of the 1857 rupture (e.g., Sieh, 1978; Scharer et al., 2014). These studies provide an unparalleled opportunity to examine patterns of recent ruptures; however, at least two significant spatial gaps in high-quality paleoseismic sites remain. At ~100 km long each, these gaps contribute up to 100 km of uncertainty to paleo-rupture lengths and could also permit a surface rupture from an earthquake up to ~M7.2 to go undetected [using scaling relationships of Wells and Coppersmith (1994)]. Given the known occurrence of an ~M7 earthquake on this portion of the SAF (1812), it is critical to fill these gaps in order to better constrain paleo-rupture lengths and to increase the probability of capturing the full spatial record of surface rupturing earthquakes.   In this study, we target a new site within the 100 km long stretch of the San Andreas Fault between the Frazier Mountain and Pallett Creek paleoseismic sites (Figure 1), near Elizabeth Lake, California. Prior excavations at the site during 1998-1999 encountered promising stratigraphy but these studies were hindered by shallow groundwater throughout the site. We began our current phase of investigations in 2012, targeting the northwestern end of a 40 x 350 m fault-parallel depression that defines the site (Figure 2). Subsequent investigations in 2013 and 2014 focused on the southeastern end of the depression where the fault trace is constrained between topographic highs and is proximal to an active drainage. In total, our paleoseismic investigations consist of 10 fault-perpendicular trenches that cross the depression (Figure 2) and expose a >2000 year depositional record. These trenches reveal that the thickest section of young stratigraphy occurs at the southeastern end of the site where the fault zone projects through an area of relatively continuous sediment accumulation from a northeast-flowing drainage. This portion of the site contains a 3-m-wide pop-up structure within the fault zone that separates alternating alluvial and paludal deposits south of the fault zone from a thick organic-rich loam on the north side of the fault zone. Faults, fissures, and tilted blocks provide evidence for 4 to 5 paleoearthquakes since ca. 1250 A.D. Radiocarbon dating established that the site has a significant component of detrital charcoal producing an age spread of up to 500 years. To supplement our age chronology we incorporated ages from collections of micro-scale organic fractions and post-IR infrared stimulated luminescence dating in order to better estimate true layer ages.

Stimulation of the basal and central amygdala in the mustached bat triggers echolocation and agonistic vocalizations within multimodal output

PubMed Central

Ma, Jie; Kanwal, Jagmeet S.

2014-01-01

The neural substrate for the perception of vocalizations is relatively well described, but how their timing and specificity are tightly coupled with accompanying physiological changes and context-appropriate behaviors remains unresolved. We hypothesized that temporally integrated vocal and emotive responses, especially the expression of fear, vigilance and aggression, originate within the amygdala. To test this hypothesis, we performed electrical microstimulation at 461 highly restricted loci within the basal and central amygdala in awake mustached bats. At a subset of these sites, high frequency stimulation with weak constant current pulses presented at near-threshold levels triggered vocalization of either echolocation pulses or social calls. At the vast majority of locations, microstimulation produced a constellation of changes in autonomic and somatomotor outputs. These changes included widespread co-activation of significant tachycardia and hyperventilation and/or rhythmic ear pinna movements (PMs). In a few locations, responses were constrained to vocalization and/or PMs despite increases in the intensity of stimulation. The probability of eliciting echolocation pulses vs. social calls decreased in a medial-posterior to anterolateral direction within the centrobasal amygdala. Microinjections of kainic acid (KA) at stimulation sites confirmed the contribution of cellular activity rather than fibers-of-passage in the control of multimodal outputs. The results suggest that localized clusters of neurons may simultaneously modulate the activity of multiple central pattern generators (CPGs) present within the brainstem. PMID:24624089

Stimulation of the basal and central amygdala in the mustached bat triggers echolocation and agonistic vocalizations within multimodal output.

PubMed

Ma, Jie; Kanwal, Jagmeet S

2014-01-01

The neural substrate for the perception of vocalizations is relatively well described, but how their timing and specificity are tightly coupled with accompanying physiological changes and context-appropriate behaviors remains unresolved. We hypothesized that temporally integrated vocal and emotive responses, especially the expression of fear, vigilance and aggression, originate within the amygdala. To test this hypothesis, we performed electrical microstimulation at 461 highly restricted loci within the basal and central amygdala in awake mustached bats. At a subset of these sites, high frequency stimulation with weak constant current pulses presented at near-threshold levels triggered vocalization of either echolocation pulses or social calls. At the vast majority of locations, microstimulation produced a constellation of changes in autonomic and somatomotor outputs. These changes included widespread co-activation of significant tachycardia and hyperventilation and/or rhythmic ear pinna movements (PMs). In a few locations, responses were constrained to vocalization and/or PMs despite increases in the intensity of stimulation. The probability of eliciting echolocation pulses vs. social calls decreased in a medial-posterior to anterolateral direction within the centrobasal amygdala. Microinjections of kainic acid (KA) at stimulation sites confirmed the contribution of cellular activity rather than fibers-of-passage in the control of multimodal outputs. The results suggest that localized clusters of neurons may simultaneously modulate the activity of multiple central pattern generators (CPGs) present within the brainstem.

Optimization of Benzoisothiazole dioxide inhibitory activity of the NS5B polymerase of HCV genotype 4 using ligand-steered homological modeling, reaction-driven scaffold-hopping and Enovo workflow.

PubMed

Mahmoud, Amr Hamed; Mohamed Abouzid, Khaled Abouzid; El Ella, Dalal Abd El Rahman Abou; Hamid Ismail, Mohamed Abdel

2011-01-01

Infection caused by hepatitis C virus (HCV) is a significant world health problem for which novel therapies are in urgent demand. The virus is highly prevalent in the Middle East and Africa particularly Egypt with more than 90% of infections due to genotype 4. Nonstructural (NS5B) viral proteins have emerged as an attractive target for HCV antivirals discovery. A potent class of inhibitors having benzisothiazole dioxide scaffold has been identified on this target, however they were mainly active on genotype 1 while exhibiting much lowered activity on other genotypes due to the high degree of mutation of its binding site. Based on this fact, we employed a novel strategy to optimize this class on genotype 4. This strategy depends on using a refined ligand-steered homological model of this genotype to study the mutation binding energies of the binding site amino acid residues, the essential features for interaction and provide a structure-based pharmacophore model that can aid optimization. This model was applied on a focused library which was generated using a reaction-driven scaffold-hopping strategy. The hits retrieved were subjected to Enovo pipeline pilot optimization workflow that employs R-group enumeration, core-constrained protein docking using modified CDOCKER and finally ranking of poses using an accurate molecular mechanics generalized Born with surface area method.

Inhibition of plasminogen activator inhibitor-1 binding to endocytosis receptors of the low-density-lipoprotein receptor family by a peptide isolated from a phage display library

PubMed Central

Jensen, Jan K.; Malmendal, Anders; Schiøtt, Birgit; Skeldal, Sune; Pedersen, Katrine E.; Celik, Leyla; Nielsen, Niels Chr.; Andreasen, Peter A.; Wind, Troels

2006-01-01

The functions of the serpin PAI-1 (plasminogen activator inhibitor-1) are based on molecular interactions with its target proteases uPA and tPA (urokinase-type and tissue-type plasminogen activator respectively), with vitronectin and with endocytosis receptors of the low-density-lipoprotein family. Understanding the significance of these interactions would be facilitated by the ability to block them individually. Using phage display, we have identified the disulfide-constrained peptide motif CFGWC with affinity for natural human PAI-1. The three-dimensional structure of a peptide containing this motif (DVPCFGWCQDA) was determined by liquid-state NMR spectroscopy. A binding site in the so-called flexible joint region of PAI-1 was suggested by molecular modelling and validated through binding studies with various competitors and site-directed mutagenesis of PAI-1. The peptide with an N-terminal biotin inhibited the binding of the uPA–PAI-1 complex to the endocytosis receptors low-density-lipoprotein-receptor-related protein 1A (LRP-1A) and very-low-density-lipoprotein receptor (VLDLR) in vitro and inhibited endocytosis of the uPA–PAI-1 complex in U937 cells. We conclude that the isolated peptide represents a novel approach to pharmacological interference with the functions of PAI-1 based on inhibition of one specific molecular interaction. PMID:16813566

Active deformation and seismicity in the Southern Alps (Italy): The Montello hill as a case study

NASA Astrophysics Data System (ADS)

Danesi, Stefania; Pondrelli, Silvia; Salimbeni, Simone; Cavaliere, Adriano; Serpelloni, Enrico; Danecek, Peter; Lovati, Sara; Massa, Marco

2015-06-01

The Montello anticline is a morphotectonic feature of the east pede-mountain of the South Alpine Chain in northern Italy, which lies ca. 40 km northwest of Venice, Italy. The purpose of this study is to characterize the present-day crustal deformation and seismotectonics of the Montello area through multi-parametric geophysical observations. We used new data obtained from the installation of a temporary network of 12 seismic stations and 6 GPS sites. The GPS observations indicate that there is ~ 1 mm/yr shortening across the Montello thrust. Sites located north of the Montello thrust front deviate from the ~ NNW-ward Adria-Eurasia convergence direction, as they are constrained by a relative rotation pole in northwestern Italy that has a NNE-ward motion trend. Over 18 months, seismographic recordings allowed us to locate 142 local seismic events with Ml 0.5-3.5 with good reliability (rms < 0.5). After cross-correlation analysis, we classified 42 of these events into six clusters, with cross-correlation thresholds > 0.80. The source focal solutions indicate that: (i) there is thrusting seismic activity on the basal, sub-horizontal, portion of the Montello structure; and (ii) strike-slip source kinematics prevail on the western edge of the Montello hill. Our observations on the source mechanisms and the measured crustal deformation confirm that the Montello thrust is tectonically active.

The effects of sample size on population genomic analyses--implications for the tests of neutrality.

PubMed

Subramanian, Sankar

2016-02-20

One of the fundamental measures of molecular genetic variation is the Watterson's estimator (θ), which is based on the number of segregating sites. The estimation of θ is unbiased only under neutrality and constant population growth. It is well known that the estimation of θ is biased when these assumptions are violated. However, the effects of sample size in modulating the bias was not well appreciated. We examined this issue in detail based on large-scale exome data and robust simulations. Our investigation revealed that sample size appreciably influences θ estimation and this effect was much higher for constrained genomic regions than that of neutral regions. For instance, θ estimated for synonymous sites using 512 human exomes was 1.9 times higher than that obtained using 16 exomes. However, this difference was 2.5 times for the nonsynonymous sites of the same data. We observed a positive correlation between the rate of increase in θ estimates (with respect to the sample size) and the magnitude of selection pressure. For example, θ estimated for the nonsynonymous sites of highly constrained genes (dN/dS < 0.1) using 512 exomes was 3.6 times higher than that estimated using 16 exomes. In contrast this difference was only 2 times for the less constrained genes (dN/dS > 0.9). The results of this study reveal the extent of underestimation owing to small sample sizes and thus emphasize the importance of sample size in estimating a number of population genomic parameters. Our results have serious implications for neutrality tests such as Tajima D, Fu-Li D and those based on the McDonald and Kreitman test: Neutrality Index and the fraction of adaptive substitutions. For instance, use of 16 exomes produced 2.4 times higher proportion of adaptive substitutions compared to that obtained using 512 exomes (24% vs 10 %).

Emissions from prescribed fire in temperate forest in south-east Australia: implications for carbon accounting

NASA Astrophysics Data System (ADS)

Possell, M.; Jenkins, M.; Bell, T. L.; Adams, M. A.

2014-09-01

We estimated of emissions of carbon, as CO2-equivalents, from planned fire in four sites in a south-eastern Australian forest. Emission estimates were calculated using measurements of fuel load and carbon content of different fuel types, before and after burning, and determination of fuel-specific emission factors. Median estimates of emissions for the four sites ranged from 20 to 139 T CO2-e ha-1. Variability in estimates was a consequence of different burning efficiencies of each fuel type from the four sites. Higher emissions resulted from more fine fuel (twigs, decomposing matter, near-surface live and leaf litter) or coarse woody debris (CWD; > 25 mm diameter) being consumed. In order to assess the effect of estimating emissions when only a few fuel variables are known, Monte-Carlo simulations were used to create seven scenarios where input parameters values were replaced by probability density functions. Calculation methods were: (1) all measured data were constrained between measured maximum and minimum values for each variable, (2) as for (1) except the proportion of carbon within a fuel type was constrained between 0 and 1, (3) as for (2) but losses of mass caused by fire were replaced with burning efficiency factors constrained between 0 and 1; and (4) emissions were calculated using default values in the Australian National Greenhouse Accounts (NGA), National Inventory Report 2011, as appropriate for our sites. Effects of including CWD in calculations were assessed for calculation Method 1, 2 and 3 but not for Method 4 as the NGA does not consider this fuel type. Simulations demonstrate that the probability of estimating true median emissions declines strongly as the amount of information available declines. Including CWD in scenarios increased uncertainty in calculations because CWD is the most variable contributor to fuel load. Inclusion of CWD in scenarios generally increased the amount of carbon lost. We discuss implications of these simulations and how emissions from prescribed burns in temperate Australian forests could be improved.

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor

PubMed Central

Yanagawa, Katsunori; Ijiri, Akira; Breuker, Anja; Sakai, Sanae; Miyoshi, Youko; Kawagucci, Shinsuke; Noguchi, Takuroh; Hirai, Miho; Schippers, Axel; Ishibashi, Jun-ichiro; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2017-01-01

Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ13C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106–198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field. PMID:27754478

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor.

PubMed

Yanagawa, Katsunori; Ijiri, Akira; Breuker, Anja; Sakai, Sanae; Miyoshi, Youko; Kawagucci, Shinsuke; Noguchi, Takuroh; Hirai, Miho; Schippers, Axel; Ishibashi, Jun-Ichiro; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2017-02-01

Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ 13 C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106-198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field.

Active constrained layer damping of geometrically nonlinear vibrations of functionally graded plates using piezoelectric fiber-reinforced composites

NASA Astrophysics Data System (ADS)

Panda, Satyajit; Ray, M. C.

2008-04-01

In this paper, a geometrically nonlinear dynamic analysis has been presented for functionally graded (FG) plates integrated with a patch of active constrained layer damping (ACLD) treatment and subjected to a temperature field. The constraining layer of the ACLD treatment is considered to be made of the piezoelectric fiber-reinforced composite (PFRC) material. The temperature field is assumed to be spatially uniform over the substrate plate surfaces and varied through the thickness of the host FG plates. The temperature-dependent material properties of the FG substrate plates are assumed to be graded in the thickness direction of the plates according to a power-law distribution while the Poisson's ratio is assumed to be a constant over the domain of the plate. The constrained viscoelastic layer of the ACLD treatment is modeled using the Golla-Hughes-McTavish (GHM) method. Based on the first-order shear deformation theory, a three-dimensional finite element model has been developed to model the open-loop and closed-loop nonlinear dynamics of the overall FG substrate plates under the thermal environment. The analysis suggests the potential use of the ACLD treatment with its constraining layer made of the PFRC material for active control of geometrically nonlinear vibrations of FG plates in the absence or the presence of the temperature gradient across the thickness of the plates. It is found that the ACLD treatment is more effective in controlling the geometrically nonlinear vibrations of FG plates than in controlling their linear vibrations. The analysis also reveals that the ACLD patch is more effective for controlling the nonlinear vibrations of FG plates when it is attached to the softest surface of the FG plates than when it is bonded to the stiffest surface of the plates. The effect of piezoelectric fiber orientation in the active constraining PFRC layer on the damping characteristics of the overall FG plates is also discussed.

Synthetic Constraint of Ecosystem C Models Using Radiocarbon and Net Primary Production (NPP) in New Zealand Grazing Land

NASA Astrophysics Data System (ADS)

Baisden, W. T.

2011-12-01

Time-series radiocarbon measurements have substantial ability to constrain the size and residence time of the soil C pools commonly represented in ecosystem models. Radiocarbon remains unique in the ability to constrain the large stabilized C pool with decadal residence times. Radiocarbon also contributes usefully to constraining the size and turnover rate of the passive pool, but typically struggles to constrain pools with residence times less than a few years. Overall, the number of pools and associated turnover rates that can be constrained depends upon the number of time-series samples available, the appropriateness of chemical or physical fractions to isolate unequivocal pools, and the utility of additional C flux data to provide additional constraints. In New Zealand pasture soils, we demonstrate the ability to constrain decadal turnover times with in a few years for the stabilized pool and reasonably constrain the passive fraction. Good constraint is obtained with two time-series samples spaced 10 or more years apart after 1970. Three or more time-series samples further improve the level of constraint. Work within this context shows that a two-pool model does explain soil radiocarbon data for the most detailed profiles available (11 time-series samples), and identifies clear and consistent differences in rates of C turnover and passive fraction in Andisols vs Non-Andisols. Furthermore, samples from multiple horizons can commonly be combined, yielding consistent residence times and passive fraction estimates that are stable with, or increase with, depth in different sites. Radiocarbon generally fails to quantify rapid C turnover, however. Given that the strength of radiocarbon is estimating the size and turnover of the stabilized (decadal) and passive (millennial) pools, the magnitude of fast cycling pool(s) can be estimated by subtracting the radiocarbon-based estimates of turnover within stabilized and passive pools from total estimates of NPP. In grazing land, these estimates can be derived primarily from measured aboveground NPP and calculated belowground NPP. Results suggest that only 19-36% of heterotrophic soil respiration is derived from the soil C with rapid turnover times. A final logical step in synthesis is the analysis of temporal variation in NPP, primarily due to climate, as driver of changes in plant inputs and resulting in dynamic changes in rapid and decadal soil C pools. In sites with good time series samples from 1959-1975, we examine the apparent impacts of measured or modelled (Biome-BGC) NPP on soil Δ14C. Ultimately, these approaches have the ability to empirically constrain, and provide limited verification, of the soil C cycle as commonly depicted ecosystem biogeochemistry models.

Illite authigenesis during faulting and fluid flow - a microstructural study of fault rocks

NASA Astrophysics Data System (ADS)

Scheiber, Thomas; Viola, Giulio; van der Lelij, Roelant; Margreth, Annina

2017-04-01

Authigenic illite can form synkinematically during slip events along brittle faults. In addition it can also crystallize as a result of fluid flow and associated mineral alteration processes in hydrothermal environments. K-Ar dating of illite-bearing fault rocks has recently become a common tool to constrain the timing of fault activity. However, to fully interpret the derived age spectra in terms of deformation ages, a careful investigation of the fault deformation history and architecture at the outcrop-scale, ideally followed by a detailed mineralogical analysis of the illite-forming processes at the micro-scale, are indispensable. Here we integrate this methodological approach by presenting microstructural observations from the host rock immediately adjacent to dated fault gouges from two sites located in the Rolvsnes granodiorite (Bømlo, western Norway). This granodiorite experienced multiple episodes of brittle faulting and fluid-induced alteration, starting in the Mid Ordovician (Scheiber et al., 2016). Fault gouges are predominantly associated with normal faults accommodating mainly E-W extension. K-Ar dating of illites separated from representative fault gouges constrains deformation and alteration due to fluid ingress from the Permian to the Cretaceous, with a cluster of ages for the finest (<0.1 µm) fraction in the early to middle Jurassic. At site one, high-resolution thin section structural mapping reveals a complex deformation history characterized by several coexisting types of calcite veins and seven different generations of cataclasite, two of which contain a significant amount of authigenic and undoubtedly deformation-related illite. At site two, fluid ingress along and adjoining the fault core induced pervasive alteration of the host granodiorite. Quartz is crosscut by calcite veinlets whereas plagioclase, K-feldspar and biotite are almost completely replaced by the main alteration products kaolin, quartz and illite. Illite-bearing micro-domains were physically separated by means of microsawing and drilling devices. K-Ar and XRD data from these separates are compared with bulk K-Ar and XRD data from the adjacent fault gouges, which may help to further unravel complex histories archived in multiply activated brittle fault zones. Scheiber, T., Viola, G., Wilkinson, C.M., Ganerød, M., Skår, Ø., and D. Gasser (2016): Direct 40Ar/39Ar dating of Late-Ordovician and Silurian brittle faulting in the southwestern Norwegian Caledonides. Terra Nova 28, 374-382.

FXR agonist activity of conformationally constrained analogs of GW 4064.

PubMed

Akwabi-Ameyaw, Adwoa; Bass, Jonathan Y; Caldwell, Richard D; Caravella, Justin A; Chen, Lihong; Creech, Katrina L; Deaton, David N; Madauss, Kevin P; Marr, Harry B; McFadyen, Robert B; Miller, Aaron B; Navas, Frank; Parks, Derek J; Spearing, Paul K; Todd, Dan; Williams, Shawn P; Bruce Wisely, G

2009-08-15

Two series of conformationally constrained analogs of the FXR agonist GW 4064 1 were prepared. Replacement of the metabolically labile stilbene with either benzothiophene or naphthalene rings led to the identification of potent full agonists 2a and 2g.

Water vapor isotopic measurements from the Atmospheric Radiation Measurement site on Graciosa Island, Azores

NASA Astrophysics Data System (ADS)

Delp, J. M.; Galewsky, J.

2017-12-01

Stable isotopic measurements of water vapor can potentially constrain the processes that govern the formation of low-clouds and how their distribution may change as the climate warms. Using off-axis integrated cavity output spectroscopy, in-situ water vapor isotopic measurements will be collected for a period of one year (beginning August 2017) at the US Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) site in the Eastern North Atlantic (ENA) located on Graciosa Island, Azores. The Azores location within the ENA is a prime setting for studying low-cloud processes. After correcting for humidity-dependent biases and normalizing the measurements to the VSMOW-SLAP scale, the measurements from the first several months of the water vapor isotopic analyzer's deployment will be compared to complementary datasets from the suite of instruments at the DOE site, including twice-daily soundings, aerosol instrumentation, and cloud radars, with the purpose of determining links between local stratocumulus and precipitation processes and their impact on the stable isotopic composition of atmospheric water vapor. The results of this study will potentially provide a new approach for linking field observations with climate models and may help better constrain the uncertainties associated with low-cloud feedbacks.

Constraining Aggregate-Scale Solar Energy Partitioning in Arctic Sea Ice Through Synthesis of Remote Sensing and Autonomous In-Situ Observations.

NASA Astrophysics Data System (ADS)

Wright, N.; Polashenski, C. M.; Deeb, E. J.; Morriss, B. F.; Song, A.; Chen, J.

2015-12-01

One of the key processes controlling sea ice mass balance in the Arctic is the partitioning of solar energy between reflection back to the atmosphere and absorption into the ice and upper ocean. We investigate the solar energy balance in the ice-ocean system using in-situ data collected from Arctic Observing Network (AON) sea ice sites and imagery from high resolution optical satellites. AON assets, including ice mass balance buoys and ice tethered profilers, monitor the storage and fluxes of heat in the ice-ocean system. High resolution satellite imagery, processed using object-based image classification techniques, allows us to quantify the evolution of surrounding ice conditions, including melt pond coverage and floe size distribution, at aggregate scale. We present results from regionally representative sites that constrain the partitioning of absorbed solar energy between ice melt and ocean storage, and quantify the strength of the ice-albedo feedback. We further demonstrate how the results can be used to validate model representations of the physical processes controlling ice-albedo feedbacks. The techniques can be extended to understand solar partitioning across the Arctic basin using additional sites and model based data integration.

Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display.

PubMed

Hacker, David E; Hoinka, Jan; Iqbal, Emil S; Przytycka, Teresa M; Hartman, Matthew C T

2017-03-17

Highly constrained peptides such as the knotted peptide natural products are promising medicinal agents because of their impressive biostability and potent activity. Yet, libraries of highly constrained peptides are challenging to prepare. Here, we present a method which utilizes two robust, orthogonal chemical steps to create highly constrained bicyclic peptide libraries. This technology was optimized to be compatible with in vitro selections by mRNA display. We performed side-by-side monocyclic and bicyclic selections against a model protein (streptavidin). Both selections resulted in peptides with mid-nanomolar affinity, and the bicyclic selection yielded a peptide with remarkable protease resistance.

Geological Development of the Izu-Bonin Forearc Since the Eocene Based on Biostratigraphic, Rock Magnetic, and Sediment Provenance Observations from IODP Expedition 352 Drill Cores

NASA Astrophysics Data System (ADS)

Petronotis, K. E.; Robertson, A.; Kutterolf, S.; Avery, A.; Baxter, A.; Schindlbeck, J. C.; Wang, K. L.; Acton, G.

2016-12-01

International Ocean Discovery Program (IODP) Expedition 352 recovered early Oligocene to recent sediments above Eocene igneous basement at 4 sites in the Izu-Bonin Forearc. The sites were selected to investigate the forearc region since subduction initiation in the Eocene, with Sites U1439 and U1442 being cored into the upper trench slope and Sites U1440 and U1441 into the lower trench slope. Postcruise studies of biostratigraphy, sediment chemistry, tephra composition and chronology and magnetic properties, along with observations from prior coring help constrain the regional geological development. Volcanic activity in the area, as inferred from its influence on sediment composition, has varied between long periods of activity and quiescence. Combined whole-rock sediment chemistry and tephra compositions suggest that during the Oligocene to earliest Miocene ( 30-22 Ma) tuffaceous input of predominantly dacitic composition was mainly derived from the intra-oceanic Izu-Bonin Arc. The early Miocene interval ( 22-15 Ma) lacks tuffaceous input, as supported by rock magnetic data. During this period, the forearc subsided beneath the carbonate compensation depth (CCD), as evidenced by radiolarian-bearing mud and metal-rich silty clay. This was followed by input of tephra with bimodal felsic and mafic compositions from the Izu-Bonin Arc from 15 to 5 Ma. Middle Miocene to Quaternary time was characterized by increased carbonate preservation, coupled with abundant, predominantly felsic tephra input, which is chemically indicative of a Japan continental arc source (Honshu), with additional chemically distinctive input from the Izu-Bonin Arc. Extending back to 32 Ma, tephra layers can be correlated between the upper-slope sites, extrapolated to the less well-dated lower-slope sites, and further correlated with onland Japanese tephra (Kutterolf et al., 2016; Goldschmidt Conference). Overall, the new results provide an improved understanding of the regional tectonic evolution.

A Constitutively Activating Mutation Alters the Dynamics and Energetics of a Key Conformational Change in a Ligand-free G Protein-coupled Receptor*

PubMed Central

Tsukamoto, Hisao; Farrens, David L.

2013-01-01

G protein-coupled receptors (GPCRs) undergo dynamic transitions between active and inactive conformations. Usually, these conversions are triggered when the receptor detects an external signal, but some so-called constitutively activating mutations, or CAMs, induce a GPCR to bind and activate G proteins in the absence of external stimulation, in ways still not fully understood. Here, we investigated how a CAM alters the structure of a GPCR and the dynamics involved as the receptor transitions between different conformations. Our approach used site-directed fluorescence labeling (SDFL) spectroscopy to compare opsin, the ligand-free form of the GPCR rhodopsin, with opsin containing the CAM M257Y, focusing specifically on key movements that occur in the sixth transmembrane helix (TM6) during GPCR activation. The site-directed fluorescence labeling data indicate opsin is constrained to an inactive conformation both in detergent micelles and lipid membranes, but when it contains the M257Y CAM, opsin is more dynamic and can interact with a G protein mimetic. Further study of these receptors using tryptophan-induced quenching (TrIQ) methods indicates that in detergent, the CAM significantly increases the population of receptors in the active state, but not in lipids. Subsequent Arrhenius analysis of the TrIQ data suggests that, both in detergent and lipids, the CAM lowers the energy barrier for TM6 movement, a key transition required for conversion between the inactive and active conformations. Together, these data suggest that the lowered energy barrier is a primary effect of the CAM on the receptor dynamics and energetics. PMID:23940032

Role of vegetation and edaphic factors in controlling diversity and use of different carbon sources in semi-arid ecosystems

NASA Astrophysics Data System (ADS)

Lohse, K. A.; McLain, J. E.; Harman, C. J.; Sivapalan, M.; Troch, P. A.

2010-12-01

Microbially-mediated soil carbon cycling is closely linked to soil moisture and temperature. Climate change is predicted to increase intra-annual precipitation variability (i.e. less frequent yet more intense precipitation events) and alter biogeochemical processes due to shifts in soil moisture dynamics and inputs of carbon. However, the responses of soil biology and chemistry to predicted climate change, and their concomitant feedbacks on ecosystem productivity and biogeochemical processes are poorly understood. We collected soils at three different elevations in the Santa Catalina Mountains, AZ and quantified carbon utilization during pre-monsoon precipitation conditions. Contrasting parent materials (schist and granite) were paired at each elevation. We expected climate to determine the overall activity of soil fungal and bacterial communities and diversity of soil C utilization, and differences in parent material to modify these responses through controls on soil physical properties. We used EcoPlateTM C utilization assays to determine the relative abundance of soil bacterial and fungal populations and rate and diversity of carbon utilization. Additional plates were incubated with inhibitors selective to fungal or bacterial activity to assess relative contribution of these microbial groups to overall C utilization. We analyzed soils for soil organic matter, total C and N, particle size analysis and soil moisture content via both gravimetric and volumetric methods to assess the influences of soil physical and chemical properties on the measured biological responses. Consistent with our expectations, overall microbial activity was highest at the uppermost conifer elevation sites compared to the middle and lower elevation sites. In contrast to our expectations, however, overall activity was lower at the mid elevation oak woodland sites compared to the low elevation desert sites. Also consistent with our expectations was the observation that overall activities were consistently higher in schist parent material compared to granite. Though differences between canopy and intercanopy carbon utilization were subtle, the diversity of carbon utilization differed, suggesting a potential role of root exudates in governing C utilization in these semiarid soils. Findings from this study suggest that soil physical properties due to parent material have primary impacts in constraining microbial growth and carbon utilization under changing climate conditions.

Constraining the Carbon Cycle through Tree Rings: A Case Study of the Valles Caldera, NM

NASA Astrophysics Data System (ADS)

Alexander, M. R.; Babst, F.; Moore, D. J.; Trouet, V.

2013-12-01

Terrestrial ecosystems take up approximately 120 Gt of carbon as Gross Primary Productivity (GPP) from the atmosphere annually, but it is challenging to track the allocation of that carbon throughout the biosphere. Here, we combine eddy covariance measurements of net carbon uptake with above ground biomass increments derived from tree-ring data to better understand the interannual variability associated with biomass accumulation. In the summer of 2012, we collected tree cores near two eddy covariance towers in the Jemez Mountains of northern New Mexico. One tower was located in an upper elevation mixed-conifer forest, and the other in a lower elevation Pinus ponderosa forest. Our analysis shows that the annual above ground biomass increment accounted for approximately 40% of the GPP at the lower elevation Pinus ponderosa site and approximately 70% of GPP at the upper elevation mixed-conifer site. We have also used the above ground biomass increment to constrain the Simple Photosynthesis EvapoTranspiration (SiPNET) model to gain a better understanding of allocation within the forest. Tree growth at both elevations was negatively influenced by spring (March-June) temperature and positively by cool season (October-April) precipitation and warm (May-September) and cool season PDSI. We also analyzed the six most extreme temperature and moisture (PDSI) years of the record to determine the response of productivity to climatic forcing. During the driest years, biomass production was reduced by 40% at the upper elevation site and 43% at the lower elevation site. During the hottest years of the record the biomass decreased 28% at the upper site and 45% at the lower site. Our results indicate that tree rings can be used to effectively constrain the above ground biomass component of a forest's carbon budget and to estimate allocation of carbon to woody biomass as a function of climate. However, many variables remain unknown. The combined results of the extreme year analyses and the derived biomass increments illustrate that the forests at the Valles Caldera are considerably less productive during years of extreme drought and warmer than average temperatures. With future projections calling for consecutive years of extreme conditions in the American Southwest, this could have a substantial effect on the overall productivity of these forests.

Assimilating AmeriFlux Site Data into the Community Land Model with Carbon-Nitrogen Coupling via the Ensemble Kalman Filter

NASA Astrophysics Data System (ADS)

Pettijohn, J. C.; Law, B. E.; Williams, M. D.; Stoeckli, R.; Thornton, P. E.; Hudiburg, T. M.; Thomas, C. K.; Martin, J.; Hill, T. C.

2009-12-01

The assimilation of terrestrial carbon, water and nutrient cycle measurements into land surface models of these processes is fundamental to improving our ability to predict how these ecosystems may respond to climate change. A combination of measurements and models, each with their own systematic biases, must be considered when constraining the nonlinear behavior of these coupled dynamics. As such, we use the sequential Ensemble Kalman Filter (EnKF) to assimilate eddy covariance (EC) and other site-level AmeriFlux measurements into the NCAR Community Land Model with Carbon-Nitrogen coupling (CLM-CN v3.5), run in single-column mode at a 30-minute time step, to improve estimates of relatively unconstrained model state variables and parameters. Specifically, we focus on a semi-arid ponderosa pine site (US-ME2) in the Pacific Northwest to identify the mechanisms by which this ecosystem responds to severe late summer drought. Our EnKF analysis includes water, carbon, energy and nitrogen state variables (e.g., 10 volumetric soil moisture levels (0-3.43 m), ponderosa pine and shrub evapotranspiration and net ecosystem exchange of carbon dioxide stocks and flux components, snow depth, etc.) and associated parameters (e.g., PFT-level rooting distribution parameters, maximum subsurface runoff coefficient, soil hydraulic conductivity decay factor, snow aging parameters, maximum canopy conductance, C:N ratios, etc.). The effectiveness of the EnKF in constraining state variables and associated parameters is sensitive to their relative frequencies, in that C-N state variables and parameters with long time constants require similarly long time series in the analysis. We apply the EnKF kernel perturbation routine to disrupt preliminary convergence of covariances, which has been found in recent studies to be a problem more characteristic of low frequency vegetation state variables and parameters than high frequency ones more heavily coupled with highly varying climate (e.g., shallow soil moisture, snow depth). Preliminary results demonstrate that the assimilation of EC and other available AmeriFlux site physical, chemical and biological data significantly helps quantify and reduce CLM-CN model uncertainties and helps to constrain ‘hidden’ states and parameters that are essential in the coupled water, carbon, energy and nutrient dynamics of these sites. Such site-level calibration of CLM-CN is an initial step in identifying model deficiencies and in forecasts of future ecosystem responses to climate change.

Development and validation of the Single Item Trait Empathy Scale (SITES).

PubMed

Konrath, Sara; Meier, Brian P; Bushman, Brad J

2018-04-01

Empathy involves feeling compassion for others and imagining how they feel. In this article, we develop and validate the Single Item Trait Empathy Scale (SITES), which contains only one item that takes seconds to complete. In seven studies (N=5,724), the SITES was found to be both reliable and valid. It correlated in expected ways with a wide variety of intrapersonal outcomes. For example, it is negatively correlated with narcissism, depression, anxiety, and alexithymia. In contrast, it is positively correlated with other measures of empathy, self-esteem, subjective well-being, and agreeableness. The SITES also correlates with a wide variety of interpersonal outcomes, especially compassion for others and helping others. The SITES is recommended in situations when time or question quantity is constrained.

A remarkable enhancement of selectivity towards versatile analytes by a strategically integrated H-bonding site containing phase.

PubMed

Mallik, Abul K; Qiu, Hongdeng; Kuwahara, Yutaka; Takafuji, Makoto; Ihara, Hirotaka

2015-09-28

A double β-alanylated L-glutamide-derived organic phase has been newly designed and synthesized in such a way that integrated H-bonding (interaction) sites make it very suitable for the separation of versatile analytes, including shape-constrained isomers, and nonpolar, polar and basic compounds. The β-alanine residues introduced into two long-chain alkyl group moieties provide ordered polar groups through H-bonding among the amide groups.

Architecture of Allosteric Materials and Edge Modes

NASA Astrophysics Data System (ADS)

Yan, Le; Ravasio, Riccardo; Brito, Carolina; Wyart, Matthieu

Allostery, a long-range elasticity-mediated interaction, remains the biggest mystery decades after its discovery in proteins. We introduce a numerical scheme to evolve functional materials that can accomplish a specified mechanical task. In this scheme, the number of solutions, their spatial architectures and the correlations among them can be computed. As an example, we consider an ``allosteric'' task, which requires the material to respond specifically to a stimulus at a distant active site. We find that functioning materials evolve a less-constrained trumpet-shaped region connecting the stimulus and active sites and that the amplitude of the elastic response varies non-monotonically along the trumpet. As previously shown for some proteins, we find that correlations appearing during evolution alone are sufficient to identify key aspects of this design. Finally, we show that the success of this architecture stems from the emergence of soft edge modes recently found to appear near the surface of marginally connected materials. Overall, our in silico evolution experiment offers a new window to study the relationship between structure, function, and correlations emerging during evolution. L.Y. was supported in part by the National Science Foundation under Grant No. NSF PHY11-25915. M.W. thanks the Swiss National Science Foundation for support under Grant No. 200021-165509 and the Simons Foundation Grant (#454953 Matthieu Wyart).

Post-approval monitoring and oversight of U.S.-initiated human subjects research in resource-constrained countries.

PubMed

Brown, Brandon; Kinsler, Janni; Folayan, Morenike O; Allen, Karen; Cáceres, Carlos F

2014-06-01

The history of human subjects research and controversial procedures in relation to it has helped form the field of bioethics. Ethically questionable elements may be identified during research design, research implementation, management at the study site, or actions by a study's investigator or other staff. Post-approval monitoring (PAM) may prevent violations from occurring or enable their identification at an early stage. In U.S.-initiated human subjects research taking place in resource-constrained countries with limited development of research regulatory structures, arranging a site visit from a U.S. research ethics committee (REC) becomes difficult, thus creating a potential barrier to regulatory oversight by the parent REC. However, this barrier may be overcome through the use of digital technologies, since much of the world has at least remote access to the Internet. Empirical research is needed to pilot test the use of these technologies for research oversight to ensure the protection of human subjects taking part in research worldwide.

Coseismic fold scarp associated with historic earthquakes upon the Yoro active blind thrust, the Nobi-Ise fault zone, central Japan

NASA Astrophysics Data System (ADS)

Ishiyama, T.; Mueller, K.; Togo, M.

2004-12-01

We present structural models constrained by tectonic geomorphology, surface geologic mapping, shallow borehole transects and a high-resolution S-wave seismic reflection profile to define the kinematic evolution of a coseismic fold scarp along the Nobi-Ise fault zone (NIFZ). The NIFZ is an active intraplate fault system in central Japan, and consists of a 110-km-long array of active, east-verging reverse faults. Fold scarps along the Yoro fault are interpreted as produced during a large historic blind-thrust earthquake. The Yoro Mountains form the stripped core of the largest structure in the NIFZ and expose Triassic-Jurassic basement that are thrust eastward over a 2-km-thick sequence of Pliocene-Pleistocene strata deposited in the Nobi basin. This basement-cored fold is underlain by an active blind thrust that is expressed as late Holocene fold scarps along its eastern flank. Drilling investigations across the fold scarp at a site near Shizu identified at least three episodes of active folding associated with large earthquakes on the Yoro fault. Radiocarbon ages constrain the latest event as having occurred in a period that contains historical evidence for a large earthquake in A.D. 1586. A high resolution, S-wave seismic reflection profile at the same site shows that the topographic fold scarp coincides with the projected surface trace of the synclinal axis, across which the buried, early Holocene to historic sedimentary units are folded. This is interpreted to indicate that the structure accommodated coseismic fault-propagation folding during the A.D. 1586 blind thrust earthquake. Flexural-slip folding associated with secondary bedding-parallel thrusts may also deform late Holocene strata and act to consume slip on the primary blind thrust across the synclinal axial surfaces. The best-fitting trishear model for folded ca. 13 ka gravels deposited across the forelimb requires a 28\\deg east-dipping thrust fault. This solution suggests that a 4.2 mm/yr of slip rate has been accommodated on the Yoro fault during the late Holocene, with an average vertical rate of 1.9 mm/yr. This is consistent with longer-term slip rates calculated by a structural relief across a ca. 7.3 ka volcanic ash horizon (1.6 mm/yr), and ca. 110 ka innerbay clays (1.3 mm/yr) deposited across the forelimb. Our trishear model is thus able to account for the bulk of the folding history accommodated at shorter millennial timescales, suggesting that this technique may be used to adequately define slip rates on blind thrust faults.

Densification behavior of ceramic and crystallizable glass materials constrained on a rigid substrate

NASA Astrophysics Data System (ADS)

Calata, Jesus N.

2005-11-01

Constrained sintering is an important process for many applications. The sintering process almost always involves some form of constraint, both internal and external, such as rigid particles, reinforcing fibers and substrates to which the porous body adheres. The densification behavior of zinc oxide and cordierite-base crystallizable glass constrained on a rigid substrate was studied to add to the understanding of the behavior of various materials undergoing sintering when subjected to external substrate constraint. Porous ZnO films were isothermally sintered at temperatures between 900°C and 1050°C. The results showed that the densification of films constrained on substrates is severely reduced. This was evident in the sintered microstructures where the particles are joined together by narrower necks forming a more open structure, instead of the equiaxed grains with wide grain boundaries observed in the freestanding films. The calculated activation energies of densification were also different. For the density range of 60 to 64%, the constrained film had an activation energy of 391 +/- 34 kJ/mole compared to 242 +/- 21 kJ/mole for the freestanding film, indicating a change in the densification mechanism. In-plane stresses were observed during the sintering of the constrained films. Yielding of the films, in which the stresses dropped slight or remained unchanged, occurred at relative densities below 60% before the stresses climbed linearly with increasing density followed by a gradual relaxation. A substantial amount of the stresses remained after cooling. Free and constrained films of the cordierite-base crystallizable glass (glass-ceramic) were sintered between 900°C and 1000°C. The substrate constraint did not have a significant effect on the densification rate but the constrained films eventually underwent expansion. Calculations of the densification activation energy showed that, on average, it was close to 1077 kJ/mole, the activation energy of the glass, indicating that the prevailing mechanism was still viscous flow. The films expanded earlier and faster with increasing sintering temperature. The expansion was traced to the formation of pores at the interface with the silicon substrate and to a lesser extent on aluminum nitride. It was significantly reduced when the silicon substrate was pre-oxidized at 900°C, leading to the conclusion that the pore formation at the interface was due to poor wetting, which in turn was caused by the loss of the thin oxide layer through a reaction with the glass.

Spatio-Temporal Dynamics of Field Cricket Calling Behaviour: Implications for Female Mate Search and Mate Choice.

PubMed

Nandi, Diptarup; Balakrishnan, Rohini

2016-01-01

Amount of calling activity (calling effort) is a strong determinant of male mating success in species such as orthopterans and anurans that use acoustic communication in the context of mating behaviour. While many studies in crickets have investigated the determinants of calling effort, patterns of variability in male calling effort in natural choruses remain largely unexplored. Within-individual variability in calling activity across multiple nights of calling can influence female mate search and mate choice strategies. Moreover, calling site fidelity across multiple nights of calling can also affect the female mate sampling strategy. We therefore investigated the spatio-temporal dynamics of acoustic signaling behaviour in a wild population of the field cricket species Plebeiogryllus guttiventris. We first studied the consistency of calling activity by quantifying variation in male calling effort across multiple nights of calling using repeatability analysis. Callers were inconsistent in their calling effort across nights and did not optimize nightly calling effort to increase their total number of nights spent calling. We also estimated calling site fidelity of males across multiple nights by quantifying movement of callers. Callers frequently changed their calling sites across calling nights with substantial displacement but without any significant directionality. Finally, we investigated trade-offs between within-night calling effort and energetically expensive calling song features such as call intensity and chirp rate. Calling effort was not correlated with any of the calling song features, suggesting that energetically expensive song features do not constrain male calling effort. The two key features of signaling behaviour, calling effort and call intensity, which determine the duration and spatial coverage of the sexual signal, are therefore uncorrelated and function independently.

Ca-Mg Carbonate Cements in Ophiolite-Hosted Creek Waters of the Del Puerto Ophiolite, CA, and their Potential Significance as a Planetary Biosignature

NASA Astrophysics Data System (ADS)

Blank, J. G.

2015-12-01

Serpentinization, the reaction at moderate pressure and temperature of water with olivine and pyroxene that are common in basalts and ultramafic rocks, results in the formation of alkaline fluids and the precipitation of a variety of secondary minerals. Terrestrial localities where active serpentinization is occurring are ideal Mars analogs for examining the characteristics of an environment that possesses two of the key features that we assume necessary to host life: water and an internally generated energy source. This study focuses on a related but different feature present where active serpentinization is occurring - namely, carbonate cements forming under plain air in the vicinity of Adobe Springs, CA. This site is located in the Del Puerto ophiolite about 150 km ESE of San Francisco, in the Coast Range of California. Two alkaline spring water compositions have been described at the site, a Ca-OH water (which is not currently being emitted by the active springs), and a Mg-CO3 water. Abundant dolomitic and calcitic carbonate cements are found in the creek drainages near the springs, associated with a diverse microbial community. We conducted a systematic study of the carbonate cements using SEM, EMP, XRD, TEM, and SIMS, focusing on sub-mm variations in texture, mineral chemistry and stable isotope (COH) composition. We compared our measurements with thermodynamic modeling results constrained by chemical analysis of water chemistry from the site and known partition coefficients and stable isotope fractionation factors. The wide range of carbonate compositions and textures observed at the Adobe Springs site suggests that more than one process is involved in their precipitation, including the possibility of microbially mediated dolomite mineralization. These carbonate cements could be a mineralogic biomarker of serpentinization and microbiological processes on Mars and other rocky planets and, therefore, prime targets for future astrobiological investigations.

The Use of Explosion Aftershock Probabilities for Planning and Deployment of Seismic Aftershock Monitoring System for an On-site Inspection

NASA Astrophysics Data System (ADS)

Labak, P.; Ford, S. R.; Sweeney, J. J.; Smith, A. T.; Spivak, A.

2011-12-01

One of four elements of CTBT verification regime is On-site inspection (OSI). Since the sole purpose of an OSI shall be to clarify whether a nuclear weapon test explosion or any other nuclear explosion has been carried out, inspection activities can be conducted and techniques used in order to collect facts to support findings provided in inspection reports. Passive seismological monitoring, realized by the seismic aftershock monitoring (SAMS) is one of the treaty allowed techniques during an OSI. Effective planning and deployment of SAMS during the early stages of an OSI is required due to the nature of possible events recorded and due to the treaty related constrains on size of inspection area, size of inspection team and length of an inspection. A method, which may help in planning the SAMS deployment is presented. An estimate of aftershock activity due to a theoretical underground nuclear explosion is produced using a simple aftershock rate model (Ford and Walter, 2010). The model is developed with data from the Nevada Test Site and Semipalatinsk Test Site, which we take to represent soft- and hard-rock testing environments, respectively. Estimates of expected magnitude and number of aftershocks are calculated using the models for different testing and inspection scenarios. These estimates can help to plan the SAMS deployment for an OSI by giving a probabilistic assessment of potential aftershocks in the Inspection Area (IA). The aftershock assessment combined with an estimate of the background seismicity in the IA and an empirically-derived map of threshold magnitude for the SAMS network could aid the OSI team in reporting. We tested the hard-rock model to a scenario similar to the 2008 Integrated Field Exercise 2008 deployment in Kazakhstan and produce an estimate of possible recorded aftershock activity.

Seismic Hazard in Haiti: A Geologic Perspective

NASA Astrophysics Data System (ADS)

Prentice, C. S.; Crone, A. J.; Gold, R. D.; Briggs, R. W.; Narcisse, R.

2012-12-01

The catastrophic M 7.0 earthquake that occurred in Haiti on 12 January 2010 highlighted the hazard associated with the Caribbean-North American plate boundary in Hispaniola. Detailed analysis and modeling of geologic, geodetic, and seismologic data showed that most of the moment release occurred on a previously unidentified, north-dipping, blind thrust fault (now named the Léogâne fault), which is north of the plate-bounding, left-lateral Enriquillo-Plantain Garden fault (EPGF). The result that the Léogâne fault was the source of the 2010 earthquake implies that the EPGF remains a significant hazard and raises the question of other potential seismic sources near Port-au-Prince (PaP). Following the earthquake, we mapped Quaternary traces of the EPGF in the field using satellite imagery, aerial photography, and LiDAR data. We identified three paleoseismic study sites along the EPGF: the Jean-Jean and Marianne sites southwest of PaP along the Momance section of the EPGF and the Riviére Grise site southeast of PaP along the Dumay section. Trenches at the Jean-Jean site show fault strands breaking nearly to the ground surface, but that did not move in the 2010 earthquake. We collected radiocarbon samples from faulted strata that we anticipate will provide constraints on the age of the most recent surface rupture. We also identified a buried channel deposit that is left-laterally offset a minimum of 3 m, and collected radiocarbon samples to constrain its age. In a natural stream cut at the Marianne site, we documented three colluvial wedges, and collected samples for optically stimulated luminescence (OSL) dating that we anticipate will provide age constraints on the three most recent earthquakes. At Riviére Grise we documented evidence for three surface ruptures in a fluvial terrace deposit, and collected OSL samples to constrain their ages. Our preliminary geomorphic analysis of a belt of low hills north of the EPGF and east of PaP suggests that these hills are young folds likely underlain by blind thrust faults. Reconnaissance field observations show that the hills are cored by folded alluvial-fan deposits of probable Quaternary age and that the folding defeated north-flowing drainages and ponded lacustrine sediment on the south flank of the folds. Radiocarbon analyses of charcoal samples collected from ponded sediments will help to constrain the age of recent deformation. These blind thrust faults are potentially additional earthquake sources that should be included in seismic hazard assessments for PaP. In our reconnaissance along the Matheux-Neiba fault north of PaP we found only weak evidence of recent deformation, and while this fault system may also be a potential earthquake source, its rate of activity is much lower than the rate on the EPGF. Because the EPGF adjacent to PaP did not rupture in 2010, and has not ruptured in at least 240 years, considerable strain remains to be released in a future earthquake, and this fault still poses a major hazard to densely populated parts of Haiti, including Port-au-Prince.

Kinetics of heavy metal adsorption and desorption in soil: Developing a unified model based on chemical speciation

NASA Astrophysics Data System (ADS)

Peng, Lanfang; Liu, Paiyu; Feng, Xionghan; Wang, Zimeng; Cheng, Tao; Liang, Yuzhen; Lin, Zhang; Shi, Zhenqing

2018-03-01

Predicting the kinetics of heavy metal adsorption and desorption in soil requires consideration of multiple heterogeneous soil binding sites and variations of reaction chemistry conditions. Although chemical speciation models have been developed for predicting the equilibrium of metal adsorption on soil organic matter (SOM) and important mineral phases (e.g. Fe and Al (hydr)oxides), there is still a lack of modeling tools for predicting the kinetics of metal adsorption and desorption reactions in soil. In this study, we developed a unified model for the kinetics of heavy metal adsorption and desorption in soil based on the equilibrium models WHAM 7 and CD-MUSIC, which specifically consider metal kinetic reactions with multiple binding sites of SOM and soil minerals simultaneously. For each specific binding site, metal adsorption and desorption rate coefficients were constrained by the local equilibrium partition coefficients predicted by WHAM 7 or CD-MUSIC, and, for each metal, the desorption rate coefficients of various binding sites were constrained by their metal binding constants with those sites. The model had only one fitting parameter for each soil binding phase, and all other parameters were derived from WHAM 7 and CD-MUSIC. A stirred-flow method was used to study the kinetics of Cd, Cu, Ni, Pb, and Zn adsorption and desorption in multiple soils under various pH and metal concentrations, and the model successfully reproduced most of the kinetic data. We quantitatively elucidated the significance of different soil components and important soil binding sites during the adsorption and desorption kinetic processes. Our model has provided a theoretical framework to predict metal adsorption and desorption kinetics, which can be further used to predict the dynamic behavior of heavy metals in soil under various natural conditions by coupling other important soil processes.

Nest site attributes and temporal patterns of northern flicker nest loss: effects of predation and competition.

PubMed

Fisher, Ryan J; Wiebe, Karen L

2006-04-01

To date, most studies of nest site selection have failed to take into account more than one source of nest loss (or have combined all sources in one analysis) when examining nest site characteristics, leaving us with an incomplete understanding of the potential trade-offs that individuals may face when selecting a nest site. Our objectives were to determine whether northern flickers (Colaptes auratus) may experience a trade-off in nest site selection in response to mammalian nest predation and nest loss to a cavity nest competitor (European starling, Sturnus vulgaris). We also document within-season temporal patterns of these two sources of nest loss with the hypothesis that flickers may also be constrained in the timing of reproduction under both predatory and competitive influence. Mammalian predators frequently depredated flicker nests that were: lower to the ground, less concealed by vegetation around the cavity entrance and at the base of the nest tree, closer to coniferous forest edges and in forest clumps with a high percentage of conifer content. Proximity to coniferous edges or coniferous trees increased the probability of nest predation, but nests near conifers were less likely to be lost to starlings. Flickers may thus face a trade-off in nest site selection with respect to safety from predators or competitors. Models suggested that peaks of nest predation and nest loss to eviction occurred at the same time, although a competing model suggested that the peak of nest loss to starlings occurred 5 days earlier than the peak of mammalian predation. Differences in peaks of mammalian predation and loss to starlings may constrain any adjustment in clutch initiation date by flickers to avoid one source of nest loss.

Empirical Green's function analysis: Taking the next step

USGS Publications Warehouse

Hough, S.E.

1997-01-01

An extension of the empirical Green's function (EGF) method is presented that involves determination of source parameters using standard EGF deconvolution, followed by inversion for a common attenuation parameter for a set of colocated events. Recordings of three or more colocated events can thus be used to constrain a single path attenuation estimate. I apply this method to recordings from the 1995-1996 Ridgecrest, California, earthquake sequence; I analyze four clusters consisting of 13 total events with magnitudes between 2.6 and 4.9. I first obtain corner frequencies, which are used to infer Brune stress drop estimates. I obtain stress drop values of 0.3-53 MPa (with all but one between 0.3 and 11 MPa), with no resolved increase of stress drop with moment. With the corner frequencies constrained, the inferred attenuation parameters are very consistent; they imply an average shear wave quality factor of approximately 20-25 for alluvial sediments within the Indian Wells Valley. Although the resultant spectral fitting (using corner frequency and ??) is good, the residuals are consistent among the clusters analyzed. Their spectral shape is similar to the the theoretical one-dimensional response of a layered low-velocity structure in the valley (an absolute site response cannot be determined by this method, because of an ambiguity between absolute response and source spectral amplitudes). I show that even this subtle site response can significantly bias estimates of corner frequency and ??, if it is ignored in an inversion for only source and path effects. The multiple-EGF method presented in this paper is analogous to a joint inversion for source, path, and site effects; the use of colocated sets of earthquakes appears to offer significant advantages in improving resolution of all three estimates, especially if data are from a single site or sites with similar site response.

Optimal vibration control of a rotating plate with self-sensing active constrained layer damping

NASA Astrophysics Data System (ADS)

Xie, Zhengchao; Wong, Pak Kin; Lo, Kin Heng

2012-04-01

This paper proposes a finite element model for optimally controlled constrained layer damped (CLD) rotating plate with self-sensing technique and frequency-dependent material property in both the time and frequency domain. Constrained layer damping with viscoelastic material can effectively reduce the vibration in rotating structures. However, most existing research models use complex modulus approach to model viscoelastic material, and an additional iterative approach which is only available in frequency domain has to be used to include the material's frequency dependency. It is meaningful to model the viscoelastic damping layer in rotating part by using the anelastic displacement fields (ADF) in order to include the frequency dependency in both the time and frequency domain. Also, unlike previous ones, this finite element model treats all three layers as having the both shear and extension strains, so all types of damping are taken into account. Thus, in this work, a single layer finite element is adopted to model a three-layer active constrained layer damped rotating plate in which the constraining layer is made of piezoelectric material to work as both the self-sensing sensor and actuator under an linear quadratic regulation (LQR) controller. After being compared with verified data, this newly proposed finite element model is validated and could be used for future research.

Understanding Methane Emission from Natural Gas Activities Using Inverse Modeling Techniques

NASA Astrophysics Data System (ADS)

Abdioskouei, M.; Carmichael, G. R.

2015-12-01

Natural gas (NG) has been promoted as a bridge fuel that can smooth the transition from fossil fuels to zero carbon energy sources by having lower carbon dioxide emission and lower global warming impacts in comparison to other fossil fuels. However, the uncertainty around the estimations of methane emissions from NG systems can lead to underestimation of climate and environmental impacts of using NG as a replacement for coal. Accurate estimates of methane emissions from NG operations is crucial for evaluation of environmental impacts of NG extraction and at larger scale, adoption of NG as transitional fuel. However there is a great inconsistency within the current estimates. Forward simulation of methane from oil and gas operation sites for the US is carried out based on NEI-2011 using the WRF-Chem model. Simulated values are compared against measurements of observations from different platforms such as airborne (FRAPPÉ field campaign) and ground-based measurements (NOAA Earth System Research Laboratory). A novel inverse modeling technique is used in this work to improve the model fit to the observation values and to constrain methane emission from oil and gas extraction sites.

Model Evaluation Report for Corrective Action Unit 98: Frenchman Flat, Nevada National Security Site, Nye County, Nevada, Revision 1

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

Ruskauff, Greg; Marutzky, Sam

Model evaluation focused solely on the PIN STRIPE and MILK SHAKE underground nuclear tests’ contaminant boundaries (CBs) because they had the largest extent, uncertainty, and potential consequences. The CAMBRIC radionuclide migration experiment also had a relatively large CB, but because it was constrained by transport data (notably Well UE-5n), there was little uncertainty, and radioactive decay reduced concentrations before much migration could occur. Each evaluation target and the associated data-collection activity were assessed in turn to determine whether the new data support, or demonstrate conservatism of, the CB forecasts. The modeling team—in this case, the same team that developed themore » Frenchman Flat geologic, source term, and groundwater flow and transport models—analyzed the new data and presented the results to a PER committee. Existing site understanding and its representation in numerical groundwater flow and transport models was evaluated in light of the new data and the ability to proceed to the CR stage of long-term monitoring and institutional control.« less

Hydrological Parameter Estimations from a Conservative Tracer Test With Variable-Density Effects at the Boise Hydrogeophysical Research Site

DTIC Science & Technology

2011-12-15

the measured porosity values can be taken as equivalent to effective porosity values for this aquifer with the risk of only very limited overestimation...information to constrain/control an increasingly ill-posed problem, and (3) risk estimation of a model with more heterogeneity than is needed to explain...coarse fluvial deposits: Boise Hydrogeophysical Research Site, Geological Society of America Bulletin, 116(9–10), 1059–1073. Barrash, W., T. Clemo

Fluid and chemical fluxes along a buried-basement ridge in the eastern Juan de Fuca Ridge flank

NASA Astrophysics Data System (ADS)

Hulme, S.; Wheat, C. G.

2010-12-01

Hydrothermal fluid circulation within oceanic crust at low temperatures affects global biogeochemical cycles, with the volume of fluid circulation rivaling that of the world’s water flux to the oceans from rivers. Our work focuses on the best studied low temperature hydrothermal system on the eastern flank of the Juan de Fuca Ridge where a buried basement ridge 100 km from the active spreading axis has been sampled with a variety of mediums. We use data from deep sea drilling, gravity coring, and submersible operations from five sites along-strike of the buried ridge to better constrain the chemical and fluid fluxes along this transect. A transport (advection-diffusion) model is applied to the data, constraining the volumetric fluid flux per unit length within the oceanic crust from 0.05 and 0.2 m3 y-1 cm-1 and identifying conservative elements within this system. Using an average fluid flux, reactive fluxes are determined for non-conservative elements within basaltic crust for twenty-four chemical species. Conservative species include K, Cl, SO4, Ba, Sr, Cs, Mo, and Y. Only Ca and the rare earth elements Ce and Gd are produced by basaltic basement. The remaining chemical species Mg, Na, ammonium, Li, Rb, Mn, Fe, Co, Zn, Cd, U, La and Yb are all consumed within upper basaltic basement. Fluxes of potentially-bioavailable redox species ammonium, Fe, and Mn into the upper basaltic basement are 3 to 20 nmol y-1cm-2. Possible mechanisms of removal are suggested, placing constraints on microbial metabolic activity and biomineralization.

Role of Host-Driven Mutagenesis in Determining Genome Evolution of Sigma Virus (DMelSV; Rhabdoviridae) in Drosophila melanogaster.

PubMed

Piontkivska, Helen; Matos, Luis F; Paul, Sinu; Scharfenberg, Brian; Farmerie, William G; Miyamoto, Michael M; Wayne, Marta L

2016-10-05

Sigma virus (DMelSV) is ubiquitous in natural populations of Drosophila melanogaster. Host-mediated, selective RNA editing of adenosines to inosines (ADAR) may contribute to control of viral infection by preventing transcripts from being transported into the cytoplasm or being translated accurately; or by increasing the viral genomic mutation rate. Previous PCR-based studies showed that ADAR mutations occur in DMelSV at low frequency. Here we use SOLiD TM deep sequencing of flies from a single host population from Athens, GA, USA to comprehensively evaluate patterns of sequence variation in DMelSV with respect to ADAR. GA dinucleotides, which are weak targets of ADAR, are strongly overrepresented in the positive strand of the virus, consistent with selection to generate ADAR resistance on this complement of the transient, double-stranded RNA intermediate in replication and transcription. Potential ADAR sites in a worldwide sample of viruses are more likely to be "resistant" if the sites do not vary among samples. Either variable sites are less constrained and hence are subject to weaker selection than conserved sites, or the variation is driven by ADAR. We also find evidence of mutations segregating within hosts, hereafter referred to as hypervariable sites. Some of these sites were variable only in one or two flies (i.e., rare); others were shared by four or even all five of the flies (i.e., common). Rare and common hypervariable sites were indistinguishable with respect to susceptibility to ADAR; however, polymorphism in rare sites were more likely to be consistent with the action of ADAR than in common ones, again suggesting that ADAR is deleterious to the virus. Thus, in DMelSV, host mutagenesis is constraining viral evolution both within and between hosts. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Monitoring ship noise to assess the impact of coastal developments on marine mammals.

PubMed

Merchant, Nathan D; Pirotta, Enrico; Barton, Tim R; Thompson, Paul M

2014-01-15

The potential impacts of underwater noise on marine mammals are widely recognised, but uncertainty over variability in baseline noise levels often constrains efforts to manage these impacts. This paper characterises natural and anthropogenic contributors to underwater noise at two sites in the Moray Firth Special Area of Conservation, an important marine mammal habitat that may be exposed to increased shipping activity from proposed offshore energy developments. We aimed to establish a pre-development baseline, and to develop ship noise monitoring methods using Automatic Identification System (AIS) and time-lapse video to record trends in noise levels and shipping activity. Our results detail the noise levels currently experienced by a locally protected bottlenose dolphin population, explore the relationship between broadband sound exposure levels and the indicators proposed in response to the EU Marine Strategy Framework Directive, and provide a ship noise assessment toolkit which can be applied in other coastal marine environments. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Predicting thunderstorm evolution using ground-based lightning detection networks

NASA Technical Reports Server (NTRS)

Goodman, Steven J.

1990-01-01

Lightning measurements acquired principally by a ground-based network of magnetic direction finders are used to diagnose and predict the existence, temporal evolution, and decay of thunderstorms over a wide range of space and time scales extending over four orders of magnitude. The non-linear growth and decay of thunderstorms and their accompanying cloud-to-ground lightning activity is described by the three parameter logistic growth model. The growth rate is shown to be a function of the storm size and duration, and the limiting value of the total lightning activity is related to the available energy in the environment. A new technique is described for removing systematic bearing errors from direction finder data where radar echoes are used to constrain site error correction and optimization (best point estimate) algorithms. A nearest neighbor pattern recognition algorithm is employed to cluster the discrete lightning discharges into storm cells and the advantages and limitations of different clustering strategies for storm identification and tracking are examined.

Hitomi observation of radio galaxy NGC 1275: The first X-ray microcalorimeter spectroscopy of Fe-Kα line emission from an active galactic nucleus

NASA Astrophysics Data System (ADS)

Hitomi Collaboration; Aharonian, Felix; Akamatsu, Hiroki; Akimoto, Fumie; Allen, Steven W.; Angelini, Lorella; Audard, Marc; Awaki, Hisamitsu; Axelsson, Magnus; Bamba, Aya; Bautz, Marshall W.; Blandford, Roger; Brenneman, Laura W.; Brown, Gregory V.; Bulbul, Esra; Cackett, Edward M.; Chernyakova, Maria; Chiao, Meng P.; Coppi, Paolo S.; Costantini, Elisa; de Plaa, Jelle; de Vries, Cor P.; den Herder, Jan-Willem; Done, Chris; Dotani, Tadayasu; Ebisawa, Ken; Eckart, Megan E.; Enoto, Teruaki; Ezoe, Yuichiro; Fabian, Andrew C.; Ferrigno, Carlo; Foster, Adam R.; Fujimoto, Ryuichi; Fukazawa, Yasushi; Furuzawa, Akihiro; Galeazzi, Massimiliano; Gallo, Luigi C.; Gandhi, Poshak; Giustini, Margherita; Goldwurm, Andrea; Gu, Liyi; Guainazzi, Matteo; Haba, Yoshito; Hagino, Kouichi; Hamaguchi, Kenji; Harrus, Ilana M.; Hatsukade, Isamu; Hayashi, Katsuhiro; Hayashi, Takayuki; Hayashida, Kiyoshi; Hiraga, Junko S.; Hornschemeier, Ann; Hoshino, Akio; Hughes, John P.; Ichinohe, Yuto; Iizuka, Ryo; Inoue, Hajime; Inoue, Yoshiyuki; Ishida, Manabu; Ishikawa, Kumi; Ishisaki, Yoshitaka; Iwai, Masachika; Kaastra, Jelle; Kallman, Tim; Kamae, Tsuneyoshi; Kataoka, Jun; Katsuda, Satoru; Kawai, Nobuyuki; Kelley, Richard L.; Kilbourne, Caroline A.; Kitaguchi, Takao; Kitamoto, Shunji; Kitayama, Tetsu; Kohmura, Takayoshi; Kokubun, Motohide; Koyama, Katsuji; Koyama, Shu; Kretschmar, Peter; Krimm, Hans A.; Kubota, Aya; Kunieda, Hideyo; Laurent, Philippe; Lee, Shiu-Hang; Leutenegger, Maurice A.; Limousin, Olivier O.; Loewenstein, Michael; Long, Knox S.; Lumb, David; Madejski, Greg; Maeda, Yoshitomo; Maier, Daniel; Makishima, Kazuo; Markevitch, Maxim; Matsumoto, Hironori; Matsushita, Kyoko; McCammon, Dan; McNamara, Brian R.; Mehdipour, Missagh; Miller, Eric D.; Miller, Jon M.; Mineshige, Shin; Mitsuda, Kazuhisa; Mitsuishi, Ikuyuki; Miyazawa, Takuya; Mizuno, Tsunefumi; Mori, Hideyuki; Mori, Koji; Mukai, Koji; Murakami, Hiroshi; Mushotzky, Richard F.; Nakagawa, Takao; Nakajima, Hiroshi; Nakamori, Takeshi; Nakashima, Shinya; Nakazawa, Kazuhiro; Nobukawa, Kumiko K.; Nobukawa, Masayoshi; Noda, Hirofumi; Odaka, Hirokazu; Ohashi, Takaya; Ohno, Masanori; Okajima, Takashi; Ota, Naomi; Ozaki, Masanobu; Paerels, Frits; Paltani, Stéphane; Petre, Robert; Pinto, Ciro; Porter, Frederick S.; Pottschmidt, Katja; Reynolds, Christopher S.; Safi-Harb, Samar; Saito, Shinya; Sakai, Kazuhiro; Sasaki, Toru; Sato, Goro; Sato, Kosuke; Sato, Rie; Sawada, Makoto; Schartel, Norbert; Serlemitsos, Peter J.; Seta, Hiromi; Shidatsu, Megumi; Simionescu, Aurora; Smith, Randall K.; Soong, Yang; Stawarz, Łukasz; Sugawara, Yasuharu; Sugita, Satoshi; Szymkowiak, Andrew; Tajima, Hiroyasu; Takahashi, Hiromitsu; Takahashi, Tadayuki; Takeda, Shin'ichiro; Takei, Yoh; Tamagawa, Toru; Tamura, Takayuki; Tanaka, Takaaki; Tanaka, Yasuo; Tanaka, Yasuyuki T.; Tashiro, Makoto S.; Tawara, Yuzuru; Terada, Yukikatsu; Terashima, Yuichi; Tombesi, Francesco; Tomida, Hiroshi; Tsuboi, Yohko; Tsujimoto, Masahiro; Tsunemi, Hiroshi; Tsuru, Takeshi Go; Uchida, Hiroyuki; Uchiyama, Hideki; Uchiyama, Yasunobu; Ueda, Shutaro; Ueda, Yoshihiro; Uno, Shin'ichiro; Urry, C. Megan; Ursino, Eugenio; Watanabe, Shin; Werner, Norbert; Wilkins, Dan R.; Williams, Brian J.; Yamada, Shinya; Yamaguchi, Hiroya; Yamaoka, Kazutaka; Yamasaki, Noriko Y.; Yamauchi, Makoto; Yamauchi, Shigeo; Yaqoob, Tahir; Yatsu, Yoichi; Yonetoku, Daisuke; Zhuravleva, Irina; Zoghbi, Abderahmen; Kawamuro, Taiki

2018-03-01

The origin of the narrow Fe-Kα fluorescence line at 6.4 keV from active galactic nuclei has long been under debate; some of the possible sites are the outer accretion disk, the broad line region, a molecular torus, or interstellar/intracluster media. In 2016 February-March, we performed the first X-ray microcalorimeter spectroscopy with the Soft X-ray Spectrometer (SXS) on board the Hitomi satellite of the Fanaroff-Riley type I radio galaxy NGC 1275 at the center of the Perseus cluster of galaxies. With the high-energy resolution of ˜5 eV at 6 keV achieved by Hitomi/SXS, we detected the Fe-Kα line with ˜5.4 σ significance. The velocity width is constrained to be 500-1600 km s-1 (FWHM for Gaussian models) at 90% confidence. The SXS also constrains the continuum level from the NGC 1275 nucleus up to ˜20 keV, giving an equivalent width of ˜20 eV for the 6.4 keV line. Because the velocity width is narrower than that of the broad Hα line of ˜2750 km s-1, we can exclude a large contribution to the line flux from the accretion disk and the broad line region. Furthermore, we performed pixel map analyses on the Hitomi/SXS data and image analyses on the Chandra archival data, and revealed that the Fe-Kα line comes from a region within ˜1.6 kpc of the NGC 1275 core, where an active galactic nucleus emission dominates, rather than that from intracluster media. Therefore, we suggest that the source of the Fe-Kα line from NGC 1275 is likely a low-covering-fraction molecular torus or a rotating molecular disk which probably extends from a parsec to hundreds of parsecs scale in the active galactic nucleus system.

Density-dependent mass gain by Wilson's Warblers during stopover

Treesearch

Jeffrey F. Kelly; Linda S. DeLay; Deborah M. Finch

2002-01-01

The need restore energetic reserves at stopover sites constrains avian migration ecology. To describe that constraint, we examined relationships among mass gained by Wilson's Warblers (Wilsonia pusilla) during stopover, abundance of Wilson's Warblers (i.e. capture rate), and arthropod abundance during autumn migration. We found that amount...

Adaptation of innate lymphoid cells to nutrient deprivation promotes type 2 barrier immunity

USDA-ARS?s Scientific Manuscript database

Survival of the host relies on the establishment of site-specific barrier defense tailored to constrain pressures imposed by commensal and parasitic exposures. The host is confronted with the additional challenge of maintaining barrier immunity in fluctuating states of dietary availability, yet how ...

Prediction of cheatgrass field germination potential using wet thermal accumulation

Treesearch

Bruce A. Roundy; Stuart P. Hardegree; Jeane C. Chambers; Alison Whittaker

2007-01-01

Invasion and dominance of weedy species is facilitated or constrained by environmental and ecological factors that affect resource availability during critical life stages. We compared the relative effects of season, annual weather, site, and disturbance on potential cheatgrass (Bromus tectorum L.) germination in big sagebrush (Artemisia...

Sanitation, Stress, and Life Stage: A Systematic Data Collection Study among Women in Odisha, India.

PubMed

Hulland, Kristyna R S; Chase, Rachel P; Caruso, Bethany A; Swain, Rojalin; Biswal, Bismita; Sahoo, Krushna Chandra; Panigrahi, Pinaki; Dreibelbis, Robert

2015-01-01

Emerging evidence demonstrates how inadequate access to water and sanitation is linked to psychosocial stress, especially among women, forcing them to navigate social and physical barriers during their daily sanitation routines. We examine sanitation-related psychosocial stress (SRPS) across women's reproductive lives in three distinct geographic sites (urban slums, rural villages, and rural tribal villages) in Odisha, India. We explored daily sanitation practices of adolescent, newly married, pregnant, and established adult women (n = 60) and identified stressors encountered during sanitation. Responding to structured data collection methods, women ranked seven sanitation activities (defecation, urination, menstruation, bathing, post-defecation cleaning, carrying water, and changing clothes) based on stress (high to low) and level of freedom (associated with greatest freedom to having the most restrictions). Women then identified common stressors they encountered when practicing sanitation and sorted stressors in constrained piles based on frequency and severity of each issue. The constellation of factors influencing SRPS varies by life stage and location. Overall, sanitation behaviors that were most restricted (i.e., menstruation) were the most stressful. Women in different sites encountered different stressors, and the level of perceived severity varied based on site and life stage. Understanding the influence of place and life stage on SRPS provides a nuanced understanding of sanitation, and may help identify areas for intervention.

Horizontal-to-Vertical Spectral Ratio for Estimating Thickness of Sedimentary Deposits across the PoroTomo site in Brady Hot Springs, Nevada (USA)

NASA Astrophysics Data System (ADS)

Parker, L.; Fratta, D.; Zeng, X.; Lord, N. E.; Wang, H. F.; Thurber, C. H.; Lin, F. C.; Feigl, K. L.; Team, P.

2016-12-01

During March 2016, the PoroTomo research team deployed more than 8700 m of DAS and DTS cable in horizontal and vertical sensing arrays, 244 three-component surface geophones, inSAR images, pressure transducers, and a vibroseis truck to actively and passively image the response of a geothermal field in Brady Hot Springs, Nevada. During the imaging period the geothermal field was manipulated to change the pore pressure in the formation. The objective of the study is to invert for poroelastic parameters within a 1500 m by 500 m by 400 m volume using tomographic techniques. Among the different imaging techniques, the research team is using passive horizontal-to-vertical spectral ratio data captured with the three-component geophones to estimate the thickness of the sedimentary deposits across the PoroTomo site. The interpretation of the inverted data is complicated due the heterogeneity in the near surface deposits at the site. These deposits include diatomaceous earth, sandy/silty layers, and hardened silica associated with the presence of fumaroles. In spite of the challenges associated with deposits of very different stiffness, the mapping of sediment thickness across the Natural Laboratory helps constrain the inversion of Multiple Channel Analysis of Surface Waves to improve the quality of the solution images.

Responses of riparian reptile communities to damming and urbanization

USGS Publications Warehouse

Hunt, Stephanie D.; Guzy, Jacquelyn C.; Price, Steven J.; Halstead, Brian J.; Eskew, Evan A.; Dorcas, Michael E.

2013-01-01

Various anthropogenic pressures, including habitat loss, threaten reptile populations worldwide. Riparian zones are critical habitat for many reptile species, but these habitats are also frequently modified by anthropogenic activities. Our study investigated the effects of two riparian habitat modifications-damming and urbanization-on overall and species-specific reptile occupancy patterns. We used time-constrained search techniques to compile encounter histories for 28 reptile species at 21 different sites along the Broad and Pacolet Rivers of South Carolina. Using a hierarchical Bayesian analysis, we modeled reptile occupancy responses to a site's distance upstream from dam, distance downstream from dam, and percent urban land use. The mean occupancy response by the reptile community indicated that reptile occupancy and species richness were maximized when sites were farther upstream from dams. Species-specific occupancy estimates showed a similar trend of lower occupancy immediately upstream from dams. Although the mean occupancy response of the reptile community was positively related to distance downstream from dams, the occupancy response to distance downstream varied among species. Percent urban land use had little effect on the occupancy response of the reptile community or individual species. Our results indicate that the conditions of impoundments and subsequent degradation of the riparian zones upstream from dams may not provide suitable habitat for a number of reptile species.

Geodatabase of sites, basin boundaries, and topology rules used to store drainage basin boundaries for the U.S. Geological Survey, Colorado Water Science Center

USGS Publications Warehouse

Dupree, Jean A.; Crowfoot, Richard M.

2012-01-01

This geodatabase and its component datasets are part of U.S. Geological Survey Digital Data Series 650 and were generated to store basin boundaries for U.S. Geological Survey streamgages and other sites in Colorado. The geodatabase and its components were created by the U.S. Geological Survey, Colorado Water Science Center, and are used to derive the numeric drainage areas for Colorado that are input into the U.S. Geological Survey's National Water Information System (NWIS) database and also published in the Annual Water Data Report and on NWISWeb. The foundational dataset used to create the basin boundaries in this geodatabase was the National Watershed Boundary Dataset. This geodatabase accompanies a U.S. Geological Survey Techniques and Methods report (Book 11, Section C, Chapter 6) entitled "Digital Database Architecture and Delineation Methodology for Deriving Drainage Basins, and Comparison of Digitally and Non-Digitally Derived Numeric Drainage Areas." The Techniques and Methods report details the geodatabase architecture, describes the delineation methodology and workflows used to develop these basin boundaries, and compares digitally derived numeric drainage areas in this geodatabase to non-digitally derived areas. 1. COBasins.gdb: This geodatabase contains site locations and basin boundaries for Colorado. It includes a single feature dataset, called BasinsFD, which groups the component feature classes and topology rules. 2. BasinsFD: This feature dataset in the "COBasins.gdb" geodatabase is a digital container that holds the feature classes used to archive site locations and basin boundaries as well as the topology rules that govern spatial relations within and among component feature classes. This feature dataset includes three feature classes: the sites for which basins have been delineated (the "Sites" feature class), basin bounding lines (the "BasinLines" feature class), and polygonal basin areas (the "BasinPolys" feature class). The feature dataset also stores the topology rules (the "BasinsFD_Topology") that constrain the relations within and among component feature classes. The feature dataset also forces any feature classes inside it to have a consistent projection system, which is, in this case, an Albers-Equal-Area projection system. 3. BasinsFD_Topology: This topology contains four persistent topology rules that constrain the spatial relations within the "BasinLines" feature class and between the "BasinLines" feature class and the "BasinPolys" feature classes. 4. Sites: This point feature class contains the digital representations of the site locations for which Colorado Water Science Center basin boundaries have been delineated. This feature class includes point locations for Colorado Water Science Center active (as of September 30, 2009) gages and for other sites. 5. BasinLines: This line feature class contains the perimeters of basins delineated for features in the "Sites" feature class, and it also contains information regarding the sources of lines used for the basin boundaries. 6. BasinPolys: This polygon feature class contains the polygonal basin areas delineated for features in the "Sites" feature class, and it is used to derive the numeric drainage areas published by the Colorado Water Science Center.

Trench logs, terrestrial lidar system imagery, and radiocarbon data from the kilometer-62 site on the Greenville Fault, southeastern Alameda County, California, 2014

USGS Publications Warehouse

Lienkaemper, James J.; DeLong, Stephen B.; Avdievitch, Nikita N.; Pickering, Alexandra J; Guilderson, Thomas P.

2015-01-01

In 2014, we investigated an abrupt 8.5-meter (m), right-laterally deflected stream channel located near the Greenville Fault in southeastern Alameda County, California (-121.56224° E, 37.53430° N) that we discovered using 0.5-m resolution, 2011 aerial lidar imagery flown along the active fault trace. Prior to trenching we surveyed the site using a terrestrial lidar system (TLS) to document the exact geomorphic expression of this deflected stream channel before excavating a trench adjacent to it. We trenched perpendicular to the fault hoping to document the prehistoric history of earthquake ruptures along the fault. However, the alluvial stratigraphy that we document in these trench logs shows conclusively that this trench did not expose any active fault trace. Using other local geomorphic evidence for the fault location, a straight fault scarp immediately north of this stream projects slightly upslope of the west end of our trench and may be the actual location of the active fault trace. Five radiocarbon samples establish age control for the alluvial sequence documented in the trench, which may in the future be useful in constraining the long-term slip rate of the Greenville Fault. The deflection had been caused by an abrupt nontectonic termination of unit u30, a relatively thick (0.15–0.35 m) silt that is more erosion resistant than the adjacent cohesionless sand and gravel. 

Active convergence between the Lesser and Greater Caucasus in Georgia: Constraints on the tectonic evolution of the Lesser-Greater Caucasus continental collision

NASA Astrophysics Data System (ADS)

Sokhadze, G.; Floyd, M.; Godoladze, T.; King, R.; Cowgill, E. S.; Javakhishvili, Z.; Hahubia, G.; Reilinger, R.

2018-01-01

We present and interpret newly determined site motions derived from GPS observations made from 2008 through 2016 in the Republic of Georgia, which constrain the rate and locus of active shortening in the Lesser-Greater Caucasus continental collision zone. Observation sites are located along two ∼160 km-long profiles crossing the Lesser-Greater Caucasus boundary zone: one crossing the Rioni Basin in western Georgia and the other crossing further east near the longitude of Tbilisi. Convergence across the Rioni Basin Profile occurs along the southern margin of the Greater Caucasus, near the surface trace of the north-dipping Main Caucasus Thrust Fault (MCTF) system, and is consistent with strain accumulation on the fault that generated the 1991 MW6.9 Racha earthquake. In contrast, convergence along the Tbilisi Profile occurs near Tbilisi and the northern boundary of the Lesser Caucasus (near the south-dipping Lesser Caucasus Thrust Fault), approximately 50-70 km south of the MCTF, which is inactive within the resolution of geodetic observations (< ± 0.5 mm/yr) at the location of the Tbilisi Profile. We suggest that the southward offset of convergence along strike of the range is related to the incipient collision of the Lesser-Greater Caucasus, and closing of the intervening Kura Basin, which is most advanced along this segment of the collision zone. The identification of active shortening near Tbilisi requires a reevaluation of seismic hazards in this area.

Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment

DOE PAGES

Bond-Lamberty, Benjamin; Bolton, Harvey; Fansler, Sarah J.; ...

2016-03-02

The effects of climate change on soil organic matter—its structure, microbial community, carbon storage, and respiration response—remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampledmore » the original 1994 soil transplants and controls, measuring CO 2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5 °C monthly maximum air temperature, +50 mm yr -1precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. Lastly, these results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.« less

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment.

PubMed

Bond-Lamberty, Ben; Bolton, Harvey; Fansler, Sarah; Heredia-Langner, Alejandro; Liu, Chongxuan; McCue, Lee Ann; Smith, Jeffrey; Bailey, Vanessa

2016-01-01

The effects of climate change on soil organic matter-its structure, microbial community, carbon storage, and respiration response-remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampled the original 1994 soil transplants and controls, measuring CO2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5°C monthly maximum air temperature, +50 mm yr-1 precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. These results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.

Integration of paleoseismic data from multiple sites to develop an objective earthquake chronology: Application to the Weber segment of the Wasatch fault zone, Utah

USGS Publications Warehouse

DuRoss, Christopher B.; Personius, Stephen F.; Crone, Anthony J.; Olig, Susan S.; Lund, William R.

2011-01-01

We present a method to evaluate and integrate paleoseismic data from multiple sites into a single, objective measure of earthquake timing and recurrence on discrete segments of active faults. We apply this method to the Weber segment (WS) of the Wasatch fault zone using data from four fault-trench studies completed between 1981 and 2009. After systematically reevaluating the stratigraphic and chronologic data from each trench site, we constructed time-stratigraphic OxCal models that yield site probability density functions (PDFs) of the times of individual earthquakes. We next qualitatively correlated the site PDFs into a segment-wide earthquake chronology, which is supported by overlapping site PDFs, large per-event displacements, and prominent segment boundaries. For each segment-wide earthquake, we computed the product of the site PDF probabilities in common time bins, which emphasizes the overlap in the site earthquake times, and gives more weight to the narrowest, best-defined PDFs. The product method yields smaller earthquake-timing uncertainties compared to taking the mean of the site PDFs, but is best suited to earthquakes constrained by broad, overlapping site PDFs. We calculated segment-wide earthquake recurrence intervals and uncertainties using a Monte Carlo model. Five surface-faulting earthquakes occurred on the WS at about 5.9, 4.5, 3.1, 1.1, and 0.6 ka. With the exception of the 1.1-ka event, we used the product method to define the earthquake times. The revised WS chronology yields a mean recurrence interval of 1.3 kyr (0.7–1.9-kyr estimated two-sigma [2δ] range based on interevent recurrence). These data help clarify the paleoearthquake history of the WS, including the important question of the timing and rupture extent of the most recent earthquake, and are essential to the improvement of earthquake-probability assessments for the Wasatch Front region.

Integration of paleoseismic data from multiple sites to develop an objective earthquake chronology: Application to the Weber segment of the Wasatch fault zone, Utah

USGS Publications Warehouse

DuRoss, C.B.; Personius, S.F.; Crone, A.J.; Olig, S.S.; Lund, W.R.

2011-01-01

We present a method to evaluate and integrate paleoseismic data from multiple sites into a single, objective measure of earthquake timing and recurrence on discrete segments of active faults. We apply this method to the Weber segment (WS) of the Wasatch fault zone using data from four fault-trench studies completed between 1981 and 2009. After systematically reevaluating the stratigraphic and chronologic data from each trench site, we constructed time-stratigraphic OxCal models that yield site probability density functions (PDFs) of the times of individual earthquakes. We next qualitatively correlated the site PDFs into a segment-wide earthquake chronology, which is supported by overlapping site PDFs, large per-event displacements, and prominent segment boundaries. For each segment-wide earthquake, we computed the product of the site PDF probabilities in common time bins, which emphasizes the overlap in the site earthquake times, and gives more weight to the narrowest, best-defined PDFs. The product method yields smaller earthquake-timing uncertainties compared to taking the mean of the site PDFs, but is best suited to earthquakes constrained by broad, overlapping site PDFs. We calculated segment-wide earthquake recurrence intervals and uncertainties using a Monte Carlo model. Five surface-faulting earthquakes occurred on the WS at about 5.9, 4.5, 3.1, 1.1, and 0.6 ka. With the exception of the 1.1-ka event, we used the product method to define the earthquake times. The revised WS chronology yields a mean recurrence interval of 1.3 kyr (0.7-1.9-kyr estimated two-sigma [2??] range based on interevent recurrence). These data help clarify the paleoearthquake history of the WS, including the important question of the timing and rupture extent of the most recent earthquake, and are essential to the improvement of earthquake-probability assessments for the Wasatch Front region.

Ecological-site based assessments of wind and water erosion: informing management of accelerated soil erosion in rangelands

NASA Astrophysics Data System (ADS)

Webb, N.; Herrick, J.; Duniway, M.

2013-12-01

This work explores how soil erosion assessments can be structured in the context of ecological sites and site dynamics to inform systems for managing accelerated soil erosion. We evaluated wind and water erosion rates for five ecological sites in southern New Mexico, USA, using monitoring data and rangeland-specific wind and water erosion models. Our results show that wind and water erosion can be highly variable within and among ecological sites. Plots in shrub-encroached and shrub-dominated states were consistently susceptible to both wind and water erosion. However, grassland plots and plots with a grass-succulent mix had a high indicated susceptibility to wind and water erosion respectively. Vegetation thresholds for controlling erosion are identified that transcend the ecological sites and their respective states. The thresholds define vegetation cover levels at which rapid (exponential) increases in erosion rates begin to occur, suggesting that erosion in the study ecosystem can be effectively controlled when bare ground cover is <20% of a site or total ground cover is >50%. Similarly, our results show that erosion can be controlled when the cover of canopy interspaces >50 cm in length reaches ~50%, the cover of canopy interspaces >100 cm in length reaches ~35% or the cover of canopy interspaces >150 cm in length reaches ~20%. This process-based understanding can be applied, along with knowledge of the differential sensitivity of vegetation states, to improve erosion management systems. Land use and management activities that alter cover levels such that they cross thresholds, and/or drive vegetation state changes, may increase the susceptibility of sites to erosion. Land use impacts that are constrained within the natural variability of sites should not result in accelerated soil erosion. Evaluating land condition against the erosion thresholds and natural variability of ecological sites will enable improved identification of where and when accelerated soil erosion occurs and the development of practical management solutions.

Straight from the source's mouth; a quantitative study of grain-size export for an entire active rift, the Corinth Rift, central Greece

NASA Astrophysics Data System (ADS)

Watkins, Stephen E.; Whittaker, Alexander C.; Bell, Rebecca E.; Brooke, Sam A. S.; McNeill, Lisa C.; Gawthorpe, Robert L.

2017-04-01

The volumes, grain sizes and characteristics of sediment supplied from source catchments fundamentally controls basin stratigraphy. However, to date, few studies have constrained sediment budgets, including grain size, released into an active rift basin at a regional scale. The Gulf of Corinth, central Greece, is one of the most rapidly extending rifts in the world, with geodetic measurements of 5 mm/yr in the East to 15 mm/yr in the West. It has well-constrained climatic and tectonic boundary conditions and bedrock lithologies are well-characterised. It is therefore an ideal natural laboratory to study the grain-size export for a rift. In the field, we visited the river mouths of 49 catchments draining into the Corinth Gulf, which in total drain 83% of the rift. At each site, hydraulic geometries, surface grain-size of channel bars and full-weighted grain-size distributions of river sediment were obtained. The surface grain-size was measured using the Wolman point count method and the full-weighted grain-size distribution of the bedload by in-situ sieving. In total, approximately 17,000 point counts and 3 tonnes of sediment were processed. The grain-size distributions show an overall increase from East to West on the southern coast of the gulf, with largest grain-sizes exported from the Western rift catchments. D84 ranges from 20 to 110 mm, however 50% of D84 grain-sizes are less than 40 mm. Subsequently, we derived the full Holocene sediment budget for the Corinth Gulf by combining our grain size data with catchment sediment fluxes, constrained using the BQART model and calibrated to known Holocene sediment volumes in the basin from seismic data (c.f. Watkins et al., in review). This is the first time such a budget has been derived for the Corinth Rift. Finally, our estimates of sediment budgets and grain sizes were compared to regional uplift constraints, fault distributions, slip rates and lithology to identify the relative importance of these controls on sediment supply to the basin.

Working with Toronto neighbourhoods toward developing indicators of community capacity.

PubMed

Jackson, Suzanne F; Cleverly, Shelley; Poland, Blake; Burman, David; Edwards, Richard; Robertson, Ann

2003-12-01

Often the goal of health and social development agencies is to assess communities and work with them to improve community capacity. Particularly for health promoters working in community settings and to ensure consistency in the definition of health promotion, the evaluation of health promotion programmes should be based on strengths and assets, yet existing information for planning and evaluation purposes usually focuses on problems and deficits. A model and definition of community capacity, grounded in community experience and focusing on strengths and assets, was developed following a 4-year, multi-site, qualitative, action research project in four Toronto neighbourhoods. There was significant community involvement in the four Community Advisory Committees, one for each study site. Semi-structured, open-ended interviews and focus groups were conducted with 161 residents and agency workers identified by the Community Advisory Committees. The data were analyzed with the assistance of NUDIST software. Thematic analysis was undertaken in two stages: (i) within each site and (ii) across sites, with the latter serving as the basis for the development of indicators of community capacity. This paper presents a summary of the research, the model and the proposed indicators. The model locates talents and skills of community members in a larger context of socioenvironmental conditions, both inside and outside the community, which can act to enable or constrain the expression of these talents and skills. The significance of the indicators of community capacity proposed in the study is that they focus on identifying and measuring the facilitating and constraining socioenvironmental conditions.

Emissions from prescribed fires in temperate forest in south-east Australia: implications for carbon accounting

NASA Astrophysics Data System (ADS)

Possell, M.; Jenkins, M.; Bell, T. L.; Adams, M. A.

2015-01-01

We estimated emissions of carbon, as equivalent CO2 (CO2e), from planned fires in four sites in a south-eastern Australian forest. Emission estimates were calculated using measurements of fuel load and carbon content of different fuel types, before and after burning, and determination of fuel-specific emission factors. Median estimates of emissions for the four sites ranged from 20 to 139 Mg CO2e ha-1. Variability in estimates was a consequence of different burning efficiencies of each fuel type from the four sites. Higher emissions resulted from more fine fuel (twigs, decomposing matter, near-surface live and leaf litter) or coarse woody debris (CWD; > 25 mm diameter) being consumed. In order to assess the effect of declining information quantity and the inclusion of coarse woody debris when estimating emissions, Monte Carlo simulations were used to create seven scenarios where input parameters values were replaced by probability density functions. Calculation methods were (1) all measured data were constrained between measured maximum and minimum values for each variable; (2) as in (1) except the proportion of carbon within a fuel type was constrained between 0 and 1; (3) as in (2) but losses of mass caused by fire were replaced with burning efficiency factors constrained between 0 and 1; and (4) emissions were calculated using default values in the Australian National Greenhouse Accounts (NGA), National Inventory Report 2011, as appropriate for our sites. Effects of including CWD in calculations were assessed for calculation Method 1, 2 and 3 but not for Method 4 as the NGA does not consider this fuel type. Simulations demonstrate that the probability of estimating true median emissions declines strongly as the amount of information available declines. Including CWD in scenarios increased uncertainty in calculations because CWD is the most variable contributor to fuel load. Inclusion of CWD in scenarios generally increased the amount of carbon lost. We discuss implications of these simulations and how emissions from prescribed burns in temperate Australian forests could be improved.

Fluid Geochemistry of the Capelinhos Vent Site. A Key to Understand the Lucky Strike Hydrothermal Vent Field (37°N, MAR).

NASA Astrophysics Data System (ADS)

Leleu, T.; Chavagnac, V.; Cannat, M.; Ceuleneer, G.; Castillo, A.; Menjot, L.

2015-12-01

The Lucky Strike hydrothermal field is situated at the mid-Atlantic ridge, south of the Azores, on top of a central volcano within the axial valley. The volcano is composed of a fossil lava lake surrounded by three volcanic cones. An Axial Magma Chamber (AMC) is reported 3.4km below the seafloor. The active venting sites are situated around the fossil lava lake and are directly linked to the heat supplied by the AMC. High temperature fluids from the Lucky Strike field were sampled in 2013, 2014 and 2015 in order to document the depth of the reaction zone, subsurface mixing, geographical control and magmatic degassing. A new active site named Capelinhos was discovered approximately 1.5km eastward from the lava lake, during exploration by ROV Victor6000 - MoMARsat cruise, 2013. It is composed of 10m-high chimneys discharging black smoker-type fluid. Fluid temperatures were 328°C in 2013 and decreased to 318°C in 2014 and 2015. Capelinhos fluids are Cl-depleted by 55% compared to seawater indicating phase separation at depth. In comparison, the other sites range from 6% enrichment (2608/Y3 site) to 22% depletion (Eiffel tower site). Si geothermobarometry of Y3 site estimates quartz equilibration at P=300 bars and T=360-380°C, coherent with Fe/Mn geothermometer (T=370±10°C). For Capelinhos, Fe/Mn suggests 398°C (±10°C) which is close to the critical point of seawater (P=300 bars and T=407°C). Other geothermobarometer uses Si/Cl vapor-like fluid to constrain depth of the top of reaction zone and predicts significant bias due to mixing along the up-flow zone. Application gives P=~370 bars, T=~435°C at Capelinhos and P=~390 bars, T=~440°C at Eiffel tower. This is further sustained by end-member 87Sr/86Sr=0.7038, which indicates little interaction of Capelinhos vent fluids with seawater-derived fluid, compared to other vapor-like sites with 87Sr/86Sr=0.7043. Because of its external location, Capelinhos site isn't influenced by the complex tectonic context of the lava lake.

Postglacial Rebound and Current Ice Loss Estimates from Space Geodesy: The New ICE-6G (VM5a) Global Model

NASA Astrophysics Data System (ADS)

Peltier, W. R.; Argus, D.; Drummond, R.; Moore, A. W.

2012-12-01

We compare, on a global basis, estimates of site velocity against predictions of the newly constructed postglacial rebound model ICE-6G (VM5a). This model is fit to observations of North American postglacial rebound thereby demonstrating that the ice sheet at last glacial maximum must have been, relative to ICE-5G,thinner in southern Manitoba, thinner near Yellowknife (northwest Territories), thicker in eastern and southern Quebec, and thicker along the British Columbia-Alberta border. The GPS based estimates of site velocity that we employ are more accurate than were previously available because they are based on GPS estimates of position as a function of time determined by incorporating satellite phase center variations [Desai et al. 2011]. These GPS estimates are constraining postglacial rebound in North America and Europe more tightly than ever before. In particular, given the high density of GPS sites in North America, and the fact that the velocity of the mass center (CM) of Earth is also more tightly constrained, the new model much more strongly constrains both the lateral extent of the proglacial forebulge and the rate at which this peripheral bulge (that was emplaced peripheral to the late Pleistocence Laurentia ice sheet) is presently collapsing. This fact proves to be important to the more accurate inference of the current rate of ice loss from both Greenland and Alaska based upon the time dependent gravity observations being provided by the GRACE satellite system. In West Antarctica we have also been able to significantly revise the previously prevalent ICE-5G deglaciation history so as to enable its predictions to be optimally consistent with GPS site velocities determined by connecting campaign WAGN measurements to those provided by observations from the permanent ANET sites. Ellsworth Land (south of the Antarctic peninsula), is observed to be rising at 6 ±3 mm/yr according to our latest analyses; the Ellsworth mountains themselves are observed to be rising at 5 ±4 mm/yr; Palmer Land is observed to be rising at 3 ±3 mm/yr. The predictions of the ICE-5G (VM2) model and those of the postglacial rebound component of the model of Simons, Ivins, and James [2010] had predicted uplift to be significantly faster than observed in this region, as previously documented in Argus et al [2011]. From a global perspective the new ICE-6G (VM5a) model is also a further significant improvement on the previous ICE-5G (VM2) model in that the degree two and order one components of its predicted time dependence of geoid height are tightly constrained by the recent inferences of Roy and Peltier [2011] of the post-GRACE-launch values of the speed and direction of true polar wander and the non-tidal acceleration of the lod. .

The November 2017 Mw 5.5 Pohang earthquake: A possible case of induced seismicity in South Korea

NASA Astrophysics Data System (ADS)

Grigoli, F.; Cesca, S.; Rinaldi, A. P.; Manconi, A.; López-Comino, J. A.; Clinton, J. F.; Westaway, R.; Cauzzi, C.; Dahm, T.; Wiemer, S.

2018-06-01

The moment magnitude (Mw) 5.5 earthquake that struck South Korea in November 2017 was one of the largest and most damaging events in that country over the past century. Its proximity to an enhanced geothermal system site, where high-pressure hydraulic injection had been performed during the previous 2 years, raises the possibility that this earthquake was anthropogenic. We have combined seismological and geodetic analyses to characterize the mainshock and its largest aftershocks, constrain the geometry of this seismic sequence, and shed light on its causal factors. According to our analysis, it seems plausible that the occurrence of this earthquake was influenced by the aforementioned industrial activities. Finally, we found that the earthquake transferred static stress to larger nearby faults, potentially increasing the seismic hazard in the area.

Variability of Kelvin wave momentum flux from high-resolution radiosonde and radio occultation data

NASA Astrophysics Data System (ADS)

Sjoberg, J. P.; Zeng, Z.; Ho, S. P.; Birner, T.; Anthes, R. A.; Johnson, R. H.

2017-12-01

Direct measurement of momentum flux from Kelvin waves in the stratosphere remains challenging. Constraining this flux from observations is an important step towards constraining the flux from models. Here we present results from analyses using linear theory to estimate the Kelvin wave amplitudes and momentum fluxes from both high-resolution radiosondes and from radio occultation (RO) data. These radiosonde data are from a contiguous 11-year span of soundings performed at two Department of Energy Atmospheric Radiation Measurement sites, while the RO data span 14 years from multiple satellite missions. Daily time series of the flux from both sources are found to be in quantitative agreement with previous studies. Climatological analyses of these data reveal the expected seasonal cycle and variability associated with the quasi-biennial oscillation. Though both data sets provide measurements on distinct spatial and temporal scales, the estimated flux from each provides insight into separate but complimentary aspects of how the Kelvin waves affect the stratosphere. Namely, flux derived from radiosonde sites provide details on the regional Kelvin wave variability, while the flux from RO data are zonal mean estimates.

Ecological site-based assessments of wind and water erosion: informing accelerated soil erosion management in rangelands

USGS Publications Warehouse

Webb, Nicholas P.; Herrick, Jeffrey E.; Duniway, Michael C.

2014-01-01

Accelerated soil erosion occurs when anthropogenic processes modify soil, vegetation or climatic conditions causing erosion rates at a location to exceed their natural variability. Identifying where and when accelerated erosion occurs is a critical first step toward its effective management. Here we explore how erosion assessments structured in the context of ecological sites (a land classification based on soils, landscape setting and ecological potential) and their vegetation states (plant assemblages that may change due to management) can inform systems for reducing accelerated soil erosion in rangelands. We evaluated aeolian horizontal sediment flux and fluvial sediment erosion rates for five ecological sites in southern New Mexico, USA, using monitoring data and rangeland-specific wind and water erosion models. Across the ecological sites, plots in shrub-encroached and shrub-dominated vegetation states were consistently susceptible to aeolian sediment flux and fluvial sediment erosion. Both processes were found to be highly variable for grassland and grass-succulent states across the ecological sites at the plot scale (0.25 Ha). We identify vegetation thresholds that define cover levels below which rapid (exponential) increases in aeolian sediment flux and fluvial sediment erosion occur across the ecological sites and vegetation states. Aeolian sediment flux and fluvial erosion in the study area can be effectively controlled when bare ground cover is 100 cm in length is less than ~35%. Land use and management activities that alter cover levels such that they cross thresholds, and/or drive vegetation state changes, may increase the susceptibility of areas to erosion. Land use impacts that are constrained within the range of natural variability should not result in accelerated soil erosion. Evaluating land condition against the erosion thresholds identified here will enable identification of areas susceptible to accelerated soil erosion and the development of practical management solutions.

Value, Cost, and Sharing: Open Issues in Constrained Clustering

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri L.

2006-01-01

Clustering is an important tool for data mining, since it can identify major patterns or trends without any supervision (labeled data). Over the past five years, semi-supervised (constrained) clustering methods have become very popular. These methods began with incorporating pairwise constraints and have developed into more general methods that can learn appropriate distance metrics. However, several important open questions have arisen about which constraints are most useful, how they can be actively acquired, and when and how they should be propagated to neighboring points. This position paper describes these open questions and suggests future directions for constrained clustering research.

Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.

PubMed

Horowitz, Scott; Dirk, Lynnette M A; Yesselman, Joseph D; Nimtz, Jennifer S; Adhikari, Upendra; Mehl, Ryan A; Scheiner, Steve; Houtz, Robert L; Al-Hashimi, Hashim M; Trievel, Raymond C

2013-10-16

S-adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer mechanism remain undefined. A survey of high-resolution crystal structures reveals that unconventional carbon-oxygen (CH···O) hydrogen bonds coordinate the AdoMet methyl group in different methyltransferases irrespective of their class, active site structure, or cofactor binding conformation. Corroborating these observations, quantum chemistry calculations demonstrate that these charged interactions formed by the AdoMet sulfonium cation are stronger than typical CH···O hydrogen bonds. Biochemical and structural studies using a model lysine methyltransferase and an active site mutant that abolishes CH···O hydrogen bonding to AdoMet illustrate that these interactions are important for high-affinity AdoMet binding and transition-state stabilization. Further, crystallographic and NMR dynamics experiments of the wild-type enzyme demonstrate that the CH···O hydrogen bonds constrain the motion of the AdoMet methyl group, potentially facilitating its alignment during catalysis. Collectively, the experimental findings with the model methyltransferase and structural survey imply that methyl CH···O hydrogen bonding represents a convergent evolutionary feature of AdoMet-dependent methyltransferases, mediating a universal mechanism for methyl transfer.

A Network of Hydrophobic Residues Impeding Helix αC Rotation Maintains Latency of Kinase Gcn2, Which Phosphorylates the α Subunit of Translation Initiation Factor 2▿

PubMed Central

Gárriz, Andrés; Qiu, Hongfang; Dey, Madhusudan; Seo, Eun-Joo; Dever, Thomas E.; Hinnebusch, Alan G.

2009-01-01

Kinase Gcn2 is activated by amino acid starvation and downregulates translation initiation by phosphorylating the α subunit of translation initiation factor 2 (eIF2α). The Gcn2 kinase domain (KD) is inert and must be activated by tRNA binding to the adjacent regulatory domain. Previous work indicated that Saccharomyces cerevisiae Gcn2 latency results from inflexibility of the hinge connecting the N and C lobes and a partially obstructed ATP-binding site in the KD. Here, we provide strong evidence that a network of hydrophobic interactions centered on Leu-856 also promotes latency by constraining helix αC rotation in the KD in a manner relieved during amino acid starvation by tRNA binding and autophosphorylation of Thr-882 in the activation loop. Thus, we show that mutationally disrupting the hydrophobic network in various ways constitutively activates eIF2α phosphorylation in vivo and bypasses the requirement for a key tRNA binding motif (m2) and Thr-882 in Gcn2. In particular, replacing Leu-856 with any nonhydrophobic residue activates Gcn2, while substitutions with various hydrophobic residues maintain kinase latency. We further provide strong evidence that parallel, back-to-back dimerization of the KD is a step on the Gcn2 activation pathway promoted by tRNA binding and autophosphorylation. Remarkably, mutations that disrupt the L856 hydrophobic network or enhance hinge flexibility eliminate the need for the conserved salt bridge at the parallel dimer interface, implying that KD dimerization facilitates the reorientation of αC and remodeling of the active site for enhanced ATP binding and catalysis. We propose that hinge remodeling, parallel dimerization, and reorientation of αC are mutually reinforcing conformational transitions stimulated by tRNA binding and secured by the ensuing autophosphorylation of T882 for stable kinase activation. PMID:19114556

A network of hydrophobic residues impeding helix alphaC rotation maintains latency of kinase Gcn2, which phosphorylates the alpha subunit of translation initiation factor 2.

PubMed

Gárriz, Andrés; Qiu, Hongfang; Dey, Madhusudan; Seo, Eun-Joo; Dever, Thomas E; Hinnebusch, Alan G

2009-03-01

Kinase Gcn2 is activated by amino acid starvation and downregulates translation initiation by phosphorylating the alpha subunit of translation initiation factor 2 (eIF2alpha). The Gcn2 kinase domain (KD) is inert and must be activated by tRNA binding to the adjacent regulatory domain. Previous work indicated that Saccharomyces cerevisiae Gcn2 latency results from inflexibility of the hinge connecting the N and C lobes and a partially obstructed ATP-binding site in the KD. Here, we provide strong evidence that a network of hydrophobic interactions centered on Leu-856 also promotes latency by constraining helix alphaC rotation in the KD in a manner relieved during amino acid starvation by tRNA binding and autophosphorylation of Thr-882 in the activation loop. Thus, we show that mutationally disrupting the hydrophobic network in various ways constitutively activates eIF2alpha phosphorylation in vivo and bypasses the requirement for a key tRNA binding motif (m2) and Thr-882 in Gcn2. In particular, replacing Leu-856 with any nonhydrophobic residue activates Gcn2, while substitutions with various hydrophobic residues maintain kinase latency. We further provide strong evidence that parallel, back-to-back dimerization of the KD is a step on the Gcn2 activation pathway promoted by tRNA binding and autophosphorylation. Remarkably, mutations that disrupt the L856 hydrophobic network or enhance hinge flexibility eliminate the need for the conserved salt bridge at the parallel dimer interface, implying that KD dimerization facilitates the reorientation of alphaC and remodeling of the active site for enhanced ATP binding and catalysis. We propose that hinge remodeling, parallel dimerization, and reorientation of alphaC are mutually reinforcing conformational transitions stimulated by tRNA binding and secured by the ensuing autophosphorylation of T882 for stable kinase activation.

Combining active and passive seismic methods for the characterization of urban sites in Cairo, Egypt

NASA Astrophysics Data System (ADS)

Adly, Ashraf; Poggi, Valerio; Fäh, Donat; Hassoup, Awad; Omran, Awad

2017-07-01

The geology at Kottamiya, Rehab City and Zahraa-Madinat-Nasr to the East of Cairo (Egypt) is composed of low-velocity sediments on top of a rigid rock basement. Such sediments include the loose sands of the Gebel Ahmar formation, marl and shales of Maadi formation, in addition to sparse quaternary soil covers. Due to the contrast of the seismic impedance with the underlying bedrock, these soft sediments have the potential of considerably amplifying the ground motion during an earthquake. For the evaluation of site-specific seismic hazard, we computed the seismic site response in these areas by developing 1-D velocity models and derived average seismic velocities, including Vs30. To do that, we applied different active and passive source techniques, including the horizontal to vertical Fourier spectral ratio of ambient vibration recordings and multichannel analysis of artificially generated surface waves. A set of models representing the velocity structure of the site is then obtained by combined inversion of Rayleigh wave dispersion curves and ellipticity functions. While dispersion curves are used to constrain the uppermost low-velocity part of the soil profile, ellipticity helps in resolving the structure at the depth of the sediment-bedrock interface. From the retrieved velocity models, numerical ground-motion amplification is finally derived using 1-D SH-wave transfer function. We account for uncertainty in amplification by using a statistical model that accounts for the misfit of all the inverted velocity profiles. The study reveals that the different sites experience an important frequency-dependent amplification, with largest amplification occurring at the resonance frequencies of the sites. Amplification up to a factor of 5 is found, with some variability depending on the soil type (Vs30 ranges between 340 and 415 m s-2). Moreover, amplification is expected in the frequency range that is important for buildings (0.8-10 Hz), which is additional confirmation for the need of microzonation analysis of the area. The obtained results will be used for the development of a new seismic hazard model.

Modeling and stabilization results for a charge or current-actuated active constrained layer (ACL) beam model with the electrostatic assumption

NASA Astrophysics Data System (ADS)

Özer, Ahmet Özkan

2016-04-01

An infinite dimensional model for a three-layer active constrained layer (ACL) beam model, consisting of a piezoelectric elastic layer at the top and an elastic host layer at the bottom constraining a viscoelastic layer in the middle, is obtained for clamped-free boundary conditions by using a thorough variational approach. The Rao-Nakra thin compliant layer approximation is adopted to model the sandwich structure, and the electrostatic approach (magnetic effects are ignored) is assumed for the piezoelectric layer. Instead of the voltage actuation of the piezoelectric layer, the piezoelectric layer is proposed to be activated by a charge (or current) source. We show that, the closed-loop system with all mechanical feedback is shown to be uniformly exponentially stable. Our result is the outcome of the compact perturbation argument and a unique continuation result for the spectral problem which relies on the multipliers method. Finally, the modeling methodology of the paper is generalized to the multilayer ACL beams, and the uniform exponential stabilizability result is established analogously.

Near Surface Seismic Hazard Characterization in the Presence of High Velocity Contrasts

NASA Astrophysics Data System (ADS)

Gribler, G.; Mikesell, D.; Liberty, L. M.

2017-12-01

We present new multicomponent surface wave processing techniques that provide accurate characterization of near-surface conditions in the presence of large lateral or vertical shear wave velocity boundaries. A common problem with vertical component Rayleigh wave analysis in the presence of high contrast subsurface conditions is Rayleigh wave propagation mode misidentification due to an overlap of frequency-phase velocity domain dispersion, leading to an overestimate of shear wave velocities. By using the vertical and horizontal inline component signals, we isolate retrograde and prograde particle motions to separate fundamental and higher mode signals, leading to more accurate and confident dispersion curve picks and shear wave velocity estimates. Shallow, high impedance scenarios, such as the case with shallow bedrock, are poorly constrained when using surface wave dispersion information alone. By using a joint inversion of dispersion and horizontal-to-vertical (H/V) curves within active source frequency ranges (down to 3 Hz), we can accurately estimate the depth to high impedance boundaries, a significant improvement compared to the estimates based on dispersion information alone. We compare our approach to body wave results that show comparable estimates of bedrock topography. For lateral velocity contrasts, we observe horizontal polarization of Rayleigh waves identified by an increase in amplitude and broadening of the horizontal spectra with little variation in the vertical component spectra. The horizontal spectra offer a means to identify and map near surface faults where there is no topographic or clear body wave expression. With these new multicomponent active source seismic data processing and inversion techniques, we better constrain a variety of near surface conditions critical to the estimation of local site response and seismic hazards.

Constraining Holocene hydrological changes in the Carpathian-Balkan region using speleothem δ18O and pollen-based temperature reconstructions

NASA Astrophysics Data System (ADS)

Drăguşin, V.; Staubwasser, M.; Hoffmann, D. L.; Ersek, V.; Onac, B. P.; Veres, D.

2014-07-01

Here we present a speleothem isotope record (POM2) from Ascunsă Cave (Romania) that provides new data on past climate changes in the Carpathian-Balkan region from 8.2 ka until the present. This paper describes an approach to constrain the effect of temperature changes on calcite δ18O values in stalagmite POM2 over the course of the middle Holocene (6-4 ka), and across the 8.2 and 3.2 ka rapid climate change events. Independent pollen temperature reconstructions are used to this purpose. The approach combines the temperature-dependent isotope fractionation of rain water during condensation and fractionation resulting from calcite precipitation at the given cave temperature. The only prior assumptions are that pollen-derived average annual temperature reflects average cave temperature, and that pollen-derived coldest and warmest month temperatures reflect the range of condensation temperatures of rain above the cave site. This approach constrains a range of values between which speleothem δ18O changes should be found if controlled only by surface temperature variations at the cave site. Deviations of the change in δ18Ocspel values from the calculated temperature-constrained range of change are interpreted towards large-scale variability of climate-hydrology. Following this approach, we show that an additional ∼0.6‰ enrichment of δ18Oc in the POM2 stalagmite was caused by changing hydrological patterns in SW Romania across the middle Holocene, most likely comprising local evaporation from the soil and an increase in Mediterranean moisture δ18O. Further, by extending the calculations to other speleothem records from around the entire Mediterranean basin, it appears that all eastern Mediterranean speleothems recorded a similar isotopic enrichment due to changing hydrology, whereas all changes recorded in speleothems from the western Mediterranean are fully explained by temperature variation alone. This highlights a different hydrological evolution between the two sides of the Mediterranean. Our results also demonstrate that during the 8.2 ka event, POM2 stable isotope data essentially fit the temperature-constrained isotopic variability. In the case of the 3.2 ka event, an additional climate-related hydrological factor is more evident. This implies a different rainfall pattern in the Southern Carpathian region during this event at the end of the Bronze Age.

Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework.

PubMed

Giovannelli, Edoardo; Procacci, Piero; Cardini, Gianni; Pagliai, Marco; Volkov, Victor; Chelli, Riccardo

2017-12-12

The fast-switching decoupling method is a powerful nonequilibrium technique to compute absolute binding free energies of ligand-receptor complexes (Sandberg et al., J. Chem. Theory Comput. 2014, 11, 423-435). Inspired by the theory of noncovalent binding association of Gilson and co-workers (Biophys. J. 1997, 72, 1047-1069), we develop two approaches, termed binded-domain and single-point alchemical-path schemes (BiD-AP and SiP-AP), based on the possibility of performing alchemical trajectories during which the ligand is constrained to fixed positions relative to the receptor. The BiD-AP scheme exploits a recent generalization of nonequilibrium work theorems to estimate the free energy difference between the coupled and uncoupled states of the ligand-receptor complex. With respect to the fast-switching decoupling method without constraints, BiD-AP prevents the ligand from leaving the binding site, but still requires an estimate of the positional binding-site volume, which may not be a simple task. On the other side, the SiP-AP scheme allows avoidance of the calculation of the binding-site volume by introducing an additional equilibrium simulation of ligand and receptor in the bound state. In the companion article (DOI: 10.1021/acs.jctc.7b00595), we show that the extra computational effort required by SiP-AP leads to a significant improvement of accuracy in the free energy estimates.

Meter-scale slopes of candidate MER landing sites from point photoclinometry

USGS Publications Warehouse

Beyer, R.A.; McEwen, A.S.; Kirk, R.L.

2003-01-01

Photoclinometry was used to analyze the small-scale roughness of areas that fall within the proposed Mars Exploration Rover (MER) 2003 landing ellipses. The landing ellipses presented in this study were those in Athabasca Valles, Elysium Planitia, Eos Chasma, Gusev Crater, Isidis Planitia, Melas Chasma, and Meridiani Planum. We were able to constrain surface slopes on length scales comparable to the image resolution (1.5 to 12 m/pixel). The MER 2003 mission has various engineering constraints that each candidate landing ellipse must satisfy. These constraints indicate that the statistical slope values at 5 m baselines are an important criterion. We used our technique to constrain maximum surface slopes across large swaths of each image, and built up slope statistics for the images in each landing ellipse. We are confident that all MER 2003 landing site ellipses in this study, with the exception of the Melas Chasma ellipse, are within the small-scale roughness constraints. Our results have provided input into the landing hazard assessment process. In addition to evaluating the safety of the landing sites, our mapping of small-scale roughnesses can also be used to better define and map morphologic units. The morphology of a surface is characterized by the slope distribution and magnitude of slopes. In looking at how slopes are distributed, we can better define landforms and determine the boundaries of morphologic units. Copyright 2003 by the American Geophysical Union.

Effect of environmental conditions on the relationship between solar-induced fluorescence and gross primary productivity at an OzFlux grassland site

NASA Astrophysics Data System (ADS)

Verma, Manish; Schimel, David; Evans, Bradley; Frankenberg, Christian; Beringer, Jason; Drewry, Darren T.; Magney, Troy; Marang, Ian; Hutley, Lindsay; Moore, Caitlin; Eldering, Annmarie

2017-03-01

Recent studies have utilized coarse spatial and temporal resolution remotely sensed solar-induced fluorescence (SIF) for modeling terrestrial gross primary productivity (GPP) at regional scales. Although these studies have demonstrated the potential of SIF, there have been concerns about the ecophysiological basis of the relationship between SIF and GPP in different environmental conditions. Launched in 2014, the Orbiting Carbon Observatory-2 (OCO-2) has enabled fine-scale (1.3 by 2.5 km) retrievals of SIF that are comparable with measurements recorded at eddy covariance towers. In this study, we examine the effect of environmental conditions on the relationship of OCO-2 SIF with tower GPP over the course of a growing season at a well-characterized natural grassland site. Combining OCO-2 SIF and eddy covariance tower data with a canopy radiative transfer and an ecosystem model, we also assess the potential of OCO-2 SIF to constrain the estimates of Vcmax, one of the most important parameters in ecosystem models. Based on the results, we suggest that although environmental conditions play a role in determining the nature of relationship between SIF and GPP, overall, the linear relationship is more robust at ecosystem scale than the theory based on leaf-level processes might suggest. Our study also shows that the ability of SIF to constrain Vcmax is weak at the selected site.

Constraining Puerto Rico - Virgin Islands microplate internal deformation with two decades of GPS observations

NASA Astrophysics Data System (ADS)

Lopez, A. M.; Jansma, P. E.; Mattioli, G. S.; James, S. A.; Ihemedu, D.; Quintana, S. M.; Salazar, J. S.

2011-12-01

The Puerto Rico - Virgin Island microplate, a crustal block within the deformation region of the Northern Caribbean Plate Boundary Zone has been monitored with campaign and permanent Global Positioning System stations for almost 20 years. Within this time period a total of 37 sites have been used to describe and quantify internal deformation of the plate and estimate elastic strain accumulation along the key geological bounding features. In June 2011, 12 of the 20 sites that comprise the campaign GPS network in Puerto Rico were re-occupied and their results were merged with at least three years of continuous GPS data from the Puerto Rico - Virgin Islands cGPS network. The remaining 8 in PR sites will be reoccupied soon, while sites from the Virgin Islands were last reoccupied in 2007. All data were processed with v5 of GOAII using an APP strategy. Here we present the latest results of the newly computed velocity field of our mixed network in both North America and Caribbean fixed frames employing the latest IGS05 reference frame and updated satellite orbits, earth orientation, and xfiles from JPL. Of particular importance in this study are the results of a three station transect across the Lajas Valley, the most seismically active area on southwestern Puerto Rico. Relative to a fixed velocity for a campaign site on Isla Magueyes in La Parguera, the southernmost site in the Lajas Valley has a residual motion of -4.38±1.39 and 2.41±2.10 mm/yr in the north and east components, respectively. This suggests that there is SSE-directed shortening across a structure located between these two sites. In contrast, sites near Mayagüez are moving toward SW at ˜2 mm/yr relative to La Parguera. These results demonstrate the PRVI block shows small internal deformation in addition to its generally westward rigid block translation relative the stable interior of the Caribbean plate.

An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair

PubMed Central

Ramezanpour, Mohsen; Lee, Jaeyong; Taneva, Svetla G.; Tieleman, D. Peter; Cornell, Rosemary B.

2018-01-01

The activity of CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme in phosphatidylcholine synthesis, is regulated by reversible interactions of a lipid-inducible amphipathic helix (domain M) with membrane phospholipids. When dissociated from membranes, a portion of the M domain functions as an auto-inhibitory (AI) element to suppress catalysis. The AI helix from each subunit binds to a pair of α helices (αE) that extend from the base of the catalytic dimer to create a four-helix bundle. The bound AI helices make intimate contact with loop L2, housing a key catalytic residue, Lys122. The impacts of the AI helix on active-site dynamics and positioning of Lys122 are unknown. Extensive MD simulations with and without the AI helix revealed that backbone carbonyl oxygens at the point of contact between the AI helix and loop L2 can entrap the Lys122 side chain, effectively competing with the substrate, CTP. In silico, removal of the AI helices dramatically increased αE dynamics at a predicted break in the middle of these helices, enabling them to splay apart and forge new contacts with loop L2. In vitro cross-linking confirmed the reorganization of the αE element upon membrane binding of the AI helix. Moreover, when αE bending was prevented by disulfide engineering, CCT activation by membrane binding was thwarted. These findings suggest a novel two-part auto-inhibitory mechanism for CCT involving capture of Lys122 and restraint of the pliable αE helices. We propose that membrane binding enables bending of the αE helices, bringing the active site closer to the membrane surface. PMID:29519816

Exploring the Connection between Parsec-scale Jet Activity and Broadband Outbursts in 3C 279

NASA Astrophysics Data System (ADS)

Rani, B.; Jorstad, S. G.; Marscher, A. P.; Agudo, I.; Sokolovsky, K. V.; Larionov, V. M.; Smith, P.; Mosunova, D. A.; Borman, G. A.; Grishina, T. S.; Kopatskaya, E. N.; Mokrushina, A. A.; Morozova, D. A.; Savchenko, S. S.; Troitskaya, Yu. V.; Troitsky, I. S.; Thum, C.; Molina, S. N.; Casadio, C.

2018-05-01

We use a combination of high-resolution very long baseline interferometry (VLBI) radio and multiwavelength flux density and polarization observations to constrain the physics of the dissipation mechanism powering the broadband flares in 3C 279 during an episode of extreme flaring activity in 2013–2014. Six bright flares superimposed on a long-term outburst are detected at γ-ray energies. Four of the flares have optical and radio counterparts. The two modes of flaring activity (faster flares sitting on top of a long-term outburst) present at radio, optical, and γ-ray frequencies are missing in X-rays. X-ray counterparts are only observed for two flares. The first three flares are accompanied by ejection of a new VLBI component (NC2), suggesting the 43 GHz VLBI core as the site of energy dissipation. Another new component, NC3, is ejected after the last three flares, which suggests that the emission is produced upstream from the core (closer to the black hole). The study therefore indicates multiple sites of energy dissipation in the source. An anticorrelation is detected between the optical percentage polarization (PP) and optical/γ-ray flux variations, while the PP has a positive correlation with optical/γ-ray spectral indices. Given that the mean polarization is inversely proportional to the number of cells in the emission region, the PP versus optical/γ-ray anticorrelation could be due to more active cells during the outburst than at other times. In addition to the turbulent component, our analysis suggests the presence of a combined turbulent and ordered magnetic field, with the ordered component transverse to the jet axis.

Multi-Sensor Systems Development for UXO Detection and Discrimination: Man-Portable Dual Magnetic/Electromagnetic Induction Sensor

DTIC Science & Technology

2008-02-01

of the magnetic data to constrain the target depth using joint or cooperative inversions ( Pasion et al. 2002). ERDC/EL TR-08-9 24 Figure 15. EM...baseline ordnance classification test site at Blossom Pt. Naval Research Laboratory. NRL/MR/6110-00-8437, March 20, 1998. Pasion , L., S. Billings, and

Bering Sea Nd isotope records of North Pacific Intermediate Water circulation

NASA Astrophysics Data System (ADS)

Rabbat, C.; Knudson, K. P.; Goldstein, S. L.

2017-12-01

North Pacific Intermediate Water (NPIW) is the primary water mass associated with Pacific meridional overturning circulation. While the relationship between Atlantic meridional overturning circulation and climate has been extensively studied, a lack of suitable sediment cores has limited past investigations of North Pacific climate and NPIW variability. Integrated Ocean Drilling Program Site U1342 (818 m water depth) on Bower's Ridge in the Bering Sea is located at a sensitive depth for detecting changes in NPIW, and it is the only available sub-arctic North Pacific site that offers long, continuous core recovery, relatively high sedimentation rates, excellent foraminifera preservation, and a well-constrained age model over multiple glacial-interglacial cycles. Previous work at Site U1342 from Knudson and Ravelo (2015), using non-quantitative circulation proxies, provides evidence for enhanced NPIW formation during extreme glacials associated with the closure of the Bering Strait and suggest that NPIW was formed locally within the Bering Sea. Our work builds on the potential importance of these results and applies more robust and potentially quantitative circulation proxies to constrain NPIW variability. Here, we present new records of NPIW circulation from Site U1342 based on Nd isotope analyses on fish debris and Fe-Mn encrusted foraminifera, which serve as semi-quantitative "water mass tracers." Weak Bering Sea NPIW formation and ventilation are reflected by relatively lower eNd values indicative of open subarctic North Pacific waters, which are presently predominant, whereas enhanced Bering Sea NPIW formation and ventilation are be reflected by relatively higher eNd values due to the input of Nd from regional volcanic rocks.

Intertidal biological indicators of coseismic subsidence during the Mw 7.8 Haida Gwaii, Canada, earthquake

USGS Publications Warehouse

Haeussler, Peter J.; Witter, Robert C.; Wang, Kelin

2015-01-01

The 28 October 2012 Mw 7.8 Haida Gwaii earthquake was a megathrust earthquake along the very obliquely convergent Queen Charlotte margin of British Columbia, Canada. Coseismic deformation is not well constrained by geodesy, with only six Global Positioning System (GPS) sites and two tide gauge stations within 250 km of the rupture area. To better constrain vertical coseismic deformation, we measured the upper growth limits of two sessile intertidal organisms, which are controlled by physical conditions, relative to sea level at 25 sites 5 months after the earthquake. We measured the positions of rockweed (Fucus distichus, 617 observations) and the common acorn barnacle (Balanus balanoides, 686 observations). The study focused on the western side of the islands where rupture models indicated that the greatest amount of vertical displacement, but we also investigated sites well away from the inferred rupture area to provide a control on the upper limit of the organisms unaffected by vertical displacement. We also made 322 measurements of sea level to relate the growth limits to a tidal datum using the TPXO7.2 tidal model, rather than ellipsoid heights determined by GPS. Three methods of examining the data all indicate 0.4–0.6 m subsidence along the western coast of Moresby Island as a result of the 28 October 2012 Haida Gwaii earthquake. Our data are, within the errors, consistent with data from two campaign GPS sites along the west coast of Haida Gwaii and with rupture models that indicate megathrust rupture offshore, but not beneath, the islands.

Discovery and structure-activity relationships of piperidinone- and piperidine-constrained phenethylamines as novel, potent, and selective dipeptidyl peptidase IV inhibitors.

PubMed

Pei, Zhonghua; Li, Xiaofeng; von Geldern, Thomas W; Longenecker, Kenton; Pireh, Daisy; Stewart, Kent D; Backes, Bradley J; Lai, Chunqiu; Lubben, Thomas H; Ballaron, Stephen J; Beno, David W A; Kempf-Grote, Anita J; Sham, Hing L; Trevillyan, James M

2007-04-19

Dipeptidyl peptidase IV (DPP4) inhibitors are emerging as a new class of therapeutic agents for the treatment of type 2 diabetes. They exert their beneficial effects by increasing the levels of active glucagon-like peptide-1 and glucose-dependent insulinotropic peptide, which are two important incretins for glucose homeostasis. Starting from a high-throughput screening hit, we were able to identify a series of piperidinone- and piperidine-constrained phenethylamines as novel DPP4 inhibitors. Optimized compounds are potent, selective, and have good pharmacokinetic profiles.

Future-oriented maintenance strategy based on automated processes is finding its way into large astronomical facilities at remote observing sites

NASA Astrophysics Data System (ADS)

Silber, Armin; Gonzalez, Christian; Pino, Francisco; Escarate, Patricio; Gairing, Stefan

2014-08-01

With expanding sizes and increasing complexity of large astronomical observatories on remote observing sites, the call for an efficient and recourses saving maintenance concept becomes louder. The increasing number of subsystems on telescopes and instruments forces large observatories, like in industries, to rethink conventional maintenance strategies for reaching this demanding goal. The implementation of full-, or semi-automatic processes for standard service activities can help to keep the number of operating staff on an efficient level and to reduce significantly the consumption of valuable consumables or equipment. In this contribution we will demonstrate on the example of the 80 Cryogenic subsystems of the ALMA Front End instrument, how an implemented automatic service process increases the availability of spare parts and Line Replaceable Units. Furthermore how valuable staff recourses can be freed from continuous repetitive maintenance activities, to allow focusing more on system diagnostic tasks, troubleshooting and the interchanging of line replaceable units. The required service activities are decoupled from the day-to-day work, eliminating dependencies on workload peaks or logistic constrains. The automatic refurbishing processes running in parallel to the operational tasks with constant quality and without compromising the performance of the serviced system components. Consequentially that results in an efficiency increase, less down time and keeps the observing schedule on track. Automatic service processes in combination with proactive maintenance concepts are providing the necessary flexibility for the complex operational work structures of large observatories. The gained planning flexibility is allowing an optimization of operational procedures and sequences by considering the required cost efficiency.

Molecular and thermodynamic mechanisms of the chloride-dependent human angiotensin-I-converting enzyme (ACE).

PubMed

Yates, Christopher J; Masuyer, Geoffrey; Schwager, Sylva L U; Akif, Mohd; Sturrock, Edward D; Acharya, K Ravi

2014-01-17

Somatic angiotensin-converting enzyme (sACE), a key regulator of blood pressure and electrolyte fluid homeostasis, cleaves the vasoactive angiotensin-I, bradykinin, and a number of other physiologically relevant peptides. sACE consists of two homologous and catalytically active N- and C-domains, which display marked differences in substrate specificities and chloride activation. A series of single substitution mutants were generated and evaluated under varying chloride concentrations using isothermal titration calorimetry. The x-ray crystal structures of the mutants provided details on the chloride-dependent interactions with ACE. Chloride binding in the chloride 1 pocket of C-domain ACE was found to affect positioning of residues from the active site. Analysis of the chloride 2 pocket R522Q and R522K mutations revealed the key interactions with the catalytic site that are stabilized via chloride coordination of Arg(522). Substrate interactions in the S2 subsite were shown to affect chloride affinity in the chloride 2 pocket. The Glu(403)-Lys(118) salt bridge in C-domain ACE was shown to stabilize the hinge-bending region and reduce chloride affinity by constraining the chloride 2 pocket. This work demonstrated that substrate composition to the C-terminal side of the scissile bond as well as interactions of larger substrates in the S2 subsite moderate chloride affinity in the chloride 2 pocket of the ACE C-domain, providing a rationale for the substrate-selective nature of chloride dependence in ACE and how this varies between the N- and C-domains.

Molecular and Thermodynamic Mechanisms of the Chloride-dependent Human Angiotensin-I-converting Enzyme (ACE)*

PubMed Central

Yates, Christopher J.; Masuyer, Geoffrey; Schwager, Sylva L. U.; Akif, Mohd; Sturrock, Edward D.; Acharya, K. Ravi

2014-01-01

Somatic angiotensin-converting enzyme (sACE), a key regulator of blood pressure and electrolyte fluid homeostasis, cleaves the vasoactive angiotensin-I, bradykinin, and a number of other physiologically relevant peptides. sACE consists of two homologous and catalytically active N- and C-domains, which display marked differences in substrate specificities and chloride activation. A series of single substitution mutants were generated and evaluated under varying chloride concentrations using isothermal titration calorimetry. The x-ray crystal structures of the mutants provided details on the chloride-dependent interactions with ACE. Chloride binding in the chloride 1 pocket of C-domain ACE was found to affect positioning of residues from the active site. Analysis of the chloride 2 pocket R522Q and R522K mutations revealed the key interactions with the catalytic site that are stabilized via chloride coordination of Arg522. Substrate interactions in the S2 subsite were shown to affect chloride affinity in the chloride 2 pocket. The Glu403-Lys118 salt bridge in C-domain ACE was shown to stabilize the hinge-bending region and reduce chloride affinity by constraining the chloride 2 pocket. This work demonstrated that substrate composition to the C-terminal side of the scissile bond as well as interactions of larger substrates in the S2 subsite moderate chloride affinity in the chloride 2 pocket of the ACE C-domain, providing a rationale for the substrate-selective nature of chloride dependence in ACE and how this varies between the N- and C-domains. PMID:24297181

Sanitation, Stress, and Life Stage: A Systematic Data Collection Study among Women in Odisha, India

PubMed Central

Hulland, Kristyna R. S.; Chase, Rachel P.; Caruso, Bethany A.; Swain, Rojalin; Biswal, Bismita; Sahoo, Krushna Chandra; Panigrahi, Pinaki; Dreibelbis, Robert

2015-01-01

Emerging evidence demonstrates how inadequate access to water and sanitation is linked to psychosocial stress, especially among women, forcing them to navigate social and physical barriers during their daily sanitation routines. We examine sanitation-related psychosocial stress (SRPS) across women’s reproductive lives in three distinct geographic sites (urban slums, rural villages, and rural tribal villages) in Odisha, India. We explored daily sanitation practices of adolescent, newly married, pregnant, and established adult women (n = 60) and identified stressors encountered during sanitation. Responding to structured data collection methods, women ranked seven sanitation activities (defecation, urination, menstruation, bathing, post-defecation cleaning, carrying water, and changing clothes) based on stress (high to low) and level of freedom (associated with greatest freedom to having the most restrictions). Women then identified common stressors they encountered when practicing sanitation and sorted stressors in constrained piles based on frequency and severity of each issue. The constellation of factors influencing SRPS varies by life stage and location. Overall, sanitation behaviors that were most restricted (i.e., menstruation) were the most stressful. Women in different sites encountered different stressors, and the level of perceived severity varied based on site and life stage. Understanding the influence of place and life stage on SRPS provides a nuanced understanding of sanitation, and may help identify areas for intervention. PMID:26551866

BOREAS RSS-17 1994 ERS-1 Level-3 Freeze/Thaw Backscatter Change Images

NASA Technical Reports Server (NTRS)

Rignot, Eric; Nickeson, Jaime (Editor); Hall, Forrest G. (Editor); Way, JoBea; McDonald, Kyle C.; Smith, David E. (Technical Monitor)

2000-01-01

The Boreal Ecosystem-Atmosphere Study (BOREAS) Remote Sensing Science (RSS)-17 team acquired and analyzed imaging radar data from the European Space Agency's (ESA's) European Remote Sensing Satellite (ERS)-1 over a complete annual cycle at the BOREAS sites in Canada in 1994 to detect shifts in radar backscatter related to varying environmental conditions. Two independent transitions corresponding to soil thaw and possible canopy thaw were revealed by the data. The results demonstrated that radar provides an ability to observe thaw transitions at the beginning of the growing season, which in turn helps constrain the length of the growing season. The data set presented here includes change maps derived from radar backscatter images that were mosaicked together to cover the southern BOREAS sites. The image values used for calculating the changes are given relative to the reference mosaic image. The data are stored in binary image format files. The imaging radar data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

Analysis of the prescribed burning practice in the pine forest of northwestern Portugal.

PubMed

Fernandes, P; Botelho, H

2004-01-01

The ignition of low-intensity fires in the dormant season in the pine stands of north-western Portugal seeks to reduce the existing fuel hazard without compromising site quality. The purpose of this study is to characterise this practice and assess its effectiveness, based on information resulting from the normal monitoring process at the management level, and using operational guidelines, fire behaviour models and a newly developed method to classify prescribed fire severity. Although the region's humid climate strongly constrains the activity of prescribed fire, 87% of the fires analysed were undertaken under acceptable meteorological and fuel moisture conditions. In fact, most operations achieved satisfactory results. On average, prescribed fire reduces by 96% the potential intensity of a wildfire occurring under extreme weather conditions, but 36% of the treated sites would still require heavy fire fighting resources to suppress such fire, and 17% would still carry it in the tree canopy. Only 10% of the prescribed burns have an excessive impact on trees or the forest floor, while 89% (normal fire weather) or 59% (extreme fire weather) comply with both ecological integrity maintenance and wildfire protection needs. Improved planning and monitoring procedures are recommended in order to overcome the current deficiencies.

Foraging habitat quality constrains effectiveness of artificial nest-site provisioning in reversing population declines in a colonial cavity nester.

PubMed

Catry, Inês; Franco, Aldina M A; Rocha, Pedro; Alcazar, Rita; Reis, Susana; Cordeiro, Ana; Ventim, Rita; Teodósio, Joaquim; Moreira, Francisco

2013-01-01

Among birds, breeding numbers are mainly limited by two resources of major importance: food supply and nest-site availability. Here, we investigated how differences in land-use and nest-site availability affected the foraging behaviour, breeding success and population trends of the colonial cavity-dependent lesser kestrel Falco naumanni inhabiting two protected areas. Both areas were provided with artificial nests to increase nest-site availability. The first area is a pseudo-steppe characterized by traditional extensive cereal cultivation, whereas the second area is a previous agricultural zone now abandoned or replaced by forested areas. In both areas, lesser kestrels selected extensive agricultural habitats, such as fallows and cereal fields, and avoided scrubland and forests. In the second area, tracked birds from one colony travelled significantly farther distances (6.2 km ± 1.7 vs. 1.8 km ± 0.4 and 1.9 km ± 0.6) and had significant larger foraging-ranges (144 km(2) vs. 18.8 and 14.8 km(2)) when compared to the birds of two colonies in the extensive agricultural area. Longer foraging trips were reflected in lower chick feeding rates, lower fledging success and reduced chick fitness. Availability and occupation of artificial nests was high in both areas but population followed opposite trends, with a positive increment recorded exclusively in the first area with a large proportion of agricultural areas. Progressive habitat loss around the studied colony in the second area (suitable habitat decreased from 32% in 1990 to only 7% in 2002) is likely the main driver of the recorded population decline and suggests that the effectiveness of bird species conservation based on nest-site provisioning is highly constrained by habitat quality in the surrounding areas. Therefore, the conservation of cavity-dependent species may be enhanced firstly by finding the best areas of remaining habitat and secondly by increasing the carrying capacity of high-quality habitat areas through safe nest-site provisioning.

Foraging Habitat Quality Constrains Effectiveness of Artificial Nest-Site Provisioning in Reversing Population Declines in a Colonial Cavity Nester

PubMed Central

Catry, Inês; Franco, Aldina M. A.; Rocha, Pedro; Alcazar, Rita; Reis, Susana; Cordeiro, Ana; Ventim, Rita; Teodósio, Joaquim; Moreira, Francisco

2013-01-01

Among birds, breeding numbers are mainly limited by two resources of major importance: food supply and nest-site availability. Here, we investigated how differences in land-use and nest-site availability affected the foraging behaviour, breeding success and population trends of the colonial cavity-dependent lesser kestrel Falco naumanni inhabiting two protected areas. Both areas were provided with artificial nests to increase nest-site availability. The first area is a pseudo-steppe characterized by traditional extensive cereal cultivation, whereas the second area is a previous agricultural zone now abandoned or replaced by forested areas. In both areas, lesser kestrels selected extensive agricultural habitats, such as fallows and cereal fields, and avoided scrubland and forests. In the second area, tracked birds from one colony travelled significantly farther distances (6.2 km ±1.7 vs. 1.8 km ±0.4 and 1.9 km ±0.6) and had significant larger foraging-ranges (144 km2 vs. 18.8 and 14.8 km2) when compared to the birds of two colonies in the extensive agricultural area. Longer foraging trips were reflected in lower chick feeding rates, lower fledging success and reduced chick fitness. Availability and occupation of artificial nests was high in both areas but population followed opposite trends, with a positive increment recorded exclusively in the first area with a large proportion of agricultural areas. Progressive habitat loss around the studied colony in the second area (suitable habitat decreased from 32% in 1990 to only 7% in 2002) is likely the main driver of the recorded population decline and suggests that the effectiveness of bird species conservation based on nest-site provisioning is highly constrained by habitat quality in the surrounding areas. Therefore, the conservation of cavity-dependent species may be enhanced firstly by finding the best areas of remaining habitat and secondly by increasing the carrying capacity of high-quality habitat areas through safe nest-site provisioning. PMID:23484016

Protein-mediated loops in supercoiled DNA create large topological domains

PubMed Central

Yan, Yan; Ding, Yue; Leng, Fenfei; Dunlap, David; Finzi, Laura

2018-01-01

Abstract Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria of fundamental DNA/chromatin transactions. For example, supercoiling affects the hierarchical organization and function of chromatin in topologically associating domains (TADs) in both eukaryotes and bacteria. On the other hand, a protein-mediated loop in DNA can constrain supercoiling within a plectonemic structure. To characterize the extent of constrained supercoiling, 400 bp, lac repressor-secured loops were formed in extensively over- or under-wound DNA under gentle tension in a magnetic tweezer. The protein-mediated loops constrained variable amounts of supercoiling that often exceeded the maximum writhe expected for a 400 bp plectoneme. Loops with such high levels of supercoiling appear to be entangled with flanking domains. Thus, loop-mediating proteins operating on supercoiled substrates can establish topological domains that may coordinate gene regulation and other DNA transactions across spans in the genome that are larger than the separation between the binding sites. PMID:29538766

Petrogenesis and depositional history of felsic pyroclastic rocks from the Melka Wakena archaeological site-complex in South central Ethiopia

NASA Astrophysics Data System (ADS)

Resom, Angesom; Asrat, Asfawossen; Gossa, Tegenu; Hovers, Erella

2018-06-01

The Melka Wakena archaeological site-complex is located at the eastern rift margin of the central sector of the Main Ethiopian Rift (MER), in south central Ethiopia. This wide, gently sloping rift shoulder, locally called the "Gadeb plain" is underlain by a succession of primary pyroclastic deposits and intercalated fluvial sediments as well as reworked volcaniclastic rocks, the top part of which is exposed by the Wabe River in the Melka Wakena area. Recent archaeological survey and excavations at this site revealed important paleoanthropological records. An integrated stratigraphic, petrological, and major and trace element geochemical study has been conducted to constrain the petrogenesis of the primary pyroclastic deposits and the depositional history of the sequence. The results revealed that the Melka Wakena pyroclastic deposits are a suite of mildly alkaline, rhyolitic pantellerites (ash falls, pumiceous ash falls and ignimbrites) and slightly dacitic ash flows. These rocks were deposited by episodic volcanic eruptions during early to middle Pleistocene from large calderas along the Wonji Fault Belt (WFB) in the central sector of the MER and from large silicic volcanic centers at the eastern rift shoulder. The rhyolitic ash falls, pumiceous ash falls and ignimbrites have been generated by fractional crystallization of a differentiating basaltic magma while the petrogenesis of the slightly dacitic ash flows involved some crustal contamination and assimilation during fractionation. Contemporaneous fluvial activities in the geomorphologically active Gadeb plain deposited overbank sedimentary sequences (archaeology bearing conglomerates and sands) along meandering river courses while a dense network of channels and streams have subsequently down-cut through the older volcanic and sedimentary sequences, redepositing the reworked volcaniclastic sediments further downstream.

The Influences of Soil Characteristics on Nest-Site Selection in Painted Turtles (Chrysemys picta)

NASA Astrophysics Data System (ADS)

Page, R.

2017-12-01

A variety of animals dig nests and lay their eggs in soil, leaving them to incubate and hatch without assistance from the parents. Nesting habitat is important for these organisms many of which exhibit temperature dependent sex determination (TSD) whereby the incubation temperature determines the sex of each hatchling. However, suitable nesting habitat may be limited due to anthropogenic activities and global temperature increases. Soil thermal properties are critical to these organisms and are positively correlated with water retention and soil carbon; carbon-rich soils result in higher incubation temperatures. We investigated nest-site selection in painted turtles (Chrysemys picta) inhabiting an anthropogenic pond in south central Pennsylvania. We surveyed for turtle nests and documented location, depth, width, temperature, canopy coverage, clutch size, and hatch success for a total of 31 turtle nests. To address the influence of soil carbon and particle size on nest selection, we analyzed samples collected from: 1) actual nests that were depredated, 2) false nests, incomplete nests aborted during digging prior to nest completion, and 3) randomized locations. Soil samples were separated into coarse, medium, and fine grain size fractions through a stack of sieves. Samples were combusted in a total carbon analyzer to measure weight percent organic carbon. We found that anthropogenic activity at this site has created homogenous, sandy, compacted soils at the uppermost layer that may limit females' access to appropriate nesting habitat. Turtle nesting activity was limited to a linear region north of the pond and was constrained by an impassable rail line. Relative to other studies, turtle nests were notably shallow (5.8±0.9 cm) and placed close to the pond. Compared to false nests and random locations, turtle-selected sites averaged greater coarse grains (35% compared to 20.24 and 20.57%) and less fine grains (47% compared to 59 and 59, respectively). Despite remarkably high soil carbon along the rail line (47.08%) turtles nested here with slightly higher hatch success. We suggest that the turtles are limited to sandy, compact soils with low heat capacities and may compensate for this by also nesting adjacent to the rail line where high soil carbon could increase incubation temperatures.

ER-PM Contacts Define Actomyosin Kinetics for Proper Contractile Ring Assembly.

PubMed

Zhang, Dan; Bidone, Tamara C; Vavylonis, Dimitrios

2016-03-07

The cortical endoplasmic reticulum (ER), an elaborate network of tubules and cisternae [1], establishes contact sites with the plasma membrane (PM) through tethering machinery involving a set of conserved integral ER proteins [2]. The physiological consequences of forming ER-PM contacts are not fully understood. Here, we reveal a kinetic restriction role of ER-PM contacts over ring compaction process for proper actomyosin ring assembly in Schizosaccharomyces pombe. We show that fission yeast cells deficient in ER-PM contacts exhibit aberrant equatorial clustering of actin cables during ring assembly and are particularly susceptible to compromised actin filament crosslinking activity. Using quantitative image analyses and computer simulation, we demonstrate that ER-PM contacts function to modulate the distribution of ring components and to constrain their compaction kinetics. We propose that ER-PM contacts have evolved as important physical modulators to ensure robust ring assembly. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Boehm, Céline; Degrande, Céline; Mattelaer, Olivier

The study of anomalous electromagnetic emission in the sky is the basis of indirect searches for dark matter. It is also a powerful tool to constrain the radiative decay of active neutrinos. Until now, quantitative analyses have focused on the flux and energy spectrum of such an emission; polarisation has never been considered. Here we show that we could be missing out on an essential piece of information. The radiative decay of neutrinos, as well as the interactions of dark matter and neutrinos with Standard Model particles can generate a circular polarisation signal in X-rays or γ-rays. If observed, thismore » could reveal important information about their spatial distribution and particle-antiparticle ratio, and could even reveal the nature of the high-energy particle physics processes taking place in astrophysical sites. The question of the observability of these polarised signatures and their separation from background astrophysical sources is left for future work.« less

Radiocesium in migratory aquatic game birds using contaminated U.S. Department of Energy reactor-cooling reservoirs: A long-term perspective.

PubMed

Kennamer, Robert A; Oldenkamp, Ricki E; Leaphart, James C; King, Joshua D; Bryan, A Lawrence; Beasley, James C

2017-05-01

Low-level releases of radiocesium into former nuclear reactor cooling-reservoirs on the U.S. Department of Energy's Savannah River Site (SRS) in South Carolina, USA, dating primarily to the late 1950s and early 1960s, have allowed examination of long-term contaminant attenuation in biota occupying these habitats. Periodic collections of migratory game birds since the 1970s have documented 137 Cs (radiocesium) activity concentrations in birds of SRS reservoirs, including mainly Par Pond and Pond B. In this study, during 2014 and 2015 we released wild-caught American coots (Fulica americana) and ring-necked ducks (Aythya collaris) onto Pond B. We made lethal collections of these same birds with residence times ranging from 32 to 173 days to examine radiocesium uptake and estimate the rate of natural attenuation. The two species achieved asymptotic whole-body activity concentrations of radiocesium at different times, with ring-necked ducks requiring almost three times longer than the 30-35 days needed by coots. We estimated ecological half-life (T e ) for Pond B coots over a 28-yr period as 16.8 yr (95% CI = 12.9-24.2 yr). Pond B coot T e was nearly four times longer than T e for coots at nearby Par Pond where radiocesium bioavailability had been constrained for decades by pumping of potassium-enriched river water into that reservoir. T e could not be estimated from long-term data for radiocesium in Pond B diving ducks, including ring-necked ducks, likely because of high variability in residence times of ducks on Pond B. Our results highlight the importance: (1) for risk managers to understand site-specific bio-geochemistry of radiocesium for successful implementation of countermeasures at contaminated sites and (2) of residence time as a critical determinant of observed radiocesium activity concentrations in highly mobile wildlife inhabiting contaminated habitats. Copyright © 2017 Elsevier Ltd. All rights reserved.

Resource Constrained Planning of Multiple Projects with Separable Activities

NASA Astrophysics Data System (ADS)

Fujii, Susumu; Morita, Hiroshi; Kanawa, Takuya

In this study we consider a resource constrained planning problem of multiple projects with separable activities. This problem provides a plan to process the activities considering a resource availability with time window. We propose a solution algorithm based on the branch and bound method to obtain the optimal solution minimizing the completion time of all projects. We develop three methods for improvement of computational efficiency, that is, to obtain initial solution with minimum slack time rule, to estimate lower bound considering both time and resource constraints and to introduce an equivalence relation for bounding operation. The effectiveness of the proposed methods is demonstrated by numerical examples. Especially as the number of planning projects increases, the average computational time and the number of searched nodes are reduced.

Community Decadal Panel for Terrestrial Analogs to Mars

NASA Astrophysics Data System (ADS)

Barlow, N. G.; Farr, T.; Baker, V. R.; Bridges, N.; Carsey, F.; Duxbury, N.; Gilmore, M. S.; Green, J. R.; Grin, E.; Hansen, V.; Keszthelyi, L.; Lanagan, P.; Lentz, R.; Marinangeli, L.; Morris, P. A.; Ori, G. G.; Paillou, P.; Robinson, C.; Thomson, B.

2001-11-01

It is well recognized that interpretations of Mars must begin with the Earth as a reference. The most successful comparisons have focused on understanding geologic processes on the Earth well enough to extrapolate to Mars' environment. Several facets of terrestrial analog studies have been pursued and are continuing. These studies include field workshops, characterization of terrestrial analog sites for Mars, instrument tests, laboratory measurements (including analysis of martian meteorites), and computer and laboratory modeling. The combination of all these activities allows scientists to constrain the processes operating in specific terrestrial environments and extrapolate how similar processes could affect Mars. The Terrestrial Analogs for Mars Community Panel is considering the following two key questions: (1) How do terrestrial analog studies tie in to the MEPAG science questions about life, past climate, and geologic evolution of Mars, and (2) How can future instrumentation be used to address these questions. The panel is considering the issues of data collection, value of field workshops, data archiving, laboratory measurements and modeling, human exploration issues, association with other areas of solar system exploration, and education and public outreach activities.

Terrestrial Analogs to Mars

NASA Astrophysics Data System (ADS)

Farr, T. G.; Arcone, S.; Arvidson, R. W.; Baker, V.; Barlow, N. G.; Beaty, D.; Bell, M. S.; Blankenship, D. D.; Bridges, N.; Briggs, G.; Bulmer, M.; Carsey, F.; Clifford, S. M.; Craddock, R. A.; Dickerson, P. W.; Duxbury, N.; Galford, G. L.; Garvin, J.; Grant, J.; Green, J. R.; Gregg, T. K. P.; Guinness, E.; Hansen, V. L.; Hecht, M. H.; Holt, J.; Howard, A.; Keszthelyi, L. P.; Lee, P.; Lanagan, P. D.; Lentz, R. C. F.; Leverington, D. W.; Marinangeli, L.; Moersch, J. E.; Morris-Smith, P. A.; Mouginis-Mark, P.; Olhoeft, G. R.; Ori, G. G.; Paillou, P.; Reilly, J. F., II; Rice, J. W., Jr.; Robinson, C. A.; Sheridan, M.; Snook, K.; Thomson, B. J.; Watson, K.; Williams, K.; Yoshikawa, K.

2002-08-01

It is well recognized that interpretations of Mars must begin with the Earth as a reference. The most successful comparisons have focused on understanding geologic processes on the Earth well enough to extrapolate to Mars' environment. Several facets of terrestrial analog studies have been pursued and are continuing. These studies include field workshops, characterization of terrestrial analog sites, instrument tests, laboratory measurements (including analysis of Martian meteorites), and computer and laboratory modeling. The combination of all these activities allows scientists to constrain the processes operating in specific terrestrial environments and extrapolate how similar processes could affect Mars. The Terrestrial Analogs for Mars Community Panel has considered the following two key questions: (1) How do terrestrial analog studies tie in to the Mars Exploration Payload Assessment Group science questions about life, past climate, and geologic evolution of Mars, and (2) How can future instrumentation be used to address these questions. The panel has considered the issues of data collection, value of field workshops, data archiving, laboratory measurements and modeling, human exploration issues, association with other areas of solar system exploration, and education and public outreach activities.

Arp2/3 complex–dependent actin networks constrain myosin II function in driving retrograde actin flow

PubMed Central

Yang, Qing; Zhang, Xiao-Feng; Pollard, Thomas D.

2012-01-01

The Arp2/3 complex nucleates actin filaments to generate networks at the leading edge of motile cells. Nonmuscle myosin II produces contractile forces involved in driving actin network translocation. We inhibited the Arp2/3 complex and/or myosin II with small molecules to investigate their respective functions in neuronal growth cone actin dynamics. Inhibition of the Arp2/3 complex with CK666 reduced barbed end actin assembly site density at the leading edge, disrupted actin veils, and resulted in veil retraction. Strikingly, retrograde actin flow rates increased with Arp2/3 complex inhibition; however, when myosin II activity was blocked, Arp2/3 complex inhibition now resulted in slowing of retrograde actin flow and veils no longer retracted. Retrograde flow rate increases induced by Arp2/3 complex inhibition were independent of Rho kinase activity. These results provide evidence that, although the Arp2/3 complex and myosin II are spatially segregated, actin networks assembled by the Arp2/3 complex can restrict myosin II–dependent contractility with consequent effects on growth cone motility. PMID:22711700

Implementing interprofessional education and practice: Lessons from a resource-constrained university.

PubMed

Frantz, J M; Rhoda, A J

2017-03-01

Interprofessional education is seen as a vehicle to facilitate collaborative practice and, therefore, address the complex health needs of populations. A number of concerns have, however, been raised with the implementation of interprofessional education. The three core concerns raised in the literature and addressed in the article include the lack of an explicit framework, challenges operationalising interprofessional education and practice, and the lack of critical mass in terms of human resources to drive activities related to interprofessional education and practice. This article aims to present lessons learnt when attempting to overcome the main challenges and implementing interprofessional education activities in a resource-constrained higher education setting in South Africa. Boyer's model of scholarship, which incorporates research, teaching integration, and application, was used to address the challenge of a lack of a framework in which to conceptualise the activities of interprofressional education. In addition, a scaffolding approach to teaching activities within a curriculum was used to operationalise interprofessional education and practice. Faculty development initiatives were additionally used to develop a critical mass that focused on driving interprofessional education. Lessons learnt highlighted that if a conceptual model is agreed upon by all, it allows for a more focused approach, and both human and financial resources may be channelled towards a common goal which may assist resource-constrained institutions in successfully implementing interprofessional activities.

Ground-rupturing earthquakes on the northern Big Bend of the San Andreas Fault, California, 800 A.D. to Present

USGS Publications Warehouse

Scharer, Katherine M.; Weldon, Ray; Biasi, Glenn; Streig, Ashley; Fumal, Thomas E.

2017-01-01

Paleoseismic data on the timing of ground-rupturing earthquakes constrain the recurrence behavior of active faults and can provide insight on the rupture history of a fault if earthquakes dated at neighboring sites overlap in age and are considered correlative. This study presents the evidence and ages for 11 earthquakes that occurred along the Big Bend section of the southern San Andreas Fault at the Frazier Mountain paleoseismic site. The most recent earthquake to rupture the site was the Mw7.7–7.9 Fort Tejon earthquake of 1857. We use over 30 trench excavations to document the structural and sedimentological evolution of a small pull-apart basin that has been repeatedly faulted and folded by ground-rupturing earthquakes. A sedimentation rate of 0.4 cm/yr and abundant organic material for radiocarbon dating contribute to a record that is considered complete since 800 A.D. and includes 10 paleoearthquakes. Earthquakes have ruptured this location on average every ~100 years over the last 1200 years, but individual intervals range from ~22 to 186 years. The coefficient of variation of the length of time between earthquakes (0.7) indicates quasiperiodic behavior, similar to other sites along the southern San Andreas Fault. Comparison with the earthquake chronology at neighboring sites along the fault indicates that only one other 1857-size earthquake could have occurred since 1350 A.D., and since 800 A.D., the Big Bend and Mojave sections have ruptured together at most 50% of the time in Mw ≥ 7.3 earthquakes.

Fate of arsenic, phosphate and ammonium plumes in a coastal aquifer affected by saltwater intrusion.

PubMed

Colombani, N; Mastrocicco, M; Prommer, H; Sbarbati, C; Petitta, M

2015-08-01

A severe groundwater contamination with extensive plumes of arsenic, phosphate and ammonium was found in a coastal aquifer beneath a former fertilizer production plant. The implementation of an active groundwater remediation strategy, based on a comprehensive pump and treat scheme, now prevents the migration of the dissolved contaminants into the marine environment. However, due to the site's proximity to the coastline, a seawater wedge was induced by the pumping scheme. Additionally the groundwater flow and salinity patterns were also strongly affected by leakage from the site's sewer system and from a seawater-fed cooling canal. The objective of this study was to elucidate the fate of arsenic and its co-contaminants over the site's history under the complex, coupled hydrodynamic and geochemical conditions that prevail at the site. A detailed geochemical characterisation of samples from sediment cores and hydrochemical data provided valuable high-resolution information. The obtained data were used to develop various conceptual models and to constrain the development and calibration of a reactive transport model. The reactive transport simulations were performed for a sub-domain (two-dimensional transect) of an earlier developed three-dimensional flow and variable density solute transport model. The results suggest that in the upper sub-oxic zone the influx of oxygenated water promoted As attenuation via co-precipitation with Al and Fe oxides and copper hydroxides. In contrast, in the deeper aquifer zone, iron reduction, associated with the release of adsorbed As and the dissolution of As bearing phases, provided and still provides to date a persistent source for groundwater pollution. The presented monitoring and modelling approach could be broadly applied to coastal polluted sites by complex contaminant mixture containing As. Copyright © 2015 Elsevier B.V. All rights reserved.

Constraining ecosystem processes from tower fluxes and atmospheric profiles.

PubMed

Hill, T C; Williams, M; Woodward, F I; Moncrieff, J B

2011-07-01

The planetary boundary layer (PBL) provides an important link between the scales and processes resolved by global atmospheric sampling/modeling and site-based flux measurements. The PBL is in direct contact with the land surface, both driving and responding to ecosystem processes. Measurements within the PBL (e.g., by radiosondes, aircraft profiles, and flask measurements) have a footprint, and thus an integrating scale, on the order of 1-100 km. We use the coupled atmosphere-biosphere model (CAB) and a Bayesian data assimilation framework to investigate the amount of biosphere process information that can be inferred from PBL measurements. We investigate the information content of PBL measurements in a two-stage study. First, we demonstrate consistency between the coupled model (CAB) and measurements, by comparing the model to eddy covariance flux tower measurements (i.e., water and carbon fluxes) and also PBL scalar profile measurements (i.e., water, carbon dioxide, and temperature) from Canadian boreal forest. Second, we use the CAB model in a set of Bayesian inversions experiments using synthetic data for a single day. In the synthetic experiment, leaf area and respiration were relatively well constrained, whereas surface albedo and plant hydraulic conductance were only moderately constrained. Finally, the abilities of the PBL profiles and the eddy covariance data to constrain the parameters were largely similar and only slightly lower than the combination of both observations.

A Fluorescent Protein Scaffold for Presenting Structurally Constrained Peptides Provides an Effective Screening System to Identify High Affinity Target-Binding Peptides

PubMed Central

Kadonosono, Tetsuya; Yabe, Etsuri; Furuta, Tadaomi; Yamano, Akihiro; Tsubaki, Takuya; Sekine, Takuya; Kuchimaru, Takahiro; Sakurai, Minoru; Kizaka-Kondoh, Shinae

2014-01-01

Peptides that have high affinity for target molecules on the surface of cancer cells are crucial for the development of targeted cancer therapies. However, unstructured peptides often fail to bind their target molecules with high affinity. To efficiently identify high-affinity target-binding peptides, we have constructed a fluorescent protein scaffold, designated gFPS, in which structurally constrained peptides are integrated at residues K131–L137 of superfolder green fluorescent protein. Molecular dynamics simulation supported the suitability of this site for presentation of exogenous peptides with a constrained structure. gFPS can present 4 to 12 exogenous amino acids without a loss of fluorescence. When gFPSs presenting human epidermal growth factor receptor type 2 (HER2)-targeting peptides were added to the culture medium of HER2-expressing cells, we could easily identify the peptides with high HER2-affinity and -specificity based on gFPS fluorescence. In addition, gFPS could be expressed on the yeast cell surface and applied for a high-throughput screening. These results demonstrate that gFPS has the potential to serve as a powerful tool to improve screening of structurally constrained peptides that have a high target affinity, and suggest that it could expedite the one-step identification of clinically applicable cancer cell-binding peptides. PMID:25084350

Regional aerosol radiative and hydrological effects over the mid-Atlantic corridor

NASA Astrophysics Data System (ADS)

Creekmore, Torreon N.

A thorough assessment of direct, indirect, and semi-direct influences of aerosols on Earth's energy budget is required to better understand climate and estimate how it may change in the future. Clear-sky surface broadband (measured and modeled) irradiance, spectral aerosol optical depth, heating rate profiles, and non-radiative flux measurements were conducted at a state-of-the-art site, developed by the NOAA-Howard University Center for Atmospheric Sciences (NCAS) program, providing a best estimate of aerosol radiative atmosphere-surface interactions. Methods developed by the Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Program were applied to: (1) temporally quantify regional aerosol forcing, (2) to derive an empirical equation describing a relationship between aerosol optical depth and normalized diffuse ratio, (3) evaluate aerosol impacts on atmospheric heating, and (4) evaluate how aerosol forcing impacts may possibly reduce latent and sensible fluxes. Measurements were obtained during the period of May--September for the years of 2005, 2006, and 2007. Atmospheric aerosols are among the key uncertainties affecting the Earth's climate and atmospheric radiative processes. Present-day increases in aerosol concentrations directly, indirectly, and semi-directly impact the Earth's energy budget (i.e., cooling the surface and heating the atmosphere), thereby contributing to climate change. The Howard University Beltsville Site (HUBS) has experienced a greater loss in mean normalized aerosol radiative forcing with time, as observations show a decrease from --0.9 in 2005 to --3.1 and --3.4 W/m2 for 2006 and 2007 respectively, in mean net surface irradiance. The mean normalized aerosol radiative forcing estimated for the period considered was --2.5 W/m2. The reduction in surface solar insolation is due to increased scattering and absorption related to increased aerosol burdens v for the period, promoting surface cooling and atmospheric heating. Calculation of radiative flux and heating rates profiles, which are constrained by HUBS observations, were performed by the 1-D Fu-Liou radiative transfer model to investigate the effect of polluted and pristine aerosol conditions on the surface energy budget and hydrological cycle. For HUBS the surface forcing (--14.2 W/m2) and atmospheric forcing (9.9 W/m2) were significantly larger than the TOA (--4.3 W/m2) radiative forcing. Associated aerosol heating, as well as reduced surface insolation, may lead to increasing near surface static stability, and reduced vertical transport of moisture into the atmospheric boundary layer, and over time, a possible spin-down of the hydrological cycle. It is shown that HUBS provides an ideal opportunity for improving measurements and datasets, thus allowing for both the study and understanding of aerosol impacts on the climate system. Further, results show that in order to provide reference quality data and constrain aerosol radiative effects over land, ground-based research sites must conform to HUBS standards of: (1) instrumentation (e.g. passive and active sensors); (2) operational protocols (e.g. calibration and routine cleaning); (3) rigorous cloud screening protocols; and (4) incorporation of ARM QC and modified FFA algorithms. HUBS surface measurements provides the reference quality data necessary and capability required to help enhance measurements and constrain current uncertainties in estimates of aerosol direct effects over land. Incorporating a combined technique of both active and passive instruments reduced the direct radiative forcing estimates by ˜82 W/m2. The analysis of aerosol effects over HUBS helps continue in bridging the gap of applying measurements for improvement of climate simulations by generating observational products, which describes aerosol and radiation field characteristics in detail.

Choosing health, constrained choices.

PubMed

Chee Khoon Chan

2009-12-01

In parallel with the neo-liberal retrenchment of the welfarist state, an increasing emphasis on the responsibility of individuals in managing their own affairs and their well-being has been evident. In the health arena for instance, this was a major theme permeating the UK government's White Paper Choosing Health: Making Healthy Choices Easier (2004), which appealed to an ethos of autonomy and self-actualization through activity and consumption which merited esteem. As a counterpoint to this growing trend of informed responsibilization, constrained choices (constrained agency) provides a useful framework for a judicious balance and sense of proportion between an individual behavioural focus and a focus on societal, systemic, and structural determinants of health and well-being. Constrained choices is also a conceptual bridge between responsibilization and population health which could be further developed within an integrative biosocial perspective one might refer to as the social ecology of health and disease.

Characterization and management of electrical noise in the new Australian military HF communication network

NASA Astrophysics Data System (ADS)

Vyden, Bruce

2000-03-01

The Australian Defense Force's (ADF's) High Frequency (HF) communication network is soon to be replaced by a modernized system. Characterization of electrical noise at the receiver sites proposed for the new system is crucial to its performance. Consequently receiver site noise will be measured under the HF Modernization implementation contract that was awarded to Boeing Australia Ltd. Unfortunately the utility of the noise measurements is constrained by the uncertainties of both the ionosphere and atmosphere. This paper discusses some of the issues related to the methodology for measuring the noise and exposes some unresolved issues.

Rationale for a Mars Pathfinder mission to Chryse Planitia and the Viking 1 lander

NASA Technical Reports Server (NTRS)

Craddock, Robert A.

1994-01-01

Presently the landing site for Mars Pathfinder will be constrained to latitudes between 0 deg and 30 deg N to facilitate communication with earth and to allow the lander and rover solar arrays to generate the maximum possible power. The reference elevation of the site must also be below 0 km so that the descent parachute, a Viking derivative, has sufficient time to open and slow the lander to the correct terminal velocity. Although Mars has as much land surface area as the continental crust of the earth, such engineering constraints immediately limit the number of possible landing sites to only three broad areas: Amazonis, Chryse, and Isidis Planitia. Of these, both Chryse and Isidis Planitia stand out as the sites offering the most information to address several broad scientific topics.

Investigation of copper(II) binding to the protein precursor of Non-Amyloid-Beta Component of Alzheimer Disease Amyloid Plaque

NASA Astrophysics Data System (ADS)

Rose, Francis; Hodak, Miroslav; Bernholc, Jerry

2007-03-01

The Non-Amyloid-Beta Component Precursor (NACP) is a natively unfolded synaptic protein that is implicated in Alzheimers and Parkinsons diseases. Its aggregation into fibrillar structures is accelerated by the binding of copper(II). Experimental studies suggest that the dominant copper binding site is located at the histidine residue in NACP. Based on this evidence we assembled a model fragment of the binding site and used DFT to analyze the conformational details of the most probable binding motifs. We investigated the overall conformational effects with classical MD by constraining the copper binding site to the most energetically favorable geometry obtained from the DFT calculations. These results are compared and contrasted with those of the unbound NACP.

Use of U and Th Decay-Series Disequilibrium to Characterize Geothermal Systems: An Example from the Coso Geothermal System

NASA Astrophysics Data System (ADS)

Leslie, B. W.; Hammond, D.

2007-12-01

Uranium and thorium decay series isotopes were measured in fluids and solids in the Coso geothermal system to assess the utility and constrain the limitations of the radioisotopic approach to the investigation of rock-water interaction. Fluid radioisotope measurements indicate substantial kilometer-scale variability in chemistry. Between 1988 and 1990, radium isotope activity ratios indicate temporal variability, which is exhibited by apparent mixing relationships observed as a function of time for single wells. Activity ratios of Ra-224/Ra-226 and Ra- 228/Ra-226, and the processes that contribute and remove these radionuclide to and from the fluids, constrain residence times of fluids and may help constrain fluid velocities in the geothermal system. Activity ratios of Ra- 224/Ra-226 > ten were measured. In groundwater and geothermal systems ratios of Ra-224/Ra-226 > ten are limited to zones of thermal upwelling or very young (days to weeks) waters in mountainous areas. Rn-222 results indicate that radon is also an effective tracer for steam velocities within the geothermal system. Analysis of carbon dioxide and Rn-222 data indicates that the residence time of steam (time since separation from the liquid) is short (probably less than four days). Estimates of fluid velocities derived from Rn-222 and radium isotopic measurements are within an order of magnitude of velocities derived from a fluorescein tracer test. Both Rn-222 and Ra-224 activities are higher in single-phase fluids in the northwest as compared to the southeast, indicating a higher rock-surface-area/water-volume ratio in the northwest. Thus, measurements of short-lived radioisotopes and gaseous phase constituents can constrain processes and characteristics of geothermal systems that are usually difficult to constrain (e.g., surface area/volume, residence times). The NRC staff views expressed herein are preliminary and do not constitute a final judgment or determination of the matters addressed or of the acceptability of a license application for a geologic repository at Yucca Mountain.

The Search for Transient Mass Loss Events on Active Stars and Their Impacts

NASA Astrophysics Data System (ADS)

Crosley, Michael K.

2018-01-01

The conditions that determine the potential habitability of exoplanets are very diverse and still poorly understood. Magnetic eruptive events, such as flares and coronal mass ejections (CME's) are one such concern. Stellar flares are routinely observed and on cool stars but clear signatures of stellar CME's have been less forthcoming. CME’s are geoeffective and contribute to space weather. Stellar coronal mass ejections remain experimentally unconstrained, unlike the stellar flare counterpart which are observed ubiquitously across the electromagnetic spectrum. Low frequency radio bursts in the form of a type II burst offer the best means of identifying and constraining the rate and properties of stellar CME’s. CME properties can be further constrained and solar scaling relationships tested by simultaneously preforming flare observations. The interpretation for the multi-wavelength analysis of type II events and their associated flares is tested by fully constrained solar observations. There we find that velocity measurements are typically accurate to within a factor of two and that mass constraints are accurate to within an order of magnitude. We take these lessons and apply them to observations of the nearby, active M dwarf stars YZ Cmi and EQ Peg. These stars have the advantage of being well observed and constrained. Their well documented high flare activity is expected to be accompanied with high CME activity. They have been shown to have low frequency radio bursts in the past, and their constrained coronal properties allows us to extract the information required to interpret the type II burst. We report on 15 hours of Low Frequency Array (10-190 MHz) observations of YZ Cmi and to 64 hours of EQ Peg observations at the Jansky Very Large Array (230-470 MHz), 20 hours of which were observed simultaneously for flares at the Apache Point Observatory. During this time, solar scaling relationships tells us that ~70 large flares should have been produced which would be associated to a corresponding CME as well. From our results we can constraint event properties, detection limits, CME models, and atmospheric models.

Present-day kinematics of the Danakil block (southern Red Sea-Afar) constrained by GPS

NASA Astrophysics Data System (ADS)

Ladron de Guevara, R.; Jonsson, S.; Ruch, J.; Doubre, C.; Reilinger, R. E.; Ogubazghi, G.; Floyd, M.; Vasyura-Bathke, H.

2017-12-01

The rifting of the Arabian plate from the Nubian and Somalian plates is primarily accommodated by seismic and magmatic activity along two rift arms of the Afar triple junction (the Red Sea and Gulf of Aden rifts). The spatial distribution of active deformation in the Afar region have been constrained with geodetic observations. However, the plate boundary configuration in which this deformation occurs is still not fully understood. South of 17°N, the Red Sea rift is composed of two parallel and overlapping rift branches separated by the Danakil block. The distribution of the extension across these two overlapping rifts, their potential connection through a transform fault zone and the counterclockwise rotation of the Danakil block have not yet been fully resolved. Here we analyze new GPS observations from the Danakil block, the Gulf of Zula area (Eritrea) and Afar (Ethiopia) together with previous geodetic survey data to better constrain the plate kinematics and active deformation of the region. The new data has been collected in 2016 and add up to 5 years to the existing geodetic observations (going back to 2000). Our improved GPS velocity field shows differences with previously modeled GPS velocities, suggesting that the rate and rotation of the Danakil block need to be updated. The new velocity field also shows that the plate-boundary strain is accommodated by broad deformation zones rather than across sharp boundaries between tectonic blocks. To better determine the spatial distribution of the strain, we first implement a rigid block model to constrain the overall regional plate kinematics and to isolate the plate-boundary deformation at the western boundary of the Danakil block. We then study whether the recent southern Red Sea rifting events have caused detectable changes in observed GPS velocities and if the observations can be used to constrain the scale of this offshore rift activity. Finally, we investigate different geometries of transform faults that might connect the two overlapping branches of the southern Red Sea rift in the Gulf of Zula region.

Effects of landscape composition and configuration on migrating songbirds: inference from and individual-based model

Treesearch

Emily Cohen; Scott Pearson; Frank Moore

2014-01-01

The behavior of long-distance migrants during stopover is constrained by the need to quickly and safely replenish energetic reserves. Replenishing fuel stores at stopover sites requires adjusting to unfamiliar landscapes with little to no information about the distribution of resources. Despite their critical importance to the success of songbird migration, the effects...

A power analysis for multivariate tests of temporal trend in species composition.

PubMed

Irvine, Kathryn M; Dinger, Eric C; Sarr, Daniel

2011-10-01

Long-term monitoring programs emphasize power analysis as a tool to determine the sampling effort necessary to effectively document ecologically significant changes in ecosystems. Programs that monitor entire multispecies assemblages require a method for determining the power of multivariate statistical models to detect trend. We provide a method to simulate presence-absence species assemblage data that are consistent with increasing or decreasing directional change in species composition within multiple sites. This step is the foundation for using Monte Carlo methods to approximate the power of any multivariate method for detecting temporal trends. We focus on comparing the power of the Mantel test, permutational multivariate analysis of variance, and constrained analysis of principal coordinates. We find that the power of the various methods we investigate is sensitive to the number of species in the community, univariate species patterns, and the number of sites sampled over time. For increasing directional change scenarios, constrained analysis of principal coordinates was as or more powerful than permutational multivariate analysis of variance, the Mantel test was the least powerful. However, in our investigation of decreasing directional change, the Mantel test was typically as or more powerful than the other models.

A Strategy for Developing Future Academic Leaders for South Africa in a Resource-Constrained Environment

PubMed Central

Lalloo, Umesh G.; Bobat, Raziya A.; Pillay, Sandy; Wassenaar, Douglas

2014-01-01

A key challenge in addressing the shortage of health care workers in resource-constrained environments is ensuring that there is optimal academic capacity for their training. South Africa’s University of KwaZulu-Natal has placed academic and research capacity building at the heart of its program with the Medical Education Partnership Initiative (MEPI) in a program called ENhancing Training, REsearch Capacity, and Expertise (ENTREE). The program is premised on the basis that research capacity development will lead to an increase in teachers who will be essential to improving the quality and quantity of health care workers needed to meet South Africa’s health challenges. This is being achieved through four components of the program: (1) infusion of the undergraduate program with research modules; (2) attraction of academically talented students in the middle of their undergraduate program into a parallel track that has research capacity as its major thrust; (3) attraction of qualified health care personnel into a supported PhD program; and (4) providing strong research ethics training and mentorship. A significant proportion of the program is being executed in rural training sites, to increase the probability that trainees will return to the sites as mentors. PMID:25072580

U and Th isotope constraints on the duration of Heinrich events H0-H4 in the southeastern Labrador Sea

NASA Astrophysics Data System (ADS)

Veiga-Pires, C. C.; Hillaire-Marcel, C.

1999-04-01

The duration and sequence of events recorded in Heinrich layers at sites near the Hudson Strait source area for ice-rafted material are still poorly constrained, notably because of the limit and uncertainties of the 14C chronology. Here we use high-resolution 230Th-excess measurements, in a 6 m sequence raised from Orphan Knoll (southern Labrador Sea), to constrain the duration of the deposition of the five most recent Heinrich (H) layers. On the basis of maximum/minimum estimates for the mean glacial 230Th-excess flux at the studied site a minimum/maximum duration of 1.0/0.6, 1.4/0.8, 1.3/0.8, 1.5/0.9, and 2.1/1.3 kyr is obtained for H0 (˜Younger Dryas), Hl, H2, H3, and H4, respectively. Thorium-230-excess inventories and other sedimentological features indicate a reduced but still significant lateral sedimentary supply by the Western Boundary Undercurrent during the glacial interval. U and Th series systematics also provide insights into source rocks of H layer sediments (i.e., into distal Irminger Basin/local Labrador Sea supplies).

Automatic Hazard Detection for Landers

NASA Technical Reports Server (NTRS)

Huertas, Andres; Cheng, Yang; Matthies, Larry H.

2008-01-01

Unmanned planetary landers to date have landed 'blind'; that is, without the benefit of onboard landing hazard detection and avoidance systems. This constrains landing site selection to very benign terrain,which in turn constrains the scientific agenda of missions. The state of the art Entry, Descent, and Landing (EDL) technology can land a spacecraft on Mars somewhere within a 20-100km landing ellipse.Landing ellipses are very likely to contain hazards such as craters, discontinuities, steep slopes, and large rocks, than can cause mission-fatal damage. We briefly review sensor options for landing hazard detection and identify a perception approach based on stereo vision and shadow analysis that addresses the broadest set of missions. Our approach fuses stereo vision and monocular shadow-based rock detection to maximize spacecraft safety. We summarize performance models for slope estimation and rock detection within this approach and validate those models experimentally. Instantiating our model of rock detection reliability for Mars predicts that this approach can reduce the probability of failed landing by at least a factor of 4 in any given terrain. We also describe a rock detector/mapper applied to large-high-resolution images from the Mars Reconnaissance Orbiter (MRO) for landing site characterization and selection for Mars missions.

The effects of an invasive seaweed on native communities vary along a gradient of land-based human impacts

PubMed Central

Badalamenti, Fabio; Iveša, Ljiljana; Mikac, Barbara; Musco, Luigi; Jaklin, Andrej; Rattray, Alex; Vega Fernández, Tomás; Benedetti-Cecchi, Lisandro

2016-01-01

The difficulty in teasing apart the effects of biological invasions from those of other anthropogenic perturbations has hampered our understanding of the mechanisms underpinning the global biodiversity crisis. The recent elaboration of global-scale maps of cumulative human impacts provides a unique opportunity to assess how the impact of invaders varies among areas exposed to different anthropogenic activities. A recent meta-analysis has shown that the effects of invasive seaweeds on native biota tend to be more negative in relatively pristine than in human-impacted environments. Here, we tested this hypothesis through the experimental removal of the invasive green seaweed, Caulerpa cylindracea, from rocky reefs across the Mediterranean Sea. More specifically, we assessed which out of land-based and sea-based cumulative impact scores was a better predictor of the direction and magnitude of the effects of this seaweed on extant and recovering native assemblages. Approximately 15 months after the start of the experiment, the removal of C. cylindracea from extant assemblages enhanced the cover of canopy-forming macroalgae at relatively pristine sites. This did not, however, result in major changes in total cover or species richness of native assemblages. Preventing C. cylindracea re-invasion of cleared plots at pristine sites promoted the recovery of canopy-forming and encrusting macroalgae and hampered that of algal turfs, ultimately resulting in increased species richness. These effects weakened progressively with increasing levels of land-based human impacts and, indeed, shifted in sign at the upper end of the gradient investigated. Thus, at sites exposed to intense disturbance from land-based human activities, the removal of C. cylindracea fostered the cover of algal turfs and decreased that of encrusting algae, with no net effect on species richness. Our results suggests that competition from C. cylindracea is an important determinant of benthic assemblage diversity in pristine environments, but less so in species-poor assemblages found at sites exposed to intense disturbance from land-based human activities, where either adverse physical factors or lack of propagules may constrain the number of potential native colonizers. Implementing measures to reduce the establishment and spread of C. cylindracea in areas little impacted by land-based human activities should be considered a priority for preserving the biodiversity of Mediterranean shallow rocky reefs. PMID:27014513

The effects of an invasive seaweed on native communities vary along a gradient of land-based human impacts.

PubMed

Bulleri, Fabio; Badalamenti, Fabio; Iveša, Ljiljana; Mikac, Barbara; Musco, Luigi; Jaklin, Andrej; Rattray, Alex; Vega Fernández, Tomás; Benedetti-Cecchi, Lisandro

2016-01-01

The difficulty in teasing apart the effects of biological invasions from those of other anthropogenic perturbations has hampered our understanding of the mechanisms underpinning the global biodiversity crisis. The recent elaboration of global-scale maps of cumulative human impacts provides a unique opportunity to assess how the impact of invaders varies among areas exposed to different anthropogenic activities. A recent meta-analysis has shown that the effects of invasive seaweeds on native biota tend to be more negative in relatively pristine than in human-impacted environments. Here, we tested this hypothesis through the experimental removal of the invasive green seaweed, Caulerpa cylindracea, from rocky reefs across the Mediterranean Sea. More specifically, we assessed which out of land-based and sea-based cumulative impact scores was a better predictor of the direction and magnitude of the effects of this seaweed on extant and recovering native assemblages. Approximately 15 months after the start of the experiment, the removal of C. cylindracea from extant assemblages enhanced the cover of canopy-forming macroalgae at relatively pristine sites. This did not, however, result in major changes in total cover or species richness of native assemblages. Preventing C. cylindracea re-invasion of cleared plots at pristine sites promoted the recovery of canopy-forming and encrusting macroalgae and hampered that of algal turfs, ultimately resulting in increased species richness. These effects weakened progressively with increasing levels of land-based human impacts and, indeed, shifted in sign at the upper end of the gradient investigated. Thus, at sites exposed to intense disturbance from land-based human activities, the removal of C. cylindracea fostered the cover of algal turfs and decreased that of encrusting algae, with no net effect on species richness. Our results suggests that competition from C. cylindracea is an important determinant of benthic assemblage diversity in pristine environments, but less so in species-poor assemblages found at sites exposed to intense disturbance from land-based human activities, where either adverse physical factors or lack of propagules may constrain the number of potential native colonizers. Implementing measures to reduce the establishment and spread of C. cylindracea in areas little impacted by land-based human activities should be considered a priority for preserving the biodiversity of Mediterranean shallow rocky reefs.

Grammatical aspect, lexical aspect, and event duration constrain the availability of events in narratives.

PubMed

Becker, Raymond B; Ferretti, Todd R; Madden-Lombardi, Carol J

2013-11-01

The present study investigates how readers' representations of narratives are constrained by three sources of temporal information; grammatical aspect, lexical aspect, and the duration of intervening events. Participants read short stories in which a target event with an intrinsic endpoint or not (lexical aspect: accomplishments/activities) was described as ongoing or completed (grammatical aspect: imperfective/perfective). An intervening sentence described either a long or short duration event before the target situation was reintroduced later in the story. The electroencephalogram time-locked to the reintroduction of the target event elicited a larger N400 for perfective versus imperfective accomplishments, and this effect occurred only after short intervening events. Alternatively, the N400 to targets in the activity condition did not vary as a function of grammatical aspect or duration of intervening events. These results provide novel insight into how the temporal properties of events interact to constrain the availability of concepts in situation models. Copyright © 2013 Elsevier B.V. All rights reserved.

The Dermis as a Delivery Site of Trypanosoma brucei for Tsetse Flies

PubMed Central

Caljon, Guy; Van Reet, Nick; De Trez, Carl; Vermeersch, Marjorie; Pérez-Morga, David; Van Den Abbeele, Jan

2016-01-01

Tsetse flies are the sole vectors of Trypanosoma brucei parasites that cause sleeping sickness. Our knowledge on the early interface between the infective metacyclic forms and the mammalian host skin is currently highly limited. Glossina morsitans flies infected with fluorescently tagged T. brucei parasites were used in this study to initiate natural infections in mice. Metacyclic trypanosomes were found to be highly infectious through the intradermal route in sharp contrast with blood stream form trypanosomes. Parasite emigration from the dermal inoculation site resulted in detectable parasite levels in the draining lymph nodes within 18 hours and in the peripheral blood within 42 h. A subset of parasites remained and actively proliferated in the dermis. By initiating mixed infections with differentially labeled parasites, dermal parasites were unequivocally shown to arise from the initial inoculum and not from a re-invasion from the blood circulation. Scanning electron microscopy demonstrated intricate interactions of these skin-residing parasites with adipocytes in the connective tissue, entanglement by reticular fibers of the periadipocytic baskets and embedment between collagen bundles. Experimental transmission experiments combined with molecular parasite detection in blood fed flies provided evidence that dermal trypanosomes can be acquired from the inoculation site immediately after the initial transmission. High resolution thermographic imaging also revealed that intradermal parasite expansion induces elevated skin surface temperatures. Collectively, the dermis represents a delivery site of the highly infective metacyclic trypanosomes from which the host is systemically colonized and where a proliferative subpopulation remains that is physically constrained by intricate interactions with adipocytes and collagen fibrous structures. PMID:27441553

A High-Resolution Chronology of Rapid Forest Transitions following Polynesian Arrival in New Zealand

PubMed Central

McWethy, David B.; Wilmshurst, Janet M.; Whitlock, Cathy; Wood, Jamie R.; McGlone, Matt S.

2014-01-01

Human-caused forest transitions are documented worldwide, especially during periods when land use by dense agriculturally-based populations intensified. However, the rate at which prehistoric human activities led to permanent deforestation is poorly resolved. In the South Island, New Zealand, the arrival of Polynesians c. 750 years ago resulted in dramatic forest loss and conversion of nearly half of native forests to open vegetation. This transformation, termed the Initial Burning Period, is documented in pollen and charcoal records, but its speed has been poorly constrained. High-resolution chronologies developed with a series of AMS radiocarbon dates from two lake sediment cores suggest the shift from forest to shrubland occurred within decades rather than centuries at drier sites. We examine two sites representing extreme examples of the magnitude of human impacts: a drier site that was inherently more vulnerable to human-set fires and a wetter, less burnable site. The astonishing rate of deforestation at the hands of small transient populations resulted from the intrinsic vulnerability of the native flora to fire and from positive feedbacks in post-fire vegetation recovery that increased landscape flammability. Spatially targeting burning in highly-flammable seral vegetation in forests rarely experiencing fire was sufficient to create an alternate fire-prone stable state. The New Zealand example illustrates how seemingly stable forest ecosystems can experience rapid and permanent conversions. Forest loss in New Zealand is among the fastest ecological transitions documented in the Holocene; yet equally rapid transitions can be expected in present-day regions wherever positive feedbacks support alternate fire-inhibiting, fire-prone stable states. PMID:25372150

Using Airborne High Spectral Resolution Lidar Data to Evaluate Combined Active Plus Passive Retrievals of Aerosol Extinction Profiles

NASA Technical Reports Server (NTRS)

Burton, S. P.; Ferrare, R. A.; Kittaka, C.; Hostetler, C. A.; Hair, J. W.; Obland, M. D.; Rogers, R. R.; Cook, A. L.; Haper, D. B.

2008-01-01

Aerosol extinction profiles are derived from backscatter data by constraining the retrieval with column aerosol optical thickness (AOT), for example from coincident MODIS observations and without reliance on a priori assumptions about aerosol type or optical properties. The backscatter data were acquired with the NASA Langley High Spectral Resolution Lidar (HSRL). The HSRL also simultaneously measures extinction independently, thereby providing an ideal data set for evaluating the constrained retrieval of extinction from backscatter. We will show constrained extinction retrievals using various sources of column AOT, and examine comparisons with the HSRL extinction measurements and with a similar retrieval using data from the CALIOP lidar on the CALIPSO satellite.

Quorum sensing control of Type VI secretion factors restricts the proliferation of quorum-sensing mutants

PubMed Central

Majerczyk, Charlotte; Schneider, Emily; Greenberg, E Peter

2016-01-01

Burkholderia thailandensis uses acyl-homoserine lactone-mediated quorum sensing systems to regulate hundreds of genes. Here we show that cell-cell contact-dependent type VI secretion (T6S) toxin-immunity systems are among those activated by quorum sensing in B. thailandensis. We also demonstrate that T6S is required to constrain proliferation of quorum sensing mutants in colony cocultures of a BtaR1 quorum-sensing signal receptor mutant and its parent. However, the BtaR1 mutant is not constrained by and outcompetes its parent in broth coculture, presumably because no cell contact occurs and there is a metabolic cost associated with quorum sensing gene activation. The increased fitness of the wild type over the BtaR1 mutant during agar surface growth is dependent on an intact T6SS-1 apparatus. Thus, quorum sensing activates B. thailandensis T6SS-1 growth inhibition and this control serves to police and constrain quorum-sensing mutants. This work defines a novel role for T6SSs in intraspecies mutant control. DOI: http://dx.doi.org/10.7554/eLife.14712.001 PMID:27183270

Strain partitioning in southeastern Alaska: Is the Chatham Strait Fault active?

USGS Publications Warehouse

Brothers, Daniel; Elliott, Julie L.; Conrad, James E.; Haeussler, Peter J.; Kluesner, Jared

2018-01-01

A 1200 km-long transform plate boundary passes through southeastern Alaska and northwestern British Columbia and represents one of the most seismically active, but poorly understood continental margins of North America. Although most of the plate motion is accommodated by the right-lateral Queen Charlotte–Fairweather Fault (QCFF) System, which has produced at least six M > 7 earthquakes since 1920, seismic hazard assessments also include the Chatham Strait Fault (CSF) as a potentially active, 400 km-long strike slip fault that cuts northward through southeastern Alaska, connecting with the Eastern Denali Fault. Nearly the entire length of the CSF is submerged beneath Chatham Strait and Lynn Canal and has never been systematically imaged using high-resolution marine geophysical approaches. In this study we present an integrated analysis of new marine seismic reflectiondata acquired across Lynn Canal and tectonic block modeling constrained by data from continuous and campaign GPS sites. Seismic profiles cross the CSF at twelve locations spanning ∼50 km of fault length; they reveal thick (up to 300 m) packages of glaciomarine sedimentary facies emplaced on an unconformity surface that formed during the Last Glacial Maximum (LGM). Localized warping of post-LGM stratigraphy (∼13.9 kyr B.P. to present) appears to correlate with sediment drape on basement topography and current-controlled deposition. There is no evidence for an active fault along the axis of Lynn Canal in the seismic reflection data. Crustal block models constrained by GPS data allow, but do not require, a maximum slip rate of 2–3 mm/yr along the CSF; higher slip rates on the CSF result in significant misfit to GPS data in the surrounding region. Based on the combined marine geophysical and GPS observations, it is plausible that the CSF has not generated resolvable coseismic deformation in the last ∼13 ka and that the modern slip-rate is <1 mm/yr. We propose that models for strain transfer between the QCFF and the Denali Fault, and seismic hazard maps in general, may need to be reevaluated.

Strain partitioning in Southeastern Alaska: Is the Chatham Strait Fault active?

NASA Astrophysics Data System (ADS)

Brothers, Daniel S.; Elliott, Julie L.; Conrad, James E.; Haeussler, Peter J.; Kluesner, Jared W.

2018-01-01

A 1200 km-long transform plate boundary passes through southeastern Alaska and northwestern British Columbia and represents one of the most seismically active, but poorly understood continental margins of North America. Although most of the plate motion is accommodated by the right-lateral Queen Charlotte-Fairweather Fault (QCFF) System, which has produced at least six M > 7 earthquakes since 1920, seismic hazard assessments also include the Chatham Strait Fault (CSF) as a potentially active, 400 km-long strike slip fault that cuts northward through southeastern Alaska, connecting with the Eastern Denali Fault. Nearly the entire length of the CSF is submerged beneath Chatham Strait and Lynn Canal and has never been systematically imaged using high-resolution marine geophysical approaches. In this study we present an integrated analysis of new marine seismic reflection data acquired across Lynn Canal and tectonic block modeling constrained by data from continuous and campaign GPS sites. Seismic profiles cross the CSF at twelve locations spanning ∼50 km of fault length; they reveal thick (up to 300 m) packages of glaciomarine sedimentary facies emplaced on an unconformity surface that formed during the Last Glacial Maximum (LGM). Localized warping of post-LGM stratigraphy (∼13.9 kyr B.P. to present) appears to correlate with sediment drape on basement topography and current-controlled deposition. There is no evidence for an active fault along the axis of Lynn Canal in the seismic reflection data. Crustal block models constrained by GPS data allow, but do not require, a maximum slip rate of 2-3 mm/yr along the CSF; higher slip rates on the CSF result in significant misfit to GPS data in the surrounding region. Based on the combined marine geophysical and GPS observations, it is plausible that the CSF has not generated resolvable coseismic deformation in the last ∼13 ka and that the modern slip-rate is <1 mm/yr. We propose that models for strain transfer between the QCFF and the Denali Fault, and seismic hazard maps in general, may need to be reevaluated.

Rigid Ankle Foot Orthosis Deteriorates Mediolateral Balance Control and Vertical Braking during Gait Initiation

PubMed Central

Delafontaine, Arnaud; Gagey, Olivier; Colnaghi, Silvia; Do, Manh-Cuong; Honeine, Jean-Louis

2017-01-01

Rigid ankle-foot orthoses (AFO) are commonly used for impeding foot drop during the swing phase of gait. They also reduce pain and improve gait kinematics in patients with weakness or loss of integrity of ankle-foot complex structures due to various pathological conditions. However, this comes at the price of constraining ankle joint mobility, which might affect propulsive force generation and balance control. The present study examined the effects of wearing an AFO on biomechanical variables and electromyographic activity of tibialis anterior (TA) and soleus muscles during gait initiation (GI). Nineteen healthy adults participated in the study. They initiated gait at a self-paced speed with no ankle constraint as well as wearing an AFO on the stance leg, or bilaterally. Constraining the stance leg ankle decreased TA activity ipsilaterally during the anticipatory postural adjustment (APA) of GI, and ipsilateral soleus activity during step execution. In the sagittal plane, the decrease in the stance leg TA activity reduced the backward displacement of the center of pressure (CoP) resulting in a reduction of the forward velocity of the center of mass (CoM) measured at foot contact (FC). In the frontal plane, wearing the AFO reduced the displacement of the CoP in the direction of the swing leg during the APA phase. The mediolateral velocity of the CoM increased during single-stance prompting a larger step width to recover balance. During step execution, the CoM vertical downward velocity is normally reduced in order to lessen the impact of the swing leg with the floor and facilitates the rise of the CoM that occurs during the subsequent double-support phase. The reduction in stance leg soleus activity caused by constraining the ankle weakened the vertical braking of the CoM during step execution. This caused the absolute instantaneous vertical velocity of the CoM at FC to be greater in the constrained conditions with respect to the control condition. From a rehabilitation perspective, passively- or actively-powered assistive AFOs could correct for the reduction in muscle activity and enhance balance control during GI of patients. PMID:28503144

Using degrees of rate control to improve selective n-butane oxidation over model MOF-encapsulated catalysts: sterically-constrained Ag 3 Pd(111)

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

Dix, Sean T.; Scott, Joseph K.; Getman, Rachel B.

2016-01-01

Metal nanoparticles encapsulated within metal organic frameworks (MOFs) offer steric restrictions near the catalytic metal that can improve selectivity, much like in enzymes. A microkinetic model is developed for the regio-selective oxidation ofn-butane to 1-butanol with O 2over a model for MOF-encapsulated bimetallic nanoparticles. The model consists of a Ag 3Pd(111) surface decorated with a 2-atom-thick ring of (immobile) helium atoms which creates an artificial pore of similar size to that in common MOFs, which sterically constrains the adsorbed reaction intermediates. The kinetic parameters are based on energies calculated using density functional theory (DFT). The microkinetic model was analysed atmore » 423 K to determine the dominant pathways and which species (adsorbed intermediates and transition states in the reaction mechanism) have energies that most sensitively affect the reaction rates to the different products, using degree-of-rate-control (DRC) analysis. This analysis revealed that activation of the C–H bond is assisted by adsorbed oxygen atoms, O*. Unfortunately, O* also abstracts H from adsorbed 1-butanol and butoxy as well, leading to butanal as the only significant product. This suggested to (1) add water to produce more OH*, thus inhibiting these undesired steps which produce OH*, and (2) eliminate most of the O 2pressure to reduce the O* coverage, thus also inhibiting these steps. Combined with increasing butane pressure, this dramatically improved the 1-butanol selectivity (from 0 to 95%) and the rate (to 2 molecules per site per s). Moreover, 40% less O 2was consumed per oxygen atom in the products. Under these conditions, a terminal H in butane is directly eliminated to the Pd site, and the resulting adsorbed butyl combines with OH* to give the desired 1-butanol. These results demonstrate that DRC analysis provides a powerful approach for optimizing catalytic process conditions, and that highly selectivity oxidation can sometimes be achieved by using a mixture of O 2and H 2O as the oxidant. This was further demonstrated by DRC analysis of a second microkinetic model based on a related but hypothetical catalyst, where the activation energies for two of the steps were modified.« less

Finding Faults: Tohoku and other Active Megathrusts/Megasplays

NASA Astrophysics Data System (ADS)

Moore, J. C.; Conin, M.; Cook, B. J.; Kirkpatrick, J. D.; Remitti, F.; Chester, F.; Nakamura, Y.; Lin, W.; Saito, S.; Scientific Team, E.

2012-12-01

Current subduction-fault drilling procedure is to drill a logging hole, identify target faults, then core and instrument them. Seismic data may constrain faults but the additional resolution of borehole logs is necessary for efficient coring and instrumentation under difficult conditions and tight schedules. Thus, refining the methodology of identifying faults in logging data has become important, and thus comparison of log signatures of faults in different locations is worthwhile. At the C0019 (JFAST) drill site, the Tohoku megathrust was principally identified as a decollement where steep cylindrically-folded bedding abruptly flattens below the basal detachment. A similar structural contrast occurs across a megasplay fault in the NanTroSEIZE transect (Site C0004). At the Tohoku decollement, a high gamma-ray value from a pelagic clay layer, predicted as a likely decollement sediment type, strengthens the megathrust interpretation. The original identification of the pelagic clay as a decollement candidate was based on results of previous coring of an oceanic reference site. Negative density anomalies, often seen as low resistivity zones, identified a subsidiary fault in the deformed prism overlying the Tohoku megathrust. Elsewhere, at Barbados, Nankai (Moroto), and Costa Rica, negative density anomalies are associated with the decollement and other faults in hanging walls. Log-based density anomalies in fault zones provide a basis for recognizing in-situ fault zone dilation. At the Tohoku Site C0019, breakouts are present above but not below the megathrust. Changes in breakout orientation and width (stress magnitude) occur across megasplay faults at Sites C0004 and C0010 in the NantroSEIZE transect. Annular pressure anomalies are not apparent at the Tohoku megathrust, but are variably associated with faults and fracture zones drilled along the NanTroSEIZE transect. Overall, images of changes in structural features, negative density anomalies, and changes in breakout occurrence and orientation provide the most common log criteria for recognizing major thrust zones in ocean drilling holes at convergent margins. In the case of JFAST, identification of faults by logging was confirmed during subsequent coring activities, and logging data was critical for successful placement of the observatory down hole.

Coupling of physical erosion and chemical weathering after phases of intense human activity

NASA Astrophysics Data System (ADS)

Schoonejans, Jerome; Vanacker, Veerle; Opfergelt, Sophie; Ameijeiras-Mariño, Yolanda; Kubik, Peter W.

2014-05-01

Anthropogenic disturbance of natural vegetation profoundly alters the lateral and vertical fluxes of soil nutrients and particles at the land surface. Human-induced acceleration of soil erosion can thereby result in an imbalance between physical erosion, soil production and chemical weathering. The (de-)coupling between physical erosion and chemical weathering in ecosystems with strong anthropogenic disturbances is not yet fully understood, as earlier studies mostly focused on natural ecosystems. In this study, we explore the chemical weathering intensity for four study sites located in the Internal Zone of the Spanish Betic Cordillera. Most of the sites belong to the Nevado-Filabres complex, but are characterized by different rates of long-term exhumation, 10Be catchment-wide denudation and hill slope morphology. Denudation rates are generally low, but show large variation between the three sites (from 23 to 246 mm kyr-1). The magnitude of denudation rates is consistent with longer-term uplift rates derived from marine deposits, fission-track measurements and vertical fault slip rates. Two to three soil profiles were sampled per study site at exposed ridge tops. All soils overly fractured mica schist, and are very thin (< 60cm). In each soil profile, we sampled 5 depth slices, rock fragments and the (weathered) bedrock. In total, 38 soil and 20 rock samples were analyzed for their chemical composition. The chemical weathering intensity is constrained by the Chemical Depletion Fraction that is based on a chemical mass balance approach using Zr as an immobile element. Chemical weathering accounts for 5 to 35% of the total mass lost due to denudation. We observe systematically higher chemical weathering intensities (CDFs) in sites with lower denudation rates (and vice versa), suggesting that weathering is supply-limited. Our measurements of soil elemental losses from 10 soil profiles suggest that the observed variation in chemical weathering is strongly associated with long-term 10Be derived denudation rates, and tectonic uplift rates. Our data do not provide direct evidence of an imbalance between soil production and chemical weathering, despite more than 2000 years of intense human activity.

Modeling and simulating networks of interdependent protein interactions.

PubMed

Stöcker, Bianca K; Köster, Johannes; Zamir, Eli; Rahmann, Sven

2018-05-21

Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of these systems emerge not only from the protein interactions themselves but also from the dependencies between these interactions, as generated by allosteric effects or mutual exclusion due to steric hindrance. Therefore, formal models for integrating and utilizing information about interaction dependencies are of high interest. Here, we describe an approach for endowing protein networks with interaction dependencies using propositional logic, thereby obtaining constrained protein interaction networks ("constrained networks"). The construction of these networks is based on public interaction databases as well as text-mined information about interaction dependencies. We present an efficient data structure and algorithm to simulate protein complex formation in constrained networks. The efficiency of the model allows fast simulation and facilitates the analysis of many proteins in large networks. In addition, this approach enables the simulation of perturbation effects, such as knockout of single or multiple proteins and changes of protein concentrations. We illustrate how our model can be used to analyze a constrained human adhesome protein network, which is responsible for the formation of diverse and dynamic cell-matrix adhesion sites. By comparing protein complex formation under known interaction dependencies versus without dependencies, we investigate how these dependencies shape the resulting repertoire of protein complexes. Furthermore, our model enables investigating how the interplay of network topology with interaction dependencies influences the propagation of perturbation effects across a large biochemical system. Our simulation software CPINSim (for Constrained Protein Interaction Network Simulator) is available under the MIT license at http://github.com/BiancaStoecker/cpinsim and as a Bioconda package (https://bioconda.github.io).

Using 10Be erosion rates and fluvial channel morphology to constrain fault throw rates in the southwestern Sacramento River Valley, California, USA

NASA Astrophysics Data System (ADS)

Cyr, A. J.

2013-12-01

The Sacramento - San Joaquin River Delta, California, USA, is a critical region for California water resources, agriculture, and threatened or endangered species. This landscape is affected by an extensive set of levees that enclose artificial islands created for agricultural use. In addition to their importance for sustaining agriculture, this levee system also supports extensive transport and power transmission infrastructure and urban/suburban development. These levees are susceptible to damage from even moderate ground shaking by either a large earthquake on one of the high-activity faults in the nearby San Francisco Bay region, or even a moderate earthquake on one of the low-activity faults in the Delta region itself. However, despite this danger the earthquake hazards in this region are poorly constrained due to our lack of understanding of faults in and near the Delta region. As part of an effort to better constrain the seismic hazard associated with known, but poorly constrained, faults in the region, a geomorphic analysis of the Dunnigan Hills, northwest of Woodland, CA, is being combined with cosmogenic 10Be catchment-averaged erosion rates. The Dunnigan Hills are a low-relief (maximum elevation 87 m) landscape generated by fault-bend folding above the west-vergent Sweitzer reverse fault that soles into a blind east-vergent reverse fault. These faults have been imaged by seismic reflection data, and local microseismicity indicates that this system is actively propagating to the east. However, the throw rates on the faults in this system remain unconstrained, despite the potential for significant shaking such as that experienced in the nearby April, 1892 earthquake sequence between Winters and Vacaville, Ca, ~25 km to the south, which has been estimated at magnitude 6.0 or greater. Geomorphic and cosmogenic 10Be analyses from 12 catchments draining the eastern flank of the Dunnigan Hills will be used to infer vertical rock uplift rates to better constrain activity on the west-vergent Sweitzer fault and the east-vergent blind reverse fault. All of the sampled catchments are underlain exclusively by Tehama Sandstone. Moreover, there are no mapped surface traces of faults in the sampled catchments. This minimizes the possibility of changes in lithogic resistance to impact the erosion rates and channel analyses. These analyses, combined with fault geometries derived from published seismic reflection data and structural cross sections, allows us to constrain the throw rates on these faults and thus better evaluate the associated seismic hazard.

Global Kinetic Analysis of Mammalian E3 Reveals pH-dependent NAD+/NADH Regulation, Physiological Kinetic Reversibility, and Catalytic Optimum*

PubMed Central

Moxley, Michael A.; Beard, Daniel A.; Bazil, Jason N.

2016-01-01

Mammalian E3 is an essential mitochondrial enzyme responsible for catalyzing the terminal reaction in the oxidative catabolism of several metabolites. E3 is a key regulator of metabolic fuel selection as a component of the pyruvate dehydrogenase complex (PDHc). E3 regulates PDHc activity by altering the affinity of pyruvate dehydrogenase kinase, an inhibitor of the enzyme complex, through changes in reduction and acetylation state of lipoamide moieties set by the NAD+/NADH ratio. Thus, an accurate kinetic model of E3 is needed to predict overall mammalian PDHc activity. Here, we have combined numerous literature data sets and new equilibrium spectroscopic experiments with a multitude of independently collected forward and reverse steady-state kinetic assays using pig heart E3. The latter kinetic assays demonstrate a pH-dependent transition of NAD+ activation to inhibition, shown here, to our knowledge, for the first time in a single consistent data set. Experimental data were analyzed to yield a thermodynamically constrained four-redox-state model of E3 that simulates pH-dependent activation/inhibition and active site redox states for various conditions. The developed model was used to determine substrate/product conditions that give maximal E3 rates and show that, due to non-Michaelis-Menten behavior, the maximal flux is different compared with the classically defined kcat. PMID:26644471

Constraining land carbon cycle process understanding with observations of atmospheric CO2 variability

NASA Astrophysics Data System (ADS)

Collatz, G. J.; Kawa, S. R.; Liu, Y.; Zeng, F.; Ivanoff, A.

2013-12-01

We evaluate our understanding of the land biospheric carbon cycle by benchmarking a model and its variants to atmospheric CO2 observations and to an atmospheric CO2 inversion. Though the seasonal cycle in CO2 observations is well simulated by the model (RMSE/standard deviation of observations <0.5 at most sites north of 15N and <1 for Southern Hemisphere sites) different model setups suggest that the CO2 seasonal cycle provides some constraint on gross photosynthesis, respiration, and fire fluxes revealed in the amplitude and phase at northern latitude sites. CarbonTracker inversions (CT) and model show similar phasing of the seasonal fluxes but agreement in the amplitude varies by region. We also evaluate interannual variability (IAV) in the measured atmospheric CO2 which, in contrast to the seasonal cycle, is not well represented by the model. We estimate the contributions of biospheric and fire fluxes, and atmospheric transport variability to explaining observed variability in measured CO2. Comparisons with CT show that modeled IAV has some correspondence to the inversion results >40N though fluxes match poorly at regional to continental scales. Regional and global fire emissions are strongly correlated with variability observed at northern flask sample sites and in the global atmospheric CO2 growth rate though in the latter case fire emissions anomalies are not large enough to account fully for the observed variability. We discuss remaining unexplained variability in CO2 observations in terms of the representation of fluxes by the model. This work also demonstrates the limitations of the current network of CO2 observations and the potential of new denser surface measurements and space based column measurements for constraining carbon cycle processes in models.

Postglacial relative sea-level history of the Prince Rupert area, British Columbia, Canada

NASA Astrophysics Data System (ADS)

Letham, Bryn; Martindale, Andrew; Macdonald, Rebecca; Guiry, Eric; Jones, Jacob; Ames, Kenneth M.

2016-12-01

This paper presents a history of relative sea level (RSL) change for the last 15,000 years in the Prince Rupert region on the northern coast of British Columbia, Canada. One hundred twenty-three radiocarbon ages of organic material from isolation basin cores, sediment sequence exposures, and archaeological sites having a recognized relation to past sea levels constrain postglacial RSL. The large number of new measurements relating to past sea-level provides a well constrained RSL curve that differs in significant ways from previously published results. After deglaciation following the Last Glacial Maximum, the region experienced an isostatically-induced rapid RSL drop from as much 50 m asl to as low as -6.3 m asl in as little as a few centuries between 14,500 BP and 13,500 BP. After a lowstand below current sea level for about 2000 years during the terminal Pleistocene, RSL rose again to a highstand at least 6 m asl after the end of the Younger Dryas. RSL slowly dropped through the Holocene to close to its current position by 2000-1500 BP, with some potential fluctuations between 3500 and 1500 BP. This study highlights variation in RSL histories across relatively short distances, which must be accounted for by local RSL reconstructions such as this one. This RSL curve aided in the identification of an 8000-9000 year old archaeological site on a 10-12 m asl terrace, which is currently the earliest dated archaeological site in the area, and it provides guidance for searching for even older archaeological remains. We highlight the utility and potential of this refined RSL history for developing surveys for other archaeological sites associated with paleoshorelines.

New Hybridized Surface Wave Approach for Geotechnical Modeling of Shear Wave Velocity at Strong Motion Recording Stations

NASA Astrophysics Data System (ADS)

Kayen, R.; Carkin, B.; Minasian, D.

2006-12-01

Strong motion recording (SMR) networks often have little or no shear wave velocity measurements at stations where characterization of site amplification and site period effects is needed. Using the active Spectral Analysis of Surface Waves (SASW) method, and passive H/V microtremor method we have investigated nearly two hundred SMR sites in California, Alaska, Japan, Australia, China and Taiwan. We are conducting these studies, in part, to develop a new hybridized method of site characterization that utilizes a parallel array of harmonic-wave sources for active-source SASW, and a single long period seismometer for passive-source microtremor measurement. Surface wave methods excel in their ability to non-invasively and rapidly characterize the variation of ground stiffness properties with depth below the surface. These methods are lightweight, inexpensive to deploy, and time-efficient. They have been shown to produce accurate and deep soil stiffness profiles. By placing and wiring shakers in a large parallel circuit, either side-by-side on the ground or in a trailer-mounted array, a strong in-phase harmonic wave can be produced. The effect of arraying many sources in parallel is to increase the amplitude of waves received at far-away spaced seismometers at low frequencies so as to extend the longest wavelengths of the captured dispersion curve. The USGS system for profiling uses this concept by arraying between two and eight electro-mechanical harmonic-wave shakers. With large parallel arrays of vibrators, a dynamic force in excess of 1000 lb can be produced to vibrate the ground and produce surface waves. We adjust the harmonic wave through a swept-sine procedure to profile surface wave dispersion down to a frequency of 1 Hz and out to surface wave-wavelengths of 200-1000 meters, depending on the site stiffness. The parallel-array SASW procedure is augmented using H/V microtremor data collected with the active source turned off. Passive array microtremor data reveal the natural and resonance characteristics of the ground by capturing persistent natural vibrations. These microtremors are the result of the interaction of surface waves arriving from distant sources and the stiffness structure of the site under investigation. As such, these resonance effects are effective in constraining the layer thicknesses of the SASW shear wave velocity structure and aid in determining the depth of the deepest layer. Together, the hybridized SASW and H/V procedure provides a complete data set for modeling the geotechnical aspects of ground amplification of earthquake motions. Data from these investigations are available at http://walrus.wr.usgs.gov/geotech.

Constrained optimal multi-phase lunar landing trajectory with minimum fuel consumption

NASA Astrophysics Data System (ADS)

Mathavaraj, S.; Pandiyan, R.; Padhi, R.

2017-12-01

A Legendre pseudo spectral philosophy based multi-phase constrained fuel-optimal trajectory design approach is presented in this paper. The objective here is to find an optimal approach to successfully guide a lunar lander from perilune (18km altitude) of a transfer orbit to a height of 100m over a specific landing site. After attaining 100m altitude, there is a mission critical re-targeting phase, which has very different objective (but is not critical for fuel optimization) and hence is not considered in this paper. The proposed approach takes into account various mission constraints in different phases from perilune to the landing site. These constraints include phase-1 ('braking with rough navigation') from 18km altitude to 7km altitude where navigation accuracy is poor, phase-2 ('attitude hold') to hold the lander attitude for 35sec for vision camera processing for obtaining navigation error, and phase-3 ('braking with precise navigation') from end of phase-2 to 100m altitude over the landing site, where navigation accuracy is good (due to vision camera navigation inputs). At the end of phase-1, there are constraints on position and attitude. In Phase-2, the attitude must be held throughout. At the end of phase-3, the constraints include accuracy in position, velocity as well as attitude orientation. The proposed optimal trajectory technique satisfies the mission constraints in each phase and provides an overall fuel-minimizing guidance command history.

40Ar/(39)Ar geochronology and paleomagnetic stratigraphy of the Lukeino and lower Chemeron Formations at Tabarin and Kapcheberek, Tugen Hills, Kenya.

PubMed

Deino, Alan L; Tauxe, Lisa; Monaghan, Marc; Hill, Andrew

2002-01-01

(40)Ar/(39)Ar single-crystal laser-fusion dating, K-Ar dating, and paleomagnetic reversal stratigraphy have been used to determine the chronostratigraphy of the Kabarnet Trachyte, Lukeino Formation, Kaparaina Basalt Formation, and Chemeron Formation at the sites of Kapcheberek (BPRP#77) and Tabarin (BPRP#77) in the Tugen Hills, Kenya. The succession ranges in age from 6.56-3.8 Ma. The upper Lukeino Formation at Kapcherberek, including the fauna from the site BPRP#76, was deposited during chron C3r and can be constrained to the interval 5.88-5.72 Ma. The Chemeron Formation at Tabarin includes at the base an ignimbrite and associated basal air-fall tuff with a combined age of 5.31+/-0.03 Ma. Sedimentary and volcaniclastic rocks of the Chemeron Formation which unconformably overlie the ignimbrite record chrons C3n.2n through C2Ar. The combined(40)Ar/(39)Ar and paleomagnetic data constrain the age of this sequence to 4.63-3.837 Ma. The age of the Tabarin mandible fragment (KNM-TH 13150) and associated fauna at site BPRP#77 in the Chemeron Formation is 4.48-4.41 Ma, marginally older than similar early hominids from Aramis, Ethiopia. Basin subsidence appears to be defining an overall accumulation rate of about 17 cm/ka over the 2.7 Ma represented at Tabarin and Kapcheberek, despite episodes of rapid accumulation and hiatuses. Copyright 2002 Academic Press.

Constrained ℋ∞ control for low bandwidth active suspensions

NASA Astrophysics Data System (ADS)

Wasiwitono, Unggul; Sutantra, I. Nyoman

2017-08-01

Low Bandwidth Active Suspension (LBAS) is shown to be more competitive to High Bandwidth Active Suspension (HBAS) when energy and cost aspects are taken into account. In this paper, the constrained ℋ∞ control scheme is applied for LBAS system. The ℋ∞ performance is used to measure ride comfort while the concept of reachable set in a state-space ellipsoid defined by a quadratic storage function is used to capture the time domain constraint that representing the requirements for road holding, suspension deflection limitation and actuator saturation. Then, the control problem is derived in the framework of Linear Matrix Inequality (LMI) optimization. The simulation is conducted considering the road disturbance as a stationary random process. The achievable performance of LBAS is analyzed for different values of bandwidth and damping ratio.

Bumetanide for autism: more eye contact, less amygdala activation.

PubMed

Hadjikhani, Nouchine; Åsberg Johnels, Jakob; Lassalle, Amandine; Zürcher, Nicole R; Hippolyte, Loyse; Gillberg, Christopher; Lemonnier, Eric; Ben-Ari, Yehezkel

2018-02-26

We recently showed that constraining eye contact leads to exaggerated increase of amygdala activation in autism. Here, in a proof of concept pilot study, we demonstrate that administration of bumetanide (a NKCC1 chloride importer antagonist that restores GABAergic inhibition) normalizes the level of amygdala activation during constrained eye contact with dynamic emotional face stimuli in autism. In addition, eye-tracking data reveal that bumetanide administration increases the time spent in spontaneous eye gaze during in a free-viewing mode of the same face stimuli. In keeping with clinical trials, our data support the Excitatory/Inhibitory dysfunction hypothesis in autism, and indicate that bumetanide may improve specific aspects of social processing in autism. Future double-blind placebo controlled studies with larger cohorts of participants will help clarify the mechanisms of bumetanide action in autism.

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

PubMed Central

Zimmerman, Naupaka B.; Vitousek, Peter M.

2012-01-01

We surveyed endophytic fungal communities in leaves of a single tree species (Metrosideros polymorpha) across wide environmental gradients (500–5,500 mm of rain/y; 10–22 °C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai’i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551 ± 134 taxonomic units per site). However, among-site diversity contributed even more than did within-site diversity to the overall richness of more than 4,200 taxonomic units observed in M. polymorpha, and this among-site variation in endophyte community composition correlated strongly with temperature and rainfall. These results are consistent with suggestions that foliar endophytic fungi are hyperdiverse. They further suggest that microbial diversity may be even greater than has been assumed and that broad-scale environmental controls such as temperature and rainfall can structure eukaryotic microbial diversity. Appropriately constrained study systems across strong environmental gradients present a useful means to understand the environmental factors that structure the diversity of microbial communities. PMID:22837398

Effects of common seagrass restoration methods on ecosystem structure in subtropical seagrass meadows.

PubMed

Bourque, Amanda S; Fourqurean, James W

2014-06-01

Seagrass meadows near population centers are subject to frequent disturbance from vessel groundings. Common seagrass restoration methods include filling excavations and applying fertilizer to encourage seagrass recruitment. We sampled macrophytes, soil structure, and macroinvertebrate infauna at unrestored and recently restored vessel grounding disturbances to evaluate the effects of these restoration methods on seagrass ecosystem structure. After a year of observations comparing filled sites to both undisturbed reference and unrestored disturbed sites, filled sites had low organic matter content, nutrient pools, and primary producer abundance. Adding a nutrient source increased porewater nutrient pools at disturbed sites and in undisturbed meadows, but not at filled sites. Environmental predictors of infaunal community structure across treatments included soil texture and nutrient pools. At the one year time scale, the restoration methods studied did not result in convergence between restored and unrestored sites. Particularly in filled sites, soil conditions may combine to constrain rapid development of the seagrass community and associated infauna. Our study is important for understanding early recovery trajectories following restoration using these methods. Published by Elsevier Ltd.

Shallow seismic imaging of folds above the Puente Hills blind-thrust fault, Los Angeles, California

USGS Publications Warehouse

Pratt, T.L.; Shaw, J.H.; Dolan, J.F.; Christofferson, S.A.; Williams, R.A.; Odum, J.K.; Plesch, A.

2002-01-01

High-resolution seismic reflection profiles image discrete folds in the shallow subsurface (<600 m) above two segments of the Puente Hills blind-thrust fault system, Los Angeles basin, California. The profiles demonstrate late Quaternary activity at the fault tip, precisely locate the axial surfaces of folds within the upper 100 m, and constrain the geometry and kinematics of recent folding. The Santa Fe Springs segment of the Puente Hills fault zone shows an upward-narrowing kink band with an active anticlinal axial surface, consistent with fault-bend folding above an active thrust ramp. The Coyote Hills segment shows an active synclinal axial surface that coincides with the base of a 9-m-high scarp, consistent with tip-line folding or the presence of a backthrust. The seismic profiles pinpoint targets for future geologic work to constrain slip rates and ages of past events on this important fault system.

A highland sample strategy for Pathfinder

NASA Technical Reports Server (NTRS)

Dehon, Rene A.

1994-01-01

Potential landing sites are confined to latitudes between 0 deg and 30 deg N and surfaces below 0 km elevation. The landing ellipse is 100 x 200 km oriented N 74 deg E. The constraints essentially eliminate the slopes of Elysium Mons, Olympus Mons, Tharsis Ridge, Lunae Plaunum, all the southern highlands, and almost all the Noachian material of Arabia Terra. Those areas that remain as potential landing sites are chiefly lowland plains of Amazonis Chryse, Isidis, and Elysium Planitia. Any attempt to sample highland material further constrains the possible landing sites by eliminating areas of Hesperian or Amazonian lavas and sediments. One possible sampling strategy is to sample materials within those few 'highland' terrains that extend to low elevations. A second strategy is to sample materials at the mouth of an outflow channel that drains from the highlands. Potential landing sites include outflow channel material at the edge of Chryse Planitia and highland materials bordering southern Amazonis Planitia.

Design and control strategy for a hybrid green energy system for mobile telecommunication sites

NASA Astrophysics Data System (ADS)

Okundamiya, Michael S.; Emagbetere, Joy O.; Ogujor, Emmanuel A.

2014-07-01

The rising energy costs and carbon footprint of operating mobile telecommunication sites in the emerging world have increased research interests in green technology. The intermittent nature of most green energy sources creates the problem of designing the optimum configuration for a given location. This study presents the design analysis and control strategy for a cost effective and reliable operation of the hybrid green energy system (HGES) for GSM base transceiver station (BTS) sites in isolated regions. The design constrains the generation and distribution of power to reliably satisfy the energy demand while ensuring safe operation of the system. The overall process control applies the genetic algorithm-based technique for optimal techno-economic sizing of system's components. The process simulation utilized meteorological data for 3 locations (Abuja, Benin City and Sokoto) with varying climatic conditions in Nigeria. Simulation results presented for green GSM BTS sites are discussed and compared with existing approaches.

Strong Purifying Selection at Synonymous Sites in D. melanogaster

PubMed Central

Lawrie, David S.; Messer, Philipp W.; Hershberg, Ruth; Petrov, Dmitri A.

2013-01-01

Synonymous sites are generally assumed to be subject to weak selective constraint. For this reason, they are often neglected as a possible source of important functional variation. We use site frequency spectra from deep population sequencing data to show that, contrary to this expectation, 22% of four-fold synonymous (4D) sites in Drosophila melanogaster evolve under very strong selective constraint while few, if any, appear to be under weak constraint. Linking polymorphism with divergence data, we further find that the fraction of synonymous sites exposed to strong purifying selection is higher for those positions that show slower evolution on the Drosophila phylogeny. The function underlying the inferred strong constraint appears to be separate from splicing enhancers, nucleosome positioning, and the translational optimization generating canonical codon bias. The fraction of synonymous sites under strong constraint within a gene correlates well with gene expression, particularly in the mid-late embryo, pupae, and adult developmental stages. Genes enriched in strongly constrained synonymous sites tend to be particularly functionally important and are often involved in key developmental pathways. Given that the observed widespread constraint acting on synonymous sites is likely not limited to Drosophila, the role of synonymous sites in genetic disease and adaptation should be reevaluated. PMID:23737754

The structure of the herpetofaunal assemblage in the Douglas-fir/hardwood forests of northwestern California and southwestern Oregon

Treesearch

Hart Welsh; A.J. Lind

1991-01-01

Terrestrial and aquatic herpetofauna were sampled by three methods, time-constrained searches, pitfall traps, and areaconstrained searches from 1984 to 1986 in northwestern California and southwestern Oregon. The 54 terrestrial and 39 aquatic study sites were in Douglas-fir/hardwood forest stands that ranged in age from 30 to 560 years. Results of these surveys are...

Hydraulic architecture and photosynthetic capacity as constraints on release from suppression in Douglas-fir and western hemlock.

Treesearch

Renninger H.J.; Meinzer F.C.; B.L. Gartner

2006-01-01

We compared hydraulic architecture, photosynthesis, and growth in Douglas-fir with that of a shade-tolerant western hemlock. The study was conducted in a site that had been thinned to release suppressed trees, and one that remained unthinned. Release seemed to be constrained initially by photosynthetic capacity in both species. After released trees increased their...

Comparison of soil organic matter dynamics at five temperate deciduous forests with physical fractionation and radiocarbon measurements

Treesearch

Karis J. McFarlane; Margaret S. Torn; Paul J. Hanson; Rachel C. Porras; Christopher W. Swanston; Mac A. Callaham; Thomas P. Guilderson

2013-01-01

Forest soils represent a significant pool for carbon sequestration and storage, but the factors controlling soil carbon cycling are not well constrained.We compared soil carbon dynamics at five broadleaf forests in the Eastern US that vary in climate, soil type, and soil ecology: two sites at the University of Michigan Biological Station (MI-Coarse, sandy;MI-Fine,...

Investigating the Mechanisms of Learning from a Constrained Preparation for Future Learning Activity

ERIC Educational Resources Information Center

Siler, Stephanie A.; Klahr, David; Price, Norman

2013-01-01

Many studies have shown benefits associated with engaging students in problem-solving activities prior to administering lessons. These problem-solving activities are assumed to activate relevant knowledge and allow students to develop some initial knowledge structures, which support understanding of the lesson. In this paper we report the results…

Three-dimensional magnetotelluric imaging of Cascadia subduction zone from an amphibious array

NASA Astrophysics Data System (ADS)

Yang, B.; Egbert, G. D.; Key, K.; Bedrosian, P.; Livelybrooks, D.; Schultz, A.

2016-12-01

We present results from three-dimensional inversion of an amphibious magnetotelluric (MT) array consisting of 71 offshore and 75 onshore sites in the central part of Cascadia, to image down-dip and along strike variations of electrical conductivity, and constrain the 3D distribution of fluids and melt in the subduction zone. A larger scale array consisting of EarthScope transportable-array data and several 2D legacy profiles (e.g. EMSLAB, CAFE-MT, SWORMT) which covers WA, OR, northern CA and northern NV has been inverted separately, to provide a broader view of the subduction zone. Inverting these datasets including seafloor data, and involving strong coast effects presents many challenges, especially for the nominal TE mode impedances which have very anomalous phases in both land and seafloor sites. We find that including realistic bathymetry and conductive seafloor sediments significantly stabilizes the inversion, and that a two stage inversion strategy, first emphasizing fit to the more challenging TE data, improved overall data fits. We have also constrained the geometry of the (assumed resistive) subducting plates by extracting morphological parameters (e.g. upper boundary and thickness) from seismological models (McCrory et al 2012, Schmandt and Humphreys 2010). These constraints improve recovery and resolution of subduction related conductivity features. With the strategies mentioned above, we improved overall data fits, resulting in a model which reveals (for the first time) a conductive oceanic asthenosphere, extending under the North America plate. The most striking model features are conductive zones along the plate interface, including a continuous stripe of high conductivity just inboard of the coast, extending from the northern limits of our model in Washington state, to north-central Oregon. High conductivities also occur in patches near the tip of the mantle wedge, at depths appropriate for eclogitization, and at greater depth beneath the arc, in places extending downdip well into the back-arc. By comparing the two inversions, with and without seafloor data, we demonstrate the role of the offshore sites in constraining important model features.

Hydraulic architecture and photosynthetic capacity as constraints on release from suppression in Douglas-fir and western hemlock.

PubMed

Renninger, Heidi J; Meinzer, Frederick C; Gartner, Barbara L

2007-01-01

We compared hydraulic architecture, photosynthesis and growth in Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), a shade-intolerant species, and western hemlock (Tsuga heterophylla (Raf.) Sarg.), a shade-tolerant species, to study the temporal pattern of release from suppressive shade. In particular, we sought to determine whether hydraulic architecture or photosynthetic capacity is most important in constraining release. The study was conducted at two sites with mixed stands of 10- to 20-year-old Douglas-fir and western hemlock. At one site, the stand had been thinned allowing release of the understory trees, whereas at the other site, the stand remained unthinned. Douglas-fir had lower height growth (from 1998-2003) and lower relative height growth (height growth from 1998 to 2003/height in 1998) than western hemlock. However, relative height growth of released versus suppressed trees was higher in Douglas-fir (130%) than in western hemlock (65%), indicating that, although absolute height growth was less, Douglas-fir did release from suppression. Release seemed to be constrained initially by a limited photosynthetic capacity in both species. Five years after release, Douglas-fir trees had 14 times the leaf area and 1.5 times the leaf nitrogen concentration (N (area)) of suppressed trees. Needles of released western hemlock trees had about twice the maximum assimilation rate (A (max)) at ambient [CO(2)] as needles of suppressed trees and exhibited no photoinhibition at the highest irradiances. After release, trees increased in leaf area, leaf N concentration and overall photosynthetic capacity. Subsequently, hydraulic architecture appeared to constrain release in Douglas-fir and, to a lesser extent, in western hemlock. Released trees had significantly less negative foliar delta(13)C values than suppressed trees and showed a positive relationship between leaf area:sapwood area ratio (A (L)/A (S)) and delta(13)C, suggesting that trees with more leaf area for a given sapwood area experienced a stomatal limitation on carbon gain. Nonetheless, these changes had no significant effects on leaf specific conductivities of suppressed versus released trees of either species, but leaf specific root conductance was significantly lower in released Douglas-fir.

Shallow structure of the InSight 2018 landing site in Elysium Planitia, Mars, from ambient vibration Rayleigh wave ellipticity: A modeling study

NASA Astrophysics Data System (ADS)

Knapmeyer-Endrun, B.; Golombek, M.; Ohrnberger, M. M.

2016-12-01

The SEIS (Seismic Experiment for Interior Structure) instrument onboard NASA's InSight mission, scheduled to land in November 2018, will be the first seismometer directly deployed on the surface of Mars. From studies on both the Earth and the Moon, it is well known that site amplification in low-velocity sediments, e.g. regolith, on top of more competent rocks has a strong influence on seismic signals, but can also be used to constrain the subsurface structure. Based on orbital data, lab measurements and terrestrial analogues, we construct a model of the shallow sub-surface at the landing site in western Elysium Planitia and simulate the ambient vibration wavefield. We show how Rayleigh wave ellipticity can be extracted from these data and inverted for shallow structure. Using reasonable variations in regolith properties, we do not expect any influence of site resonances on teleseismic quakes recorded by InSight, but recordings of local events will likely be affected. We find that higher mode ellipticity information might be extracted from the data, significantly reducing uncertainties in the inversion. Though the data are most sensitive to properties of the upper-most layer and show a strong trade-off between layer depth and velocity, it is possible to estimate the velocity and thickness of the sub-regolith layer and distinguish between different models by using reasonable constraints on regolith properties. Model parameters are best constrained if either higher mode data can be used or additional constraints on regolith properties, e.g. from analysis of hammer strokes of the HP3 heat flow probe or orbital mapping of regolith thickness from the onset diameter of rocky ejecta craters, are available. In addition, Rayleigh wave ellipticity can differentiate between models with a constant regolith velocity and models with increasing velocity with depth. We also discuss the influence of lander and leveling system mechanical noise on the identification of site resonances.

Characterizing Sediment Supply to Rivers: Effects of Lithology, Climate, Weathering and Erosion on Rock-fragment Abundance in Granitic, Hillslope Soils

NASA Astrophysics Data System (ADS)

Riebe, C. S.; Marshall, J. A.; Sklar, L. S.; Granger, D. E.

2008-12-01

River incision sets the pace of landscape evolution and so is crucial to linkages among climate, tectonics and topography. Theoretical and experimental studies indicate that bedrock river incision should be regulated by both the quantity and caliber of sediment supply, which together affect the availability and persistence of bed-scouring tools in the channel. Rates of sediment supply are now quantified routinely using cosmogenic- radionuclide-based (CRN) measurements of hillslope erosion rates. Although grain-size data are also measured routinely (e.g., as part of state and federal soil surveys), they are not widely available for soils with well-constrained rates of erosion and weathering. As a result, there is much to learn about how weathering and erosion interrelate to regulate grain-size distributions in hillslope soils. Moreover, we lack a strong empirical basis for investigating how the rate and caliber of sediment supply affect bedrock river incision in natural systems. Here we compare new grain-size data with existing CRN-based rates of erosion and weathering for a series of granitic soils at two climatically diverse sites in the Sierra Nevada, California. Our results indicate that the percentage of coarse material---which presumably becomes the bedload that abrades and lowers channels---varies significantly across each site. At the colder, wetter site, differences in grain size and soil depth are substantial, despite little variability in erosion rates; coarse material abundance appears to increase with the density of bedrock outcrops, which increases with hillslope gradients, according to previous work. At the hotter, drier site, where rates of erosion and weathering vary by 10-fold, soil thickness and texture and the abundance of outcrops do not vary systematically across the landscape. We speculate that the differences in soil development across our two sites partly reflect effects of small differences in the ratio of biotite to hornblende in the parent rock. We discuss implications for constraining the rate and caliber of sediment supply to rivers.

Constraining Resurgence through Lake Sediment Paleomagnetism on Resurgent Dome Samosir Island in Toba Caldera, Sumatra, Indonesia

NASA Astrophysics Data System (ADS)

Solada, K.; de Silva, S. L.; Stoner, J. S.; Mucek, A. E.; Reilly, B. T.; Hatfield, R. G.; Pratomo, I.; Bowers, J.; Jamil, R.; Setianto, B.

2017-12-01

Around 74 ka, a supervolcano, Toba Caldera in Sumatra, Indonesia erupted, producing the Youngest Toba Tuff and its associated caldera. After this catastrophic eruption, a lake filled the caldera, sedimentation within the lake occurred, and the process known as resurgence began. Today, the resurgent dome, Samosir Island, is uplifted 700 m above the lake with the upper 100 m composed of these post eruption lake sediments. These sediments and their ages offer insight to the resurgent uplift history. To constrain sediment chronology, we collected discrete paleomagnetic 8 cm3 cubes and 43 radiocarbon samples from 10 sites around the island. Bulk organic carbon 14C ages provide an initial chronostratigraphic framework, which is improved by correlating paleomagnetic signals between site sections. Additionally, nearby marine sediment paleomagnetic records show large amplitude changes in inclination over the past 74 ka, providing a good template to compare the sediment chronology. 27 radiocarbon samples have already been dated, with the oldest dating at 38 ka. However, our radiocarbon and paleomagnetic correlation suggest that this record extends even older. Natural and laboratory magnetizations on discrete samples were studied using alternating field (AF) demagnetization at the Oregon State University P-Mag Lab. Although there is variability in magnetic susceptibility between study sites and natural remanant magnetization intensities are often relatively low ( 10-4 (A/m)), AF demagnetization behavior suggests a primary magnetization is recorded. Characteristic remanent magnetizations are reasonably well-defined using a principal component analysis with maximum angular deviation values < 15°, though stronger samples typically have better resolved magnetizations. Data from 4 sites with 14C ages ranging from 23 ka to 38 ka, show low inclination values, averaging around -5° compared with geocentric axial dipole prediction for the site location of approximately 4°. This is consistent with the negative inclination anomaly associated with this region. These observations and similar patterns between sections suggest that a reliable record is preserved that is suitable for magnetic stratigraphy.

Deep aquifer as driver for mineral authigenesis in Gulf of Alaska sediments (IODP Expedition 341, Site U1417)

NASA Astrophysics Data System (ADS)

Zindorf, Mark; März, Christian; Wagner, Thomas; Strauss, Harald; Gulick, Sean P. S.; Jaeger, John M.; LeVay, Leah J.

2016-04-01

Bacterial sulphate reduction plays a key role in authigenic mineral formation in marine sediments. Usually, decomposition of organic matter follows a sequence of microbial metabolic pathways, where microbial sulphate reduction leads to sulphate depletion deeper in the sediment. When sulphate is consumed completely from the pore waters, methanogenesis commences. The contact of sulphate- and methane-containing pore waters is a well-defined biogeochemical boundary (the sulphate-methane transition zone, SMTZ). Here authigenic pyrite, barite and carbonates form. Pyrite formation is directly driven by bacterial sulphate reduction since pyrite precipitates from produced hydrogen sulphide. Barite and carbonate formation are secondary effects resulting from changes of the chemical milieu due to microbial activity. However, this mineral authigenesis is ultimately linked to abiotic processes that determine the living conditions for microorganisms. At IODP Site U1417 in the Gulf of Alaska, a remarkable diagenetic pattern has been observed: Between sulphate depletion and methane enrichment, a ~250 m wide gap exists. Consequently, no SMTZ can be found under present conditions, but enrichments of pyrite indicate that such zones have existed in the past. Solid layers consisting of authigenic carbonate-cemented sand were partly recovered right above the methane production zone, likely preventing continued upward methane diffusion. At the bottom of the sediment succession, the lower boundary of the methanogenic zone is constrained by sulphate-rich pore waters that appear to originate from a deeper source. Here, a well-established SMTZ exists, but in reversed order (sulphate diffusing up, methane diffusing down). Sulphur isotopes of pyrite reveal that sulphate reduction here does not occur under closed system conditions. This indicates that a deep aquifer is actively recharging the deep sulphate pool. Similar deep SMTZs have been found at other sites, yet mostly in geologically active environments such as ridge flanks or above subduction zones. Therefore Site U1417, in a relatively inactive intraplate environment, represents a so far under-sampled geochemical setting. Calculated accumulation times for authigenic minerals in the deep SMTZ are on the same order of magnitude as the onset of subduction-related bending of the Pacific Plate, suggesting that both processes are linked. Plate bending could create fractures in the overlying sediments allowing seawater to penetrate and recharge a deep aquifer. Our study provides insights into a newly discovered geological process suitable for delivering sulphate-rich water deep into the sediments and installing diagenetically active environments where microbial activity would otherwise be very limited.

CD8+ T-cell immunosurveillance constrains lymphoid pre-metastatic myeloid cell accumulation

PubMed Central

Li, Wenzhao; Deng, Jiehui; Herrmann, Andreas; Priceman, Saul J.; Liang, Wei; Shen, Shudan; Pal, Sumanta K.; Hoon, Dave S.B.; Yu, Hua

2014-01-01

Increasing evidence suggests that pre-metastatic niches, consisting mainly of myeloid cells, provide microenvironment critical for cancer cell recruitment and survival to facilitate metastasis. While CD8+ T cells exert immunosurveillance in primary human tumors, whether they can exert similar effects on myeloid cells in the pre-metastatic environment is unknown. Here, we show that CD8+ T cells are capable of constraining pre-metastatic myeloid cell accumulation by inducing myeloid cell apoptosis in C57BL/6 mice. Antigen-specific CD8+ T-cell cytotoxicity against myeloid cells in pre-metastatic lymph nodes is compromised by Stat3. We demonstrate here that Stat3 ablation in myeloid cells leads to CD8+ T-cell activation and increased levels of IFN-γ and granzyme B in the pre-metastatic environment. Furthermore, Stat3 negatively regulates soluble antigen cross-presentation by myeloid cells to CD8+ T cells in the pre-metastatic niche. Importantly, in tumor-free lymph nodes of melanoma patients, infiltration of activated CD8+ T cells inversely correlates with STAT3 activity, which is associated with a decrease in number of myeloid cells. Our study suggested a novel role for CD8+ T cells in constraining myeloid cell activity through direct killing in the pre-metastatic environment, and the therapeutic potential by targeting Stat3 in myeloid cells to improve CD8+ T-cell immunosurveillance against metastasis. PMID:25310972

Evaluation of the performance of a passive-active vibration isolation system

NASA Astrophysics Data System (ADS)

Sun, L. L.; Hansen, C. H.; Doolan, C.

2015-01-01

The behavior of a feedforward active isolation system subjected to actuator output constraints is investigated. Distributed parameter models are developed to analyze the system response, and to produce a transfer matrix for the design of an integrated passive-active isolation system. Cost functions considered here comprise a combination of the vibration transmission energy and the sum of the squared control forces. The example system considered is a rigid body connected to a simply supported plate via two isolation mounts. The overall isolation performance is evaluated by numerical simulation. The results show that the control strategies which rely on unconstrained actuator outputs may give substantial power transmission reductions over a wide frequency range, but also require large control force amplitudes to control excited vibration modes of the system. Expected power transmission reductions for modified control strategies that incorporate constrained actuator outputs are considerably less than typical reductions with unconstrained actuator outputs. The active system with constrained control force outputs is shown to be more effective at the resonance frequencies of the supporting plate. However, in the frequency range in which rigid body modes are present, the control strategies employed using constrained actuator outputs can only achieve 5-10 dB power transmission reduction, while at off-resonance frequencies, little or no power transmission reduction can be obtained with realistic control forces. Analysis of the wave effects in the passive mounts is also presented.

Neurofunctional changes after a single mirror therapy intervention in chronic ischemic stroke.

PubMed

Novaes, Morgana M; Palhano-Fontes, Fernanda; Peres, Andre; Mazzetto-Betti, Kelley; Pelicioni, Maristela; Andrade, Kátia C; Dos Santos, Antonio Carlos; Pontes-Neto, Octavio; Araujo, Draulio

2018-03-20

Mirror therapy (MT) is becoming an alternative rehabilitation strategy for various conditions, including stroke. Although recent studies suggest the positive benefit of MT in chronic stroke motor recovery, little is known about its neural mechanisms. To identify functional brain changes induced by a single MT intervention in ischemic stroke survivors, assessed by both transcranial magnetic stimulation (TMS) and functional magnetic resonance imaging (fMRI). TMS and fMRI were used to investigate 15 stroke survivors immediately before and after a single 30-min MT session. We found statistically significant increase in post-MT motor evoked potential (MEP) amplitude (increased excitability) from the affected primary motor cortex (M1), when compared to pre-MT MEP. Post-MT fMRI maps were associated with a more organized and constrained pattern, with a more focal M1 activity within the affected hemisphere after MT, limited to the cortical area of hand representation. Furthermore, we find a change in the balance of M1 activity toward the affected hemisphere. In addition, significant correlation was found between decreased fMRI β-values and increased MEP amplitude post-MT, in the affected hemisphere. Our study suggests that a single MT intervention in stroke survivors is related to increased MEP of the affected limb, and a more constrained activity of the affected M1, as if activity had become more constrained and limited to the affected hemisphere.

Rates and extent of microbial debromination in the deep subseafloor biosphere

NASA Astrophysics Data System (ADS)

Berg, R. D.; Solomon, E. A.; Morris, R. M.

2013-12-01

Recent genomic and porewater geochemical data suggest that reductive dehalogenation of a wide range of halogenated organic compounds could represent an important energy source for deep subseafloor microbial communities. At continental slope sites worldwide, there is a remarkably linear relationship between porewater profiles of ammonium and bromide, indicating that the factors controlling the distribution and rates of dehalogenation have the potential to influence carbon and nitrogen cycling in the deep subsurface biosphere. Though this metabolic pathway could play an important role in the cycling of otherwise refractory pools of carbon and nitrogen in marine sediments and provide energy to microbial communities in the deep subsurface biosphere, the rates and extent of dehalogenation in marine sediments are poorly constrained. Here we report net reaction rate profiles of debromination activity in continental slope sediments, calculated from numerical modeling of porewater bromide profiles from several margins worldwide. The reaction rate profiles indicate three common zones of debromination activity in slope sediments: 1) low rates of debromination, and a potential bromine sink, in the upper sediment column correlating to the sulfate reduction zone, with net bromide removal rates from -3.6 x 10^-2 to -4.85 x 10^-1 μmol m^-2 yr^-1, 2) high rates of debromination from the sulfate-methane transition zone to ~40-100 mbsf, with net bromide release rates between 7.1 x 10^-2 to 3.9 x 10^-1 μmol m^-2 yr^-1, and 3) an inflection point at ~40-100 mbsf, below which net rates of debromination decrease by an order of magnitude and at several sites are indistinguishable from zero. These results indicate that dehalogenating activity is widely distributed in marine sediments, providing energy to fuel deep subseafloor microbial communities, with potentially important consequences for the global bromine and nitrogen cycles.

A New Seismic Hazard Model for Mainland China

NASA Astrophysics Data System (ADS)

Rong, Y.; Xu, X.; Chen, G.; Cheng, J.; Magistrale, H.; Shen, Z. K.

2017-12-01

We are developing a new seismic hazard model for Mainland China by integrating historical earthquake catalogs, geological faults, geodetic GPS data, and geology maps. To build the model, we construct an Mw-based homogeneous historical earthquake catalog spanning from 780 B.C. to present, create fault models from active fault data, and derive a strain rate model based on the most complete GPS measurements and a new strain derivation algorithm. We divide China and the surrounding regions into about 20 large seismic source zones. For each zone, a tapered Gutenberg-Richter (TGR) magnitude-frequency distribution is used to model the seismic activity rates. The a- and b-values of the TGR distribution are calculated using observed earthquake data, while the corner magnitude is constrained independently using the seismic moment rate inferred from the geodetically-based strain rate model. Small and medium sized earthquakes are distributed within the source zones following the location and magnitude patterns of historical earthquakes. Some of the larger earthquakes are distributed onto active faults, based on their geological characteristics such as slip rate, fault length, down-dip width, and various paleoseismic data. The remaining larger earthquakes are then placed into the background. A new set of magnitude-rupture scaling relationships is developed based on earthquake data from China and vicinity. We evaluate and select appropriate ground motion prediction equations by comparing them with observed ground motion data and performing residual analysis. To implement the modeling workflow, we develop a tool that builds upon the functionalities of GEM's Hazard Modeler's Toolkit. The GEM OpenQuake software is used to calculate seismic hazard at various ground motion periods and various return periods. To account for site amplification, we construct a site condition map based on geology. The resulting new seismic hazard maps can be used for seismic risk analysis and management.

A biogeochemical and genetic survey of acetylene fermentation by environmental samples and bacterial isolates

USGS Publications Warehouse

Miller, Laurence G.; Baesman, Shaun M.; Kirshtein, Julie; Voytek, Mary A.; Oremland, Ronald S.

2013-01-01

Anoxic samples (sediment and groundwater) from 13 chemically diverse field sites were assayed for their ability to consume acetylene (C2H2). Over incubation periods ranging from ˜ 10 to 80 days, selected samples from 7 of the 13 tested sites displayed significant C2H2 removal. No significant formation of ethylene was noted in these incubations; therefore, C2H2 consumption could be attributed to acetylene hydratase (AH) rather than nitrogenase activity. This putative AH (PAH) activity was observed in only 21% of the total of assayed samples, while amplification of AH genes from extracted DNA using degenerate primers derived from Pelobacter acetylenicus occurred in even fewer (9.8%) samples. Acetylene-fermenting bacteria were isolated as a pure culture from the sediments of a tidal mudflat in San Francisco Bay (SFB93) and as an enrichment culture from freshwater Searsville Lake (SV7). Comparison of 16S rDNA clone libraries revealed that SFB93 was closely related to P. carbolinicus, while SV7 consisted of several unrelated bacteria. AH gene was amplified from SFB93 but not SV7. The inability of the primers to generate amplicons in the SV7 enrichment, as well as from several of the environmental samples that displayed PAH activity, implied that either the primers were too highly constrained in their specificity or that there was a different type of AH gene in these environmental samples than occurs in P. acetylenicus. The significance of this work with regard to the search for life in the outer Solar System, where C2HL2 is abundant, is discussed.

Run-Reversal Equilibrium for Clinical Trial Randomization

PubMed Central

Grant, William C.

2015-01-01

In this paper, we describe a new restricted randomization method called run-reversal equilibrium (RRE), which is a Nash equilibrium of a game where (1) the clinical trial statistician chooses a sequence of medical treatments, and (2) clinical investigators make treatment predictions. RRE randomization counteracts how each investigator could observe treatment histories in order to forecast upcoming treatments. Computation of a run-reversal equilibrium reflects how the treatment history at a particular site is imperfectly correlated with the treatment imbalance for the overall trial. An attractive feature of RRE randomization is that treatment imbalance follows a random walk at each site, while treatment balance is tightly constrained and regularly restored for the overall trial. Less predictable and therefore more scientifically valid experiments can be facilitated by run-reversal equilibrium for multi-site clinical trials. PMID:26079608

Dating Tectonic Activity on Mercury’s Large-Scale Lobate-Scarp Thrust Faults

NASA Astrophysics Data System (ADS)

Barlow, Nadine G.; E Banks, Maria

2017-10-01

Mercury’s widespread large-scale lobate-scarp thrust faults reveal that the planet’s tectonic history has been dominated by global contraction, primarily due to cooling of its interior. Constraining the timing and duration of this contraction provides key insight into Mercury’s thermal and geologic evolution. We combine two techniques to enhance the statistical validity of size-frequency distribution crater analyses and constrain timing of the 1) earliest and 2) most recent detectable activity on several of Mercury’s largest lobate-scarp thrust faults. We use the sizes of craters directly transected by or superposed on the edge of the scarp face to define a count area around the scarp, a method we call the Modified Buffered Crater Counting Technique (MBCCT). We developed the MBCCT to avoid the issue of a near-zero scarp width since feature widths are included in area calculations of the commonly used Buffered Crater Counting Technique (BCCT). Since only craters directly intersecting the scarp face edge conclusively show evidence of crosscutting relations, we increase the number of craters in our analysis (and reduce uncertainties) by using the morphologic degradation state (i.e. relative age) of these intersecting craters to classify other similarly degraded craters within the count area (i.e., those with the same relative age) as superposing or transected. The resulting crater counts are divided into two categories: transected craters constrain the earliest possible activity and superposed craters constrain the most recent detectable activity. Absolute ages are computed for each population using the Marchi et al. [2009] model production function. A test of the Blossom lobate scarp indicates the MBCCT gives statistically equivalent results to the BCCT. We find that all scarps in this study crosscut surfaces Tolstojan or older in age (>~3.7 Ga). The most recent detectable activity along lobate-scarp thrust faults ranges from Calorian to Kuiperian (~3.7 Ga to present). Our results complement previous relative-age studies with absolute ages and indicate global contraction continued over the last ~3-4 Gyr. At least some thrust fault activity occurred on Mercury in relatively recent times (<280 Ma).

Double quick, double click reversible peptide "stapling".

PubMed

Grison, Claire M; Burslem, George M; Miles, Jennifer A; Pilsl, Ludwig K A; Yeo, David J; Imani, Zeynab; Warriner, Stuart L; Webb, Michael E; Wilson, Andrew J

2017-07-01

The development of constrained peptides for inhibition of protein-protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine ( h Cys) amino acids spaced at i and i + 4 positions by double substitution. The constraint can be readily removed by displacement of the maleimide using excess thiol. This new constraining methodology results in enhanced α-helical conformation (BID and RNase S peptide) as demonstrated by circular dichroism and molecular dynamics simulations, resistance to proteolysis (BID) as demonstrated by trypsin proteolysis experiments and retained or enhanced potency of inhibition for Bcl-2 family protein-protein interactions (BID), or greater capability to restore the hydrolytic activity of the RNAse S protein (RNase S peptide). Finally, use of a dibromomaleimide functionalized with an alkyne permits further divergent functionalization through alkyne-azide cycloaddition chemistry on the constrained peptide with fluorescein, oligoethylene glycol or biotin groups to facilitate biophysical and cellular analyses. Hence this methodology may extend the scope and accessibility of peptide stapling.

Balancing computation and communication power in power constrained clusters

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

Piga, Leonardo; Paul, Indrani; Huang, Wei

Systems, apparatuses, and methods for balancing computation and communication power in power constrained environments. A data processing cluster with a plurality of compute nodes may perform parallel processing of a workload in a power constrained environment. Nodes that finish tasks early may be power-gated based on one or more conditions. In some scenarios, a node may predict a wait duration and go into a reduced power consumption state if the wait duration is predicted to be greater than a threshold. The power saved by power-gating one or more nodes may be reassigned for use by other nodes. A cluster agentmore » may be configured to reassign the unused power to the active nodes to expedite workload processing.« less

Constraining Atmospheric Particle Size in Gale Crater Using REMS UV Measurements and Mastcam Observations at 440 and 880 nm

NASA Astrophysics Data System (ADS)

Mason, E. L.; Lemmon, M. T.; de la Torre-Juárez, M.; Vicente-Retortillo, A.; Martinez, G.

2015-12-01

Optical depth measured in Gale crater has been shown to vary seasonally, and this variation is potentially linked to a change in dust size visible from the surface. The Mast Camera (Mastcam) on the Mars Science Laboratory (MSL) has performed cross-sky brightness surveys similar to those obtained at the Phoenix Lander site. Since particle size can be constrained by observing airborne dust across multiple wavelengths and angles, surveys at 440 and 880 nm can be used to characterize atmospheric dust within and above the crater. In addition, Rover Environmental Monitoring Station (REMS) on MSL provides downward radiation flux from 250 nm (UVD) to 340 nm (UVA), which would further constrain aerosol properties. The dust, which is not spherical and likely contains irregular particles, can be modeled using randomly oriented triaxial ellipsoids with predetermined microphysical optical properties and fit to sky survey observations to retrieve an effective radius. This work provides a discussion on the constraints of particle size distribution using REMS measurements as well as shape of the particle in Gale crater in comparison to Mastcam at the specified wavelengths.

Multiscale Data Assimilation for Large-Eddy Simulations

NASA Astrophysics Data System (ADS)

Li, Z.; Cheng, X.; Gustafson, W. I., Jr.; Xiao, H.; Vogelmann, A. M.; Endo, S.; Toto, T.

2017-12-01

Large-eddy simulation (LES) is a powerful tool for understanding atmospheric turbulence, boundary layer physics and cloud development, and there is a great need for developing data assimilation methodologies that can constrain LES models. The U.S. Department of Energy Atmospheric Radiation Measurement (ARM) User Facility has been developing the capability to routinely generate ensembles of LES. The LES ARM Symbiotic Simulation and Observation (LASSO) project (https://www.arm.gov/capabilities/modeling/lasso) is generating simulations for shallow convection days at the ARM Southern Great Plains site in Oklahoma. One of major objectives of LASSO is to develop the capability to observationally constrain LES using a hierarchy of ARM observations. We have implemented a multiscale data assimilation (MSDA) scheme, which allows data assimilation to be implemented separately for distinct spatial scales, so that the localized observations can be effectively assimilated to constrain the mesoscale fields in the LES area of about 15 km in width. The MSDA analysis is used to produce forcing data that drive LES. With such LES workflow we have examined 13 days with shallow convection selected from the period May-August 2016. We will describe the implementation of MSDA, present LES results, and address challenges and opportunities for applying data assimilation to LES studies.

Expansion of the CRISPR-Cas9 genome targeting space through the use of H1 promoter-expressed guide RNAs.

PubMed

Ranganathan, Vinod; Wahlin, Karl; Maruotti, Julien; Zack, Donald J

2014-08-08

The repurposed CRISPR-Cas9 system has recently emerged as a revolutionary genome-editing tool. Here we report a modification in the expression of the guide RNA (gRNA) required for targeting that greatly expands the targetable genome. gRNA expression through the commonly used U6 promoter requires a guanosine nucleotide to initiate transcription, thus constraining genomic-targeting sites to GN19NGG. We demonstrate the ability to modify endogenous genes using H1 promoter-expressed gRNAs, which can be used to target both AN19NGG and GN19NGG genomic sites. AN19NGG sites occur ~15% more frequently than GN19NGG sites in the human genome and the increase in targeting space is also enriched at human genes and disease loci. Together, our results enhance the versatility of the CRISPR technology by more than doubling the number of targetable sites within the human genome and other eukaryotic species.

Short-term prey field lability constrains individual specialisation in resource selection and foraging site fidelity in a marine predator.

PubMed

Courbin, Nicolas; Besnard, Aurélien; Péron, Clara; Saraux, Claire; Fort, Jérôme; Perret, Samuel; Tornos, Jérémy; Grémillet, David

2018-04-16

Spatio-temporally stable prey distributions coupled with individual foraging site fidelity are predicted to favour individual resource specialisation. Conversely, predators coping with dynamic prey distributions should diversify their individual diet and/or shift foraging areas to increase net intake. We studied individual specialisation in Scopoli's shearwaters (Calonectris diomedea) from the highly dynamic Western Mediterranean, using daily prey distributions together with resource selection, site fidelity and trophic-level analyses. As hypothesised, we found dietary diversification, low foraging site fidelity and almost no individual specialisation in resource selection. Crucially, shearwaters switched daily foraging tactics, selecting areas with contrasting prey of varying trophic levels. Overall, information use and plastic resource selection of individuals with reduced short-term foraging site fidelity allow predators to overcome prey field lability. Our study is an essential step towards a better understanding of individual responses to enhanced environmental stochasticity driven by global changes, and of pathways favouring population persistence. © 2018 John Wiley & Sons Ltd/CNRS.

Molybdenum and Phosphorus Interact to Constrain Asymbiotic Nitrogen Fixation in Tropical Forests

PubMed Central

Wurzburger, Nina; Bellenger, Jean Philippe; Kraepiel, Anne M. L.; Hedin, Lars O.

2012-01-01

Biological di-nitrogen fixation (N2) is the dominant natural source of new nitrogen to land ecosystems. Phosphorus (P) is thought to limit N2 fixation in many tropical soils, yet both molybdenum (Mo) and P are crucial for the nitrogenase reaction (which catalyzes N2 conversion to ammonia) and cell growth. We have limited understanding of how and when fixation is constrained by these nutrients in nature. Here we show in tropical forests of lowland Panama that the limiting element on asymbiotic N2 fixation shifts along a broad landscape gradient in soil P, where Mo limits fixation in P-rich soils while Mo and P co-limit in P-poor soils. In no circumstance did P alone limit fixation. We provide and experimentally test a mechanism that explains how Mo and P can interact to constrain asymbiotic N2 fixation. Fixation is uniformly favored in surface organic soil horizons - a niche characterized by exceedingly low levels of available Mo relative to P. We show that soil organic matter acts to reduce molybdate over phosphate bioavailability, which, in turn, promotes Mo limitation in sites where P is sufficient. Our findings show that asymbiotic N2 fixation is constrained by the relative availability and dynamics of Mo and P in soils. This conceptual framework can explain shifts in limitation status across broad landscape gradients in soil fertility and implies that fixation depends on Mo and P in ways that are more complex than previously thought. PMID:22470462

Sustaining Lesson Study: Resources and Factors that Support and Constrain Mathematics Teachers' Ability to Continue After the Grant Ends

NASA Astrophysics Data System (ADS)

Druken, Bridget Kinsella

Lesson study, a teacher-led vehicle for inquiring into teacher practice through creating, enacting, and reflecting on collaboratively designed research lessons, has been shown to improve mathematics teacher practice in the United States, such as improving knowledge about mathematics, changing teacher practice, and developing communities of teachers. Though it has been described as a sustainable form of professional development, little research exists on what might support teachers in continuing to engage in lesson study after a grant ends. This qualitative and multi-case study investigates the sustainability of lesson study as mathematics teachers engage in a district scale-up lesson study professional experience after participating in a three-year California Mathematics Science Partnership (CaMSP) grant to improve algebraic instruction. To do so, I first provide a description of material (e.g. curricular materials and time), human (attending district trainings and interacting with mathematics coaches), and social (qualities like trust, shared values, common goals, and expectations developed through relationships with others) resources present in the context of two school districts as reported by participants. I then describe practices of lesson study reported to have continued. I also report on teachers' conceptions of what it means to engage in lesson study. I conclude by describing how these results suggest factors that supported and constrained teachers' in continuing lesson study. To accomplish this work, I used qualitative methods of grounded theory informed by a modified sustainability framework on interview, survey, and case study data about teachers, principals, and Teachers on Special Assignment (TOSAs). Four cases were selected to show the varying levels of lesson study practices that continued past the conclusion of the grant. Analyses reveal varying levels of integration, linkage, and synergy among both formally and informally arranged groups of teachers. High levels of integration and linkage among groups of teachers supported them in sustaining lesson study practices. Groups of teachers with low levels of integration but with linked individuals sustained some level of practices, whereas teachers with low levels of integration and linkage constrained them in continuing lesson study at their site. Additionally, teachers' visions of lesson study and its uses shaped the types of activities teachers engaged, with well-developed conceptions of lesson study supporting and limited visions constraining the ability to attract or align resources to continue lesson study practices. Principals' support, teacher autonomy, and cultures of collaboration or isolation were also factors that either supported or constrained teachers' ability to continue lesson study. These analyses provide practical implications on how to support mathematics teachers in continuing lesson study, and theoretical contributions on developing the construct of sustainability within mathematics education research.

Microseismicity of an Unstable Rock Mass: From Field Monitoring to Laboratory Testing

NASA Astrophysics Data System (ADS)

Colombero, C.; Comina, C.; Vinciguerra, S.; Benson, P. M.

2018-02-01

The field-scale microseismic (MS) activity of an unstable rock mass is known to be an important tool to assess damage and cracking processes eventually leading to macroscopic failures. However, MS-event rates alone may not be enough for a complete understanding of the trigger mechanisms of mechanical instabilities. Acoustic Emission (AE) techniques at the laboratory scale can be used to provide complementary information. In this study, we report a MS/AE comparison to assess the stability of a granitic rock mass in the northwestern Italian Alps (Madonna del Sasso). An attempt to bridge the gap between the two different scales of observation, and the different site and laboratory conditions, is undertaken to gain insights on the rock mass behavior as a function of external governing factors. Time- and frequency-domain parameters of the MS/AE waveforms are compared and discussed with this aim. At the field scale, special attention is devoted to the correlation of the MS-event rate with meteorological parameters (air temperature and rainfalls). At the laboratory scale, AE rates, waveforms, and spectral content, recorded under controlled temperature and fluid conditions, are analyzed in order to better constrain the physical mechanisms responsible for the observed field patterns. The factors potentially governing the mechanical instability at the site were retrieved from the integration of the results. Abrupt thermal variations were identified as the main cause of the site microsesimicity, without highlighting irreversible acceleration in the MS-event rate potentially anticipating the rock mass collapse.

Collaborative community hazard exposure mapping: Distant Early Warning radar sites in Alaska's North Slope

NASA Astrophysics Data System (ADS)

Brady, M.

2015-12-01

A method to produce hazard exposure maps that are developed in collaboration with local coastal communities is the focus of this research. Typically efforts to map community exposure to climate threats over large areas have limited consideration of local perspectives about associated risks, constraining their utility for local management. This problem is especially acute in remote locations such as the Arctic where there are unique vulnerabilities to coastal threats that can be fully understood only through inclusion of community stakeholders. Through collaboration with community members, this study identifies important coastal assets and places and surveys local perspectives of exposure to climate threats along Alaska's vast North Slope coastline spanning multiple municipalities. To model physical exposure, the study adapts the U.S. Geological Survey's (USGS) coastal vulnerability index (CVI) to the Arctic context by incorporating the effects of open water distance determined by sea ice extent, and assigning CVI values to coastal assets and places according to direction and proximity. The study found that in addition to concerns about exposed municipal and industrial assets, North Slope communities viewed exposure of traditional activity sites as presenting a particular risk for communities. Highly exposed legacy Cold War Distant Early Warning Line sites are of particular concern with impacts ranging from financial risk to contamination of sensitive coastal marine environments. This research demonstrates a method to collaboratively map community exposure to coastal climate threats to better understand local risks and produce locally usable exposure maps.

Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils

PubMed Central

Koyama, Akihiro; Wallenstein, Matthew D.; Simpson, Rodney T.; Moore, John C.

2014-01-01

The pool of soil organic carbon (SOC) in the Arctic is disproportionally large compared to those in other biomes. This large quantity of SOC accumulated over millennia due to slow rates of decomposition relative to net primary productivity. Decomposition is constrained by low temperatures and nutrient concentrations, which limit soil microbial activity. We investigated how nutrients limit bacterial and fungal biomass and community composition in organic and mineral soils within moist acidic tussock tundra ecosystems. We sampled two experimental arrays of moist acidic tussock tundra that included fertilized and non-fertilized control plots. One array included plots that had been fertilized annually since 1989 and the other since 2006. Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site. The relative abundance of copiotrophic α-Proteobacteria and β-Proteobacteria was higher in fertilized than control soils, and oligotrophic Acidobacteria were less abundant in fertilized than control soils at the 1989 site. Fungal community composition was less sensitive to increased nutrient availability, and fungal responses to fertilization were not consistent between soil horizons and sites. We detected two ectomycorrhizal genera, Russula and Cortinarius spp., associated with shrubs. Their relative abundance was not affected by fertilization despite increased dominance of their host plants in the fertilized plots. Our results indicate that fertilization, which has been commonly used to simulate warming in Arctic tundra, has limited applicability for investigating fungal dynamics under warming. PMID:25324836

α-SNAP regulates dynamic, on-site assembly and calcium selectivity of Orai1 channels

PubMed Central

Li, Peiyao; Miao, Yong; Dani, Adish; Vig, Monika

2016-01-01

Orai1 forms a highly calcium-selective pore of the calcium release activated channel, and α-SNAP is necessary for its function. Here we show that α-SNAP regulates on-site assembly of Orai1 dimers into calcium-selective multimers. We find that Orai1 is a dimer in resting primary mouse embryonic fibroblasts but displays variable stoichiometry in the plasma membrane of store-depleted cells. Remarkably, α-SNAP depletion induces formation of higher-order Orai1 oligomers, which permeate significant levels of sodium via Orai1 channels. Sodium permeation in α-SNAP–deficient cells cannot be corrected by tethering multiple Stim1 domains to Orai1 C-terminal tail, demonstrating that α-SNAP regulates functional assembly and calcium selectivity of Orai1 multimers independently of Stim1 levels. Fluorescence nanoscopy reveals sustained coassociation of α-SNAP with Stim1 and Orai1, and α-SNAP–depleted cells show faster and less constrained mobility of Orai1 within ER-PM junctions, suggesting Orai1 and Stim1 coentrapment without stable contacts. Furthermore, α-SNAP depletion significantly reduces fluorescence resonance energy transfer between Stim1 and Orai1 N-terminus but not C-terminus. Taken together, these data reveal a unique role of α-SNAP in the on-site functional assembly of Orai1 subunits and suggest that this process may, in part, involve enabling crucial low-affinity interactions between Orai1 N-terminus and Stim1. PMID:27335124

Environmental Monitoring of Endemic Cholera

NASA Astrophysics Data System (ADS)

ElNemr, W.; Jutla, A. S.; Constantin de Magny, G.; Hasan, N. A.; Islam, M.; Sack, R.; Huq, A.; Hashem, F.; Colwell, R.

2012-12-01

Cholera remains a major public health threat. Since Vibrio cholerae, the causative agent of the disease, is autochthonous to riverine, estuarine, and coastal waters, it is unlikely the bacteria can be eradicated from its natural habitat. Prediction of disease, in conjunction with preventive vaccination can reduce the prevalence rate of a disease. Understanding the influence of environmental parameters on growth and proliferation of bacteria is an essential first step in developing prediction methods for outbreaks. Large scale geophysical variables, such as SST and coastal chlorophyll, are often associated with conditions favoring growth of V. cholerae. However, local environmental factors, meaning biological activity in ponds from where the bulk of populations in endemic regions derive water for daily usage, are either neglected or oversimplified. Using data collected from several sites in two geographically distinct locations in South Asia, we have identified critical local environmental factors associated with cholera outbreak. Of 18 environmental variables monitored for water sources in Mathbaria (a coastal site near the Bay of Bengal) and Bakergonj (an inland site) of Bangladesh, water depth and chlorophyll were found to be important factors associated with initiation of cholera outbreaks. Cholera in coastal regions appears to be related to intrusion. However, monsoonal flooding creates conditions for cholera epidemics in inland regions. This may be one of the first attempts to relate in-situ environmental observations with cholera. We anticipate that it will be useful for further development of prediction models in the resource constrained regions.

An Ethical Governor for Constraining Lethal Action in an Autonomous System

DTIC Science & Technology

2009-01-01

property is prohibited from being attacked, including buildings dedicated to religion, art , science … Activity Active Logical Form TargetDiscriminated...attacked, including buildings dedicated to religion, art , science , charitable purposes, and historic monuments. Prohibition LOW Civilian

Nest site selection by Kentish plover suggests a trade-off between nest-crypsis and predator detection strategies.

PubMed

Gómez-Serrano, Miguel Ángel; López-López, Pascual

2014-01-01

Predation is one of the main causes of adult mortality and breeding failure for ground-nesting birds. Micro-habitat structure around nests plays a critical role in minimizing predation risk. Plovers nest in sites with little vegetation cover to maximize the incubating adult visibility, but many studies suggest a trade-off between nest-crypsis and predator detection strategies. However, this trade-off has not been explored in detail because methods used so far do not allow estimating the visibility with regards to critical factors such as slope or plant permeability to vision. Here, we tested the hypothesis that Kentish plovers select exposed sites according to a predator detection strategy, and the hypothesis that more concealed nests survive longer according to a crypsis strategy. To this end, we obtained an accurate estimation of the incubating adult's field of vision through a custom built inverted periscope. Our results showed that plovers selected nest sites with higher visibility than control points randomly selected with regards to humans and dogs, although nests located in sites with higher vegetation cover survived longer. In addition, the flushing distance (i.e., the distance at which incubating adults leave the nest when they detect a potential predator) decreased with vegetation cover. Consequently, the advantages of concealing the nest were limited by the ability to detect predators, thus indirectly supporting the existence of the trade-off between crypsis and predator detection. Finally, human disturbance also constrained nest choice, forcing plovers to move to inland sites that were less suitable because of higher vegetation cover, and modulated flushing behavior, since plovers that were habituated to humans left their nests closer to potential predators. This constraint on the width of suitable breeding habitat is particularly relevant for the conservation of Kentish Plover in sand beaches, especially under the current context of coastal regression and increase of recreational activities.

Nest Site Selection by Kentish Plover Suggests a Trade-Off between Nest-Crypsis and Predator Detection Strategies

PubMed Central

Gómez-Serrano, Miguel Ángel; López-López, Pascual

2014-01-01

Predation is one of the main causes of adult mortality and breeding failure for ground-nesting birds. Micro-habitat structure around nests plays a critical role in minimizing predation risk. Plovers nest in sites with little vegetation cover to maximize the incubating adult visibility, but many studies suggest a trade-off between nest-crypsis and predator detection strategies. However, this trade-off has not been explored in detail because methods used so far do not allow estimating the visibility with regards to critical factors such as slope or plant permeability to vision. Here, we tested the hypothesis that Kentish plovers select exposed sites according to a predator detection strategy, and the hypothesis that more concealed nests survive longer according to a crypsis strategy. To this end, we obtained an accurate estimation of the incubating adult's field of vision through a custom built inverted periscope. Our results showed that plovers selected nest sites with higher visibility than control points randomly selected with regards to humans and dogs, although nests located in sites with higher vegetation cover survived longer. In addition, the flushing distance (i.e., the distance at which incubating adults leave the nest when they detect a potential predator) decreased with vegetation cover. Consequently, the advantages of concealing the nest were limited by the ability to detect predators, thus indirectly supporting the existence of the trade-off between crypsis and predator detection. Finally, human disturbance also constrained nest choice, forcing plovers to move to inland sites that were less suitable because of higher vegetation cover, and modulated flushing behavior, since plovers that were habituated to humans left their nests closer to potential predators. This constraint on the width of suitable breeding habitat is particularly relevant for the conservation of Kentish Plover in sand beaches, especially under the current context of coastal regression and increase of recreational activities. PMID:25208045

Resource and activity substitutes for recreational salmon fishing in New Zealand

Treesearch

Bo Shelby

1985-01-01

Substitutes become an issue when people are constrained from participating in desired activities. This study investigates and compares activity and resource substitutes for recreational salmon fishing in New Zealand. Results suggest that resource substitution and inventories need more attention, user perceptions of substitutes are important, substitutes can be...

Carbon Flux and Isotopic Character of Soil and Soil Gas in Stabilized and Active Thaw Slumps in Northwest Alaska

NASA Astrophysics Data System (ADS)

Jensen, A.; Crosby, B. T.; Mora, C. I.; Lohse, K. A.

2012-12-01

Permafrost soils store nearly half the world's global carbon. Warming of arctic landscape results in permafrost thaw which causes ground subsidence or thermokarst. On hillslopes, these features rapidly and dramatically alter soil structure, temperature, and moisture, as well as the content and quality of soil organic matter. These changes alter both the rate and mechanism of carbon cycling in permafrost soils, making frozen soils available to both anaerobic and aerobic decomposition. In order to improve our predictive capabilities, we use a chronosequence thaw slumps to examine how fluxes from active and stabilized features differ. Our study site is along the Selawik River in northwest Alaska where a retrogressive thaw slump initiated in the spring of 2004. It has grown to a surface area of 50,000 m2. Products of the erosion are stored on the floor of the feature, trapped on a fan or flushed into the Selawik River. North of slump is undisturbed tundra and adjacent to the west is a slump feature that stabilized and is now covered with a second generation of spruce trees. In this 2 year study, we use measurements of CO2 efflux, δC13 in soil profiles and CO2 and CH4 abundance to constrain the response of belowground carbon emissions. We also focused on constraining which environmental factors govern C emissions within each of the above ecosystems. To this end, we measured soil temperature, and moisture, abundance and quality of soil organic carbon (SOC), water content, and bulk carbon compositions. Preliminary data from the summer of 2011 suggest that vegetation composition and soil temperature exert the strong control on CO2 efflux. The floor of the active slump and fan are bare mineral soils and are generally 10 to 15°C warmer than the tundra and stabilized slump. Consistently decreasing δC13 soil gas profiles in the recovered slump confirm that this region is a well-drained soil dominated by C3 vegetation. The δC13 gas profiles for the tundra, active slump floor, and active fan tend to be more variable as a consequence of less consistently structured soils. This could be due to either the predominance of older carbon being recycled within these profiles or a skewed balance between anaerobic vs. aerobic respiration.

Insights into Methyltransferase Specificity and Bioactivity of Derivatives of the Antibiotic Plantazolicin

DOE PAGES

Hao, Yue; Blair, Patricia M.; Sharma, Abhishek; ...

2015-01-30

Peptide antibiotics represent a class of conformationally-constrained natural products of growing pharmaceutical interest. Plantazolicin (PZN) is a linear, polyheterocyclic natural product with highly selective and potent activity against the anthrax-causing bacterium, Bacillus anthracis. The bioactivity of PZN is contingent on dimethylation of its N-terminal Arg residue by an S-adenosylmethionine-dependent methyltransferase. Here in this paper, we explore the substrate tolerances of two homologous PZN methyltransferases by carrying out kinetic analyses of the enzymes against a synthetic panel of truncated PZN analogs containing the N-terminal Arg residue. X-ray cocrystal structures of the PZN methyltransferases with each of these heterocycle-containing substrates provide amore » rationale for understanding the strict substrate specificity of these enzymes. Kinetic studies of structure-guided, site-specific variants allowed for the assignment of residues governing catalysis and substrate scope. Microbiological testing further revealed that upon dimethylation of the N-terminal Arg, a pentaheterocyclized PZN analog retained potent anti-B. anthracis activity, nearly equal to that of full-length PZN. These studies may be useful in the biosynthetic engineering of natural product analogs with different bioactivity profiles, as demonstrated by our identification of a truncated plantazolicin derivative that is active against methicillin-resistant Staphylococcus aureus (MRSA).« less

Insights into Methyltransferase Specificity and Bioactivity of Derivatives of the Antibiotic Plantazolicin

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

Hao, Yue; Blair, Patricia M.; Sharma, Abhishek

Peptide antibiotics represent a class of conformationally-constrained natural products of growing pharmaceutical interest. Plantazolicin (PZN) is a linear, polyheterocyclic natural product with highly selective and potent activity against the anthrax-causing bacterium, Bacillus anthracis. The bioactivity of PZN is contingent on dimethylation of its N-terminal Arg residue by an S-adenosylmethionine-dependent methyltransferase. Here in this paper, we explore the substrate tolerances of two homologous PZN methyltransferases by carrying out kinetic analyses of the enzymes against a synthetic panel of truncated PZN analogs containing the N-terminal Arg residue. X-ray cocrystal structures of the PZN methyltransferases with each of these heterocycle-containing substrates provide amore » rationale for understanding the strict substrate specificity of these enzymes. Kinetic studies of structure-guided, site-specific variants allowed for the assignment of residues governing catalysis and substrate scope. Microbiological testing further revealed that upon dimethylation of the N-terminal Arg, a pentaheterocyclized PZN analog retained potent anti-B. anthracis activity, nearly equal to that of full-length PZN. These studies may be useful in the biosynthetic engineering of natural product analogs with different bioactivity profiles, as demonstrated by our identification of a truncated plantazolicin derivative that is active against methicillin-resistant Staphylococcus aureus (MRSA).« less

Differential Activation of Fast-Spiking and Regular-Firing Neuron Populations During Movement and Reward in the Dorsal Medial Frontal Cortex

PubMed Central

Insel, Nathan; Barnes, Carol A.

2015-01-01

The medial prefrontal cortex is thought to be important for guiding behavior according to an animal's expectations. Efforts to decode the region have focused not only on the question of what information it computes, but also how distinct circuit components become engaged during behavior. We find that the activity of regular-firing, putative projection neurons contains rich information about behavioral context and firing fields cluster around reward sites, while activity among putative inhibitory and fast-spiking neurons is most associated with movement and accompanying sensory stimulation. These dissociations were observed even between adjacent neurons with apparently reciprocal, inhibitory–excitatory connections. A smaller population of projection neurons with burst-firing patterns did not show clustered firing fields around rewards; these neurons, although heterogeneous, were generally less selective for behavioral context than regular-firing cells. The data suggest a network that tracks an animal's behavioral situation while, at the same time, regulating excitation levels to emphasize high valued positions. In this scenario, the function of fast-spiking inhibitory neurons is to constrain network output relative to incoming sensory flow. This scheme could serve as a bridge between abstract sensorimotor information and single-dimensional codes for value, providing a neural framework to generate expectations from behavioral state. PMID:24700585

Performance analysis of smart laminated composite plate integrated with distributed AFC material undergoing geometrically nonlinear transient vibrations

NASA Astrophysics Data System (ADS)

Shivakumar, J.; Ashok, M. H.; Khadakbhavi, Vishwanath; Pujari, Sanjay; Nandurkar, Santosh

2018-02-01

The present work focuses on geometrically nonlinear transient analysis of laminated smart composite plates integrated with the patches of Active fiber composites (AFC) using Active constrained layer damping (ACLD) as the distributed actuators. The analysis has been carried out using generalised energy based finite element model. The coupled electromechanical finite element model is derived using Von Karman type nonlinear strain displacement relations and a first-order shear deformation theory (FSDT). Eight-node iso-parametric serendipity elements are used for discretization of the overall plate integrated with AFC patch material. The viscoelastic constrained layer is modelled using GHM method. The numerical results shows the improvement in the active damping characteristics of the laminated composite plates over the passive damping for suppressing the geometrically nonlinear transient vibrations of laminated composite plates with AFC as patch material.

Integrative application of active controls (IAAC) technology to an advanced subsonic transport project. Initial act configuration design study

NASA Technical Reports Server (NTRS)

1980-01-01

The performance and economic benefits of a constrained application of Active Controls Technology (ACT) are identified, and the approach to airplane design is established for subsequent steps leading to the development of a less constrained final ACT configuration. The active controls configurations are measured against a conventional baseline configuration, a state-of-the-art transport, to determine whether the performance and economic changes resulting from ACT merit proceeding with the project. The technology established by the conventional baseline configuration was held constant except for the addition of ACT. The wing, with the same planform, was moved forward on the initial ACT configuration to move the loading range aft relative to the wing mean aerodynamic chord. Wing trailing-edge surfaces and surface controls also were reconfigured for load alleviation and structural stabilization.

A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination

PubMed Central

González-Ramírez, Laura R.; Ahmed, Omar J.; Cash, Sydney S.; Wayne, C. Eugene; Kramer, Mark A.

2015-01-01

Epilepsy—the condition of recurrent, unprovoked seizures—manifests in brain voltage activity with characteristic spatiotemporal patterns. These patterns include stereotyped semi-rhythmic activity produced by aggregate neuronal populations, and organized spatiotemporal phenomena, including waves. To assess these spatiotemporal patterns, we develop a mathematical model consistent with the observed neuronal population activity and determine analytically the parameter configurations that support traveling wave solutions. We then utilize high-density local field potential data recorded in vivo from human cortex preceding seizure termination from three patients to constrain the model parameters, and propose basic mechanisms that contribute to the observed traveling waves. We conclude that a relatively simple and abstract mathematical model consisting of localized interactions between excitatory cells with slow adaptation captures the quantitative features of wave propagation observed in the human local field potential preceding seizure termination. PMID:25689136

Targeting kinase signaling pathways with constrained peptide scaffolds

PubMed Central

Hanold, Laura E.; Fulton, Melody D.; Kennedy, Eileen J.

2017-01-01

Kinases are amongst the largest families in the human proteome and serve as critical mediators of a myriad of cell signaling pathways. Since altered kinase activity is implicated in a variety of pathological diseases, kinases have become a prominent class of proteins for targeted inhibition. Although numerous small molecule and antibody-based inhibitors have already received clinical approval, several challenges may still exist with these strategies including resistance, target selection, inhibitor potency and in vivo activity profiles. Constrained peptide inhibitors have emerged as an alternative strategy for kinase inhibition. Distinct from small molecule inhibitors, peptides can provide a large binding surface area that allows them to bind shallow protein surfaces rather than defined pockets within the target protein structure. By including chemical constraints within the peptide sequence, additional benefits can be bestowed onto the peptide scaffold such as improved target affinity and target selectivity, cell permeability and proteolytic resistance. In this review, we highlight examples of diverse chemistries that are being employed to constrain kinase-targeting peptide scaffolds and highlight their application to modulate kinase signaling as well as their potential clinical implications. PMID:28185915

Analysis of Keystone Enzyme in Agar Hydrolysis Provides Insight into the Degradation (of a Polysaccharide from) Red Seaweeds*

PubMed Central

Hehemann, Jan-Hendrik; Smyth, Leo; Yadav, Anuj; Vocadlo, David J.; Boraston, Alisdair B.

2012-01-01

Agars are abundant polysaccharides from marine red algae, and their chemical structure consists of alternating d-galactose and 3,6-anhydro-l-galactose residues, the latter of which are presumed to make the polymer recalcitrant to degradation by most terrestrial bacteria. Here we study a family 117 glycoside hydrolase (BpGH117) encoded within a recently discovered locus from the human gut bacterium Bacteroides plebeius. Consistent with this locus being involved in agarocolloid degradation, we show that BpGH117 is an exo-acting 3,6-anhydro-α-(1,3)-l-galactosidase that removes the 3,6-anhydrogalactose from the non-reducing end of neoagaro-oligosaccharides. A Michaelis complex of BpGH117 with neoagarobiose reveals the distortion of the constrained 3,6-anhydro-l-galactose into a conformation that favors catalysis. Furthermore, this complex, supported by analysis of site-directed mutants, provides evidence for an organization of the active site and positioning of the catalytic residues that are consistent with an inverting mechanism of catalysis and suggests that a histidine residue acts as the general acid. This latter feature differs from the vast majority of glycoside hydrolases, which use a carboxylic acid, highlighting the alternative strategies that enzymes may utilize in catalyzing the cleavage of glycosidic bonds. PMID:22393053

Correlating the chemical composition and size of various metal oxide substrates with the catalytic activity and stability of as-deposited Pt nanoparticles for the methanol oxidation reaction

DOE PAGES

Megan E. Scofield; Wong, Stanislaus S.; Koenigsmann, Christopher; ...

2015-12-09

The performance of electrode materials in conventional direct alcohol fuel cells (DAFC) is constrained by (i) the low activity of the catalyst materials relative to their overall cost, (ii) the poisoning of the active sites due to the presence of partially oxidized carbon species (such as but not limited to CO, formate, and acetate) produced during small molecule oxidation, and (iii) the lack of catalytic stability and durability on the underlying commercial carbon support. Therefore, as a viable alternative, we have synthesized various metal oxide and perovskite materials of different sizes and chemical compositions as supports for Pt nanoparticles (NPs).more » Our results including unique mechanistic studies demonstrate that the SrRuO 3 substrate with immobilized Pt NPs at its surface evinces the best methanol oxidation performance as compared with all of the other substrate materials tested herein, including commercial carbon itself. In addition, data from electron energy loss spectroscopy (EELS) and X-ray photoelectron spectroscopy (XPS) confirmed the presence of electron transfer from bound Pt NPs to surface Ru species within the SrRuO 3 substrate itself, thereby suggesting that favorable metal support interactions are responsible for the increased methanol oxidation reaction (MOR) activity of Pt species with respect to the underlying SrRuO 3 composite catalyst material.« less

The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed

PubMed Central

2014-01-01

Background Because amino acid activation is rate-limiting for uncatalyzed protein synthesis, it is a key puzzle in understanding the origin of the genetic code. Two unrelated classes (I and II) of contemporary aminoacyl-tRNA synthetases (aaRS) now translate the code. Observing that codons for the most highly conserved, Class I catalytic peptides, when read in the reverse direction, are very nearly anticodons for Class II defining catalytic peptides, Rodin and Ohno proposed that the two superfamilies descended from opposite strands of the same ancestral gene. This unusual hypothesis languished for a decade, perhaps because it appeared to be unfalsifiable. Results The proposed sense/antisense alignment makes important predictions. Fragments that align in antiparallel orientations, and contain the respective active sites, should catalyze the same two reactions catalyzed by contemporary synthetases. Recent experiments confirmed that prediction. Invariant cores from both classes, called Urzymes after Ur = primitive, authentic, plus enzyme and representing ~20% of the contemporary structures, can be expressed and exhibit high, proportionate rate accelerations for both amino-acid activation and tRNA acylation. A major fraction (60%) of the catalytic rate acceleration by contemporary synthetases resides in segments that align sense/antisense. Bioinformatic evidence for sense/antisense ancestry extends to codons specifying the invariant secondary and tertiary structures outside the active sites of the two synthetase classes. Peptides from a designed, 46-residue gene constrained by Rosetta to encode Class I and II ATP binding sites with fully complementary sequences both accelerate amino acid activation by ATP ~400 fold. Conclusions Biochemical and bioinformatic results substantially enhance the posterior probability that ancestors of the two synthetase classes arose from opposite strands of the same ancestral gene. The remarkable acceleration by short peptides of the rate-limiting step in uncatalyzed protein synthesis, together with the synergy of synthetase Urzymes and their cognate tRNAs, introduce a new paradigm for the origin of protein catalysts, emphasize the potential relevance of an operational RNA code embedded in the tRNA acceptor stems, and challenge the RNA-World hypothesis. Reviewers This article was reviewed by Dr. Paul Schimmel (nominated by Laura Landweber), Dr. Eugene Koonin and Professor David Ardell. PMID:24927791

Constraining Source Terms, Regional Attenuation Models, and Site Effects (Postprint)

DTIC Science & Technology

2012-03-22

YAK ZRNK 10245 10831 11116 11346 12278...MDJ KAR NIL PDG QIZ RAYN SSE TATO TKM2TLG TLY UCHULHL ULN USP VOS WMQ WUS XAN YAK ZRNK 10245 10831 11116 11346 12278 12376 12574 12937 1311713130...LSA LZH MAKZUZ MDJ KAR NIL PDG QIZ RAYN SSE TATO TKM2TLG TLY UCHULHL ULN USP VOS WMQ WUS XAN YAK ZRNK 10245 10831 11116 11346 12278 12376 12574

Analysis and Simulation of Far-Field Seismic Data from the Source Physics Experiment

DTIC Science & Technology

2012-09-01

ANALYSIS AND SIMULATION OF FAR-FIELD SEISMIC DATA FROM THE SOURCE PHYSICS EXPERIMENT Arben Pitarka, Robert J. Mellors, Arthur J. Rodgers, Sean...Security Site (NNSS) provides new data for investigating the excitation and propagation of seismic waves generated by buried explosions. A particular... seismic model. The 3D seismic model includes surface topography. It is based on regional geological data, with material properties constrained by shallow

Eocene greenhouse climate revealed by coupled clumped isotope-Mg/Ca thermometry.

PubMed

Evans, David; Sagoo, Navjit; Renema, Willem; Cotton, Laura J; Müller, Wolfgang; Todd, Jonathan A; Saraswati, Pratul Kumar; Stassen, Peter; Ziegler, Martin; Pearson, Paul N; Valdes, Paul J; Affek, Hagit P

2018-02-06

Past greenhouse periods with elevated atmospheric CO 2 were characterized by globally warmer sea-surface temperatures (SST). However, the extent to which the high latitudes warmed to a greater degree than the tropics (polar amplification) remains poorly constrained, in particular because there are only a few temperature reconstructions from the tropics. Consequently, the relationship between increased CO 2 , the degree of tropical warming, and the resulting latitudinal SST gradient is not well known. Here, we present coupled clumped isotope (Δ 47 )-Mg/Ca measurements of foraminifera from a set of globally distributed sites in the tropics and midlatitudes. Δ 47 is insensitive to seawater chemistry and therefore provides a robust constraint on tropical SST. Crucially, coupling these data with Mg/Ca measurements allows the precise reconstruction of Mg/Ca sw throughout the Eocene, enabling the reinterpretation of all planktonic foraminifera Mg/Ca data. The combined dataset constrains the range in Eocene tropical SST to 30-36 °C (from sites in all basins). We compare these accurate tropical SST to deep-ocean temperatures, serving as a minimum constraint on high-latitude SST. This results in a robust conservative reconstruction of the early Eocene latitudinal gradient, which was reduced by at least 32 ± 10% compared with present day, demonstrating greater polar amplification than captured by most climate models.

Carbon-shell-constrained silicon cluster derived from Al-Si alloy as long-cycling life lithium ion batteries anode

NASA Astrophysics Data System (ADS)

Su, Junming; Zhang, Congcong; Chen, Xiang; Liu, Siyang; Huang, Tao; Yu, Aishui

2018-03-01

Although silicon is the most promising anode material for Li-ion batteries, large volume expansion during lithiation and delithiation is the main obstacle limiting the commercial application of silicon anodes. There are two ways to alleviate volume expansion and prevent further pulverization of a Si anode: fabrication of a rational nanostructure possessing void spaces and uniform distribution of the conducting sites, without a good balance effect in mitigating the limiting factors and enhancing battery performance. In this paper, we propose a novel nanostructure - a carbon-shell-constrained Si cluster (Si/C shell) with both adequate void space and good distribution of electrical contact sites to guarantee homogeneous lithiation in the initial cycle. Benefiting from the ability to maintain electrical conductivity of the outer carbon shell, even after cluster fragmentation, the Si/C shell synthesized from low-cost commercial Al-Si alloy spheres can deliver 0.03% capacity loss from 100th to 1000th cycles at a current density of 1 A g-1. The Si/C shell sample with the dual functional structure mentioned above can also maintain its own nanostructure during cycling and deliver excellent rate performance. It is a concise and scalable strategy which can simplify the preparation of other alloy anode materials for Li-ion batteries.

High spectral and spatial resolution hyperspectral imagery for quantifying Russian wheat aphid infestation in wheat using the constrained energy minimization classifier

NASA Astrophysics Data System (ADS)

Mirik, Mustafa; Ansley, R. James; Steddom, Karl; Rush, Charles M.; Michels, Gerald J.; Workneh, Fekede; Cui, Song; Elliott, Norman C.

2014-01-01

The effects of insect infestation in agricultural crops are of major ecological and economic interest because of reduced yield, increased cost of pest control and increased risk of environmental contamination from insecticide application. The Russian wheat aphid (RWA, Diuraphis noxia) is an insect pest that causes damage to wheat (Triticum aestivum L.). We proposed that concentrated RWA feeding areas, referred to as "hot spots," could be identified and isolated from uninfested areas within a field for site specific aphid management using remotely sensed data. Our objectives were to (1) investigate the reflectance characteristics of infested and uninfested wheat by RWA and (2) evaluate utility of airborne hyperspectral imagery with 1-m spatial resolution for detecting, quantifying, and mapping RWA infested areas in commercial winter wheat fields using the constrained energy minimization classifier. Percent surface reflectance from uninfested wheat was lower in the visible and higher in the near infrared portions of the spectrum when compared with RWA-infested wheat. The overall classification accuracies of >89% for damage detection were achieved. These results indicate that hyperspectral imagery can be effectively used for accurate detection and quantification of RWA infestation in wheat for site-specific aphid management.

A strategy for developing future academic leaders for South Africa in a resource-constrained environment.

PubMed

Lalloo, Umesh G; Bobat, Raziya A; Pillay, Sandy; Wassenaar, Douglas

2014-08-01

A key challenge in addressing the shortage of health care workers in resource-constrained environments is ensuring that there is optimal academic capacity for their training. South Africa's University of KwaZulu-Natal has placed academic and research capacity building at the heart of its program with the Medical Education Partnership Initiative in a program called ENhancing Training and REsearch capacity and Expertise (ENTREE). The program aims to increase the quantity, quality, and retention of health care graduates. It is premised on the basis that research capacity development will lead to an increase in teachers who will be essential to improving the quality and quantity of health care workers needed to meet South Africa's health challenges. This is being achieved through four components of the program: (1) infusion of the undergraduate program with research modules; (2) attraction of academically talented students in the middle of their undergraduate program into a parallel track that has research capacity as its major thrust; (3) attraction of qualified health care personnel into a supported PhD program; and (4) providing strong research ethics training and mentorship. A significant proportion of the program is being executed in rural training sites, to increase the probability that trainees will return to the sites as mentors.

A new velocity field for Africa from combined GPS and DORIS space geodetic Solutions: Contribution to the definition of the African reference frame (AFREF)

NASA Astrophysics Data System (ADS)

Saria, E.; Calais, E.; Altamimi, Z.; Willis, P.; Farah, H.

2013-04-01

We analyzed 16 years of GPS and 17 years of Doppler orbitography and radiopositioning integrated by satellite (DORIS) data at continuously operating geodetic sites in Africa and surroundings to describe the present-day kinematics of the Nubian and Somalian plates and constrain relative motions across the East African Rift. The resulting velocity field describes horizontal and vertical motion at 133 GPS sites and 9 DORIS sites. Horizontal velocities at sites located on stable Nubia fit a single plate model with a weighted root mean square residual of 0.6 mm/yr (maximum residual 1 mm/yr), an upper bound for plate-wide motions and for regional-scale deformation in the seismically active southern Africa and Cameroon volcanic line. We confirm significant southward motion ( ˜ 1.5 mm/yr) in Morocco with respect to Nubia, consistent with earlier findings. We propose an updated angular velocity for the divergence between Nubia and Somalia, which provides the kinematic boundary conditions to rifting in East Africa. We update a plate motion model for the East African Rift and revise the counterclockwise rotation of the Victoria plate and clockwise rotation of the Rovuma plate with respect to Nubia. Vertical velocities range from - 2 to +2 mm/yr, close to their uncertainties, with no clear geographic pattern. This study provides the first continent-wide position/velocity solution for Africa, expressed in International Terrestrial Reference Frame (ITRF2008), a contribution to the upcoming African Reference Frame (AFREF). Except for a few regions, the African continent remains largely under-sampled by continuous space geodetic data. Efforts are needed to augment the geodetic infrastructure and openly share existing data sets so that the objectives of AFREF can be fully reached.

Environmental Argumentation as Sociocultural Activity

ERIC Educational Resources Information Center

Oliveira, Alandeom W.; Akerson, Valarie L.; Oldfield, Martha

2012-01-01

While environmental argumentation has recently received much attention from science educators, little consideration has been given to how personal identities and social relationships can either support or constrain student argumentation. This study attends to this issue by examining environmental argumentation as a sociocultural activity (how…

Rayleigh Wave Ellipticity Modeling and Inversion for Shallow Structure at the Proposed InSight Landing Site in Elysium Planitia, Mars

NASA Astrophysics Data System (ADS)

Knapmeyer-Endrun, Brigitte; Golombek, Matthew P.; Ohrnberger, Matthias

2017-10-01

The SEIS (Seismic Experiment for Interior Structure) instrument onboard the InSight mission will be the first seismometer directly deployed on the surface of Mars. From studies on the Earth and the Moon, it is well known that site amplification in low-velocity sediments on top of more competent rocks has a strong influence on seismic signals, but can also be used to constrain the subsurface structure. Here we simulate ambient vibration wavefields in a model of the shallow sub-surface at the InSight landing site in Elysium Planitia and demonstrate how the high-frequency Rayleigh wave ellipticity can be extracted from these data and inverted for shallow structure. We find that, depending on model parameters, higher mode ellipticity information can be extracted from single-station data, which significantly reduces uncertainties in inversion. Though the data are most sensitive to properties of the upper-most layer and show a strong trade-off between layer depth and velocity, it is possible to estimate the velocity and thickness of the sub-regolith layer by using reasonable constraints on regolith properties. Model parameters are best constrained if either higher mode data can be used or additional constraints on regolith properties from seismic analysis of the hammer strokes of InSight's heat flow probe HP3 are available. In addition, the Rayleigh wave ellipticity can distinguish between models with a constant regolith velocity and models with a velocity increase in the regolith, information which is difficult to obtain otherwise.

Syntectonic remagnetization in the southern Methow block: Resolving large displacements in the southern Canadian Cordillera

USGS Publications Warehouse

Enkin, R.J.; Mahoney, J.B.; Baker, J.; Kiessling, M.; Haugerud, R.A.

2002-01-01

The Upper Cretaceous Ventura Member of the Goat Wall unit in the southern Methow block of southern British Columbia and northern Washington State holds a syntectonic magnetization. Eight new sites from Manning Park in British Columbia give a mean direction of D = 27.5??, I = 60.1??, k = 304.7, ??95 = 3.2?? after optimal partial tilt correction. Of five groups of bedded sites from farther south in the basin reported by Bazard et al. [1990], four have a syntectonic remanence with a direction similar to what we observe. The exception is one group which has optimal concentration of remanence directions on >100% untilting and an abherent direction which must be rejected. Combining the accepted sites, the optimal differential syntilting direction is D = 11.8??, I = 61.5??, k = 39.3, ??95 = 3.4?? (N = 47), giving a mean pole of 79.8??N, 359.2??E, K = 19.5, and A95 = 4.8??. The age of the remagnetization is constrained to be between 88 and 80 Ma. Compared to cratonic North America, this result indicates that the southern Methow block was displaced from the south by 1800 ?? 500 km, meaning it lay south of the Sierra Nevada subduction zone but well north of other paleomagnetically constrained Cretaceous rock units from the Insular superterrane, including correlative strata of the Mount Tatlow area in the northern Methow block. Among several possibilities to reconcile this discrepancy, the most plausible has the whole Methow block translated coherently but with the southern Methow block strata remagnetized during transit.

A chronological framework for a long and persistent archaeological record: Melka Kunture, Ethiopia.

PubMed

Morgan, Leah E; Renne, Paul R; Kieffer, Guy; Piperno, Marcello; Gallotti, Rosalia; Raynal, Jean-Paul

2012-01-01

New (40)Ar/(39)Ar geochronological data for several volcanic ash horizons from Melka Kunture, Ethiopia, allow for significantly more precise age constraints to be placed upon the lithostratigraphy, archaeology and paleontology from this long record. Ashes from the Melka Kunture Formation at Gombore yielded the most reliable age constraints, from 1.393 ± 0.162 Ma(2) (millions of years ago) near the base of the section to 0.709 ± 0.013 Ma near the top. Dating the Garba section proved more problematic, but the base of the section, which contains numerous Oldowan obsidian artifacts, may be >1.719 ± 0.199 Ma, while the top is securely dated to 0.869 ± 0.020 Ma. The large ignimbrite from the Kella Formation at Kella and Melka Garba is dated to 1.262 ± 0.034 Ma and pre-dates Acheulean artifacts in the area. The Gombore II site, which has yielded two Homo skull fragments, 'twisted bifaces,' and a preserved butchery site, is now constrained between 0.875 ± 0.010 Ma and 0.709 ± 0.013 Ma. Additional ashes from these and other sites further constrain the timing of deposition throughout the section. Integration with previously published magnetostratigraphy has allowed for the first time a relatively complete, reliable timeline for the deposition of sediments, environmental changes, archaeology, and paleontology at Melka Kunture. Copyright © 2011 Elsevier Ltd. All rights reserved.

Community and family perspectives on addressing overweight in urban, African-American youth.

PubMed

Burnet, Deborah L; Plaut, Andrea J; Ossowski, Kathryn; Ahmad, Afshan; Quinn, Michael T; Radovick, Sally; Gorawara-Bhat, Rita; Chin, Marshall H

2008-02-01

To assess weight-related beliefs and concerns of overweight urban, African-American children, their parents, and community leaders before developing a family-based intervention to reduce childhood overweight and diabetes risk. We conducted 13 focus groups with overweight children and their parents and eight semistructured interviews with community leaders. Focus group participants (N = 67) from Chicago's South Side were recruited through flyers in community sites. Interview participants (N = 9) were recruited to sample perspectives from health, fitness, education, civics, and faith leaders. Community leaders felt awareness was higher for acute health conditions than for obesity. Parents were concerned about their children's health, but felt stressed by competing priorities and constrained by lack of knowledge, parenting skills, time, and financial resources. Parents defined overweight in functional terms, whereas children relied upon physical appearances. Children perceived negative social consequences of overweight. Parents and children expressed interest in family-based interventions to improve nutrition and physical activity and offered suggestions for making programs interesting. This study provides insights into the perspectives of urban, African-American overweight children, their parents, and community leaders regarding nutrition and physical activity. The specific beliefs of these respondents can become potential leverage points in interventions.

Amino acid production exceeds plant nitrogen demand in Siberian tundra

NASA Astrophysics Data System (ADS)

Wild, Birgit; Eloy Alves, Ricardo J.; Bárta, Jiři; Čapek, Petr; Gentsch, Norman; Guggenberger, Georg; Hugelius, Gustaf; Knoltsch, Anna; Kuhry, Peter; Lashchinskiy, Nikolay; Mikutta, Robert; Palmtag, Juri; Prommer, Judith; Schnecker, Jörg; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Richter, Andreas

2018-03-01

Arctic plant productivity is often limited by low soil N availability. This has been attributed to slow breakdown of N-containing polymers in litter and soil organic matter (SOM) into smaller, available units, and to shallow plant rooting constrained by permafrost and high soil moisture. Using 15N pool dilution assays, we here quantified gross amino acid and ammonium production rates in 97 active layer samples from four sites across the Siberian Arctic. We found that amino acid production in organic layers alone exceeded literature-based estimates of maximum plant N uptake 17-fold and therefore reject the hypothesis that arctic plant N limitation results from slow SOM breakdown. High microbial N use efficiency in organic layers rather suggests strong competition of microorganisms and plants in the dominant rooting zone. Deeper horizons showed lower amino acid production rates per volume, but also lower microbial N use efficiency. Permafrost thaw together with soil drainage might facilitate deeper plant rooting and uptake of previously inaccessible subsoil N, and thereby promote plant productivity in arctic ecosystems. We conclude that changes in microbial decomposer activity, microbial N utilization and plant root density with soil depth interactively control N availability for plants in the Arctic.

Pooling the resources of the CMS Tier-1 sites

DOE PAGES

Apyan, A.; Badillo, J.; Cruz, J. Diaz; ...

2015-12-23

The CMS experiment at the LHC relies on 7 Tier-1 centres of the WLCG to perform the majority of its bulk processing activity, and to archive its data. During the first run of the LHC, these two functions were tightly coupled as each Tier-1 was constrained to process only the data archived on its hierarchical storage. This lack of flexibility in the assignment of processing workflows occasionally resulted in uneven resource utilisation and in an increased latency in the delivery of the results to the physics community.The long shutdown of the LHC in 2013-2014 was an opportunity to revisit thismore » mode of operations, disentangling the processing and archive functionalities of the Tier-1 centres. The storage services at the Tier-1s were redeployed breaking the traditional hierarchical model: each site now provides a large disk storage to host input and output data for processing, and an independent tape storage used exclusively for archiving. Movement of data between the tape and disk endpoints is not automated, but triggered externally through the WLCG transfer management systems.With this new setup, CMS operations actively controls at any time which data is available on disk for processing and which data should be sent to archive. Thanks to the high-bandwidth connectivity guaranteed by the LHCOPN, input data can be freely transferred between disk endpoints as needed to take advantage of free CPU, turning the Tier-1s into a large pool of shared resources. The output data can be validated before archiving them permanently, and temporary data formats can be produced without wasting valuable tape resources. Lastly, the data hosted on disk at Tier-1s can now be made available also for user analysis since there is no risk any longer of triggering chaotic staging from tape.In this contribution, we describe the technical solutions adopted for the new disk and tape endpoints at the sites, and we report on the commissioning and scale testing of the service. We detail the procedures implemented by CMS computing operations to actively manage data on disk at Tier-1 sites, and we give examples of the benefits brought to CMS workflows by the additional flexibility of the new system.« less

Pooling the resources of the CMS Tier-1 sites

NASA Astrophysics Data System (ADS)

Apyan, A.; Badillo, J.; Diaz Cruz, J.; Gadrat, S.; Gutsche, O.; Holzman, B.; Lahiff, A.; Magini, N.; Mason, D.; Perez, A.; Stober, F.; Taneja, S.; Taze, M.; Wissing, C.

2015-12-01

The CMS experiment at the LHC relies on 7 Tier-1 centres of the WLCG to perform the majority of its bulk processing activity, and to archive its data. During the first run of the LHC, these two functions were tightly coupled as each Tier-1 was constrained to process only the data archived on its hierarchical storage. This lack of flexibility in the assignment of processing workflows occasionally resulted in uneven resource utilisation and in an increased latency in the delivery of the results to the physics community. The long shutdown of the LHC in 2013-2014 was an opportunity to revisit this mode of operations, disentangling the processing and archive functionalities of the Tier-1 centres. The storage services at the Tier-1s were redeployed breaking the traditional hierarchical model: each site now provides a large disk storage to host input and output data for processing, and an independent tape storage used exclusively for archiving. Movement of data between the tape and disk endpoints is not automated, but triggered externally through the WLCG transfer management systems. With this new setup, CMS operations actively controls at any time which data is available on disk for processing and which data should be sent to archive. Thanks to the high-bandwidth connectivity guaranteed by the LHCOPN, input data can be freely transferred between disk endpoints as needed to take advantage of free CPU, turning the Tier-1s into a large pool of shared resources. The output data can be validated before archiving them permanently, and temporary data formats can be produced without wasting valuable tape resources. Finally, the data hosted on disk at Tier-1s can now be made available also for user analysis since there is no risk any longer of triggering chaotic staging from tape. In this contribution, we describe the technical solutions adopted for the new disk and tape endpoints at the sites, and we report on the commissioning and scale testing of the service. We detail the procedures implemented by CMS computing operations to actively manage data on disk at Tier-1 sites, and we give examples of the benefits brought to CMS workflows by the additional flexibility of the new system.

Reversibly constraining spliceosome-substrate complexes by engineering disulfide crosslinks.

PubMed

McCarthy, Patrick; Garside, Erin; Meschede-Krasa, Yonatan; MacMillan, Andrew; Pomeranz Krummel, Daniel

2017-08-01

The spliceosome is a highly dynamic mega-Dalton enzyme, formed in part by assembly of U snRNPs onto its pre-mRNA substrate transcripts. Early steps in spliceosome assembly are challenging to study biochemically and structurally due to compositional and conformational dynamics. We detail an approach to covalently and reversibly constrain or trap non-covalent pre-mRNA/protein spliceosome complexes. This approach involves engineering a single disulfide bond between a thiol-bearing cysteine sidechain and a proximal backbone phosphate of the pre-mRNA, site-specifically modified with an N-thioalkyl moiety. When distance and angle between reactants is optimal, the sidechain will react with the single N-thioalkyl to form a crosslink upon oxidation. We provide protocols detailing how this has been applied successfully to trap an 11-subunit RNA-protein assembly, the human U1 snRNP, in complex with a pre-mRNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Role of slack variables in quasi-Newton methods for constrained optimization

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

Tapia, R.A.

In constrained optimization the technique of converting an inequality constraint into an equality constraint by the addition of a squared slack variable is well known but rarely used. In choosing an active constraint philosophy over the slack variable approach, researchers quickly justify their choice with the standard criticisms: the slack variable approach increases the dimension of the problem, is numerically unstable, and gives rise to singular systems. It is shown that these criticisms of the slack variable approach need not apply and the two seemingly distinct approaches are actually very closely related. In fact, the squared slack variable formulation canmore » be used to develop a superior and more comprehensive active constraint philosophy.« less

Exploring the biological consequences of conformational changes in aspartame models containing constrained analogues of phenylalanine.

PubMed

Mollica, Adriano; Mirzaie, Sako; Costante, Roberto; Carradori, Simone; Macedonio, Giorgia; Stefanucci, Azzurra; Dvoracsko, Szabolcs; Novellino, Ettore

2016-12-01

The dipeptide aspartame (Asp-Phe-OMe) is a sweetener widely used in replacement of sucrose by food industry. 2',6'-Dimethyltyrosine (DMT) and 2',6'-dimethylphenylalanine (DMP) are two synthetic phenylalanine-constrained analogues, with a limited freedom in χ-space due to the presence of methyl groups in position 2',6' of the aromatic ring. These residues have shown to increase the activity of opioid peptides, such as endomorphins improving the binding to the opioid receptors. In this work, DMT and DMP have been synthesized following a diketopiperazine-mediated route and the corresponding aspartame derivatives (Asp-DMT-OMe and Asp-DMP-OMe) have been evaluated in vivo and in silico for their activity as synthetic sweeteners.

Effect of constrained weight shift on the static balance and muscle activation of stroke patients

PubMed Central

Kang, Kyung Woo; Kim, Kyoung; Lee, Na Kyung; Kwon, Jung Won; Son, Sung Min

2015-01-01

[Purpose] The purpose of this study was to evaluate the effects of constrained weight shift induced by shoe lift beneath the unaffected lower extremity, on balance functions and electromyography of the affected lower extremity of stroke patients. [Subjects and Methods] Twelve patients with unilateral stroke were recruited as volunteers for this study. The subjects were repeatedly measured in a randomized order under three conditions: no-shoe lift, and shoe lifts of 5 mm and 10 mm heights beneath the unaffected lower extremity. [Results] Standing with a 10 mm shoe lift for the unaffected lower extremity decreased the mean velocity of mediolateral sway compared to no-shoe lift. Regarding the velocity of anteroposterior sway, standing with 5 mm and 10 mm shoe lifts decreased the mean velocity of anteroposterior sway. The muscle activation of the affected lower extremity was not significantly different among the no-shoe lift, 5 mm shoe lift and 10 mm shoe lift conditions; however, the muscle activities of the rectus femoris, biceps femoris, tibialis anterior, and medial gastrocnemius of the affected lower extremity progressively improved with increasing height of the shoe lift. [Conclusion] A constrained weight shift to the affected side elicited by a shoe insole of 10 mm height on the unaffected side can improve the static standing balance of stroke patients, and it resulted in 14–24% increases in the muscle activities of the affected leg. PMID:25931729

2500 pyroclast puzzle: probing eruptive scenarios at Volcán de Colima, Mexico

NASA Astrophysics Data System (ADS)

Kueppers, U.; Varley, N. R.; Alatorre-Ibarguengoitia, M. A.; Lavallee, Y.; Becker, S.; Berninger, N.; Goldstein, F.; Hanson, J. B.; Kolzenburg, S.; Dingwell, D. B.

2009-12-01

The Colima volcanic complex is comprised by two edifices, the extinct Nevado de Colima to the North and the active Fuego de Colima in the South. Since 1998, a dome-building phase has shown repeated shifts between lava effusion and short-lived explosive activity. Lava extrusion rates were usually low leading to the build-up of domes inside the crater but occasionally, lava spilled over the crater rim and flowed down the flanks. This effusive activity was usually associated with several ash explosions and gas exhalation events per day. In 2005, occasional block-and-ash flows from dome-collapse events travelled down the Western flanks and reached La Lumbre valley. Later that year, violent explosive eruptions destroyed the dome and sent pyroclastic flows to valleys in the South (Monte Grande) and South-East (La Arena). The transition from effusive to short-lived but highly explosive eruptive behaviour presents an interesting opportunity to study pyroclastic flow deposits from different generating mechanisms. Gas at overpressure in bubbly magma is one of the main driving forces of explosive eruptions. The change of the physical properties of evolved magmas after the fragmentation is minor. Therefore, a detailed characterisation of volcanic products reveals much information and is vital for a correct understanding of volcanic deposits. Comparing different units allows constraining the bandwidth of possible eruptive scenarios. Here, we thoroughly characterized the deposits of the above described events on site. In the field, we 1) measured the density distribution of 100 surficial juvenile and lithic clasts at 24 localities (1 * 1 m) across the length and width of the pyroclastic flow deposits; 2) sieved the matrix (approx. 30 * 30 * 30 cm) at each locality; and 3) created detailed stratigraphic logs. We observe a lower mean density and a greater variance for clasts generated by the explosive eruption. Our results highlight the different origin of the 2005 deposits on Colima. Ergo, the physical properties of eruptive products allow the constraining of eruptive scenarios and may help to better interpret volcanic deposits that have not been eye-witnessed.

The Europa Imaging System (EIS): High-Resolution, 3-D Insight into Europa's Geology, Ice Shell, and Potential for Current Activity

NASA Astrophysics Data System (ADS)

Turtle, E. P.; McEwen, A. S.; Collins, G. C.; Fletcher, L. N.; Hansen, C. J.; Hayes, A.; Hurford, T., Jr.; Kirk, R. L.; Barr, A.; Nimmo, F.; Patterson, G.; Quick, L. C.; Soderblom, J. M.; Thomas, N.

2015-12-01

The Europa Imaging System will transform our understanding of Europa through global decameter-scale coverage, three-dimensional maps, and unprecedented meter-scale imaging. EIS combines narrow-angle and wide-angle cameras (NAC and WAC) designed to address high-priority Europa science and reconnaissance goals. It will: (A) Characterize the ice shell by constraining its thickness and correlating surface features with subsurface structures detected by ice penetrating radar; (B) Constrain formation processes of surface features and the potential for current activity by characterizing endogenic structures, surface units, global cross-cutting relationships, and relationships to Europa's subsurface structure, and by searching for evidence of recent activity, including potential plumes; and (C) Characterize scientifically compelling landing sites and hazards by determining the nature of the surface at scales relevant to a potential lander. The NAC provides very high-resolution, stereo reconnaissance, generating 2-km-wide swaths at 0.5-m pixel scale from 50-km altitude, and uses a gimbal to enable independent targeting. NAC observations also include: near-global (>95%) mapping of Europa at ≤50-m pixel scale (to date, only ~14% of Europa has been imaged at ≤500 m/pixel, with best pixel scale 6 m); regional and high-resolution stereo imaging at <1-m/pixel; and high-phase-angle observations for plume searches. The WAC is designed to acquire pushbroom stereo swaths along flyby ground-tracks, generating digital topographic models with 32-m spatial scale and 4-m vertical precision from 50-km altitude. These data support characterization of cross-track clutter for radar sounding. The WAC also performs pushbroom color imaging with 6 broadband filters (350-1050 nm) to map surface units and correlations with geologic features and topography. EIS will provide comprehensive data sets essential to fulfilling the goal of exploring Europa to investigate its habitability and perform collaborative science with other investigations, including cartographic and geologic maps, regional and high-resolution digital topography, GIS products, color and photometric data products, a geodetic control network tied to radar altimetry, and a database of plume-search observations.

Retesting of liquefaction and nonliquefaction case histories from the 1976 Tangshan earthquake

USGS Publications Warehouse

Moss, R.E.S.; Kayen, R.E.; Tong, L.-Y.; Liu, S.-Y.; Cai, G.-J.; Wu, J.

2011-01-01

A field investigation was performed to retest liquefaction and nonliquefaction sites from the 1976 Tangshan earthquake in China. These sites were carefully investigated in 1978 and 1979 by using standard penetration test (SPT) and cone penetration test (CPT) equipment; however, the CPT measurements are obsolete because of the now nonstandard cone that was used at the time. In 2007, a modern cone was mobilized to retest 18 selected sites that are particularly important because of the intense ground shaking they sustained despite their high fines content and/or because the site did not liquefy. Of the sites reinvestigated and carefully reprocessed, 13 were considered accurate representative case histories. Two of the sites that were originally investigated for liquefaction have been reinvestigated for cyclic failure of fine-grained soil and removed from consideration for liquefaction triggering. The most important outcome of these field investigations was the collection of more accurate data for three nonliquefaction sites that experienced intense ground shaking. Data for these three case histories is now included in an area of the liquefaction triggering database that was poorly populated and will help constrain the upper bound of future liquefaction triggering curves. ?? 2011 American Society of Civil Engineers.

Notch signalling mediates reproductive constraint in the adult worker honeybee

PubMed Central

Duncan, Elizabeth J.; Hyink, Otto; Dearden, Peter K.

2016-01-01

The hallmark of eusociality is the reproductive division of labour, in which one female caste reproduces, while reproduction is constrained in the subordinate caste. In adult worker honeybees (Apis mellifera) reproductive constraint is conditional: in the absence of the queen and brood, adult worker honeybees activate their ovaries and lay haploid male eggs. Here, we demonstrate that chemical inhibition of Notch signalling can overcome the repressive effect of queen pheromone and promote ovary activity in adult worker honeybees. We show that Notch signalling acts on the earliest stages of oogenesis and that the removal of the queen corresponds with a loss of Notch protein in the germarium. We conclude that the ancient and pleiotropic Notch signalling pathway has been co-opted into constraining reproduction in worker honeybees and we provide the first molecular mechanism directly linking ovary activity in adult worker bees with the presence of the queen. PMID:27485026

Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data

PubMed Central

Pnevmatikakis, Eftychios A.; Soudry, Daniel; Gao, Yuanjun; Machado, Timothy A.; Merel, Josh; Pfau, David; Reardon, Thomas; Mu, Yu; Lacefield, Clay; Yang, Weijian; Ahrens, Misha; Bruno, Randy; Jessell, Thomas M.; Peterka, Darcy S.; Yuste, Rafael; Paninski, Liam

2016-01-01

SUMMARY We present a modular approach for analyzing calcium imaging recordings of large neuronal ensembles. Our goal is to simultaneously identify the locations of the neurons, demix spatially overlapping components, and denoise and deconvolve the spiking activity from the slow dynamics of the calcium indicator. Our approach relies on a constrained nonnegative matrix factorization that expresses the spatiotemporal fluorescence activity as the product of a spatial matrix that encodes the spatial footprint of each neuron in the optical field and a temporal matrix that characterizes the calcium concentration of each neuron over time. This framework is combined with a novel constrained deconvolution approach that extracts estimates of neural activity from fluorescence traces, to create a spatiotemporal processing algorithm that requires minimal parameter tuning. We demonstrate the general applicability of our method by applying it to in vitro and in vivo multineuronal imaging data, whole-brain light-sheet imaging data, and dendritic imaging data. PMID:26774160

Tapered whiskers are required for active tactile sensation.

PubMed

Hires, Samuel Andrew; Pammer, Lorenz; Svoboda, Karel; Golomb, David

2013-11-19

Many mammals forage and burrow in dark constrained spaces. Touch through facial whiskers is important during these activities, but the close quarters makes whisker deployment challenging. The diverse shapes of facial whiskers reflect distinct ecological niches. Rodent whiskers are conical, often with a remarkably linear taper. Here we use theoretical and experimental methods to analyze interactions of mouse whiskers with objects. When pushed into objects, conical whiskers suddenly slip at a critical angle. In contrast, cylindrical whiskers do not slip for biologically plausible movements. Conical whiskers sweep across objects and textures in characteristic sequences of brief sticks and slips, which provide information about the tactile world. In contrast, cylindrical whiskers stick and remain stuck, even when sweeping across fine textures. Thus the conical whisker structure is adaptive for sensor mobility in constrained environments and in feature extraction during active haptic exploration of objects and surfaces. DOI: http://dx.doi.org/10.7554/eLife.01350.001.

The effect of constraining eye-contact during dynamic emotional face perception—an fMRI study

PubMed Central

Zurcher, Nicole R.; Lassalle, Amandine; Hippolyte, Loyse; Ward, Noreen; Johnels, Jakob Åsberg

2017-01-01

Abstract Eye-contact modifies how we perceive emotions and modulates activity in the social brain network. Here, using fMRI, we demonstrate that adding a fixation cross in the eye region of dynamic facial emotional stimuli significantly increases activation in the social brain of healthy, neurotypical participants when compared with activation for the exact same stimuli observed in a free-viewing mode. In addition, using PPI analysis, we show that the degree of amygdala connectivity with the rest of the brain is enhanced for the constrained view for all emotions tested except for fear, and that anxiety and alexithymia modulate the strength of amygdala connectivity for each emotion differently. Finally, we show that autistic traits have opposite effects on amygdala connectivity for fearful and angry emotional expressions, suggesting that these emotions should be treated separately in studies investigating facial emotion processing. PMID:28402536

Spatiotemporal changes of seismic attenuation caused by injected CO2 at the Frio-II pilot site, Dayton, TX, USA

NASA Astrophysics Data System (ADS)

Zhu, Tieyuan; Ajo-Franklin, Jonathan B.; Daley, Thomas M.

2017-09-01

A continuous active source seismic monitoring data set was collected with crosswell geometry during CO2 injection at the Frio-II brine pilot, near Liberty, TX. Previous studies have shown that spatiotemporal changes in the P wave first arrival time reveal the movement of the injected CO2 plume in the storage zone. To further constrain the CO2 saturation, particularly at higher saturation levels, we investigate spatial-temporal changes in the seismic attenuation of the first arrivals. The attenuation changes over the injection period are estimated by the amount of the centroid frequency shift computed by local time-frequency analysis. We observe that (1) at receivers above the injection zone seismic attenuation does not change in a physical trend; (2) at receivers in the injection zone attenuation sharply increases following injection and peaks at specific points varying with distributed receivers, which is consistent with observations from time delays of first arrivals; then, (3) attenuation decreases over the injection time. The attenuation change exhibits a bell-shaped pattern during CO2 injection. Under Frio-II field reservoir conditions, White's patchy saturation model can quantitatively explain both the P wave velocity and attenuation response observed. We have combined the velocity and attenuation change data in a crossplot format that is useful for model-data comparison and determining patch size. Our analysis suggests that spatial-temporal attenuation change is not only an indicator of the movement and saturation of CO2 plumes, even at large saturations, but also can quantitatively constrain CO2 plume saturation when used jointly with seismic velocity.

Patterns of megafloral change across the Cretaceous-Tertiary boundary in the Northern Great Plains and Rocky Mountains

NASA Technical Reports Server (NTRS)

Johnson, Kirk R.; Hickey, Leo J.

1988-01-01

The spatial and temporal distribution of vegetation in the terminal Cretaceous of Western Interior North America was a complex mosaic resulting from the interaction of factors including a shifting coastline, tectonic activity, a mild, possibly deteriorating climate, dinosaur herbivory, local facies effects, and a hypothesized bolide impact. In order to achieve sufficient resolution to analyze this vegetational pattern, over 100 megafloral collecting sites were established, yielding approximately 15,000 specimens, in Upper Cretaceous and lower Paleocene strata in the Williston, Powder River, and Bighorn basins in North Dakota, Montana, and Wyoming. These localities were integrated into a lithostratigraphic framework that is based on detailed local reference sections and constrained by vertebrate and palynomorph biostratigraphy, magnetostratigraphy, and sedimentary facies analysis. A regional biostratigraphy based on well located and identified plant megafossils that can be used to address patterns of floral evolution, ecology, and extinction is the goal of this research. Results of the analyses are discussed.

Spatio-Temporal Convergence of Maximum Daily Light-Use Efficiency Based on Radiation Absorption by Canopy Chlorophyll

NASA Astrophysics Data System (ADS)

Zhang, Yao; Xiao, Xiangming; Wolf, Sebastian; Wu, Jin; Wu, Xiaocui; Gioli, Beniamino; Wohlfahrt, Georg; Cescatti, Alessandro; van der Tol, Christiaan; Zhou, Sha; Gough, Christopher M.; Gentine, Pierre; Zhang, Yongguang; Steinbrecher, Rainer; Ardö, Jonas

2018-04-01

Light-use efficiency (LUE), which quantifies the plants' efficiency in utilizing solar radiation for photosynthetic carbon fixation, is an important factor for gross primary production estimation. Here we use satellite-based solar-induced chlorophyll fluorescence as a proxy for photosynthetically active radiation absorbed by chlorophyll (APARchl) and derive an estimation of the fraction of APARchl (fPARchl) from four remotely sensed vegetation indicators. By comparing maximum LUE estimated at different scales from 127 eddy flux sites, we found that the maximum daily LUE based on PAR absorption by canopy chlorophyll (ɛmaxchl), unlike other expressions of LUE, tends to converge across biome types. The photosynthetic seasonality in tropical forests can also be tracked by the change of fPARchl, suggesting the corresponding ɛmaxchl to have less seasonal variation. This spatio-temporal convergence of LUE derived from fPARchl can be used to build simple but robust gross primary production models and to better constrain process-based models.

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

R Vasquez-Del Carpio; T Silverstein; S Lone

Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase {Kappa} (Pol{Kappa}), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Pol{Kappa} in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure revealsmore » a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Pol{Kappa} in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.« less

The importance of hydration thermodynamics in fragment-to-lead optimization.

PubMed

Ichihara, Osamu; Shimada, Yuzo; Yoshidome, Daisuke

2014-12-01

Using a computational approach to assess changes in solvation thermodynamics upon ligand binding, we investigated the effects of water molecules on the binding energetics of over 20 fragment hits and their corresponding optimized lead compounds. Binding activity and X-ray crystallographic data of published fragment-to-lead optimization studies from various therapeutically relevant targets were studied. The analysis reveals a distinct difference between the thermodynamic profile of water molecules displaced by fragment hits and those displaced by the corresponding optimized lead compounds. Specifically, fragment hits tend to displace water molecules with notably unfavorable excess entropies-configurationally constrained water molecules-relative to those displaced by the newly added moieties of the lead compound during the course of fragment-to-lead optimization. Herein we describe the details of this analysis with the goal of providing practical guidelines for exploiting thermodynamic signatures of binding site water molecules in the context of fragment-to-lead optimization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stable Isotope Measurements of Martian Atmospheric CO2 at the Phoenix Landing Site

NASA Astrophysics Data System (ADS)

Niles, Paul B.; Boynton, William V.; Hoffman, John H.; Ming, Douglas W.; Hamara, Dave

2010-09-01

Carbon dioxide is a primary component of the martian atmosphere and reacts readily with water and silicate rocks. Thus, the stable isotopic composition of CO2 can reveal much about the history of volatiles on the planet. The Mars Phoenix spacecraft measurements of carbon isotopes [referenced to the Vienna Pee Dee belemnite (VPDB)] [δ13CVPDB = -2.5 ± 4.3 per mil (‰)] and oxygen isotopes [referenced to the Vienna standard mean ocean water (VSMOW)] (δ18OVSMOW = 31.0 ± 5.7‰), reported here, indicate that CO2 is heavily influenced by modern volcanic degassing and equilibration with liquid water. When combined with data from the martian meteorites, a general model can be constructed that constrains the history of water, volcanism, atmospheric evolution, and weathering on Mars. This suggests that low-temperature water-rock interaction has been dominant throughout martian history, carbonate formation is active and ongoing, and recent volcanic degassing has played a substantial role in the composition of the modern atmosphere.

On the discovery of new potent human farnesyltransferase inhibitors: emerging pyroglutamic derivatives.

PubMed

Homerin, Germain; Lipka, Emmanuelle; Rigo, Benoît; Farce, Amaury; Dubois, Joëlle; Ghinet, Alina

2017-10-04

In the current context of lack of emergence of innovative human farnesyltransferase inhibitors families, and given all new therapeutic perspectives that open up for such molecules in rare diseases (e.g. Hutchinson-Gilford progeria syndrome), and in delta hepatitis, cardiovascular or neuroinflammatory diseases, we have just discovered a new series of powerful inhibitors. These molecules are pyroglutamic acid derivatives, and were evaluated on human farnesyltransferase in vitro then modeled in silico on the active site of the protein. Three main points of the pyroglutamic acid cycle have undergone chemical modulations pyroglutamides in position 5 (compounds 7a-h), constrained bicyclic analogues of pyrroloimidazoledione type (compounds 1a-h), modulation of the position 3 (compounds 2-5 and 8), and allowed the first SAR in the field. Five derivatives in the current work have IC 50 values in the small nanomolar range (2-5 nM). These new lead compounds open the way for the next generation of farnesyltransferase inhibitors.

Constraining the alteration history of a Late Cretaceous Patagonian volcaniclastic bentonite-ash-mudstone sequence using K-Ar and 40Ar/39Ar isotopes

NASA Astrophysics Data System (ADS)

Warr, L. N.; Hofmann, H.; van der Pluijm, B. A.

2017-01-01

Smectite is typically considered unsuitable for radiometric dating, as argon (40Ar) produced from decay of exchangeable potassium (40K) located in the interlayer sites can be lost during fluid-rock interaction and/or during wet sample preparation in the laboratory. However, age analysis of Late Cretaceous Argentinian bentonites and associated volcaniclastic rocks from Lago Pellegrini, Northern Patagonia, indicates that, in the case of these very low-permeability rocks, the radioactive 40Ar was retained and thus can provide information on smectite age and the timing of rock alteration. This study presents isotopic results that indicate the ash-to-bentonite conversion and alteration of the overlying tuffaceous mudstones in Northern Patagonia was complete 13-17 my after middle Campanian sedimentation when the system isotopically closed. The general absence of illite in these smectite-rich lithologies reflects the low activity of K and the low temperature (<60 °C) of the formation waters that altered the parent ash.

Scattering theory of efficient quantum transport across finite networks

NASA Astrophysics Data System (ADS)

Walschaers, Mattia; Mulet, Roberto; Buchleitner, Andreas

2017-11-01

We present a scattering theory for the efficient transmission of an excitation across a finite network with designed disorder. We show that the presence of randomly positioned network sites allows significant acceleration of the excitation transfer processes as compared to a dimer structure, but only if the disordered Hamiltonians are constrained to be centrosymmetric and exhibit a dominant doublet in their spectrum. We identify the cause of this efficiency enhancement to be the constructive interplay between disorder-induced fluctuations of the dominant doublet’s splitting and the coupling strength between the input and output sites to the scattering channels. We find that the characteristic strength of these fluctuations together with the channel coupling fully control the transfer efficiency.

Mechanism for transient migration of xenon in UO{sub 2}

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

Liu, X.-Y.; Uberuaga, B. P.; Andersson, D. A.

2011-04-11

In this letter, we report recent work on atomistic modeling of diffusion migration events of the fission gas product xenon in UO{sub 2} nuclear fuel. Under nonequilibrium conditions, Xe atoms can occupy the octahedral interstitial site, in contrast to the thermodynamically most stable uranium substitutional site. A transient migration mechanism involving Xe and two oxygen atoms is identified using basin constrained molecular dynamics employing a Buckingham type interatomic potential. This mechanism is then validated using density functional theory calculations using the nudged elastic band method. An overall reduction in the migration barrier of 1.6-2.7 eV is obtained compared to vacancy-mediatedmore » diffusion on the uranium sublattice.« less

Neoproterozoic paleomagnetic poles in the Taoudeni basin (West Africa)

NASA Astrophysics Data System (ADS)

Boudzoumou, Florent; Vandamme, Didier; Affaton, Pascal; Gattacceca, Jérôme

2011-04-01

A palaeomagnetic study was carried out on Neoproterozoic samples from seven sites of the sub-basins of Gourma and Bobo Dioulasso, which include a Marinoan glaciogenic deposit. Magnetic mineralogy is represented essentially by magnetite and hematite. The mean directions of the sites are calculated on the high temperature component (500-670 °C). Two locations provide data constrained by statistical reversal and fold tests and determining Neoproterozoic virtual geomagnetic poles. The palaeolatitudes display very low values which place the West-African craton in the sub-equatorial position during the Marinoan glaciation. This result enhances the Snowball Earth hypothesis, which places most of the continental landmasses, and notably Africa, at low latitudes during the Neoproterozoic.

Development of Kinematic 3D Laser Scanning System for Indoor Mapping and As-Built BIM Using Constrained SLAM

PubMed Central

Jung, Jaehoon; Yoon, Sanghyun; Ju, Sungha; Heo, Joon

2015-01-01

The growing interest and use of indoor mapping is driving a demand for improved data-acquisition facility, efficiency and productivity in the era of the Building Information Model (BIM). The conventional static laser scanning method suffers from some limitations on its operability in complex indoor environments, due to the presence of occlusions. Full scanning of indoor spaces without loss of information requires that surveyors change the scanner position many times, which incurs extra work for registration of each scanned point cloud. Alternatively, a kinematic 3D laser scanning system, proposed herein, uses line-feature-based Simultaneous Localization and Mapping (SLAM) technique for continuous mapping. Moreover, to reduce the uncertainty of line-feature extraction, we incorporated constrained adjustment based on an assumption made with respect to typical indoor environments: that the main structures are formed of parallel or orthogonal line features. The superiority of the proposed constrained adjustment is its reduction for uncertainties of the adjusted lines, leading to successful data association process. In the present study, kinematic scanning with and without constrained adjustment were comparatively evaluated in two test sites, and the results confirmed the effectiveness of the proposed system. The accuracy of the 3D mapping result was additionally evaluated by comparison with the reference points acquired by a total station: the Euclidean average distance error was 0.034 m for the seminar room and 0.043 m for the corridor, which satisfied the error tolerance for point cloud acquisition (0.051 m) according to the guidelines of the General Services Administration for BIM accuracy. PMID:26501292

SupportNet for Frontline Behavioral Health Providers

DTIC Science & Technology

2013-07-01

hired. (Objective 3) d) We have facilitated six, on -site Focus Group meetings at Fort Carson. (Objective 3) (Appendix VII) e) We have reviewed the...Based on these results, the final model with factor loadings and the covariance constrained to be equal across both groups (Model 6; Table 3) was...and 2.17 hours of group clinical supervision per month. On average, they were receiving peer support by discussing the patients with colleagues on

Behind the Scenes: Patient Safety in the Operating Room and Central Materiel Service During Deployments

DTIC Science & Technology

2005-01-01

The surgical hand scrub plays a significant role in preventing nosocomial and surgical site infections . After approval from the Infection Control...stressful conditions in a time- constrained environment. As a result, they are more comfortable with the hands - on aspects of patient care within the...amount of dust, organic debris, and microbial load in surgical environments. Proper cleaning of surfaces can greatly reduce the risk of nosocomial

Northeast Parallel Architectures Center (NPAC) at Syracuse University

DTIC Science & Technology

1990-12-01

lattice models. On the CM-2 we will fun a lattice gauge theory simulation of quantum chromodynamics ( QCD ), and on the CM-1 we will investigate the...into a three-dimensional grid with the stipulation that adjacent processors in the lattice correspond to proximate regions of space. Light paths will...be constrained to follow lattice links and the sum over all paths from light sources to each lattice site will be computed inductively by all

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

Apyan, A.; Badillo, J.; Cruz, J. Diaz

The CMS experiment at the LHC relies on 7 Tier-1 centres of the WLCG to perform the majority of its bulk processing activity, and to archive its data. During the first run of the LHC, these two functions were tightly coupled as each Tier-1 was constrained to process only the data archived on its hierarchical storage. This lack of flexibility in the assignment of processing workflows occasionally resulted in uneven resource utilisation and in an increased latency in the delivery of the results to the physics community.The long shutdown of the LHC in 2013-2014 was an opportunity to revisit thismore » mode of operations, disentangling the processing and archive functionalities of the Tier-1 centres. The storage services at the Tier-1s were redeployed breaking the traditional hierarchical model: each site now provides a large disk storage to host input and output data for processing, and an independent tape storage used exclusively for archiving. Movement of data between the tape and disk endpoints is not automated, but triggered externally through the WLCG transfer management systems.With this new setup, CMS operations actively controls at any time which data is available on disk for processing and which data should be sent to archive. Thanks to the high-bandwidth connectivity guaranteed by the LHCOPN, input data can be freely transferred between disk endpoints as needed to take advantage of free CPU, turning the Tier-1s into a large pool of shared resources. The output data can be validated before archiving them permanently, and temporary data formats can be produced without wasting valuable tape resources. Lastly, the data hosted on disk at Tier-1s can now be made available also for user analysis since there is no risk any longer of triggering chaotic staging from tape.In this contribution, we describe the technical solutions adopted for the new disk and tape endpoints at the sites, and we report on the commissioning and scale testing of the service. We detail the procedures implemented by CMS computing operations to actively manage data on disk at Tier-1 sites, and we give examples of the benefits brought to CMS workflows by the additional flexibility of the new system.« less

Episodic fluid flow in the Nankai accretionary complex: Timescale, geochemistry, flow rates, and fluid budget

USGS Publications Warehouse

Saffer, D.M.; Bekins, B.A.

1998-01-01

Down-hole geochemical anomalies encountered in active accretionary systems can be used to constrain the timing, rates, and localization of fluid flow. Here we combine a coupled flow and solute transport model with a kinetic model for smectite dehydration to better understand and quantify fluid flow in the Nankai accretionary complex offshore of Japan. Compaction of sediments and clay dehydration provide fluid sources which drive the model flow system. We explicitly include the consolidation rate of underthrust sediments in our calculations to evaluate the impact that variations in this unknown quantity have on pressure and chloride distribution. Sensitivity analysis of steady state pressure solutions constrains bulk and flow conduit permeabilities. Steady state simulations with 30% smectite in the incoming sedimentary sequence result in minimum chloride concentrations at site 808 of 550 mM, but measured chlorinity is as low as 447 mM. We simulate the transient effects of hydrofracture or a strain event by assuming an instantaneous permeability increase of 3-4 orders of magnitude along a flow conduit (in this case the de??collement), using steady state results as initial conditions. Transient results with an increase in de??collement permeability from 10-16 m2 to 10-13 m2 and 20% smectite reproduce the observed chloride profile at site 808 after 80-160 kyr. Modeled chloride concentrations are highly sensitive to the consolidation rate of underthrust sediments, such that rapid compaction of underthrust material leads to increased freshening. Pressures within the de??collement during transient simulations rise rapidly to a significant fraction of lithostatic and remain high for at least 160 kyr, providing a mechanism for maintaining high permeability. Flow rates at the deformation front for transient simulations are in good agreement with direct measurements, but steady state flow rates are 2-3 orders of magnitude smaller than observed. Fluid budget calculations indicate that nearly 71% of the incoming water in the sediments leaves the accretionary wedge via diffuse flow out the seafloor, 0-5% escapes by focused flow along the de??collement, and roughly 1% is subducted. Copyright 1998 by the American Geophysical Union.

How consistent are top-down hydrocarbon emissions based on formaldehyde observations from GOME-2 and OMI?

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

Stavrakou, T.; Muller, J. F.; Bauwens, M.

2015-10-26

The vertical columns of formaldehyde (HCHO) retrieved from two satellite instruments, the Global Ozone Monitoring Instrument-2 (GOME-2) on Metop-A and the Ozone Monitoring Instrument (OMI) on Aura, are used to constrain global emissions of HCHO precursors from open fires, vegetation and human activities in the year 2010. To this end, the emissions are varied and optimized using the ad-joint model technique in the IMAGESv2 global CTM (chem-ical transport model) on a monthly basis and at the model res-olution. Given the different local overpass times of GOME- 2 (09:30 LT) and OMI (13:30 LT), the simulated diurnal cy-cle of HCHO columnsmore » is investigated and evaluated against ground-based optical measurements at seven sites in Europe, China and Africa. The modeled diurnal cycle exhibits large variability, reflecting competition between photochemistry and emission variations, with noon or early afternoon max-ima at remote locations (oceans) and in regions dominated by anthropogenic emissions, late afternoon or evening max-ima over fire scenes, and midday minima in isoprene-rich re-gions. The agreement between simulated and ground-based columns is generally better in summer (with a clear after-noon maximum at mid-latitude sites) than in winter, and the annually averaged ratio of afternoon to morning columns is slightly higher in the model (1.126) than in the ground-based measurements (1.043).The anthropogenic VOC (volatile organic compound) sources are found to be weakly constrained by the inversions on the global scale, mainly owing to their generally minor contribution to the HCHO columns, except over strongly pol-luted regions, like China. The OMI-based inversion yields total flux estimates over China close to the bottom-up inven-tory (24.6 vs. 25.5 TgVOC yr -1 in the a priori) with, how-ever, pronounced increases in the northeast of China and re-ductions in the south. Lower fluxes are estimated based on GOME-2 HCHO columns (20.6 TgVOC yr -1), in particular over the northeast, likely reflecting mismatches between the observed and the modeled diurnal cycle in this region.« less

Stress/strain changes and triggered seismicity following the MW7.3 Landers, California, earthquake

USGS Publications Warehouse

Gomberg, J.

1996-01-01

Calculations of dynamic stresses and strains, constrained by broadband seismograms, are used to investigate their role in generating the remotely triggered seismicity that followed the June 28, 1992, MW7.3 Landers, California earthquake. I compare straingrams and dynamic Coulomb failure functions calculated for the Landers earthquake at sites that did experience triggered seismicity with those at sites that did not. Bounds on triggering thresholds are obtained from analysis of dynamic strain spectra calculated for the Landers and MW,6.1 Joshua Tree, California, earthquakes at various sites, combined with results of static strain investigations by others. I interpret three principal results of this study with those of a companion study by Gomberg and Davis [this issue]. First, the dynamic elastic stress changes themselves cannot explain the spatial distribution of triggered seismicity, particularly the lack of triggered activity along the San Andreas fault system. In addition to the requirement to exceed a Coulomb failure stress level, this result implies the need to invoke and satisfy the requirements of appropriate slip instability theory. Second, results of this study are consistent with the existence of frequency- or rate-dependent stress/strain triggering thresholds, inferred from the companion study and interpreted in terms of earthquake initiation involving a competition of processes, one promoting failure and the other inhibiting it. Such competition is also part of relevant instability theories. Third, the triggering threshold must vary from site to site, suggesting that the potential for triggering strongly depends on site characteristics and response. The lack of triggering along the San Andreas fault system may be correlated with the advanced maturity of its fault gouge zone; the strains from the Landers earthquake were either insufficient to exceed its larger critical slip distance or some other critical failure parameter; or the faults failed stably as aseismic creep events. Variations in the triggering threshold at sites of triggered seismicity may be attributed to variations in gouge zone development and properties. Finally, these interpretations provide ready explanations for the time delays between the Landers earthquake and the triggered events.

What makes up marginal lands and how can it be defined and classified?

NASA Astrophysics Data System (ADS)

Ivanina, Vadym

2017-04-01

Definitions of marginal lands are often not explicit. The term "marginal" is not supported by either a precise definition or research to determine which lands fall into this category. To identify marginal lands terminology/methodology is used which varies between physical characteristics and the current land use of a site as basic perspective. The term 'Marginal' is most commonly followed by 'degraded' lands, and other widely used terms such as 'abandoned', 'idle', 'pasture', 'surplus agricultural land', 'Conservation Reserve Programme' (CRP)', 'barren and carbon-poor land', etc. Some terms are used synonymously. To the category of "marginal" lands are predominantly included lands which are excluded from cultivation due to economic infeasibility or physical restriction for growing conventional crops. Such sites may still have potential to be used for alternative agricultural practice, e.g. bioenergy feedstock production. The existing categorizing of marginal lands does not allow evaluating soil fertility potential or to define type and level of constrains for growing crops as the reason of a low practical value with regards to land use planning. A new marginal land classification has to be established and developed. This classification should be built on criteria of soil biophysical properties, ecologic, environment and climate handicaps for growing crops, be easy in use and of high practical value. The SEEMLA consortium made steps to build such a marginal land classification which is based on direct criteria depicting soil properties and constrains, and defining their productivity potential. By this classification marginal lands are divided into eleven categories: shallow rooting, low fertility, stony texture, sandy texture, clay texture, salinic, sodicic, acidic, overwet, eroded, and contaminated. The basis of this classification was taken criteria modified after and adapted from Regulation EU (1305)2013. To define an area of marginal lands with climate and economic limitations, SEEMLA established and implemented the term "area of land marginality" with a broader on marginal lands. This term includes marginal lands themselves, evaluation of climate constrains and economic efficiency to grow crops. This approach allows to define, categorize and classify marginal land by direct indicators of soil biophysical properties, ecologic and environment constrains, and provides additional evaluation of lands marginality with regards to suitability for growing crops based on climate criteria.

Student Activism: An Exploration of Pre-Service Teacher Engagement

ERIC Educational Resources Information Center

van Tol, Jason

2017-01-01

This study investigated university student activism from both a theoretical and applied perspective. The aims were to explore some of the elements that might enable or constrain student activism and to facilitate the students' opportunity to act on an issue of their choice. The three elements of self-efficacy, group work, and time were reviewed in…

Chronology of Late Quaternary Glacial Cycles in the Bering Trough, Gulf of Alaska: Constraints from Core-Log-Seismic Integration across the Continental Shelf and Slope

NASA Astrophysics Data System (ADS)

Clary, W. A.; Worthington, L. L.; Daigle, H.; Slagle, A. L.; Gulick, S. P. S.

2016-12-01

Sediments offshore Southern Alaska offer a natural laboratory to study glacial erosion, sediment deposition, and orogenesis. A major goal of Integrated Ocean Drilling Program (IODP) Expedition 341 was investigation of interrelationships among tectonic processes, paleoclimate, and glacial activity. Here, we focus on core-log-seismic integration of IODP Sites U1420 and U1421 on the shallow shelf and slope near the Bering Trough, a glacially derived shelf-crossing landform. These sites sample glacial and marine sediments that record a history of sedimentation following the onset of glacial intensification near the mid-Pleistocene transition (1.2 Ma) and Yakutat microplate convergence with North America. Ocean drilling provides important stratigraphic, physical properties, and age data in depth which support development of a stratigraphic model that can be extended across the shelf if carefully calibrated to local and regional seismic surveys. We use high resolution multichannel seismic, core, and logging data to develop a time-depth relationship (TDR) and update the developing chronostratigraphic model based on correlation of seismic sequence boundaries and drilling-related data, including biostratigraphic and paleomagnetic age controls. We calibrate, combine, and interpolate core and logging data at each site to minimize gaps in physical property information and generate synthetic seismic traces. At Site U1421, vertical seismic profiling further constrains the TDR, and provides input for the initial velocity model during the tie. Finally, we match reflectors in the synthetic trace with events in nearby seismic reflection data to establish a TDR at each site. We can use this relationship to better interpret the development of the Bering Trough, a recurring and favored path for ice streams and glacial advance. Initial results suggest late Pleistocene sedimentation rates of at least 1 km/m.y. on average, and variable sedimentation rates which are possibly correlated with paleoenvironmental indicators such as sea ice related species of diatoms.

Inter- and Intra-method Variability of VS Profiles and VS30 at ARRA-funded Sites

NASA Astrophysics Data System (ADS)

Yong, A.; Boatwright, J.; Martin, A. J.

2015-12-01

The 2009 American Recovery and Reinvestment Act (ARRA) funded geophysical site characterizations at 191 seismographic stations in California and in the central and eastern United States. Shallow boreholes were considered cost- and environmentally-prohibitive, thus non-invasive methods (passive and active surface- and body-wave techniques) were used at these stations. The drawback, however, is that these techniques measure seismic properties indirectly and introduce more uncertainty than borehole methods. The principal methods applied were Array Microtremor (AM), Multi-channel Analysis of Surface Waves (MASW; Rayleigh and Love waves), Spectral Analysis of Surface Waves (SASW), Refraction Microtremor (ReMi), and P- and S-wave refraction tomography. Depending on the apparent geologic or seismic complexity of the site, field crews applied one or a combination of these methods to estimate the shear-wave velocity (VS) profile and calculate VS30, the time-averaged VS to a depth of 30 meters. We study the inter- and intra-method variability of VS and VS30 at each seismographic station where combinations of techniques were applied. For each site, we find both types of variability in VS30 remain insignificant (5-10% difference) despite substantial variability observed in the VS profiles. We also find that reliable VS profiles are best developed using a combination of techniques, e.g., surface-wave VS profiles correlated against P-wave tomography to constrain variables (Poisson's ratio and density) that are key depth-dependent parameters used in modeling VS profiles. The most reliable results are based on surface- or body-wave profiles correlated against independent observations such as material properties inferred from outcropping geology nearby. For example, mapped geology describes station CI.LJR as a hard rock site (VS30 > 760 m/s). However, decomposed rock outcrops were found nearby and support the estimated VS30 of 303 m/s derived from the MASW (Love wave) profile.

Geologic implications of gas hydrates in the offshore of India: results of the National Gas Hydrate Program Expedition 01

USGS Publications Warehouse

Collett, Timothy S.; Boswell, Ray; Cochran, J.R.; Kumar, Pushpendra; Lall, Malcolm; Mazumdar, Aninda; Ramana, Mangipudi Venkata; Ramprasad, Tammisetti; Riedel, Michael; Sain, Kalachand; Sathe, Arun Vasant; Vishwanath, Krishna

2014-01-01

One of the specific objectives of this expedition was to test gas hydrate formation models and constrain model parameters, especially those that account for the formation of concentrated gas hydrate accumulations. The necessary data for characterizing the occurrence of in situ gas hydrate, such as interstitial water chlorinities, core-derived gas chemistry, physical and sedimentological properties, thermal images of the recovered cores, and downhole measured logging data (LWD and/or conventional wireline log data), were obtained from most of the drill sites established during NGHP-01. Almost all of the drill sites yielded evidence for the occurrence of gas hydrate; however, the inferred in situ concentration of gas hydrate varied substantially from site to site. For the most part, the interpretation of downhole logging data, core thermal images, interstitial water analyses, and pressure core images from the sites drilled during NGHP-01 indicate that the occurrence of concentrated gas hydrate is mostly associated with the presence of fractures in the sediments, and in some limited cases, by coarser grained (mostly sand-rich) sediments.

Abundance and local-scale processes contribute to multi-phyla gradients in global marine diversity

PubMed Central

Edgar, Graham J.; Alexander, Timothy J.; Lefcheck, Jonathan S.; Bates, Amanda E.; Kininmonth, Stuart J.; Thomson, Russell J.; Duffy, J. Emmett; Costello, Mark J.; Stuart-Smith, Rick D.

2017-01-01

Among the most enduring ecological challenges is an integrated theory explaining the latitudinal biodiversity gradient, including discrepancies observed at different spatial scales. Analysis of Reef Life Survey data for 4127 marine species at 2406 coral and rocky sites worldwide confirms that the total ecoregion richness peaks in low latitudes, near +15°N and −15°S. However, although richness at survey sites is maximal near the equator for vertebrates, it peaks at high latitudes for large mobile invertebrates. Site richness for different groups is dependent on abundance, which is in turn correlated with temperature for fishes and nutrients for macroinvertebrates. We suggest that temperature-mediated fish predation and herbivory have constrained mobile macroinvertebrate diversity at the site scale across the tropics. Conversely, at the ecoregion scale, richness responds positively to coral reef area, highlighting potentially huge global biodiversity losses with coral decline. Improved conservation outcomes require management frameworks, informed by hierarchical monitoring, that cover differing site- and regional-scale processes across diverse taxa, including attention to invertebrate species, which appear disproportionately threatened by warming seas. PMID:29057321

Abundance and local-scale processes contribute to multi-phyla gradients in global marine diversity.

PubMed

Edgar, Graham J; Alexander, Timothy J; Lefcheck, Jonathan S; Bates, Amanda E; Kininmonth, Stuart J; Thomson, Russell J; Duffy, J Emmett; Costello, Mark J; Stuart-Smith, Rick D

2017-10-01

Among the most enduring ecological challenges is an integrated theory explaining the latitudinal biodiversity gradient, including discrepancies observed at different spatial scales. Analysis of Reef Life Survey data for 4127 marine species at 2406 coral and rocky sites worldwide confirms that the total ecoregion richness peaks in low latitudes, near +15°N and -15°S. However, although richness at survey sites is maximal near the equator for vertebrates, it peaks at high latitudes for large mobile invertebrates. Site richness for different groups is dependent on abundance, which is in turn correlated with temperature for fishes and nutrients for macroinvertebrates. We suggest that temperature-mediated fish predation and herbivory have constrained mobile macroinvertebrate diversity at the site scale across the tropics. Conversely, at the ecoregion scale, richness responds positively to coral reef area, highlighting potentially huge global biodiversity losses with coral decline. Improved conservation outcomes require management frameworks, informed by hierarchical monitoring, that cover differing site- and regional-scale processes across diverse taxa, including attention to invertebrate species, which appear disproportionately threatened by warming seas.

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

Venteris, Erik R.; McBride, Robert; Coleman, Andre M.

Locating sites for new algae cultivation facilities is a complex task. The climate must support high growth rates, and cultivation ponds require appropriate land and water resources as well as key utility and transportation infrastructure. We employ our spatiotemporal Biomass Assessment Tool (BAT) to select promising locations based on the open-pond cultivation of Arthrospira sp. and a strain of the order Desmidiales. 64,000 potential sites across the southern United States were evaluated. We progressively apply a range of screening criteria and track their impact on the number of selected sites, geographic location, and biomass productivity. Both strains demonstrate maximum productivitymore » along the Gulf of Mexico coast, with the highest values on the Florida peninsula. In contrast, sites meeting all selection criteria for Arthrospira were located along the southern coast of Texas and for Desmidiales were located in Louisiana and southern Arkansas. Site selection was driven mainly by the lack of oil pipeline access in Florida and elevated groundwater salinity in southern Texas. The requirement for low salinity freshwater (<400 mg L-1) constrained Desmidiales locations; siting flexibility is greater for salt-tolerant species such as Arthrospira. Combined siting factors can result in significant departures from regions of maximum productivity but are within the expected range of site-specific process improvements.« less

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.

Conformationally Constrained Analogues of N'-(4-t-Butylbenzyl)-N-(4-Methylsulfonylaminobenzyl)Thiourea as TRPV1 Antagonists

PubMed Central

Ryu, HyungChul; Lim, Ju-Ok; Kang, Dong Wook; Pearce, Larry V.; Tran, Richard; Toth, Attila; Lee, Jeewoo; Blumberg, Peter M.

2012-01-01

A series of bicyclic analogues having indan and tetrahydronaphthalene templates in the A-region were designed as conformationally constrained analogues of our previously reported potent TRPV1 antagonists (1, 3). The activities for rat TRPV1 of the conformationally restricted analogues were moderately or markedly diminished, particularly in the case of the tetrahydronaphthalene analogues. The analysis indicated that steric constraints at the benzylic position in the bicyclic analogues were an important factor for their unfavorable interaction with the receptor. PMID:18406014

Cell cycle stage-specific differential expression of topoisomerase I in tobacco BY-2 cells and its ectopic overexpression and knockdown unravels its crucial role in plant morphogenesis and development.

PubMed

Singh, Badri Nath; Mudgil, Yashwanti; John, Riffat; Achary, V Mohan Murali; Tripathy, Manas Kumar; Sopory, Sudhir K; Reddy, Malireddy K; Kaul, Tanushri

2015-11-01

DNA topoisomerases catalyze the inter-conversion of different topological forms of DNA. Cell cycle coupled differential accumulation of topoisomerase I (Topo I) revealed biphasic expression maximum at S-phase and M/G1-phase of cultured synchronized tobacco BY-2 cells. This suggested its active role in resolving topological constrains during DNA replication (S-phase) and chromosome decondensation (M/G1 phase). Immuno-localization revealed high concentrations of Topo I in nucleolus. Propidium iodide staining and Br-UTP incorporation patterns revealed direct correlation between immunofluorescence intensity and rRNA transcription activity within nucleolus. Immuno-stained chromosomes during metaphase and anaphase suggested possible role of Topo I in resolving topological constrains during mitotic chromosome condensation. Inhibitor studies showed that in comparison to Topo I, Topo II was essential in resolving topological constrains during chromosome condensation. Probably, Topo II substituted Topo I functioning to certain extent during chromosome condensation, but not vice-versa. Transgenic Topo I tobacco lines revealed morphological abnormalities and highlighted its crucial role in plant morphogenesis and development. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Nighttime lidar water vapor mixing ratio profiling over Warsaw - impact of the relative humidity profile on cloud formation

NASA Astrophysics Data System (ADS)

Costa Surós, Montserrat; Stachlewska, Iwona S.

2016-04-01

A long-term study, assessing ground-based remote Raman lidar versus in-situ radiosounding has been conducted with the aim of improving the knowledge on the water content vertical profile through the atmosphere, and thus the conditions for cloud formation processes. Water vapor mixing ratio (WVMR) and relative humidity (RH) profiles were retrieved from ADR Lidar (PollyXT-type, EARLINET site in Warsaw). So far, more than 100 nighttime profiles averaged over 1h around midnight from July 2013 to December 2015 have been investigated. Data were evaluated with molecular extinctions calculated using two approximations: the US62 standard atmosphere and the radiosounding launched in Legionowo (12374). The calibration factor CH2O for lidar retrievals was obtained for each profile using the regression method and the profile method to determine the best calibration factor approximation to be used in the final WVMR and RH calculation. Thus, statistically representative results for comparisons between lidar WVMR median profiles obtained by calibrating using radiosounding profiles and using atmospheric synthetic profiles, all of them with the best calibration factor, will be presented. Finally, in order to constrain the conditions of cloud formation in function of the RH profile, the COS14 algorithm, capable of deriving cloud bases and tops by applying thresholds to the RH profiles, was applied to find the cloud vertical structure (CVS). The algorithm was former applied to radiosounding profiles at SGP-ARM site and tested against the CVS obtained from the Active Remote Sensing of Clouds (ARSCL) data. Similarly, it was applied for lidar measurements at the Warsaw measurement site.

Initial results from geophysical surveys and shallow coring of the Northeast Greenland Ice Stream (NEGIS)

NASA Astrophysics Data System (ADS)

Vallelonga, P.; Christianson, K.; Alley, R. B.; Anandakrishnan, S.; Christian, J. E. M.; Dahl-Jensen, D.; Gkinis, V.; Holme, C.; Jacobel, R. W.; Karlsson, N. B.; Keisling, B. A.; Kipfstuhl, S.; Kjær, H. A.; Kristensen, M. E. L.; Muto, A.; Peters, L. E.; Popp, T.; Riverman, K. L.; Svensson, A. M.; Tibuleac, C.; Vinther, B. M.; Weng, Y.; Winstrup, M.

2014-07-01

The Northeast Greenland Ice Stream (NEGIS) is the sole interior Greenlandic ice stream. Fast flow initiates near the summit dome, and the ice stream terminates approximately 1000 km downstream in three large outlet glaciers that calve into the Greenland Sea. To better understand this important system, in the summer of 2012 we drilled a 67 m firn core and conducted ground-based radio-echo sounding (RES) and active-source seismic surveys at a site approximately 150 km downstream from the onset of streaming flow (NEGIS firn core, 75°37.61' N, 35°56.49' W). The site is representative of the upper part of the ice stream, while also being in a crevasse-free area for safe surface operations. Annual cycles were observed for insoluble dust, sodium and ammonium concentrations and for electrolytic conductivity, allowing a seasonally resolved chronology covering the past 400 yr. Annual layer thicknesses averaged 0.11 m ice equivalent (i.e.) for the period 1607-2011, although accumulation varied between 0.08 and 0.14 m i.e., likely due to flow-related changes in surface topography. Tracing of RES layers from the NGRIP (North Greenland Ice Core Project) ice core site shows that the ice at NEGIS preserves a climatic record of at least the past 51 kyr. We demonstrate that deep ice core drilling in this location can provide a reliable Holocene and late-glacial climate record, as well as helping to constrain the past dynamics and ice-lithosphere interactions of the Greenland Ice Sheet.

Initial results from geophysical surveys and shallow coring of the Northeast Greenland Ice Stream (NEGIS)

NASA Astrophysics Data System (ADS)

Vallelonga, P.; Christianson, K.; Alley, R. B.; Anandakrishnan, S.; Christian, J. E. M.; Dahl-Jensen, D.; Gkinis, V.; Holme, C.; Jacobel, R. W.; Karlsson, N.; Keisling, B. A.; Kipfstuhl, S.; Kjær, H. A.; Kristensen, M. E. L.; Muto, A.; Peters, L. E.; Popp, T.; Riverman, K. L.; Svensson, A. M.; Tibuleac, C.; Vinther, B. M.; Weng, Y.; Winstrup, M.

2014-01-01

The Northeast Greenland Ice Stream (NEGIS) is the sole interior Greenlandic ice stream. Fast flow initiates near the summit dome, and the ice stream terminates approximately 1000 km downstream in three large outlet glaciers that calve into the Greenland Sea. To better understand this important system, in the summer of 2012 we drilled a 67 m firn core and conducted ground-based radio-echo sounding (RES) and active-source seismic surveys at a site approximately 150 km downstream from the onset of streaming flow (NEGIS firn core, 75° 37.61' N, 35°56.49' W). The site is representative of the upper part of the ice stream, while also being in a crevasse-free area for safe surface operations. Annual cycles were observed for insoluble dust, sodium and ammonium concentrations and for electrolytic conductivity, allowing a seasonally resolved chronology covering the past 400 yr. Annual layer thicknesses averaged 0.11 m ice equivalent (i.e.) for the period 1607-2011, although accumulation varied between 0.08 and 0.14 m i.e., likely due to flow-related changes in surface topography. Tracing of RES layers from the NGRIP ice core site shows that the ice at NEGIS preserves a climatic record of at least the past 51 kyr. We demonstrate that a deep ice core drilling in this location can provide a reliable Holocene and late-glacial climate record, as well as helping to constrain the past dynamics and ice-lithosphere interactions of the Greenland Ice Sheet.

Origin of an Assemblage Massively Dominated by Carnivorans from the Miocene of Spain

PubMed Central

Domingo, M. Soledad; Alberdi, M. Teresa; Azanza, Beatriz; Silva, Pablo G.; Morales, Jorge

2013-01-01

Carnivoran-dominated fossil sites provide precious insights into the diversity and ecology of species rarely recovered in the fossil record. The lower level assemblage of Batallones-1 fossil site (Late Miocene; Madrid Basin, Spain) has yielded one of the most abundant and diversified carnivoran assemblage ever known from the Cenozoic record of mammals. A comprehensive taphonomic study is carried out here in order to constrain the concentration mode of this remarkable assemblage. Another distinctive feature of Batallones-1 is that the accumulation of carnivoran remains took place in the context of a geomorphological landform (cavity formation through a piping process) practically unknown in the generation of fossil sites. Two characteristics of the assemblage highly restrict the probable causes for the accumulation of the remains: (1) the overwhelming number of carnivorans individuals; and (2) the mortality profiles estimated for the four most abundant taxa do not correspond to the classic mortality types but rather were the consequence of the behavior of the taxa. This evidence together with other taphonomic data supports the hypothesis that carnivoran individuals actively entered the cavity searching for resources (food or water) and were unable to exit. The scarcity of herbivores implies that the shaft was well visible and avoided by these taxa. Fossil bones exhibit a very good preservation state as a consequence of their deposition in the restricted and protective environment of the chamber. Batallones-1 had another assemblage (upper level assemblage) that was dominated by herbivore remains and that potentially corresponded to the final stages of the cavity filling. PMID:23650542

Dominant controls of transpiration along a hillslope transect inferred from ecohydrological measurements and thermodynamic limits

NASA Astrophysics Data System (ADS)

Renner, Maik; Hassler, Sibylle K.; Blume, Theresa; Weiler, Markus; Hildebrandt, Anke; Guderle, Marcus; Schymanski, Stanislaus J.; Kleidon, Axel

2016-05-01

We combine ecohydrological observations of sap flow and soil moisture with thermodynamically constrained estimates of atmospheric evaporative demand to infer the dominant controls of forest transpiration in complex terrain. We hypothesize that daily variations in transpiration are dominated by variations in atmospheric demand, while site-specific controls, including limiting soil moisture, act on longer timescales. We test these hypotheses with data of a measurement setup consisting of five sites along a valley cross section in Luxembourg. Both hillslopes are covered by forest dominated by European beech (Fagus sylvatica L.). Two independent measurements are used to estimate stand transpiration: (i) sap flow and (ii) diurnal variations in soil moisture, which were used to estimate the daily root water uptake. Atmospheric evaporative demand is estimated through thermodynamically constrained evaporation, which only requires absorbed solar radiation and temperature as input data without any empirical parameters. Both transpiration estimates are strongly correlated to atmospheric demand at the daily timescale. We find that neither vapor pressure deficit nor wind speed add to the explained variance, supporting the idea that they are dependent variables on land-atmosphere exchange and the surface energy budget. Estimated stand transpiration was in a similar range at the north-facing and the south-facing hillslopes despite the different aspect and the largely different stand composition. We identified an inverse relationship between sap flux density and the site-average sapwood area per tree as estimated by the site forest inventories. This suggests that tree hydraulic adaptation can compensate for heterogeneous conditions. However, during dry summer periods differences in topographic factors and stand structure can cause spatially variable transpiration rates. We conclude that absorption of solar radiation at the surface forms a dominant control for turbulent heat and mass exchange and that vegetation across the hillslope adjusts to this constraint at the tree and stand level. These findings should help to improve the description of land-surface-atmosphere exchange at regional scales.

[A site index model for Larix principis-rupprechtii plantation in Saihanba, north China].

PubMed

Wang, Dong-zhi; Zhang, Dong-yan; Jiang, Feng-ling; Bai, Ye; Zhang, Zhi-dong; Huang, Xuan-rui

2015-11-01

It is often difficult to estimate site indices for different types of plantation by using an ordinary site index model. The objective of this paper was to establish a site index model for plantations in varied site conditions, and assess the site qualities. In this study, a nonlinear mixed site index model was constructed based on data from the second class forest resources inventory and 173 temporary sample plots. The results showed that the main limiting factors for height growth of Larix principis-rupprechtii were elevation, slope, soil thickness and soil type. A linear regression model was constructed for the main constraining site factors and dominant tree height, with the coefficient of determination being 0.912, and the baseline age of Larix principis-rupprechtii determined as 20 years. The nonlinear mixed site index model parameters for the main site types were estimated (R2 > 0.85, the error between the predicted value and the actual value was in the range of -0.43 to 0.45, with an average root mean squared error (RMSE) in the range of 0.907 to 1.148). The estimation error between the predicted value and the actual value of dominant tree height for the main site types was in the confidence interval of [-0.95, 0.95]. The site quality of the high altitude-shady-sandy loam-medium soil layer was the highest and that of low altitude-sunny-sandy loam-medium soil layer was the lowest, while the other two sites were moderate.

Nonlinear activity of acoustically driven gas bubble near a rigid boundary

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

Maksimov, Alexey

2015-10-28

The presence of a boundary can produce considerable changes in the oscillation amplitude of the bubble and its scattered echo. The present study fills a gap in the literature, in that it is concerned theoretically with the bubble activity at relatively small distances from the rigid boundary. It was shown that the bi-spherical coordinates provide separation of variables and are more suitable for analysis of the dynamics of these constrained bubbles. Explicit formulas have been derived which describe the dependence of the bubble emission near a rigid wall on its size and the separation distance between the bubble and themore » boundary. As applications, time reversal technique for gas leakage detection and radiation forces that are induced by an acoustic wave on a constrained bubble were analyzed.« less

Management of groundwater in-situ bioremediation system using reactive transport modelling under parametric uncertainty: field scale application

NASA Astrophysics Data System (ADS)

Verardo, E.; Atteia, O.; Rouvreau, L.

2015-12-01

In-situ bioremediation is a commonly used remediation technology to clean up the subsurface of petroleum-contaminated sites. Forecasting remedial performance (in terms of flux and mass reduction) is a challenge due to uncertainties associated with source properties and the uncertainties associated with contribution and efficiency of concentration reducing mechanisms. In this study, predictive uncertainty analysis of bio-remediation system efficiency is carried out with the null-space Monte Carlo (NSMC) method which combines the calibration solution-space parameters with the ensemble of null-space parameters, creating sets of calibration-constrained parameters for input to follow-on remedial efficiency. The first step in the NSMC methodology for uncertainty analysis is model calibration. The model calibration was conducted by matching simulated BTEX concentration to a total of 48 observations from historical data before implementation of treatment. Two different bio-remediation designs were then implemented in the calibrated model. The first consists in pumping/injection wells and the second in permeable barrier coupled with infiltration across slotted piping. The NSMC method was used to calculate 1000 calibration-constrained parameter sets for the two different models. Several variants of the method were implemented to investigate their effect on the efficiency of the NSMC method. The first variant implementation of the NSMC is based on a single calibrated model. In the second variant, models were calibrated from different initial parameter sets. NSMC calibration-constrained parameter sets were sampled from these different calibrated models. We demonstrate that in context of nonlinear model, second variant avoids to underestimate parameter uncertainty which may lead to a poor quantification of predictive uncertainty. Application of the proposed approach to manage bioremediation of groundwater in a real site shows that it is effective to provide support in management of the in-situ bioremediation systems. Moreover, this study demonstrates that the NSMC method provides a computationally efficient and practical methodology of utilizing model predictive uncertainty methods in environmental management.

Explaining evolution via constrained persistent perfect phylogeny

PubMed Central

2014-01-01

Background The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to explain efficiently data that do not conform with the classical perfect phylogeny model. PMID:25572381

Using Close White Dwarf + M Dwarf Stellar Pairs to Constrain the Flare Rates in Close Stellar Binaries

NASA Astrophysics Data System (ADS)

Morgan, Dylan P.; West, Andrew A.; Becker, Andrew C.

2016-05-01

We present a study of the statistical flare rates of M dwarfs (dMs) with close white dwarf (WD) companions (WD+dM; typical separations <1 au). Our previous analysis demonstrated that dMs with close WD companions are more magnetically active than their field counterparts. One likely implication of having a close binary companion is increased stellar rotation through disk-disruption, tidal effects, and/or angular momentum exchange; increased stellar rotation has long been associated with an increase in stellar activity. Previous studies show a strong correlation between dMs that are magnetically active (showing Hα in emission) and the frequency of stellar flare rates. We examine the difference between the flare rates observed in close WD+dM binary systems and field dMs. Our sample consists of a subset of 181 close WD+dM pairs from Morgan et al. observed in the Sloan Digital Sky Survey Stripe 82, where we obtain multi-epoch observations in the Sloan ugriz-bands. We find an increase in the overall flaring fraction in the close WD+dM pairs (0.09 ± 0.03%) compared to the field dMs (0.0108 ± 0.0007%) and a lower flaring fraction for active WD+dMs (0.05 ± 0.03%) compared to active dMs (0.28 ± 0.05%). We discuss how our results constrain both the single and binary dM flare rates. Our results also constrain dM multiplicity, our knowledge of the Galactic transient background, and may be important for the habitability of attending planets around dMs with close companions.

Extending the Aircraft Availability Model to a Constrained Depot Environment Using Activity-Based Costing and the Theory of Constraints

DTIC Science & Technology

2004-06-01

Overselling Activity-Based Concepts,” Management Accounting , September 1992:26-35. Kaplan, Robert S . and Robin Cooper. Cost & Effect. Using... Accounting .............................................14 Increasing Need for Cost Information...15 Implications for Costs Accounting Systems ....................................................17 Section 2 – Costs and Resources

Spatial, Hysteretic, and Adaptive Host-Guest Chemistry in a Metal-Organic Framework with Open Watson-Crick Sites.

PubMed

Cai, Hong; Li, Mian; Lin, Xiao-Rong; Chen, Wei; Chen, Guang-Hui; Huang, Xiao-Chun; Li, Dan

2015-09-01

Biological and artificial molecules and assemblies capable of supramolecular recognition, especially those with nucleobase pairing, usually rely on autonomous or collective binding to function. Advanced site-specific recognition takes advantage of cooperative spatial effects, as in local folding in protein-DNA binding. Herein, we report a new nucleobase-tagged metal-organic framework (MOF), namely ZnBTCA (BTC=benzene-1,3,5-tricarboxyl, A=adenine), in which the exposed Watson-Crick faces of adenine residues are immobilized periodically on the interior crystalline surface. Systematic control experiments demonstrated the cooperation of the open Watson-Crick sites and spatial effects within the nanopores, and thermodynamic and kinetic studies revealed a hysteretic host-guest interaction attributed to mild chemisorption. We further exploited this behavior for adenine-thymine binding within the constrained pores, and a globally adaptive response of the MOF host was observed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Achieving full connectivity of sites in the multiperiod reserve network design problem

USGS Publications Warehouse

Jafari, Nahid; Nuse, Bryan L.; Moore, Clinton; Dilkina, Bistra; Hepinstall-Cymerman, Jeffrey

2017-01-01

The conservation reserve design problem is a challenge to solve because of the spatial and temporal nature of the problem, uncertainties in the decision process, and the possibility of alternative conservation actions for any given land parcel. Conservation agencies tasked with reserve design may benefit from a dynamic decision system that provides tactical guidance for short-term decision opportunities while maintaining focus on a long-term objective of assembling the best set of protected areas possible. To plan cost-effective conservation over time under time-varying action costs and budget, we propose a multi-period mixed integer programming model for the budget-constrained selection of fully connected sites. The objective is to maximize a summed conservation value over all network parcels at the end of the planning horizon. The originality of this work is in achieving full spatial connectivity of the selected sites during the schedule of conservation actions.

Detritus in K/T boundary clays of western North America - Evidence against a single oceanic impact

NASA Technical Reports Server (NTRS)

Sharpton, V. L.; Schuraytz, B. C.; Burke, K.; Murali, A. V.; Ryder, G.

1990-01-01

Understanding the crustal signature of impact ejecta contained in the Cretaceous/Tertiary (K/T) boundary layer is crucial to constraining the possible site(s) of the postulated K/T impact event. The relatively unaltered clastic constituents of the boundary layer at widely separated outcrops within the western interior of North America are not compatible with a single oceanic impact but require instead an impact site on a continent or continental margin. On the other hand, chemical compositions of highly altered K/T boundary layer components in some marine sections have suggested to others an impact into oceanic crust. We suspect that post-depositional alteration within the marine setting accounts for this apparent oceanic affinity. If, however, this is not the case, multiple simultaneous impacts, striking continent as well as ocean floor, would seem to be required.

Observations of hydrotectonic stress/strain events at a basement high at the Nicoya outer rise

NASA Astrophysics Data System (ADS)

Tryon, M. D.; Brown, K. M.

2005-12-01

There is substantial and growing evidence from heat flow and coring investigations that the oceanic plate off Costa Rica is highly hydrologically active and that this activity is responsible for one of the most anomalously cold thermal environments encountered in the oceanic environment. Recent work by Fisher, et al. has identified limited regions above certain topographic highs with extremely high heat flows. Pore water profiles from cores above these thinly sedimented basement highs suggest upward flow on the order of ~1 cm/yr. These highs may be the principal regions of out-flow from the basement in this region and, thus, can potentially be used to constrain the general level of hydrologic activity. The nine Chemical and Aqueous Transport (CAT) meters we deployed at one of the highest heatflow sites provide a temporal record of both in-flow and out-flow of aqueous fluids at rates as low as 0.1 mm/yr. Our objective was to provide a direct measurement of long term flow rates to address the following questions: (1) What are the characteristic fluid fluxes at basement highs of the low heat flow region of the northern Costa Rican incoming plate, and (2) is this flow temporally variable? The results of the instrument deployments agree quite closely in general with the coring results in that the background rates are on the order of 1 cm/yr or less. There is, however, considerable detail in the temporal records which suggest small scale tectonic stress transients causing temporary increases in flow rate. While this is certainly not an area of major tectonic activity, the site is located at the top of the outer rise where one would expect bending-related stress and fault reactivation to occur. The CAT meters are capable of detecting minute strain events in the underlying sediments and therefore may be detecting small localized strain events. Two periods of increased flow lasting a few weeks each occur during the 5 month deployment and are indicated on all of the instruments. A few indicate downflow while the others show upflow. This sort of response would be expected during a stress event causing regions of compression and dilation. These results suggest that ridge flank basement highs may be good sites to monitor stress/strain events as well as basement hydrology.

Attenuation and Transport Mechanisms of Depleted Uranium in Groundwater at Lawrence Livermore National Laboratory Site 300

NASA Astrophysics Data System (ADS)

Danny, K. R.; Taffet, M. J.; Brusseau, M. L. L.; Chorover, J.

2015-12-01

Lawrence Livermore National Laboratory (LLNL) Site 300 was established in 1955 to support weapons research and development. Depleted uranium was used as a proxy for fissile uranium-235 (235U) in open-air explosives tests conducted at Building 812. As a result, oxidized depleted uranium was deposited on the ground, eventually migrating to the underlying sandstone aquifer. Uranium (U) groundwater concentrations exceed the California and Federal Maximum Contaminant Level of 20 pCi L-1 (30 ug L-1). However, the groundwater plume appears to attenuate within 60 m of the source, beyond which no depleted U is detected. This study will determine the relative contribution of physical (e.g. dilution), chemical (e.g. surface adsorption, mineral precipitation), and biological (e.g. biotransformation) processes that contribute to the apparent attenuation of U, which exists as uranyl (UO22+) complexes, at the site. Methods of investigation include evaluating 15 yr of hydrogeologic and chemical data, creating a site conceptual model, and applying equilibrium (e.g. aqueous species complexation, mineral saturation indices) and reactive transport models using Geochemist's WorkbenchTM. Reactive transport results are constrained by direct field observations, including U major ion, and dissolved O2 concentrations, pH, and others, under varying chemical and hydraulic conditions. Aqueous speciation calculations indicate that U primarily exists as anionic CaUO2(CO3)32- or neutral Ca2UO2(CO3)30 species. Additionally, nucleation and growth of Ca/Mg uranyl carbonate solids are predicted to affect attenuation. Initial reactive transport results suggest surface adsorption (e.g. ion exchange, surface complexation) to layer silicate clays is limited under the aqueous geochemical conditions of the site. Current and future work includes XRD analysis of aquifer solids to constrain iron and aluminum (oxy)hydroxides, and coupling advective-dispersive transport with the chemical and physical processes. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-675707.

Eddy-covariance methane flux measurements over a European beech forest

NASA Astrophysics Data System (ADS)

Gentsch, Lydia; Siebicke, Lukas; Knohl, Alexander

2015-04-01

The role of forests in global methane (CH4) turnover is currently not well constrained, partially because of the lack of spatially integrative forest-scale measurements of CH4 fluxes. Soil chamber measurements imply that temperate forests generally act as CH4 sinks. Upscaling of chamber observations to the forest scale is however problematic, if the upscaling is not constrained by concurrent 'top-down' measurements, such as of the eddy-covariance type, which provide sufficient integration of spatial variations and of further potential CH4 flux components within forest ecosystems. Ongoing development of laser absorption-based optical instruments, resulting in enhanced measurement stability, precision and sampling speed, has recently improved the prospects for meaningful eddy-covariance measurements at sites with presumably low CH4 fluxes, hence prone to reach the flux detection limit. At present, we are launching eddy-covariance CH4 measurements at a long-running ICOS flux tower site (Hainich National Park, Germany), located in a semi natural, unmanaged, beech dominated forest. Eddy-covariance measurements will be conducted with a laser spectrometer for parallel CH4, H2Ov and CO2 measurements (FGGA, Los Gatos Research, USA). Independent observations of the CO2 flux by the FGGA and a standard Infrared Gas Analyser (LI-7200, LI-COR, USA) will allow to evaluate data quality of measured CH4 fluxes. Here, we want to present first results with a focus on uncertainties of the calculated CH4 fluxes with regard to instrument precision, data processing and site conditions. In future, we plan to compare eddy-covariance flux estimates to side-by-side turbulent flux observations from a novel eddy accumulation system. Furthermore, soil CH4 fluxes will be measured with four automated chambers situated within the tower footprint. Based on a previous soil chamber study at the same site, we expect the Hainich forest site to act as a CH4 sink. However, we hypothesize that our measurements might also reveal short CH4 emission periods when soils become water-saturated. Nonetheless, CH4 emissions by plants could also result in a close to neutral net CH4 flux.

On the Ability of Space- Based Passive and Active Remote Sensing Observations of CO2 to Detect Flux Perturbations to the Carbon Cycle

NASA Technical Reports Server (NTRS)

Crowell, Sean M. R.; Kawa, S. Randolph; Browell, Edward V.; Hammerling, Dorit M.; Moore, Berrien; Schaefer, Kevin; Doney, Scott C.

2018-01-01

Space-borne observations of CO2 are vital to gaining understanding of the carbon cycle in regions of the world that are difficult to measure directly, such as the tropical terrestrial biosphere, the high northern and southern latitudes, and in developing nations such as China. Measurements from passive instruments such as GOSAT (Greenhouse Gases Observing Satellite) and OCO-2 (Orbiting Carbon Observatory 2), however, are constrained by solar zenith angle limitations as well as sensitivity to the presence of clouds and aerosols. Active measurements such as those in development for the Active Sensing of CO2 Emissions over Nights, Days and Seasons (ASCENDS) mission show strong potential for making measurements in the high-latitude winter and in cloudy regions. In this work we examine the enhanced flux constraint provided by the improved coverage from an active measurement such as ASCENDS. The simulation studies presented here show that with sufficient precision, ASCENDS will detect permafrost thaw and fossil fuel emissions shifts at annual and seasonal time scales, even in the presence of transport errors, representativeness errors, and biogenic flux errors. While OCO-2 can detect some of these perturbations at the annual scale, the seasonal sampling provided by ASCENDS provides the stronger constraint. Plain Language Summary: Active and passive remote sensors show the potential to provide unprecedented information on the carbon cycle. With the all-season sampling, active remote sensors are more capable of constraining high-latitude emissions. The reduced sensitivity to cloud and aerosol also makes active sensors more capable of providing information in cloudy and polluted scenes with sufficient accuracy. These experiments account for errors that are fundamental to the top-down approach for constraining emissions, and even including these sources of error, we show that satellite remote sensors are critical for understanding the carbon cycle.

Strong Effects of a Shelfbreak Jet on Microbial Enzyme Activities

NASA Astrophysics Data System (ADS)

Hoarfrost, A.; Balmonte, J. P.; Ziervogel, K.; Ghobrial, S.; Gawarkiewicz, G.; Arnosti, C.

2016-02-01

The activities of extracellular enzymes are critical in initiating microbial cycling of organic carbon, yet the dynamics of heterotrophic enzyme activities in marine environments are still poorly understood. Variations at a given site in rates of activity and the spectrum of organic substrates hydrolyzed may depend upon environmental context. We measured the extracellular enzymatic hydrolysis of 13 high- and low-molecular-weight organic substrates in surface and bottom waters along a closely spaced 4-station transect at 71 W on the North Atlantic continental shelf, in the vicinity of the shelfbreak front. This transect intersects a robust upwelling cell that typically shows high biologic productivity, and is locatable by changes in T/S profiles and chl a concentrations along sharp spatial gradients. At the time of sampling, cold pool waters over the continental shelf were relatively cold, 3.5 Deg. C, compared to 12 Deg. C over the upper continental slope. Satellite thermal imagery indicated that shelf water extended offshore and interacted with a large crest of the Gulf Stream. The surface and bottom waters associated with the upwelling jet were characterized by enzyme activities a factor of 20 more rapid than closer inshore waters, and surface water chl a concentrations that were two to three times higher than the inshore waters. The spectrum of enzyme activities also differed markedly between surface and bottom waters both within the jet and at near-shore stations. Microbial extracellular enzymatic activities were strongly influenced by differences in their environmental context along the continental slope and shelfbreak front. Constraining the factors controlling heterotrophic activity across the diverse marine environment is an important step in understanding microbial controls on carbon cycling.

Chance-constrained multi-objective optimization of groundwater remediation design at DNAPLs-contaminated sites using a multi-algorithm genetically adaptive method

NASA Astrophysics Data System (ADS)

Ouyang, Qi; Lu, Wenxi; Hou, Zeyu; Zhang, Yu; Li, Shuai; Luo, Jiannan

2017-05-01

In this paper, a multi-algorithm genetically adaptive multi-objective (AMALGAM) method is proposed as a multi-objective optimization solver. It was implemented in the multi-objective optimization of a groundwater remediation design at sites contaminated by dense non-aqueous phase liquids. In this study, there were two objectives: minimization of the total remediation cost, and minimization of the remediation time. A non-dominated sorting genetic algorithm II (NSGA-II) was adopted to compare with the proposed method. For efficiency, the time-consuming surfactant-enhanced aquifer remediation simulation model was replaced by a surrogate model constructed by a multi-gene genetic programming (MGGP) technique. Similarly, two other surrogate modeling methods-support vector regression (SVR) and Kriging (KRG)-were employed to make comparisons with MGGP. In addition, the surrogate-modeling uncertainty was incorporated in the optimization model by chance-constrained programming (CCP). The results showed that, for the problem considered in this study, (1) the solutions obtained by AMALGAM incurred less remediation cost and required less time than those of NSGA-II, indicating that AMALGAM outperformed NSGA-II. It was additionally shown that (2) the MGGP surrogate model was more accurate than SVR and KRG; and (3) the remediation cost and time increased with the confidence level, which can enable decision makers to make a suitable choice by considering the given budget, remediation time, and reliability.

A tsunami deposit from Vancouver Island, Canada ― Geological evidence for the penultimate great Cascadia earthquake?

NASA Astrophysics Data System (ADS)

Tanigawa, K.; Sawai, Y.; Bobrowsky, P. T.; Huntley, D.; Goff, J. R.; Shinozaki, T.

2017-12-01

We examined tsunami deposits within salt marshes at Tofino, Ucluelet and Port Alberni along the west coast of Vancouver Island aligned with the Cascadia Subduction Zone. Previous studies in 1990s reported tsunami deposits associated with the 1964 Alaska, the 1700 Cascadia and older earthquakes from these sites (Clague and Bobrowsky, 1994a; b). However, the ages of older tsunami deposits were not well constrained. We excavated pits and collected salt marsh sediments in 2015 and 2016. Sand layers interbedded within peat and mud deposits occur at widely separated sites on Vancouver Island. Two visible sand layers were observed in Tofino, four in Ucluelet and three in Port Alberni; which is consistent with previous studies. We used a combination of 210Pb, 137Cs and 14C dating to constrain the depositional ages of sand layers. Plant microfossils and insects obtained directly above and below each sand layer were used for radiocarbon dating. Radiocarbon ages indicate that the sand layer prior to the 1700 tsunami sediments was deposited between 550-300 calendar years before present. This depositional age is correlative to the T2 event of the Cascadia Subduction Zone turbidite history (Goldfinger et al., 2012). References: Clague and Bobrowsky (1994a) Quaternary Research, 41, 176-184. Clague and Bobrowsky (1994b) GSA Bulletin 106, 1293-1303. Goldfinger et al. (2012) USGS Professional Paper 1661-F, 170 p.

Connectivity constraints on cortical reorganization of neural circuits involved in object naming.

PubMed

Papagno, Costanza; Gallucci, Marcello; Casarotti, Alessandra; Castellano, Antonella; Falini, Andrea; Fava, Enrica; Giussani, Carlo; Carrabba, Giorgio; Bello, Lorenzo; Caramazza, Alfonso

2011-04-01

The brain's plasticity in response to sensory deprivation and other perturbations is well established. While the functional properties of the reorganized areas are under vigorous investigation, the factors that constrain cortical reorganization remain poorly understood. One factor constraining such reorganization may be long-distance subcortical connectivity between relevant cortical regions-reorganization attempts to preserve the functionality of subcortical connections. Here we provide human neurophysiological evidence for the role of the subcortical connections in shaping cortical reorganization of the networks involved in object naming following perturbation of normal function. We used direct electrical stimulation (DES) during surgical removal of gliomas to identify the sites that are involved in naming different categories of objects. The sites that were selectively inhibited in naming either living or non-living objects were displaced relative to those observed with other subject populations, possibly reflecting cortical reorganization due to slowly evolving brain damage. Subcortical DES applied to the white matter underlying these regions also led to category-specific naming deficits. The existence of these subcortical fiber pathways was confirmed using diffusion tensor tractography. These results constitute the first neurophysiological evidence for the critical role of subcortical pathways as part of the neural circuits that are involved in object naming; they also highlight the importance of subcortical connectivity in shaping cortical reorganization following perturbations of normal function. Copyright © 2011 Elsevier Inc. All rights reserved.

Higher risk of gastrointestinal parasite infection at lower elevation suggests possible constraints in the distributional niche of Alpine marmots.

PubMed

Zanet, Stefania; Miglio, Giacomo; Ferrari, Caterina; Bassano, Bruno; Ferroglio, Ezio; von Hardenberg, Achaz

2017-01-01

Alpine marmots Marmota marmota occupy a narrow altitudinal niche within high elevation alpine environments. For animals living at such high elevations where resources are limited, parasitism represents a potential major cost in life history. Using occupancy models, we tested if marmots living at higher elevation have a reduced risk of being infected with gastro-intestinal helminths, possibly compensating the lower availability of resources (shorter feeding season, longer snow cover and lower temperature) than marmots inhabiting lower elevations. Detection probability of eggs and oncospheres of two gastro-intestinal helminthic parasites, Ascaris laevis and Ctenotaenia marmotae, sampled in marmot feces, was used as a proxy of parasite abundance. As predicted, the models showed a negative relationship between elevation and parasite detectability (i.e. abundance) for both species, while there appeared to be a negative effect of solar radiance only for C. marmotae. Site-occupancy models are used here for the first time to model the constrains of gastrointestinal parasitism on a wild species and the relationship existing between endoparasites and environmental factors in a population of free-living animals. The results of this study suggest the future use of site-occupancy models as a viable tool to account for parasite imperfect detection in eco-parasitological studies, and give useful insights to further investigate the hypothesis of the contribution of parasite infection in constraining the altitudinal niche of Alpine marmots.

New U/Th ages for Pleistocene megafauna deposits of southeastern Queensland, Australia

NASA Astrophysics Data System (ADS)

Price, Gilbert J.; Zhao, Jian-xin; Feng, Yue-xing; Hocknull, Scott A.

2009-02-01

Arguments over the extinction of Pleistocene megafauna have become particularly polarised in recent years. Causes for the extinctions are widely debated with climate change, human hunting and/or habitat modification, or a combination of those factors, being the dominant hypotheses. However, a lack of a spatially constrained chronology for many megafauna renders most hypotheses difficult to test. Here, we present several new U/Th dates for a series of previously undated, megafauna-bearing localities from southeastern Queensland, Australia. The sites were previously used to argue for or against various megafauna extinction hypotheses, and are the type localities for two now-extinct Pleistocene marsupials (including the giant koala, Phascolarctos stirtoni). The new dating allows the deposits to be placed in a spatially- and temporally constrained context relevant to the understanding of Australian megafaunal extinctions. The results indicate that The Joint (Texas Caves) megafaunal assemblage is middle Pleistocene or older (>292 ky); the Cement Mills (Gore) megafaunal assemblage is late Pleistocene or older (>53 ky); and the Russenden Cave Bone Chamber (Texas Caves) megafaunal assemblage is late Pleistocene (˜55 ky). Importantly, the new results broadly show that the sites date prior to the hypothesised megafaunal extinction 'window' (i.e., ˜30-50 ky), and therefore, cannot be used to argue exclusively for or against human/climate change extinction models, without first exploring their palaeoecological significance on wider temporal and spatial scales.

Tectonics and soil edaphics as controls on animal migrations and early human inhabitance in the Kenya Rift

NASA Astrophysics Data System (ADS)

Kübler, Simon; Rucina, Stephen; Reynolds, Sally; Fürgut, Felix; Bailey, Geoffrey; King, Geoffrey

2017-04-01

Animal movements in the tectonically active East African Rift Valley today are influenced by a combination of topography and soil nutrient distribution (soil edaphics). These patterns would have been the same in the past when hominins inhabited the area. Our study in the Kenya Rift shows that soil edaphics and active rift structures play a key role in present day animal movements as well as the for the location of early hominin sites. We carried out field analysis at Olorgesailie and Kariandusi, two key hominin sites in the southern and central Kenya Rift, respectiveley. Based on studying the relationship between the geology, tectonics and soil development we identified 'good' and 'bad' regions both in terms of edaphics and accessibility for grazing animals. We further sampled a large number of soils that developed on the volcanic bedrock and sediments of the region and interviewed the local Maasai shepherds to learn about present-day good and bad grazing sites. Ultimately, we created palaeoenvironmental and spatio-temporal reconstructions for interpreting human land use and exploitation of large mammals in the Kenya Rift for the relevant time frame of approximately 1 Ma BP. At Olorgesailie the hominin site is located in lacustrine sediments at the southern edge of a playa that extends north and northwest of Mt. Olorgesailie. The lakebeds are now tilted and eroded by motion on two north-south striking faults. The lake was trapped by volcanic flows and alluvial fans from Mt. Olorgesailie and was released by the fault motion leading to deep river incision and exposure of the site. To the west and the north steep fault scarps bound the playa forming a natural barrier for animals. Field observations and information from local shepherds suggest that the abundant trachytes at the valley floor produce poor soils whereas the soils developed on lacustrine and alluvial sediments close to the hominin site provide much more attractive grazing sites for present-day animals. This is supported by our soil analysis. With a lake in the past the Olorgesailie site represents an key example of how early hominins may have used the landscape for their strategic advantage. At Kariandusi site we investigated the tectonic and volcanic history of the region, and the system of lakes that have undergone periodic expansion and contraction during the Pleistocene in response to climatic and tectonic controls. We used this information to reconstruct topographic features as they would have existed at different periods of the past and their likely influence on patterns of large-mammal movements, and linked this with information from soil analysis. Our results show that Kariandusi occupied a unique window of opportunity in place and time for trapping mammals constrained to move through a narrowly defined topographic bottleneck between edaphically-rich areas during the lake highstand 1 Ma BP. Results of our study suggests that both Olorgesailie and Kariandusi sites were used for a simple form of ambush hunting.

Estimating rates of local extinction and colonization in colonial species and an extension to the metapopulation and community levels

USGS Publications Warehouse

Barbraud, C.; Nichols, J.D.; Hines, J.E.; Hafner, H.

2003-01-01

Coloniality has mainly been studied from an evolutionary perspective, but relatively few studies have developed methods for modelling colony dynamics. Changes in number of colonies over time provide a useful tool for predicting and evaluating the responses of colonial species to management and to environmental disturbance. Probabilistic Markov process models have been recently used to estimate colony site dynamics using presence-absence data when all colonies are detected in sampling efforts. Here, we define and develop two general approaches for the modelling and analysis of colony dynamics for sampling situations in which all colonies are, and are not, detected. For both approaches, we develop a general probabilistic model for the data and then constrain model parameters based on various hypotheses about colony dynamics. We use Akaike's Information Criterion (AIC) to assess the adequacy of the constrained models. The models are parameterised with conditional probabilities of local colony site extinction and colonization. Presence-absence data arising from Pollock's robust capture-recapture design provide the basis for obtaining unbiased estimates of extinction, colonization, and detection probabilities when not all colonies are detected. This second approach should be particularly useful in situations where detection probabilities are heterogeneous among colony sites. The general methodology is illustrated using presence-absence data on two species of herons (Purple Heron, Ardea purpurea and Grey Heron, Ardea cinerea). Estimates of the extinction and colonization rates showed interspecific differences and strong temporal and spatial variations. We were also able to test specific predictions about colony dynamics based on ideas about habitat change and metapopulation dynamics. We recommend estimators based on probabilistic modelling for future work on colony dynamics. We also believe that this methodological framework has wide application to problems in animal ecology concerning metapopulation and community dynamics.

Expanding Spatial Coverage of Geomagnetic Field Models Using Submarine Basaltic Glass

NASA Astrophysics Data System (ADS)

Schoeller, L. M.; Bowles, J. A.; Dreyer, B.; Clague, D. A.

2009-12-01

In recent years, paleointensity of submarine basaltic glass (SBG) has been used to constrain the ages of young mid-ocean ridge flows, often in the absence of more precise age data. In the present study, samples taken from the Co-Axial segment of the Juan de Fuca Ridge allow for further testing of the paleointensity dating technique; they also provide an assessment of the feasibility of incorporating SBG data into geomagnetic field models when independent age constraints are available. The nine sampled sites include six for which 14C dating of overlying sediments provides minimum ages (950 - 6400 ybp) for the flows, and three sites from historical flows. Absolute paleointensity estimates were derived using a Thellier-type method. The paleointensities of the samples ranged from 51.8 µT to 71.1 µT (VADM 8.3 to 11.6 x 1022 Am2). We compare results from the young (historical) flows directly with the International Geomagnetic Reference Field (IGRF), and two out of three sites are consistent with IGRF. The third gives paleointensity values that are considerably higher than would be expected based on IGRF. The rest of the samples can be compared with geomagnetic field models based on archeomagnetic and paleomagnetic data. Paleointensity values from samples < 3ka are consistent with the CALS3K.3 model (Korte et al., Geochem. Geophys. Geosys., 10, Q06008, doi:10.1029/2008GC002297, 2009), given the approximate ages provided by the 14C dating of the overlying sediments. Data constraining current geomagnetic field models are spatially quite limited, with the vast majority restricted to northern hemispheric continental regions. We suggest that data from mid-ocean ridges are suitable for incorporation into such models, with the potential to greatly expand spatial coverage.

Multichannel analysis of surface-waves and integration of downhole acoustic televiewer imaging, ultrasonic Vs and Vp, and vertical seismic profiling in an NEHRP-standard classification, South of Concordia, Kansas, USA

NASA Astrophysics Data System (ADS)

Raef, Abdelmoneam; Gad, Sabreen; Tucker-Kulesza, Stacey

2015-10-01

Seismic site characteristics, as pertaining to earthquake hazard reduction, are a function of the subsurface elastic moduli and the geologic structures. This study explores how multiscale (surface, downhole, and laboratory) datasets can be utilized to improve "constrained" average Vs30 (shear-wave velocity to a 30-meter depth). We integrate borehole, surface and laboratory measurements for a seismic site classification based on the standards of the National Earthquake Hazard Reduction Program (NEHRP). The seismic shear-wave velocity (Vs30) was derived from a geophysical inversion workflow that utilized multichannel analysis of surface-waves (MASW) and downhole acoustic televiewer imaging (DATI). P-wave and S-wave velocities, based on laboratory measurements of arrival times of ultrasonic-frequency signals, supported the workflow by enabling us to calculate Poisson's ratio, which was incorporated in building an initial model for the geophysical inversion of MASW. Extraction of core samples from two boreholes provided lithology and thickness calibration of the amplitudes of the acoustic televiewer imaging for each layer. The MASW inversion, for calculating Vs sections, was constrained with both ultrasonic laboratory measurements (from first arrivals of Vs and Vp waveforms at simulated in situ overburden stress conditions) and the downhole acoustic televiewer (DATV) amplitude logs. The Vs30 calculations enabled categorizing the studied site as NEHRP-class "C" - very dense soil and soft rock. Unlike shallow fractured carbonates in the studied area, S-wave and P-wave velocities at ultrasonic frequency for the deeper intact shale core-samples from two boreholes were in better agreement with the corresponding velocities from both a zero-offset vertical seismic profiling (VSP) and inversion of Rayleigh-wave velocity dispersion curves.

A scrutiny of heterogeneity at the TCE Source Area BioREmediation (SABRE) test site

NASA Astrophysics Data System (ADS)

Rivett, M.; Wealthall, G. P.; Mcmillan, L. A.; Zeeb, P.

2015-12-01

A scrutiny of heterogeneity at the UK's Source Area BioREmediation (SABRE) test site is presented to better understand how spatial heterogeneity in subsurface properties and process occurrence may constrain performance of enhanced in-situ bioremediation (EISB). The industrial site contained a 25 to 45 year old trichloroethene (TCE) dense non-aqueous phase liquid (DNAPL) that was exceptionally well monitored via a network of multilevel samplers and high resolution core sampling. Moreover, monitoring was conducted within a 3-sided sheet-pile cell that allowed a controlled streamtube of flow to be drawn through the source zone by an extraction well. We primarily focus on the longitudinal transect of monitoring along the length of the cell that provides a 200 groundwater point sample slice along the streamtube of flow through the DNAPL source zone. TCE dechlorination is shown to be significant throughout the cell domain, but spatially heterogeneous in occurrence and progress of dechlorination to lesser chlorinated ethenes - it is this heterogeneity in dechlorination that we primarily scrutinise. We illustrate the diagnostic use of the relative occurrence of TCE parent and daughter compounds to confirm: dechlorination in close proximity to DNAPL and enhanced during the bioremediation; persistent layers of DNAPL into which gradients of dechlorination products are evident; fast flowpaths through the source zone where dechlorination is less evident; and, the importance of underpinning flow regime understanding on EISB performance. Still, even with such spatial detail, there remains uncertainty over the dataset interpretation. These includes poor closure of mass balance along the cell length for the multilevel sampler based monitoring and points to needs to still understand lateral flows (even in the constrained cell), even greater spatial resolution of point monitoring and potentially, not easily proven, ethene degradation loss.

Solution NMR Refinement of a Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods

PubMed Central

Chakravorty, Dhruva K.; Wang, Bing; Lee, Chul Won; Guerra, Alfredo J.; Giedroc, David P.; Merz, Kenneth M.

2013-01-01

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational dynamics in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies. PMID:23609042

A Novel Approach to Constrain Near-Surface Seismic Wave Speed Based on Polarization Analysis

NASA Astrophysics Data System (ADS)

Park, S.; Ishii, M.

2016-12-01

Understanding the seismic responses of cities around the world is essential for the risk assessment of earthquake hazards. One of the important parameters is the elastic structure of the sites, in particular, near-surface seismic wave speed, that influences the level of ground shaking. Many methods have been developed to constrain the elastic structure of the populated sites or urban basins, and here, we introduce a new technique based on analyzing the polarization content or the three-dimensional particle motion of seismic phases arriving at the sites. Polarization analysis of three-component seismic data was widely used up to about two decades ago, to detect signals and identify different types of seismic arrivals. Today, we have good understanding of the expected polarization direction and ray parameter for seismic wave arrivals that are calculated based on a reference seismic model. The polarization of a given phase is also strongly sensitive to the elastic wave speed immediately beneath the station. This allows us to compare the observed and predicted polarization directions of incoming body waves and infer the near-surface wave speed. This approach is applied to High-Sensitivity Seismograph Network in Japan, where we benchmark the results against the well-log data that are available at most stations. There is a good agreement between our estimates of seismic wave speeds and those from well logs, confirming the efficacy of the new method. In most urban environments, where well logging is not a practical option for measuring the seismic wave speeds, this method can provide a reliable, non-invasive, and computationally inexpensive estimate of near-surface elastic properties.

The isolation of the temperature effect on branched GDGT distribution in an elevation transect of the Eastern Cordillera, Colombia

NASA Astrophysics Data System (ADS)

Anderson, V. J.; Shanahan, T. M.; Saylor, J.; Horton, B. K.

2012-12-01

Recently, the distribution of branched GDGT's (glycerol dialkyl glycerol tetraethers) has been proposed as a proxy for temperature and pH in soils via the MBT/CBT index, and has been used to reconstruct past temperature variations in a number of settings ranging from marine sediments to loess deposits and paleosols. However, empirical calibrations of the MBT/CBT index against temperature show significant scatter, leading to uncertainties as large as ±2 degrees C . In this study we seek to add to and improve upon the existing soil calibration using a new set of samples spanning a large elevation (and temperature) gradient in the Eastern Cordillera of Colombia. At each site we buried temperature loggers to constrain the diurnal and seasonal temperature experienced by each soil sample. Located only 5 degrees north of the equator, our sites experience a very small seasonal temperature variation - most sites display an annual range of less than 4 degrees C. In addition, the pH of all of the soils is almost invariant across the transect, with the vast majority of samples having pH's between 4 and 5. This dataset represents a "best-case" scenario - small variations in seasonal temperature, pH, and well-constrained instrumental data - which allow us to examine the brGDGT-temperature relationship in the absence of major confounding factors such as seasonality and soil chemistry. Interestingly, the relationship between temperature and the MBT/CBT index is not improved using this dataset, suggesting that these factors are not the cause of the anomalous scatter in the calibration dataset. However, we find that using other parameterizations for the regression equation instead of the MBT and CBT indices, the errors in our temperature estimates are significantly reduced.

Coronal Structures in Cool Stars

NASA Technical Reports Server (NTRS)

Oliversen, Ronald (Technical Monitor); Dupree, Andrea K.

2004-01-01

Many papers have been published that further elucidate the structure of coronas in cool stars as determined from EUVE, HST, FUSE, Chandra, and XMM-Newton observations. In addition we are exploring the effects of coronas on the He I 1083081 transition that is observed in the infrared. Highlights of these are summarized below including publications during this reporting period and presentations. Ground-based magnetic Doppler imaging of cool stars suggests that active stars have active regions located at high latitudes on their surface. We have performed similar imaging in X-ray to locate the sites of enhanced activity using Chandra spectra. Chandra HETG observations of the bright eclipsing contact binary 44i Boo and Chandra LETG observations for the eclipsing binary VW Cep show X-ray line profiles that are Doppler-shifted by orbital motion. After careful analysis of the spectrum of each binary, a composite line-profile is constructed by adding the individual spectral lines. This high signal-to-noise ratio composite line-profile yields orbital velocities for these binaries that are accurate to 30 km/sec and allows their orbital motion to be studied at higher time resolutions. In conjunction with X-ray lightcurves, the phase-binned composite line-profiles constrain coronal structures to be small and located at high latitudes. These observations and techniques show the power of the Doppler Imaging Technique applied to X-ray line emission.

Protease-Resistant Peptide Ligands from a Knottin Scaffold Library

PubMed Central

Getz, Jennifer A.; Rice, Jeffrey J.; Daugherty, Patrick S.

2011-01-01

Peptides within the knottin family have been shown to possess inherent stability, making them attractive scaffolds for the development of therapeutic and diagnostic agents. Given its remarkable stability to proteases, the cyclic peptide kalata B1 was employed as a scaffold to create a large knottin library displayed on the surface of E. coli. A library exceeding 109 variants was constructed by randomizing seven amino acids within a loop of the kalata B1 scaffold and screened using fluorescence-activated cell sorting to identify peptide ligands specific for the active site of human thrombin. Refolded thrombin binders exhibited high nanomolar affinities in solution, slow dissociation rates, and were able to inhibit thrombin’s enzymatic activity. Importantly, 80% of a knottin-based thrombin inhibitor remained intact after a two hour incubation both with trypsin and with chymotrypsin, demonstrating that modifying the kalata B1 sequence did not compromise its stability properties. In addition, the knottin variant mediated 20-fold enhanced affinity for thrombin, when compared to the same seven residue binding epitope constrained by a single disulfide bond. Our results indicate that peptide libraries derived from the kalata B1 scaffold can yield high affinity protein ligands that retain the remarkable protease resistance associated with the parent scaffold. More generally, this strategy may prove useful in the development of stable peptide ligands suitable for in vivo applications. PMID:21615106

SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals.

PubMed

Oosterveen, Tony; Kurdija, Sanja; Ensterö, Mats; Uhde, Christopher W; Bergsland, Maria; Sandberg, Magnus; Sandberg, Rickard; Muhr, Jonas; Ericson, Johan

2013-04-30

The reiterative deployment of a small cadre of morphogen signals underlies patterning and growth of most tissues during embyogenesis, but how such inductive events result in tissue-specific responses remains poorly understood. By characterizing cis-regulatory modules (CRMs) associated with genes regulated by Sonic hedgehog (Shh), retinoids, or bone morphogenetic proteins in the CNS, we provide evidence that the neural-specific interpretation of morphogen signaling reflects a direct integration of these pathways with SoxB1 proteins at the CRM level. Moreover, expression of SoxB1 proteins in the limb bud confers on mesodermal cells the potential to activate neural-specific target genes upon Shh, retinoid, or bone morphogenetic protein signaling, and the collocation of binding sites for SoxB1 and morphogen-mediatory transcription factors in CRMs faithfully predicts neural-specific gene activity. Thus, an unexpectedly simple transcriptional paradigm appears to conceptually explain the neural-specific interpretation of pleiotropic signaling during vertebrate development. Importantly, genes induced in a SoxB1-dependent manner appear to constitute repressive gene regulatory networks that are directly interlinked at the CRM level to constrain the regional expression of patterning genes. Accordingly, not only does the topology of SoxB1-driven gene regulatory networks provide a tissue-specific mode of gene activation, but it also determines the spatial expression pattern of target genes within the developing neural tube.

Acoustic and temporal partitioning of cicada assemblages in city and mountain environments.

PubMed

Shieh, Bao-Sen; Liang, Shih-Hsiung; Chiu, Yuh-Wen

2015-01-01

Comparing adaptations to noisy city environments with those to natural mountain environments on the community level can provide significant insights that allow an understanding of the impact of anthropogenic noise on invertebrates that employ loud calling songs for mate attraction, especially when each species has its distinct song, as in the case of cicadas. In this study, we investigated the partitioning strategy of cicada assemblages in city and mountain environments by comparing the acoustic features and calling activity patterns of each species, recorded using automated digital recording systems. Our comparison of activity patterns of seasonal and diel calling revealed that there was no significant temporal partitioning of cicada assemblages in either environment. In addition, there was no correlation between the acoustic distance based on spectral features and temporal segregation. Heterospecific spectral overlap was low in both city and mountain environments, although city and mountain cicada assemblages were subject to significantly different levels of anthropogenic or interspecific noise. Furthermore, for the common species found in both environments, the calling activity patterns at both seasonal and diel time scales were significantly consistent across sites and across environments. We suggest that the temporal calling activity is constrained by endogenous factors for each species and is less flexible in response to external factors, such as anthropogenic noise. As a result, cicada assemblages in city environments with low species diversity do not demonstrate a more significant temporal partitioning than those in mountain environments with high species diversity.

Acoustic and Temporal Partitioning of Cicada Assemblages in City and Mountain Environments

PubMed Central

Shieh, Bao-Sen; Liang, Shih-Hsiung; Chiu, Yuh-Wen

2015-01-01

Comparing adaptations to noisy city environments with those to natural mountain environments on the community level can provide significant insights that allow an understanding of the impact of anthropogenic noise on invertebrates that employ loud calling songs for mate attraction, especially when each species has its distinct song, as in the case of cicadas. In this study, we investigated the partitioning strategy of cicada assemblages in city and mountain environments by comparing the acoustic features and calling activity patterns of each species, recorded using automated digital recording systems. Our comparison of activity patterns of seasonal and diel calling revealed that there was no significant temporal partitioning of cicada assemblages in either environment. In addition, there was no correlation between the acoustic distance based on spectral features and temporal segregation. Heterospecific spectral overlap was low in both city and mountain environments, although city and mountain cicada assemblages were subject to significantly different levels of anthropogenic or interspecific noise. Furthermore, for the common species found in both environments, the calling activity patterns at both seasonal and diel time scales were significantly consistent across sites and across environments. We suggest that the temporal calling activity is constrained by endogenous factors for each species and is less flexible in response to external factors, such as anthropogenic noise. As a result, cicada assemblages in city environments with low species diversity do not demonstrate a more significant temporal partitioning than those in mountain environments with high species diversity. PMID:25590620

Identification and characterization of the active hydrothermal deposits in Okinawa Trough, SW Japan: Estimates from logging-while-drilling

NASA Astrophysics Data System (ADS)

Saito, S.; Sanada, Y.; Moe, K.; Kido, Y. N.; Hamada, Y.; Kumagai, H.; Nozaki, T.; Takai, K.; Suzuki, K.

2015-12-01

A scientific drilling expedition was conducted at an active hydrothermal field on the Iheya-North Knoll by D/V Chikyu in 2014 (Expedition 907) as a part of "Next-generation Technology for Ocean Resources Survey" of the Cross-ministerial Strategic Innovation Promotion Program. During the expedition logging while drilling (LWD) was deployed to constrain the area of the fluid reservoir beneath seafloor followed by three coring holes down to 150 meter below the seafloor (mbsf). The LWD system is composed of arcVISION for resistivity and natural gamma ray measurement and TeleScope for real-time transmission of drilling parameters and arcVISION data. Five sites (C9011-15) at the Iheya-North Original Site and one site (C9016) at Aki Site were drilled with LWD. At C9012 and C9016, the arcVISION detected temperature anomaly up to 84℃ at 234 mbsf and up to 39℃ at 80 mbsf, respectively. The temperature quickly increases at that depth and it would reflect the existence of high-temperature heat source along borehole. Due to the continuous fluid circulation during drilling, the measured temperature does not indicate in-situ temperature, but it reflects the heat disturbed by the cold circulated water instead. High quality resistivity and natural gamma ray data were acquired at six sites. The log curves at Site C9016 show characteristic response; the natural gamma ray log exhibits extremely high radiation (>500 gAPI) at 7-13 and 23-31 mbsf (Zone A). In the underlying interval of 31-40 mbsf, the resistivity log exhibits extremely low value (<0.2 ohm-m) (Zone B). Then the resistivity log exhibits higher value (~10 ohm-m) and the natural gamma ray log shows very low radiation (<50 gAPI) at the interval of 41-48 mbsf (Zone C). The log characteristics in Zone A, B, and C can be interpreted as a series of K-rich alteration zone, sulfide zone, and low-K hard (silicified) sediments, respectively. The LWD-based lithological interpretation was confirmed by the following core description. Zones A and B can be correlated to altered clay zone and sulfide zone including sphalerite, galena, chalcopyrite, and pyrite. Our results show that LWD is a powerful tool for the identification and characterization of submarine hydrothermal deposits and LWD survey enhances the successful recovery of sulfide samples.

Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes.

PubMed

Minkah, Nana; Hwang, Young; Perry, Kay; Van Duyne, Gregory D; Hendrickson, Robert; Lefkowitz, Elliot J; Hannenhalli, Sridhar; Bushman, Frederic D

2007-08-15

Topoisomerase enzymes regulate superhelical tension in DNA resulting from transcription, replication, repair, and other molecular transactions. Poxviruses encode an unusual type IB topoisomerase that acts only at conserved DNA sequences containing the core pentanucleotide 5'-(T/C)CCTT-3'. In X-ray structures of the variola virus topoisomerase bound to DNA, protein-DNA contacts were found to extend beyond the core pentanucleotide, indicating that the full recognition site has not yet been fully defined in functional studies. Here we report quantitation of DNA cleavage rates for an optimized 13 bp site and for all possible single base substitutions (40 total sites), with the goals of understanding the molecular mechanism of recognition and mapping topoisomerase sites in poxvirus genome sequences. The data allow a precise definition of enzyme-DNA interactions and the energetic contributions of each. We then used the resulting "action matrix" to show that favorable topoisomerase sites are distributed all along the length of poxvirus DNA sequences, consistent with a requirement for local release of superhelical tension in constrained topological domains. In orthopox genomes, an additional central cluster of sites was also evident. A negative correlation of predicted topoisomerase sites was seen relative to early terminators, but no correlation was seen with early or late promoters. These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo.

Recognition of Earthquake-Induced Damage in the Abakainon Necropolis (NE Sicily): Results From Geomorphological, Geophysical and Numerical Analyses

NASA Astrophysics Data System (ADS)

Bottari, C.; Albano, M.; Capizzi, P.; D'Alessandro, A.; Doumaz, F.; Martorana, R.; Moro, M.; Saroli, M.

2018-01-01

Seismotectonic activity and slope instability are a permanent threat in the archaeological site of Abakainon and in the nearby village of Tripi in NE Sicily. In recent times, signs of an ancient earthquake have been identified in the necropolis of Abakainon which dating was ascertained to the first century AD earthquake. The site is located on a slope of Peloritani Mts. along the Tindari Fault Line and contains evidence for earthquake-induced landslide, including fallen columns and blocks, horizontal shift and counter slope tilting of the tomb basements. In this paper, we used an integrated geomorphological and geophysical analysis to constrain the landslide. The research was directed to the acquisition of deep geological data for the reconstruction of slope process and the thickness of mobilized materials. The applied geophysical techniques included seismic refraction tomography and electrical resistivity tomography. The surveys were performed to delineate the sliding surface and to assess approximately the thickness of mobilized materials. The geophysical and geomorphologic data confirmed the presence of different overlapped landslides in the studied area. Moreover, a numerical simulation of the slope under seismic loads supports the hypothesis of a mobilization of the landslide mass in case of strong earthquakes (PGA > 0.3 g). However, numerical results highlight that the main cause of destruction for the Abakainon necropolis is the amplification of the seismic waves, occasionally accompanied by surficial sliding.

AnchorDock for Blind Flexible Docking of Peptides to Proteins.

PubMed

Slutzki, Michal; Ben-Shimon, Avraham; Niv, Masha Y

2017-01-01

Due to increasing interest in peptides as signaling modulators and drug candidates, several methods for peptide docking to their target proteins are under active development. The "blind" docking problem, where the peptide-binding site on the protein surface is unknown, presents one of the current challenges in the field. AnchorDock protocol was developed by Ben-Shimon and Niv to address this challenge.This protocol narrows the docking search to the most relevant parts of the conformational space. This is achieved by pre-folding the free peptide and by computationally detecting anchoring spots on the surface of the unbound protein. Multiple flexible simulated annealing molecular dynamics (SAMD) simulations are subsequently carried out, starting from pre-folded peptide conformations, constrained to the various precomputed anchoring spots.Here, AnchorDock is demonstrated using two known protein-peptide complexes. A PDZ-peptide complex provides a relatively easy case due to the relatively small size of the protein, and a typical peptide conformation and binding region; a more challenging example is a complex between USP7 N-term and a p53-derived peptide, where the protein is larger, and the peptide conformation and a binding site are generally assumed to be unknown. AnchorDock returned native-like solutions ranked first and third for the PDZ and USP7 complexes, respectively. We describe the procedure step by step and discuss possible modifications where applicable.

High-Resolution Holocene Records of Paleoceanographic and Paleoclimatic Variability from the Southern Alaskan Continental Margin

NASA Astrophysics Data System (ADS)

Finney, B. P.; Jaeger, J. M.; Mix, A. C.; Cowan, E. A.; Gulick, S. S.; Mayer, L. A.; Pisias, N. G.; Powell, R. D.; Prahl, F.; Stoner, J. S.

2004-12-01

We are investigating sediments from the fjords and continental margin of southern Alaska to develop high-resolution climatic and oceanographic records for the Late Quaternary. Our goal is to better understand linkages between climatic, terrestrial and oceanic systems in this tectonically active and biologically productive region. A field program was conducted aboard the R/V Maurice Ewing in August/September 2004 utilizing geophysical surveys (high-resolution swath bathymetric and backscatter imaging, shallow sub-bottom profiling, and where permitted, high-resolution seismic reflection profiling), piston and multi-coring, and CTD/water sampling at about 30 sites in this region. Cores are being analyzed for sedimentological, microfossil, geochemical and stable isotopic proxies, with chronologies constrained by Pb-210, AMS radiocarbon, tephrochronolgic and paleomagnetic dating. Our preliminary results demonstrate that these rapidly accumulating sedimentary archives can resolve environmental changes on annual to decadal timescales. Records of recent changes in lithogenic sediment accumulation and biological productivity on the Gulf of Alaska shelf track historical climatic data that extends to the early 20th century in this region. The records also correlate with multi-decadal climate regimes during the Little Ice Age as suggested by tree-ring, glacial advance and salmon abundance records from nearby coastal sites. Jack Dymond's enthusiasm for collaborative, interdisciplinary research will help guide us in unraveling the fingerprints of key processes in this relatively unexplored region.

Accurate de novo design of hyperstable constrained peptides

PubMed Central

Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Bahl, Christopher D.; Gilmore, Jason M.; Harvey, Peta J.; Cheneval, Olivier; Buchko, Garry W.; Pulavarti, Surya V.S.R.K.; Kaas, Quentin; Eletsky, Alexander; Huang, Po-Ssu; Johnsen, William A.; Greisen, Per; Rocklin, Gabriel J.; Song, Yifan; Linsky, Thomas W.; Watkins, Andrew; Rettie, Stephen A.; Xu, Xianzhong; Carter, Lauren P.; Bonneau, Richard; Olson, James M.; Coutsias, Evangelos; Correnti, Colin E.; Szyperski, Thomas; Craik, David J.; Baker, David

2016-01-01

Summary Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for de novo design of conformationally-restricted peptides, and the use of these methods to design 15–50 residue disulfide-crosslinked and heterochiral N-C backbone-cyclized peptides. These peptides are exceptionally stable to thermal and chemical denaturation, and twelve experimentally-determined X-ray and NMR structures are nearly identical to the computational models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs. PMID:27626386

Predicting ecosystem dynamics at regional scales: an evaluation of a terrestrial biosphere model for the forests of northeastern North America.

PubMed

Medvigy, David; Moorcroft, Paul R

2012-01-19

Terrestrial biosphere models are important tools for diagnosing both the current state of the terrestrial carbon cycle and forecasting terrestrial ecosystem responses to global change. While there are a number of ongoing assessments of the short-term predictive capabilities of terrestrial biosphere models using flux-tower measurements, to date there have been relatively few assessments of their ability to predict longer term, decadal-scale biomass dynamics. Here, we present the results of a regional-scale evaluation of the Ecosystem Demography version 2 (ED2)-structured terrestrial biosphere model, evaluating the model's predictions against forest inventory measurements for the northeast USA and Quebec from 1985 to 1995. Simulations were conducted using a default parametrization, which used parameter values from the literature, and a constrained model parametrization, which had been developed by constraining the model's predictions against 2 years of measurements from a single site, Harvard Forest (42.5° N, 72.1° W). The analysis shows that the constrained model parametrization offered marked improvements over the default model formulation, capturing large-scale variation in patterns of biomass dynamics despite marked differences in climate forcing, land-use history and species-composition across the region. These results imply that data-constrained parametrizations of structured biosphere models such as ED2 can be successfully used for regional-scale ecosystem prediction and forecasting. We also assess the model's ability to capture sub-grid scale heterogeneity in the dynamics of biomass growth and mortality of different sizes and types of trees, and then discuss the implications of these analyses for further reducing the remaining biases in the model's predictions.

Analysis of Peer Interaction in Learning Activities with Personal Handhelds and Shared Displays

ERIC Educational Resources Information Center

Liu, Chen-Chung; Chung, Chen-Wei; Chen, Nian-Shing; Liu, Baw-Jhiune

2009-01-01

Collaborative learning is extensively applied in classroom activities, but the screens on handheld devices are designed for individual-user mobile applications and may constrain interaction among group learners. The small screen size may lead to fragmented and tete-a-tete communication patterns and frequently obstruct the externalization of the…

Neural Activation to Emotional Faces in Adolescents with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Weng, Shih-Jen; Carrasco, Melisa; Swartz, Johnna R.; Wiggins, Jillian Lee; Kurapati, Nikhil; Liberzon, Israel; Risi, Susan; Lord, Catherine; Monk, Christopher S.

2011-01-01

Background: Autism spectrum disorders (ASD) involve a core deficit in social functioning and impairments in the ability to recognize face emotions. In an emotional faces task designed to constrain group differences in attention, the present study used functional MRI to characterize activation in the amygdala, ventral prefrontal cortex (vPFC), and…

Constraining gross primary production and ecosystem respiration estimates for North America using atmospheric observations of carbonyl sulfide (OCS) and CO2

NASA Astrophysics Data System (ADS)

He, W.; Ju, W.; Chen, H.; Peters, W.; van der Velde, I.; Baker, I. T.; Andrews, A. E.; Zhang, Y.; Launois, T.; Campbell, J. E.; Suntharalingam, P.; Montzka, S. A.

2016-12-01

Carbonyl sulfide (OCS) is a promising novel atmospheric tracer for studying carbon cycle processes. OCS shares a similar pathway as CO2 during photosynthesis but not released through a respiration-like process, thus could be used to partition Gross Primary Production (GPP) from Net Ecosystem-atmosphere CO2 Exchange (NEE). This study uses joint atmospheric observations of OCS and CO2 to constrain GPP and ecosystem respiration (Re). Flask data from tower and aircraft sites over North America are collected. We employ our recently developed CarbonTracker (CT)-Lagrange carbon assimilation system, which is based on the CT framework and the Weather Research and Forecasting - Stochastic Time-Inverted Lagrangian Transport (WRF-STILT) model, and the Simple Biosphere model with simulated OCS (SiB3-OCS) that provides prior GPP, Re and plant uptake fluxes of OCS. Derived plant OCS fluxes from both process model and GPP-scaled model are tested in our inversion. To investigate the ability of OCS to constrain GPP and understand the uncertainty propagated from OCS modeling errors to constrained fluxes in a dual-tracer system including OCS and CO2, two inversion schemes are implemented and compared: (1) a two-step scheme, which firstly optimizes GPP using OCS observations, and then simultaneously optimizes GPP and Re using CO2 observations with OCS-constrained GPP in the first step as prior; (2) a joint scheme, which simultaneously optimizes GPP and Re using OCS and CO2 observations. We will evaluate the result using an estimated GPP from space-borne solar-induced fluorescence observations and a data-driven GPP upscaled from FLUXNET data with a statistical model (Jung et al., 2011). Preliminary result for the year 2010 shows the joint inversion makes simulated mole fractions more consistent with observations for both OCS and CO2. However, the uncertainty of OCS simulation is larger than that of CO2. The two-step and joint schemes perform similarly in improving the consistence with observations for OCS, implicating that OCS could provide independent constraint in joint inversion. Optimization makes less total GPP and Re but more NEE, when testing with prior CO2 fluxes from two biosphere models. This study gives an in-depth insight into the role of joint atmospheric OCS and CO2 observations in constraining CO2 fluxes.

'Constrained collaboration': Patient empowerment discourse as resource for countervailing power.

PubMed

Vinson, Alexandra H

2016-11-01

Countervailing powers constrain the authority and autonomy of the medical profession. One countervailing power is patient consumerism, a movement with roots in health social movements. Patient empowerment discourses that emerge from health social movements suggest that active patienthood is a normative good, and that patients should inform themselves, claim their expertise, and participate in their care. Yet, little is known about how patient empowerment is understood by physicians. Drawing on ethnographic fieldwork in an American medical school, this article examines how physicians teach medical students to carry out patient encounters while adhering to American cultural expectations of a collaborative physician-patient relationship. Overt medical paternalism is characterised by professors as 'here's the orders' paternalism, and shown to be counterproductive to 'closing the deal' - achieving patient agreement to a course of treatment. To explain how physicians accomplish their therapeutic goals without violating cultural mandates of patient empowerment I develop the concept of 'constrained collaboration'. This analysis of constrained collaboration contrasts with structural-level narratives of diminishing professional authority and contributes to a theory of the micro-level reproduction of medical authority as a set of interactional practices. © 2016 Foundation for the Sociology of Health & Illness.

Time-series measurements of bubble plume variability and water column methane distribution above Southern Hydrate Ridge, Oregon

NASA Astrophysics Data System (ADS)

Philip, Brendan T.; Denny, Alden R.; Solomon, Evan A.; Kelley, Deborah S.

2016-03-01

An estimated 500-2500 gigatons of methane carbon is sequestered in gas hydrate at continental margins and some of these deposits are associated with overlying methane seeps. To constrain the impact that seeps have on methane concentrations in overlying ocean waters and to characterize the bubble plumes that transport methane vertically into the ocean, water samples and time-series acoustic images were collected above Southern Hydrate Ridge (SHR), a well-studied hydrate-bearing seep site ˜90 km west of Newport, Oregon. These data were coregistered with robotic vehicle observations to determine the origin of the seeps, the plume rise heights above the seafloor, and the temporal variability in bubble emissions. Results show that the locations of seep activity and bubble release remained unchanged over the 3 year time-series investigation, however, the magnitude of gas release was highly variable on hourly time scales. Bubble plumes were detected to depths of 320-620 m below sea level (mbsl), in several cases exceeding the upper limit of hydrate stability by ˜190 m. For the first time, sustained gas release was imaged at the Pinnacle site and in-between the Pinnacle and the Summit area of venting, indicating that the subseafloor transport of fluid and gas is not restricted to the Summit at SHR, requiring a revision of fluid-flow models. Dissolved methane concentrations above background levels from 100 to 300 mbsl are consistent with long-term seep gas transport into the upper water column, which may lead to the build-up of seep-derived carbon in regional subsurface waters and to increases in associated biological activity.

Comparison of localized injections of spinosad and selected insecticides for the control of Cryptotermes brevis (Isoptera: Kalotermitidae) in naturally infested structural mesocosms.

PubMed

Woodrow, R Joseph; Grace, J Kenneth; Oshiro, Robert J

2006-08-01

We investigated the efficacy of various chemical injections against Cryptotermes brevis (Walker) (Isoptera: Kalotermitidae) in hardwood shipping pallets. We had three principle interests: efficacy in whole structures, relative efficacy of the active ingredients, and whether acoustic evidence augmented treatment site selection. Infested pallets were delineated into boards with four monitoring sites each. Six chemical treatments were compared: chlorpyrifos aerosol, aqueous disodium octaborate tetrahydrate (DOT), resmethrin aerosol, distilled water (control), and two treatments of spinosad SC (one treatment applied based upon visual and the other treatment upon acoustic [AE] evidence). Individual boards were split apart; efficacy was determined by percentage mortality and pre- and posttreatment AE counts. Injections were constrained to a single point per board with the greatest level of termite activity. In whole pallets, mean percentage mortality ranged from 53.3 to 58.7% for the visual and AE spinosad treatments, respectively, whereas water averaged 6.8%. Remaining treatment mortalities were 33.2, 30.4, and 18.1% for chlorpyrifos, DOT, and resmethrin, respectively. Analysis of whole-pallet data indicated that none of the insecticides produced commercially acceptable mortality; localized injections of insecticides were not comparable with whole-structure treatments. We delineated independent groups of board sections (sectional aggregates; SA) that were connected by galleries. When treated SA were analyzed, spinosad and DOT treatments were significantly different from controls, whereas remaining treatments were not different from controls or spinosad and DOT. AE readings and visual termite evidence were compared with presence or absence of termites in SA, and it was determined that both AE and visual evidence were effective predictors of termite presence.

DNA Resection at Chromosome Breaks Promotes Genome Stability by Constraining Non-Allelic Homologous Recombination

PubMed Central

Koshland, Douglas

2012-01-01

DNA double-strand breaks impact genome stability by triggering many of the large-scale genome rearrangements associated with evolution and cancer. One of the first steps in repairing this damage is 5′→3′ resection beginning at the break site. Recently, tools have become available to study the consequences of not extensively resecting double-strand breaks. Here we examine the role of Sgs1- and Exo1-dependent resection on genome stability using a non-selective assay that we previously developed using diploid yeast. We find that Saccharomyces cerevisiae lacking Sgs1 and Exo1 retains a very efficient repair process that is highly mutagenic to genome structure. Specifically, 51% of cells lacking Sgs1 and Exo1 repair a double-strand break using repetitive sequences 12–48 kb distal from the initial break site, thereby generating a genome rearrangement. These Sgs1- and Exo1-independent rearrangements depend partially upon a Rad51-mediated homologous recombination pathway. Furthermore, without resection a robust cell cycle arrest is not activated, allowing a cell with a single double-strand break to divide before repair, potentially yielding multiple progeny each with a different rearrangement. This profusion of rearranged genomes suggests that cells tolerate any dangers associated with extensive resection to inhibit mutagenic pathways such as break-distal recombination. The activation of break-distal recipient repeats and amplification of broken chromosomes when resection is limited raise the possibility that genome regions that are difficult to resect may be hotspots for rearrangements. These results may also explain why mutations in resection machinery are associated with cancer. PMID:22479212

Decreases in Soil Moisture and Organic Matter Quality Suppress Microbial Decomposition Following a Boreal Forest Fire

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

Holden, Sandra R.; Berhe, Asmeret A.; Treseder, Kathleen K.

Climate warming is projected to increase the frequency and severity of wildfires in boreal forests, and increased wildfire activity may alter the large soil carbon (C) stocks in boreal forests. Changes in boreal soil C stocks that result from increased wildfire activity will be regulated in part by the response of microbial decomposition to fire, but post-fire changes in microbial decomposition are poorly understood. Here, we investigate the response of microbial decomposition to a boreal forest fire in interior Alaska and test the mechanisms that control post-fire changes in microbial decomposition. We used a reciprocal transplant between a recently burnedmore » boreal forest stand and a late successional boreal forest stand to test how post-fire changes in abiotic conditions, soil organic matter (SOM) composition, and soil microbial communities influence microbial decomposition. We found that SOM decomposing at the burned site lost 30.9% less mass over two years than SOM decomposing at the unburned site, indicating that post-fire changes in abiotic conditions suppress microbial decomposition. Our results suggest that moisture availability is one abiotic factor that constrains microbial decomposition in recently burned forests. In addition, we observed that burned SOM decomposed more slowly than unburned SOM, but the exact nature of SOM changes in the recently burned stand are unclear. Finally, we found no evidence that post-fire changes in soil microbial community composition significantly affect decomposition. Taken together, our study has demonstrated that boreal forest fires can suppress microbial decomposition due to post-fire changes in abiotic factors and the composition of SOM. Models that predict the consequences of increased wildfires for C storage in boreal forests may increase their predictive power by incorporating the observed negative response of microbial decomposition to boreal wildfires.« less

Geological and edaphic constraints on early hominin landscape exploitation in the Kenya Rift

NASA Astrophysics Data System (ADS)

Kuebler, S.; King, G. C. P.; Rucina, S.

2017-12-01

Our study in the Kenya Rift shows that soil edaphics and active rift structures play a key role in present day animal movements as well as the for the location of early hominin sites. Based on studying the relationship between the geology, tectonics and soil development we identified 'good' and 'bad' regions both in terms of edaphics and accessibility for grazing animals. We created palaeoenvironmental reconstructions for interpreting human land use and exploitation of large mammals in the Kenya Rift for the relevant time frame of 1 Ma BP. At Olorgesailie the hominin site is located in lacustrine sediments at the southern edge of a playa that extends north and northwest of Mt. Olorgesailie. Lakebeds are now tilted and eroded by motion on two north-south striking faults. The lake was trapped by volcanic flows and alluvial fans from Mt. Olorgesailie and was released by fault motion leading to deep river incision and exposure of the site. To the west and the north steep fault scarps bound the playa forming a natural barrier for animals. Field observations and information from local shepherds suggest that the abundant trachytes at the valley floor produce poor soils whereas the soils developed on lacustrine and alluvial sediments close to the hominin site provide much more attractive grazing sites for present-day animals. This is supported by our soil analysis. With a lake in the past the Olorgesailie site represents an key example of how early hominins may have used the landscape for their strategic advantage. At Kariandusi site we investigated the tectonic and volcanic history of the region, and the system of lakes that have undergone periodic expansion and contraction during the Pleistocene in response to climatic and tectonic controls. We used this information to reconstruct topographic features as they would have existed at different periods of the past and their likely influence on patterns of large-mammal movements, and linked this with information from soil analysis. Our results show that Kariandusi occupied a unique window of opportunity in place and time for trapping mammals constrained to move through a narrowly defined topographic bottleneck between edaphically-rich areas during the lake highstand 1 Ma BP. Results of our study suggests that both Olorgesailie and Kariandusi sites were used for a simple form of ambush hunting.

Synthesis and structure-activity relationships of constrained heterocyclic analogues of combretastatin A4.

PubMed

Arthuis, Martin; Pontikis, Renée; Chabot, Guy G; Seguin, Johanne; Quentin, Lionel; Bourg, Stéphane; Morin-Allory, Luc; Florent, Jean-Claude

2011-09-05

A series of combretastatin A4 (CA4) analogues with a lactam or lactone ring fused to the trimethoxyphenyl or the B-phenyl moiety were synthesized in an efficient and stereoselective manner by using a domino Heck-Suzuki-Miyaura coupling reaction. The vascular-disrupting potential of these conformationally restricted CA4 analogues was assessed by various in vitro assays: inhibition of tubulin polymerization, modification of endothelial cell morphology, and disruption of endothelial cell cords. Compounds were also evaluated for their growth inhibitory effects against murine and human tumor cells. B-ring-constrained derivatives that contain an oxindole ring (in contrast to compounds with a benzofuranone ring) as well as analogues bearing a six-membered lactone core fused to the trimethoxyphenyl ring are endowed with significant biological activity. The most potent compound of this series (oxindole 9 b) is of particular interest, as it combines chemical stability and a biological activity profile characteristic of a vascular-disrupting agent. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Worldwide data sets constrain the water vapor uptake coefficient in cloud formation

PubMed Central

Raatikainen, Tomi; Nenes, Athanasios; Seinfeld, John H.; Morales, Ricardo; Moore, Richard H.; Lathem, Terry L.; Lance, Sara; Padró, Luz T.; Lin, Jack J.; Cerully, Kate M.; Bougiatioti, Aikaterini; Cozic, Julie; Ruehl, Christopher R.; Chuang, Patrick Y.; Anderson, Bruce E.; Flagan, Richard C.; Jonsson, Haflidi; Mihalopoulos, Nikos; Smith, James N.

2013-01-01

Cloud droplet formation depends on the condensation of water vapor on ambient aerosols, the rate of which is strongly affected by the kinetics of water uptake as expressed by the condensation (or mass accommodation) coefficient, αc. Estimates of αc for droplet growth from activation of ambient particles vary considerably and represent a critical source of uncertainty in estimates of global cloud droplet distributions and the aerosol indirect forcing of climate. We present an analysis of 10 globally relevant data sets of cloud condensation nuclei to constrain the value of αc for ambient aerosol. We find that rapid activation kinetics (αc > 0.1) is uniformly prevalent. This finding resolves a long-standing issue in cloud physics, as the uncertainty in water vapor accommodation on droplets is considerably less than previously thought. PMID:23431189

Worldwide data sets constrain the water vapor uptake coefficient in cloud formation.

PubMed

Raatikainen, Tomi; Nenes, Athanasios; Seinfeld, John H; Morales, Ricardo; Moore, Richard H; Lathem, Terry L; Lance, Sara; Padró, Luz T; Lin, Jack J; Cerully, Kate M; Bougiatioti, Aikaterini; Cozic, Julie; Ruehl, Christopher R; Chuang, Patrick Y; Anderson, Bruce E; Flagan, Richard C; Jonsson, Haflidi; Mihalopoulos, Nikos; Smith, James N

2013-03-05

Cloud droplet formation depends on the condensation of water vapor on ambient aerosols, the rate of which is strongly affected by the kinetics of water uptake as expressed by the condensation (or mass accommodation) coefficient, αc. Estimates of αc for droplet growth from activation of ambient particles vary considerably and represent a critical source of uncertainty in estimates of global cloud droplet distributions and the aerosol indirect forcing of climate. We present an analysis of 10 globally relevant data sets of cloud condensation nuclei to constrain the value of αc for ambient aerosol. We find that rapid activation kinetics (αc > 0.1) is uniformly prevalent. This finding resolves a long-standing issue in cloud physics, as the uncertainty in water vapor accommodation on droplets is considerably less than previously thought.

Integrating Levels of Analysis in Systems and Cognitive Neurosciences: Selective Attention as a Case Study.

PubMed

Itthipuripat, Sirawaj; Serences, John T

2016-06-01

Neuroscience is inherently interdisciplinary, rapidly expanding beyond its roots in biological sciences to many areas of the social and physical sciences. This expansion has led to more sophisticated ways of thinking about the links between brains and behavior and has inspired the development of increasingly advanced tools to characterize the activity of large populations of neurons. However, along with these advances comes a heightened risk of fostering confusion unless efforts are made to better integrate findings across different model systems and to develop a better understanding about how different measurement techniques provide mutually constraining information. Here we use selective visuospatial attention as a case study to highlight the importance of these issues, and we suggest that exploiting multiple measures can better constrain models that relate neural activity to animal behavior. © The Author(s) 2015.

Visitor constraints to physical activity in park and recreation areas: differences by race and ethnicity

Treesearch

Sonja A. Wilhelm Stanis; Ingrid E. Schneider; Deborah J Chavez; Kimberly J. Shinew

2009-01-01

Health benefits of physical activity are well recognized and documented, yet inactivity and obesity rates remain high in the U.S., particularly among racially and ethnically diverse populations. A greater understanding of factors that constrain physical activity in parks and recreation areas across various racial and ethnic groups may improve an agency’s ability to...

Stoichiometry constrains microbial response to root exudation - insights from a model and a field experiment in a temperate forest

NASA Astrophysics Data System (ADS)

Drake, J. E.; Darby, B. A.; Giasson, M.-A.; Kramer, M. A.; Phillips, R. P.; Finzi, A. C.

2012-06-01

Healthy plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exo-enzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The causal role of exudation, however, is difficult to isolate with in-situ observations, given the complex nature of the rhizosphere environment. We investigated the potential effects of root exudation on microbial and exo-enzyme activity using a theoretical model of decomposition and a field experiment, with a specific focus on the stoichiometric constraint of nitrogen (N) availability. The field experiment isolated the effect of exudation by pumping solutions of exudate mimics through microlysimeter "root simulators" into intact forest soils over two 50-day periods. Using a combined model-experiment approach, we tested two hypotheses: (1) exudation alone is sufficient to stimulate microbial and exo-enzyme activity in rhizosphere soils, and (2) microbial response to C-exudates (carbohydrates and organic acids) is constrained by N-limitation. Experimental delivery of exudate mimics containing C and N significantly increased microbial respiration, microbial biomass, and the activity of exo-enzymes that decompose labile components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exo-enzymes that degrade recalcitrant SOM (e.g., polyphenols, lignin). However, delivery of C-only exudates had no effect on microbial biomass or overall exo-enzyme activity, and only increased microbial respiration. The theoretical decomposition model produced complementary results; the modeled microbial response to C-only exudates was constrained by limited N supply to support the synthesis of N-rich microbial biomass and exo-enzymes, while exuding C and N together elicited an increase in modeled microbial biomass, exo-enzyme activity, and decomposition. Thus, hypothesis (2) was supported, while hypothesis (1) was only supported when C and N compounds were exuded together. This study supports a cause-and-effect relationship between root exudation and enhanced microbial activity, and suggests that exudate stoichiometry is an important and underappreciated driver of microbial activity in rhizosphere soils.

Final Report, University of California Merced: Uranium and strontium fate in waste-weathered sediments: Scaling of molecular processes to predict reactive transport

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

Chorover, Jon; Mueller, Karl; O'Day, Peggy Anne

2016-06-30

Objectives of the Project: 1. Determine the process coupling that occurs between mineral transformation and contaminant (U and Sr) speciation in acid-uranium waste weathered Hanford sediments. 2. Establish linkages between molecular-scale contaminant speciation and meso-scale contaminant lability, release and reactive transport. 3. Make conjunctive use of molecular- to bench-scale data to constrain the development of a mechanistic, reactive transport model that includes coupling of contaminant sorption-desorption and mineral transformation reactions. Hypotheses Tested: Uranium and strontium speciation in legacy sediments from the U-8 and U-12 Crib sites can be reproduced in bench-scale weathering experiments conducted on unimpacted Hanford sediments from themore » same formations; Reactive transport modeling of future uranium and strontium releases from the vadose zone of acid-waste weathered sediments can be effectively constrained by combining molecular-scale information on contaminant bonding environment with grain-scale information on contaminant phase partitioning, and meso-scale kinetic data on contaminant release from the waste-weathered porous media; Although field contamination and laboratory experiments differ in their diagenetic time scales (decades for field vs. months to years for lab), sediment dissolution, neophase nucleation, and crystal growth reactions that occur during the initial disequilibrium induced by waste-sediment interaction leave a strong imprint that persists over subsequent longer-term equilibration time scales and, therefore, give rise to long-term memory effects. Enabling Capabilities Developed: Our team developed an iterative measure-model approach that is broadly applicable to elucidate the mechanistic underpinnings of reactive contaminant transport in geomedia subject to active weathering.« less

Improved Location of Microseismic Events in Borehole Monitoring by Inclusion of Particle Motion Analysis: a Case Study at a CBM Field in Indonesia

NASA Astrophysics Data System (ADS)

Verdhora Ry, Rexha; Septyana, T.; Widiyantoro, S.; Nugraha, A. D.; Ardjuna, A.

2017-04-01

Microseismic monitoring and constraining its hypocenters in and around hydrocarbon reservoirs provides insight into induced deformation related to hydraulic fracturing. In this study, we used data from a single vertical array of sensors in a borehole, providing measures of arrival times and polarizations. Microseismic events are located using 1-D velocity models and arrival times of P- and S-waves. However, in the case of all the sensors being deployed in a near-vertical borehole, there is a high ambiguity in the source location. Herein, we applied a procedure using azimuth of P-wave particle motion to constrain and improve the source location. We used a dataset acquired during 1-day of fracture stimulation at a CBM field in Indonesia. We applied five steps of location procedure to investigate microseismic events induced by these hydraulic fracturing activities. First, arrival times for 1584 candidate events were manually picked. Then we refined the arrival times using energy ratio method to obtain high consistency picking. Using these arrival times, we estimated back-azimuth using P-wave polarization analysis. We also added the combination of polarities analysis to remove 180° ambiguity. In the end, we determined hypocenter locations using grid-search method that guided in the back-azimuth trace area to minimize the misfit function of arrival times. We have successfully removed the ambiguity and produced a good solution for hypocenter locations as indicated statistically by small RMS. Most of the events clusters highlight coherent structures around the treatment well site and revealed faults. The same procedure can be applied to various other cases such as microseismic monitoring in the field of geothermal and shale gas/oil exploration, also CCS (Carbon Capture and Storage) development.

Australopithecus sediba at 1.977 Ma and implications for the origins of the genus Homo.

PubMed

Pickering, Robyn; Dirks, Paul H G M; Jinnah, Zubair; de Ruiter, Darryl J; Churchil, Steven E; Herries, Andy I R; Woodhead, Jon D; Hellstrom, John C; Berger, Lee R

2011-09-09

Newly exposed cave sediments at the Malapa site include a flowstone layer capping the sedimentary unit containing the Australopithecus sediba fossils. Uranium-lead dating of the flowstone, combined with paleomagnetic and stratigraphic analysis of the flowstone and underlying sediments, provides a tightly constrained date of 1.977 ± 0.002 million years ago (Ma) for these fossils. This refined dating suggests that Au. sediba from Malapa predates the earliest uncontested evidence for Homo in Africa.

A Stepwise Iterative Procedure to Constrain Stress Drop, Regional Attenuation Models, and Site Effects

DTIC Science & Technology

2010-09-01

Source parameter estimates for 8 crustal pairs near I.NTS using all regional data (left) and restricting the data by magnitude/distance (right). A... tectonic implications of aftershocks of the Mw 7.6 Bhuj earthquake of 26 January 2001, Bull. Seismol. Soc.Am., 94: 818-827. Bodin, P., L...Seismol. Soc. Am.,94:1658-1669. Brune, J. N. (1970). Tectonic stress and the spectra of seismic shear waves from earthquakes, J. Geophys. Res., 75

Self-constrained inversion of microgravity data along a segment of the Irpinia fault

NASA Astrophysics Data System (ADS)

Lo Re, Davide; Florio, Giovanni; Ferranti, Luigi; Ialongo, Simone; Castiello, Gabriella

2016-01-01

A microgravity survey was completed to precisely locate and better characterize the near-surface geometry of a recent fault with small throw in a mountainous area in the Southern Apennines (Italy). The site is on a segment of the Irpinia fault, which is the source of the M6.9 1980 earthquake. This fault cuts a few meter of Mesozoic carbonate bedrock and its younger, mostly Holocene continental deposits cover. The amplitude of the complete Bouguer anomaly along two profiles across the fault is about 50 μGal. The data were analyzed and interpreted according to a self-constrained strategy, where some rapid estimation of source parameters was later used as constraint for the inversion. The fault has been clearly identified and localized in its horizontal position and depth. Interesting features in the overburden have been identified and their interpretation has allowed us to estimate the fault slip-rate, which is consistent with independent geological estimates.

Feasibility analysis of cislunar flight using the Shuttle Orbiter

NASA Technical Reports Server (NTRS)

Haynes, Davy A.

1991-01-01

A first order orbital mechanics analysis was conducted to examine the possibility of utilizing the Space Shuttle Orbiter to perform payload delivery missions to lunar orbit. In the analysis, the earth orbit of departure was constrained to be that of Space Station Freedom. Furthermore, no enhancements of the Orbiter's thermal protection system were assumed. Therefore, earth orbit insertion maneuvers were constrained to be all propulsive. Only minimal constraints were placed on the lunar orbits and no consideration was given to possible landing sites for lunar surface payloads. The various phases and maneuvers of the mission are discussed for both a conventional (Apollo type) and an unconventional mission profile. The velocity impulses needed, and the propellant masses required are presented for all of the mission maneuvers. Maximum payload capabilities were determined for both of the mission profiles examined. In addition, other issues relating to the feasibility of such lunar shuttle missions are discussed. The results of the analysis indicate that the Shuttle Orbiter would be a poor vehicle for payload delivery missions to lunar orbit.

Observing Solar Radio Bursts from the Lunar Surface

NASA Technical Reports Server (NTRS)

MacDowall, R. J.; Gopalswamy, N.; Kaiser, M. L.; Lazio, T. J.; Jones, D. L.; Bale, S. D.; Burns, J.; Kasper, J. C.; Weiler, K. W.

2011-01-01

Locating low frequency radio observatories on the lunar surface has a number of advantages, including fixes locations for the antennas and no terrestrial interference on the far side of the moon. Here, we describe the Radio Observatory for Lunar Sortie Science (ROLSS), a concept for a low frequency, radio imaging interferometric array designed to study particle acceleration in the corona and inner heliosphere. ROLSS would be deployed during an early lunar sortie or by a robotic rover as part of an unmanned landing. The prime science mission is to image type II and type III solar radio bursts with the aim of determining the sites at and mechanisms by which the radiating particles are accelerated. Secondary science goals include constraining the density of the lunar ionosphere by searching for a low radio frequency cutoff of the solar radio emissions and constraining the low energy electron population in astrophysical sources. Furthermore, ROLSS serves a pathfinder function for larger lunar radio arrays designed for faint sources.

Lunar and Planetary Science XXXV: Mars: Wind, Dust Sand, and Debris

NASA Technical Reports Server (NTRS)

2004-01-01

The session "Mars: Wind, Dust Sand, and Debris" included: Mars Exploration Rovers: Laboratory Simulations of Aeolian Interactions; Thermal and Spectral Analysis of an Intracrater Dune Field in Amazonis Planitia; How High is that Dune? A Comparison of Methods Used to Constrain the Morphometry of Aeolian Bedforms on Mars; Dust Devils on Mars: Scaling of Dust Flux Based on Laboratory Simulations; A Close Encounter with a Terrestrial Dust Devil; Interpretation of Wind Direction from Eolian Features: Herschel Crater, Mars Erosion Rates at the Viking 2 Landing Site; Mars Dust: Characterization of Particle Size and Electrostatic Charge Distributions; Simple Non-fluvial Models of Planetary Surface Modification, with Application to Mars; Comparison of Geomorphically Determined Winds with a General Circulation Model: Herschel Crater, Mars; Analysis of Martian Debris Aprons in Eastern Hellas Using THEMIS; Origin of Martian Northern Hemisphere Mid-Latitude Lobate Debris Aprons; Debris Aprons in the Tempe/Mareotis Region of Mars;and Constraining Flow Dynamics of Mass Movements on Earth and Mars.

Constrained Source Apportionment of Coarse Particulate Matter and Selected Trace Elements in Three Cities from the Multi-Ethnic Study of Atherosclerosis

PubMed Central

Sturtz, Timothy M.; Adar, Sara D.; Gould, Timothy; Larson, Timothy V.

2016-01-01

PM10-2.5 mass and trace element concentrations were measured in Winston-Salem, Chicago, and St. Paul at up to 60 sites per city during two different seasons in 2010. Positive Matrix Factorization (PMF) was used to explore the underlying sources of variability. Information on previously reported PM10-2.5 tire and brake wear profiles was used to constrain these features in PMF by prior specification of selected species ratios. We also modified PMF to allow for combining the measurements from all three cities into a single model while preserving city-specific soil features. Relatively minor differences were observed between model predictions with and without the prior ratio constraints, increasing confidence in our ability to identify separate brake wear and tire wear features. Brake wear, tire wear, fertilized soil, and re-suspended soil were found to be important sources of copper, zinc, phosphorus, and silicon respectively across all three urban areas. PMID:27468256

Mixed Integer Programming and Heuristic Scheduling for Space Communication Networks

NASA Technical Reports Server (NTRS)

Cheung, Kar-Ming; Lee, Charles H.

2012-01-01

We developed framework and the mathematical formulation for optimizing communication network using mixed integer programming. The design yields a system that is much smaller, in search space size, when compared to the earlier approach. Our constrained network optimization takes into account the dynamics of link performance within the network along with mission and operation requirements. A unique penalty function is introduced to transform the mixed integer programming into the more manageable problem of searching in a continuous space. The constrained optimization problem was proposed to solve in two stages: first using the heuristic Particle Swarming Optimization algorithm to get a good initial starting point, and then feeding the result into the Sequential Quadratic Programming algorithm to achieve the final optimal schedule. We demonstrate the above planning and scheduling methodology with a scenario of 20 spacecraft and 3 ground stations of a Deep Space Network site. Our approach and framework have been simple and flexible so that problems with larger number of constraints and network can be easily adapted and solved.

Constrained source apportionment of coarse particulate matter and selected trace elements in three cities from the multi-ethnic study of atherosclerosis

NASA Astrophysics Data System (ADS)

Sturtz, Timothy M.; Adar, Sara D.; Gould, Timothy; Larson, Timothy V.

2014-02-01

PM10-2.5 mass and trace element concentrations were measured in Winston-Salem, Chicago, and St. Paul at up to 60 sites per city during two different seasons in 2010. Positive Matrix Factorization (PMF) was used to explore the underlying sources of variability. Information on previously reported PM10-2.5 tire and brake wear profiles was used to constrain these features in PMF by prior specification of selected species ratios. We also modified PMF to allow for combining the measurements from all three cities into a single model while preserving city-specific soil features. Relatively minor differences were observed between model predictions with and without the prior ratio constraints, increasing confidence in our ability to identify separate brake wear and tire wear features. Brake wear, tire wear, fertilized soil, and resuspended soil were found to be important sources of copper, zinc, phosphorus, and silicon, respectively, across all three urban areas.

Toward Building a New Seismic Hazard Model for Mainland China

NASA Astrophysics Data System (ADS)

Rong, Y.; Xu, X.; Chen, G.; Cheng, J.; Magistrale, H.; Shen, Z.

2015-12-01

At present, the only publicly available seismic hazard model for mainland China was generated by Global Seismic Hazard Assessment Program in 1999. We are building a new seismic hazard model by integrating historical earthquake catalogs, geological faults, geodetic GPS data, and geology maps. To build the model, we construct an Mw-based homogeneous historical earthquake catalog spanning from 780 B.C. to present, create fault models from active fault data using the methodology recommended by Global Earthquake Model (GEM), and derive a strain rate map based on the most complete GPS measurements and a new strain derivation algorithm. We divide China and the surrounding regions into about 20 large seismic source zones based on seismotectonics. For each zone, we use the tapered Gutenberg-Richter (TGR) relationship to model the seismicity rates. We estimate the TGR a- and b-values from the historical earthquake data, and constrain corner magnitude using the seismic moment rate derived from the strain rate. From the TGR distributions, 10,000 to 100,000 years of synthetic earthquakes are simulated. Then, we distribute small and medium earthquakes according to locations and magnitudes of historical earthquakes. Some large earthquakes are distributed on active faults based on characteristics of the faults, including slip rate, fault length and width, and paleoseismic data, and the rest to the background based on the distributions of historical earthquakes and strain rate. We evaluate available ground motion prediction equations (GMPE) by comparison to observed ground motions. To apply appropriate GMPEs, we divide the region into active and stable tectonics. The seismic hazard will be calculated using the OpenQuake software developed by GEM. To account for site amplifications, we construct a site condition map based on geology maps. The resulting new seismic hazard map can be used for seismic risk analysis and management, and business and land-use planning.

Synthesizing trait correlations and functional relationships across multiple scales: A Hierarchical Bayes approach

NASA Astrophysics Data System (ADS)

Shiklomanov, A. N.; Cowdery, E.; Dietze, M.

2016-12-01

Recent syntheses of global trait databases have revealed that although the functional diversity among plant species is immense, this diversity is constrained by trade-offs between plant strategies. However, the use of among-trait and trait-environment correlations at the global scale for both qualitative ecological inference and land surface modeling has several important caveats. An alternative approach is to preserve the existing PFT-based model structure while using statistical analyses to account for uncertainty and variability in model parameters. In this study, we used a hierarchical Bayesian model of foliar traits in the TRY database to test the following hypotheses: (1) Leveraging the covariance between foliar traits will significantly constrain our uncertainty in their distributions; and (2) Among-trait covariance patterns are significantly different among and within PFTs, reflecting differences in trade-offs associated with biome-level evolution, site-level community assembly, and individual-level ecophysiological acclimation. We found that among-trait covariance significantly constrained estimates of trait means, and the additional information provided by across-PFT covariance led to more constraint still, especially for traits and PFTs with low sample sizes. We also found that among-trait correlations were highly variable among PFTs, and were generally inconsistent with correlations within PFTs. The hierarchical multivariate framework developed in our study can readily be enhanced with additional levels of hierarchy to account for geographic, species, and individual-level variability.

Simulating carbon and water fluxes at Arctic and boreal ecosystems in Alaska by optimizing the modified BIOME-BGC with eddy covariance data

NASA Astrophysics Data System (ADS)

Ueyama, M.; Kondo, M.; Ichii, K.; Iwata, H.; Euskirchen, E. S.; Zona, D.; Rocha, A. V.; Harazono, Y.; Nakai, T.; Oechel, W. C.

2013-12-01

To better predict carbon and water cycles in Arctic ecosystems, we modified a process-based ecosystem model, BIOME-BGC, by introducing new processes: change in active layer depth on permafrost and phenology of tundra vegetation. The modified BIOME-BGC was optimized using an optimization method. The model was constrained using gross primary productivity (GPP) and net ecosystem exchange (NEE) at 23 eddy covariance sites in Alaska, and vegetation/soil carbon from a literature survey. The model was used to simulate regional carbon and water fluxes of Alaska from 1900 to 2011. Simulated regional fluxes were validated with upscaled GPP, ecosystem respiration (RE), and NEE based on two methods: (1) a machine learning technique and (2) a top-down model. Our initial simulation suggests that the original BIOME-BGC with default ecophysiological parameters substantially underestimated GPP and RE for tundra and overestimated those fluxes for boreal forests. We will discuss how optimization using the eddy covariance data impacts the historical simulation by comparing the new version of the model with simulated results from the original BIOME-BGC with default ecophysiological parameters. This suggests that the incorporation of the active layer depth and plant phenology processes is important to include when simulating carbon and water fluxes in Arctic ecosystems.

Out of the reach of children? Young people's health-seeking practices and agency in Africa's newly-emerging therapeutic landscapes.

PubMed

Hampshire, Kate R; Porter, Gina; Owusu, Samuel Asiedu; Tanle, Augustine; Abane, Albert

2011-09-01

Despite a dominant view within Western biomedicine that children and medicines should be kept apart, a growing literature suggests that children and adolescents often take active roles in health-seeking. Here, we consider young people's health-seeking practices in Ghana: a country with a rapidly-changing therapeutic landscape, characterised by the recent introduction of a National Health Insurance Scheme, mass advertising of medicines, and increased use of mobile phones. Qualitative and quantitative data are presented from eight field-sites in urban and rural Ghana, including 131 individual interviews, focus groups, plus a questionnaire survey of 1005 8-to-18-year-olds. The data show that many young people in Ghana play a major role in seeking healthcare for themselves and others. Young people's ability to secure effective healthcare is often constrained by their limited access to social, economic and cultural resources and information; however, many interviewees actively generated, developed and consolidated such resources in their quest for healthcare. Health insurance and the growth of telecommunications and advertising present new opportunities and challenges for young people's health-seeking practices. We argue that policy should take young people's medical realities as a starting point for interventions to facilitate safe and effective health-seeking. Copyright © 2011 Elsevier Ltd. All rights reserved.

Genes on a Wire: The Nucleoid-Associated Protein HU Insulates Transcription Units in Escherichia coli

PubMed Central

Berger, Michael; Gerganova, Veneta; Berger, Petya; Rapiteanu, Radu; Lisicovas, Viktoras; Dobrindt, Ulrich

2016-01-01

The extent to which chromosomal gene position in prokaryotes affects local gene expression remains an open question. Several studies have shown that chromosomal re-positioning of bacterial transcription units does not alter their expression pattern, except for a general decrease in gene expression levels from chromosomal origin to terminus proximal positions, which is believed to result from gene dosage effects. Surprisingly, the question as to whether this chromosomal context independence is a cis encoded property of a bacterial transcription unit, or if position independence is a property conferred by factors acting in trans, has not been addressed so far. For this purpose, we established a genetic test system assessing the chromosomal positioning effects by means of identical promoter-fluorescent reporter gene fusions inserted equidistantly from OriC into both chromosomal replichores of Escherichia coli K-12. Our investigations of the reporter activities in mutant cells lacking the conserved nucleoid associated protein HU uncovered various drastic chromosomal positional effects on gene transcription. In addition we present evidence that these positional effects are caused by transcriptional activity nearby the insertion site of our reporter modules. We therefore suggest that the nucleoid-associated protein HU is functionally insulating transcription units, most likely by constraining transcription induced DNA supercoiling. PMID:27545593

Prediction of ground motion and dynamic stress change in Baekdusan (Changbaishan) volcano caused by a North Korean nuclear explosion.

PubMed

Hong, Tae-Kyung; Choi, Eunseo; Park, Seongjun; Shin, Jin Soo

2016-02-17

Strong ground motions induce large dynamic stress changes that may disturb the magma chamber of a volcano, thus accelerating the volcanic activity. An underground nuclear explosion test near an active volcano constitutes a direct treat to the volcano. This study examined the dynamic stress changes of the magma chamber of Baekdusan (Changbaishan) that can be induced by hypothetical North Korean nuclear explosions. Seismic waveforms for hypothetical underground nuclear explosions at North Korean test site were calculated by using an empirical Green's function approach based on a source-spectral model of a nuclear explosion; such a technique is efficient for regions containing poorly constrained velocity structures. The peak ground motions around the volcano were estimated from empirical strong-motion attenuation curves. A hypothetical M7.0 North Korean underground nuclear explosion may produce peak ground accelerations of 0.1684 m/s(2) in the horizontal direction and 0.0917 m/s(2) in the vertical direction around the volcano, inducing peak dynamic stress change of 67 kPa on the volcano surface and ~120 kPa in the spherical magma chamber. North Korean underground nuclear explosions with magnitudes of 5.0-7.6 may induce overpressure in the magma chamber of several tens to hundreds of kilopascals.

How peer-review constrains cognition: on the frontline in the knowledge sector.

PubMed

Cowley, Stephen J

2015-01-01

Peer-review is neither reliable, fair, nor a valid basis for predicting 'impact': as quality control, peer-review is not fit for purpose. Endorsing the consensus, I offer a reframing: while a normative social process, peer-review also shapes the writing of a scientific paper. In so far as 'cognition' describes enabling conditions for flexible behavior, the practices of peer-review thus constrain knowledge-making. To pursue cognitive functions of peer-review, however, manuscripts must be seen as 'symbolizations', replicable patterns that use technologically enabled activity. On this bio-cognitive view, peer-review constrains knowledge-making by writers, editors, reviewers. Authors are prompted to recursively re-aggregate symbolizations to present what are deemed acceptable knowledge claims. How, then, can recursive re-embodiment be explored? In illustration, I sketch how the paper's own content came to be re-aggregated: agonistic review drove reformatting of argument structure, changes in rhetorical ploys and careful choice of wordings. For this reason, the paper's knowledge-claims can be traced to human activity that occurs in distributed cognitive systems. Peer-review is on the frontline in the knowledge sector in that it delimits what can count as knowing. Its systemic nature is therefore crucial to not only discipline-centered 'real' science but also its 'post-academic' counterparts.

Double quick, double click reversible peptide “stapling”† †Electronic supplementary information (ESI) available: Synthesis and characterization, additional biophysical and biochemical analyses. See DOI: 10.1039/c7sc01342f Click here for additional data file. Click here for additional data file. Click here for additional data file.

PubMed Central

Grison, Claire M.; Burslem, George M.; Miles, Jennifer A.; Pilsl, Ludwig K. A.; Yeo, David J.; Imani, Zeynab; Warriner, Stuart L.; Webb, Michael E.

2017-01-01

The development of constrained peptides for inhibition of protein–protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine (hCys) amino acids spaced at i and i + 4 positions by double substitution. The constraint can be readily removed by displacement of the maleimide using excess thiol. This new constraining methodology results in enhanced α-helical conformation (BID and RNase S peptide) as demonstrated by circular dichroism and molecular dynamics simulations, resistance to proteolysis (BID) as demonstrated by trypsin proteolysis experiments and retained or enhanced potency of inhibition for Bcl-2 family protein–protein interactions (BID), or greater capability to restore the hydrolytic activity of the RNAse S protein (RNase S peptide). Finally, use of a dibromomaleimide functionalized with an alkyne permits further divergent functionalization through alkyne–azide cycloaddition chemistry on the constrained peptide with fluorescein, oligoethylene glycol or biotin groups to facilitate biophysical and cellular analyses. Hence this methodology may extend the scope and accessibility of peptide stapling. PMID:28970902

Constraining the location of rapid gamma-ray flares in the flat spectrum radio quasar 3C 273 [Constraining the location of rapid gamma-ray flares in the FSRQ 3C 273

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

Rani, B.; Lott, B.; Krichbaum, T. P.

2013-09-02

Here, we present a γ-ray photon flux and spectral variability study of the flat-spectrum radio quasar 3C 273 over a rapid flaring activity period between September 2009 to April 2010. Five major flares were observed in the source during this period. The most rapid flare observed in the source has a flux doubling time of 1.1 hr. The rapid γ-ray flares allow us to constrain the location and size of the γ-ray emission region in the source. The γγ-opacity constrains the Doppler factor δ γ ≥ 10 for the highest energy (15 GeV) photon observed by the Fermi-Large Area Telescopemore » (LAT). Causality arguments constrain the size of the emission region to 1.6 × 10 15 cm. The γ-ray spectra measured over this period show clear deviations from a simple power law with a break in the 1–2 GeV energy range. We discuss possible explanations for the origin of the γ-ray spectral breaks. Our study suggests that the γ-ray emission region in 3C 273 is located within the broad line region (< 1.6 pc). As a result, the spectral behavior and temporal characteristics of the individual flares indicate the presence of multiple shock scenarios at the base of the jet.« less

Directional constraint of endpoint force emerges from hindlimb anatomy.

PubMed

Bunderson, Nathan E; McKay, J Lucas; Ting, Lena H; Burkholder, Thomas J

2010-06-15

Postural control requires the coordination of force production at the limb endpoints to apply an appropriate force to the body. Subjected to horizontal plane perturbations, quadruped limbs stereotypically produce force constrained along a line that passes near the center of mass. This phenomenon, referred to as the force constraint strategy, may reflect mechanical constraints on the limb or body, a specific neural control strategy or an interaction among neural controls and mechanical constraints. We used a neuromuscular model of the cat hindlimb to test the hypothesis that the anatomical constraints restrict the mechanical action of individual muscles during stance and constrain the response to perturbations to a line independent of perturbation direction. In a linearized neuromuscular model of the cat hindlimb, muscle lengthening directions were highly conserved across 10,000 different muscle activation patterns, each of which produced an identical, stance-like endpoint force. These lengthening directions were closely aligned with the sagittal plane and reveal an anatomical structure for directionally constrained force responses. Each of the 10,000 activation patterns was predicted to produce stable stance based on Lyapunov stability analysis. In forward simulations of the nonlinear, seven degree of freedom model under the action of 200 random muscle activation patterns, displacement of the endpoint from its equilibrium position produced restoring forces, which were also biased toward the sagittal plane. The single exception was an activation pattern based on minimum muscle stress optimization, which produced destabilizing force responses in some perturbation directions. The sagittal force constraint increased during simulations as the system shifted from an inertial response during the acceleration phase to a viscoelastic response as peak velocity was obtained. These results qualitatively match similar experimental observations and suggest that the force constraint phenomenon may result from the anatomical arrangement of the limb.

Directional constraint of endpoint force emerges from hindlimb anatomy

PubMed Central

Bunderson, Nathan E.; McKay, J. Lucas; Ting, Lena H.; Burkholder, Thomas J.

2010-01-01

Postural control requires the coordination of force production at the limb endpoints to apply an appropriate force to the body. Subjected to horizontal plane perturbations, quadruped limbs stereotypically produce force constrained along a line that passes near the center of mass. This phenomenon, referred to as the force constraint strategy, may reflect mechanical constraints on the limb or body, a specific neural control strategy or an interaction among neural controls and mechanical constraints. We used a neuromuscular model of the cat hindlimb to test the hypothesis that the anatomical constraints restrict the mechanical action of individual muscles during stance and constrain the response to perturbations to a line independent of perturbation direction. In a linearized neuromuscular model of the cat hindlimb, muscle lengthening directions were highly conserved across 10,000 different muscle activation patterns, each of which produced an identical, stance-like endpoint force. These lengthening directions were closely aligned with the sagittal plane and reveal an anatomical structure for directionally constrained force responses. Each of the 10,000 activation patterns was predicted to produce stable stance based on Lyapunov stability analysis. In forward simulations of the nonlinear, seven degree of freedom model under the action of 200 random muscle activation patterns, displacement of the endpoint from its equilibrium position produced restoring forces, which were also biased toward the sagittal plane. The single exception was an activation pattern based on minimum muscle stress optimization, which produced destabilizing force responses in some perturbation directions. The sagittal force constraint increased during simulations as the system shifted from an inertial response during the acceleration phase to a viscoelastic response as peak velocity was obtained. These results qualitatively match similar experimental observations and suggest that the force constraint phenomenon may result from the anatomical arrangement of the limb. PMID:20511528

Integration of real-time mapping technology in disaster relief distribution.

DOT National Transportation Integrated Search

2013-02-01

Vehicle routing for disaster relief distribution involves many challenges that distinguish this problem from those in commercial settings, given the time sensitive and resource constrained nature of relief activities. While operations research approa...

Isotopic tracking of Hanford 300 area derived uranium in the Columbia River.

PubMed

Christensen, John N; Dresel, P Evan; Conrad, Mark E; Patton, Gregory W; DePaolo, Donald J

2010-12-01

Our objectives in this study are to quantify the discharge rate of uranium (U) to the Columbia River from the Hanford Site's 300 Area and to follow that U downriver to constrain its fate. Uranium from the Hanford Site has variable isotopic composition due to nuclear industrial processes carried out at the site. This characteristic makes it possible to use high-precision isotopic measurements of U in environmental samples to identify even trace levels of contaminant U, determine its sources, and estimate discharge rates. Our data on river water samples indicate that as much as 3.2 kg/day can enter the Columbia River from the 300 Area, which is only a small fraction of the total load of dissolved natural background U carried by the Columbia River. This very low level of Hanford-derived U can be discerned, despite dilution to <1% of natural background U, 400 km downstream from the Hanford Site. These results indicate that isotopic methods can allow the amounts of U from the 300 Area of the Hanford Site entering the Columbia River to be measured accurately to ascertain whether they are an environmental concern or insignificant relative to natural uranium background in the Columbia River.

The EUROSEISTEST Experimental Test Site in Greece

NASA Astrophysics Data System (ADS)

Pitilakis, K.; Manos, G.; Raptakis, D.; Anastasiadis, A.; Makra, K.; Manakou, M.

2009-04-01

The European experimental site EUROSEISTEST has been established since 1993 in the epicentral area of the June 20th 1978 earthquake (40.8˚ N, 23.2˚ E, Ms 6.5, Imax VIII+ MSK, Papazachos et al., 1979), located in the active tectonic Mygdonian basin, 30km NNE from Thessaloniki, Greece. Euroseistest has been funded by the European Commission - Directorate General for Research and Development under the framework of consecutive EC research projects (EuroseisTest, EuroseisMod and Eurroseisrisk). It is specially designed and dedicated to conduct experimental and theoretical studies on site effects, soil and site characterization and soil-foundation-structure interaction phenomena. The geological, geophysical and geotechnical conditions of the Euroseistest valley (Mygdonian graben) is very well constrained through numerous in situ campaigns and laboratory tests. The permanent accelerometric network comprises 21 digital 3D stations, including vertical arrays down to 200m (schist bedrock), covering a surface of about 100 sq Km. The site is also covered by a permanent seismological network. A number of high quality recordings, from temporary and permanent arrays, gave the possibility to perform advanced experimental and theoretical studies on site effects (e.g. Raptakis et al., 1998; Pitilakis et al., 1999; Raptakis et al., 2000; Chávez-García et al., 2000; Makra, 2000; Makra et al., 2001 & 2005). The main advantage of Euroseistest is the detailed knowledge of the 3D geological-geotechnical structure of the basin (Manakou, 2007) and its dense permanent accelerometric network. For this reason the site has been recently selected by CEA to validate and check the advanced numerical codes to be used in Cadarache ITER project. Besides the study of site effects, Euroseistest offers interesting possibilities to study SSI problems through two model structures (scaled 1:3). A 6-storey building and a bridge pier, which have been constructed and instrumented in the centre of the valley, close to the main vertical array. Euroseistest experimental site provides a rigorous high quality database comprising geological, geotechnical, geophysical and seismological data, as well as a valuable set of experimental facilities to study both experimentally and theoretically complex site effects and soil-foundation structure problems. Numerous publications have been already released (see in the web page). It is foreseen to strengthen in the near future the possibility to provide wide access to European and international scientific community to perform joint studies, to validate their models and to improve or develop new ones.

Magnetochronology and stratigraphy at Gran Dolina section, Atapuerca (Burgos, Spain).

PubMed

Parés, J M; Pérez-González, A

1999-01-01

The Atapuerca Site (Burgos, N. Spain) is an extensive archaeological site which has yielded numerous human fossil remains. The Gran Dolina section, one of the open-air excavations and subject of this study, consists of a sedimentary infilling of 18 m thickness in a gallery originated by karstification of the host Cretaceous limestones. In this paper we present new stratigraphic and paleomagnetic evidence for the age and the sedimentary environment of the karst infilling where the archaeological site is located. Paleomagnetic dating places the hominids (Aurora stratum) in the Matuyama reversed Chron, hence before 780 ka. We also report evidence for a short normal polarity event at the bottom of the section that we speculate as being Jaramillo or Kamikatsura. The early and well-constrained date of the Atapuerca archaeological site, its location in the cul-de-sac we know as Europe, its stratigraphic context, the abundant fossil remains and the stone tool industry make it one of the most important localities for the question of the earliest human occupation in Europe. Copyright 1999 Academic Press.

Constrained fixed-fulcrum reverse shoulder arthroplasty improves functional outcome in epileptic patients with recurrent shoulder instability

PubMed Central

Thangarajah, Tanujan; Higgs, Deborah; Bayley, J I L; Lambert, Simon M

2016-01-01

AIM: To report the results of fixed-fulcrum fully constrained reverse shoulder arthroplasty for the treatment of recurrent shoulder instability in patients with epilepsy. METHODS: A retrospective review was conducted at a single facility. Cases were identified using a computerized database and all clinic notes and operative reports were reviewed. All patients with epilepsy and recurrent shoulder instability were included for study. Between July 2003 and August 2011 five shoulders in five consecutive patients with epilepsy underwent fixed-fulcrum fully constrained reverse shoulder arthroplasty for recurrent anterior shoulder instability. The mean duration of epilepsy in the cohort was 21 years (range, 5-51) and all patients suffered from grand mal seizures. RESULTS: Mean age at the time of surgery was 47 years (range, 32-64). The cohort consisted of four males and one female. Mean follow-up was 4.7 years (range, 4.3-5 years). There were no further episodes of instability, and no further stabilisation or revision procedures were performed. The mean Oxford shoulder instability score improved from 8 preoperatively (range, 5-15) to 30 postoperatively (range, 16-37) (P = 0.015) and the mean subjective shoulder value improved from 20 (range, 0-50) preoperatively to 60 (range, 50-70) postoperatively (P = 0.016). Mean active forward elevation improved from 71° preoperatively (range, 45°-130°) to 100° postoperatively (range, 80°-90°) and mean active external rotation improved from 15° preoperatively (range, 0°-30°) to 40° (20°-70°) postoperatively. No cases of scapular notching or loosening were noted. CONCLUSION: Fixed-fulcrum fully constrained reverse shoulder arthroplasty should be considered for the treatment of recurrent shoulder instability in patients with epilepsy. PMID:27458554

The Activation of Embedded Words in Spoken Word Identification Is Robust but Constrained: Evidence from the Picture-Word Interference Paradigm

ERIC Educational Resources Information Center

Bowers, Jeffrey S.; Davis, Colin J.; Mattys, Sven L.; Damian, Markus F.; Hanley, Derek

2009-01-01

Three picture-word interference (PWI) experiments assessed the extent to which embedded subset words are activated during the identification of spoken superset words (e.g., "bone" in "trombone"). Participants named aloud pictures (e.g., "brain") while spoken distractors were presented. In the critical condition,…

Children's Weekend Activities in Four Countries: Context for Personal and Social Development

ERIC Educational Resources Information Center

Ozdogru, Asil Ali

2010-01-01

Out-of-school time constitutes a major context of social and emotional development for children across cultures. Because it is not constrained by school attendance, weekend time allows cultural and gender differences in time usage to emerge. In this study, children's weekend activities, choice, and some of the related emotional outcomes were…

Developing Inventory and Monitoring Programs Based on Multiple Objectives

Treesearch

Daniel L. Schmoldt; David L. Peterson; David G. Silsbee

1995-01-01

Resource inventory and monitoring (I&M) programs in national parks combine multiple objectives in order to create a plan of action over a finite time horizon. Because all program activities are constrained by time and money, it is critical to plan I&M activities that make the best use of available agency resources. However, multiple objectives complicate a...

Role of the Microcomputer-Based Laboratory Display in Supporting the Construction of New Understandings in Thermal Physics

ERIC Educational Resources Information Center

Russell, David W.; Lucas, Keith B.; McRobbie, Campbell J.

2004-01-01

Teachers' failure to use the microcomputer-based laboratory (MBL) more widely may be a result of not recognizing its capacity to transform laboratory activities. This research aimed to increase understanding of how MBL activities designed to be consistent with a constructivist theory of learning support or constrain student construction of…

α-SNAP regulates dynamic, on-site assembly and calcium selectivity of Orai1 channels.

PubMed

Li, Peiyao; Miao, Yong; Dani, Adish; Vig, Monika

2016-08-15

Orai1 forms a highly calcium-selective pore of the calcium release activated channel, and α-SNAP is necessary for its function. Here we show that α-SNAP regulates on-site assembly of Orai1 dimers into calcium-selective multimers. We find that Orai1 is a dimer in resting primary mouse embryonic fibroblasts but displays variable stoichiometry in the plasma membrane of store-depleted cells. Remarkably, α-SNAP depletion induces formation of higher-order Orai1 oligomers, which permeate significant levels of sodium via Orai1 channels. Sodium permeation in α-SNAP-deficient cells cannot be corrected by tethering multiple Stim1 domains to Orai1 C-terminal tail, demonstrating that α-SNAP regulates functional assembly and calcium selectivity of Orai1 multimers independently of Stim1 levels. Fluorescence nanoscopy reveals sustained coassociation of α-SNAP with Stim1 and Orai1, and α-SNAP-depleted cells show faster and less constrained mobility of Orai1 within ER-PM junctions, suggesting Orai1 and Stim1 coentrapment without stable contacts. Furthermore, α-SNAP depletion significantly reduces fluorescence resonance energy transfer between Stim1 and Orai1 N-terminus but not C-terminus. Taken together, these data reveal a unique role of α-SNAP in the on-site functional assembly of Orai1 subunits and suggest that this process may, in part, involve enabling crucial low-affinity interactions between Orai1 N-terminus and Stim1. © 2016 Li, Miao, et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo.

PubMed

Tal, Asaf; Arbel-Goren, Rinat; Costantino, Nina; Court, Donald L; Stavans, Joel

2014-05-20

The search for specific sequences on long genomes is a key process in many biological contexts. How can specific target sequences be located with high efficiency, within physiologically relevant times? We addressed this question for viral integration, a fundamental mechanism of horizontal gene transfer driving prokaryotic evolution, using the infection of Escherichia coli bacteria with bacteriophage λ and following the establishment of a lysogenic state. Following the targeting process in individual live E. coli cells in real time revealed that λ DNA remains confined near the entry point of a cell following infection. The encounter between the 15-bp-long target sequence on the chromosome and the recombination site on the viral genome is facilitated by the directed motion of bacterial DNA generated during chromosome replication, in conjunction with constrained diffusion of phage DNA. Moving the native bacterial integration site to different locations on the genome and measuring the integration frequency in these strains reveals that the frequencies of the native site and a site symmetric to it relative to the origin are similar, whereas both are significantly higher than when the integration site is moved near the terminus, consistent with the replication-driven mechanism we propose. This novel search mechanism is yet another example of the exquisite coevolution of λ with its host.

Using ecological null models to assess the potential for marine protected area networks to protect biodiversity.

PubMed

Semmens, Brice X; Auster, Peter J; Paddack, Michelle J

2010-01-27

Marine protected area (MPA) networks have been proposed as a principal method for conserving biological diversity, yet patterns of diversity may ultimately complicate or compromise the development of such networks. We show how a series of ecological null models can be applied to assemblage data across sites in order to identify non-random biological patterns likely to influence the effectiveness of MPA network design. We use fish census data from Caribbean fore-reefs as a test system and demonstrate that: 1) site assemblages were nested, such that species found on sites with relatively few species were subsets of those found on sites with relatively many species, 2) species co-occurred across sites more than expected by chance once species-habitat associations were accounted for, and 3) guilds were most evenly represented at the richest sites and richness among all guilds was correlated (i.e., species and trophic diversity were closely linked). These results suggest that the emerging Caribbean marine protected area network will likely be successful at protecting regional diversity even if planning is largely constrained by insular, inventory-based design efforts. By recasting ecological null models as tests of assemblage patterns likely to influence management action, we demonstrate how these classic tools of ecological theory can be brought to bear in applied conservation problems.

Optimal Sensor Management and Signal Processing for New EMI Systems

DTIC Science & Technology

2010-09-01

adaptive techniques that would improve the speed of data collection and increase the mobility of a TEMTADS system. Although an active learning technique...data, SIG has simulated the active selection based on the data already collected at Camp SLO. In this setup, the active learning approach was constrained...to work only on a 5x5 grid (corresponding to twenty five transmitters and co-located receivers). The first technique assumes that active learning will

Cosmogenic exposure age constraints on deglaciation and flow behaviour of a marine-based ice stream in western Scotland, 21-16 ka

NASA Astrophysics Data System (ADS)

Small, David; Benetti, Sara; Dove, Dayton; Ballantyne, Colin K.; Fabel, Derek; Clark, Chris D.; Gheorghiu, Delia M.; Newall, Jennifer; Xu, Sheng

2017-07-01

Understanding how marine-based ice streams operated during episodes of deglaciation requires geochronological data that constrain both timing of deglaciation and changes in their flow behaviour, such as that from unconstrained ice streaming to topographically restricted flow. We present seventeen new 10Be exposure ages from glacial boulders and bedrock at sites in western Scotland within the area drained by the Hebrides Ice Stream, a marine-based ice stream that drained a large proportion of the former British-Irish Ice Sheet. Exposure ages from Tiree constrain deglaciation of a topographic high within the central zone of the ice stream, from which convergent flowsets were produced during ice streaming. These ages thus constrain thinning of the Hebrides Ice Stream, which, on the basis of supporting information, we infer to represent cessation of ice streaming at 20.6 ± 1.2 ka, 3-4 ka earlier than previously inferred. A period of more topographically restricted flow produced flow indicators superimposed on those relating to full ice stream conditions, and exposure ages from up-stream of these constrain deglaciation to 17.5 ± 1.0 ka. Complete deglaciation of the marine sector of the Hebrides Ice Stream occurred by 17-16 ka at which time the ice margin was located near the present coastline. Exposure ages from the southernmost Outer Hebrides (Mingulay and Barra) indicate deglaciation at 18.9 ± 1.0 and 17.1 ± 1.0 ka respectively, demonstrating that an independent ice cap persisted on the southern Outer Hebrides for 3-4 ka after initial ice stream deglaciation. This suggests that deglaciation of the Hebrides Ice Stream was focused along major submarine troughs. Collectively, our data constrain initial deglaciation and changes in flow regime of the Hebrides Ice Stream, final deglaciation of its marine sector, and deglaciation of the southern portion of the independent Outer Hebrides Ice Cap, providing chronological constraints on future numerical reconstructions of this key sector of the former British-Irish Ice Sheet.

Effect of soil property uncertainties on permafrost thaw projections: a calibration-constrained analysis: Modeling Archive

DOE Data Explorer

J.C. Rowland; D.R. Harp; C.J. Wilson; A.L. Atchley; V.E. Romanovsky; E.T. Coon; S.L. Painter

2016-02-02

This Modeling Archive is in support of an NGEE Arctic publication available at doi:10.5194/tc-10-341-2016. This dataset contains an ensemble of thermal-hydro soil parameters including porosity, thermal conductivity, thermal conductivity shape parameters, and residual saturation of peat and mineral soil. The ensemble was generated using a Null-Space Monte Carlo analysis of parameter uncertainty based on a calibration to soil temperatures collected at the Barrow Environmental Observatory site by the NGEE team. The micro-topography of ice wedge polygons present at the site is included in the analysis using three 1D column models to represent polygon center, rim and trough features. The Arctic Terrestrial Simulator (ATS) was used in the calibration to model multiphase thermal and hydrological processes in the subsurface.

Ancillary Care in South African HIV Vaccine Trials: Addressing Needs, Drafting Protocols, and Engaging Community

PubMed Central

Slack, Catherine M.

2014-01-01

There has been debate about sponsor-investigator ethical responsibilities to address participants’ medical needs in trials in resource-constrained contexts. Certain ethical guidelines make detailed recommendations. This study explored whether ethical guideline recommendations for care in HIV vaccine trials were being met, and whether stakeholders were facing difficulties addressed by guidelines. It sampled key stakeholders involved in two trials across five sites in South Africa, and reviewed relevant documentation. It concluded that sites were largely meeting guideline recommendations for addressing needs, with some exceeding these. Recommendations for writing protocols were only partially achieved. Recommendations for engaging participating community were mostly met, except for “moral negotiation” recommendations. Suggestions are made to strengthen practices, and to improve guidelines so they address empirical concerns. PMID:24572086

Binding Isotope Effects for para-Aminobenzoic Acid with Dihydropteroate Synthase from Staphylococcus aureus and Plasmodium falciparum.

PubMed

Stratton, Christopher F; Namanja-Magliano, Hilda A; Cameron, Scott A; Schramm, Vern L

2015-10-16

Dihydropteroate synthase is a key enzyme in folate biosynthesis and is the target of the sulfonamide class of antimicrobials. Equilibrium binding isotope effects and density functional theory calculations indicate that the substrate binding sites for para-aminobenzoic acid on the dihydropteroate synthase enzymes from Staphylococcus aureus and Plasmodium falciparum present distinct chemical environments. Specifically, we show that para-aminobenzoic acid occupies a more sterically constrained vibrational environment when bound to dihydropteroate synthase from P. falciparum relative to that of S. aureus. Deletion of a nonhomologous, parasite-specific insert from the plasmodial dihydropteroate synthase abrogated the binding of para-aminobenzoic acid. The loop specific to P. falciparum is important for effective substrate binding and therefore plays a role in modulating the chemical environment at the substrate binding site.

Ancillary care in South African HIV vaccine trials: addressing needs, drafting protocols, and engaging community.

PubMed

Slack, Catherine M

2014-02-01

There has been debate about sponsor-investigator ethical responsibilities to address participants' medical needs in trials in resource-constrained contexts. Certain ethical guidelines make detailed recommendations. This study explored whether ethical guideline recommendations for care in HIV vaccine trials were being met, and whether stakeholders were facing difficulties addressed by guidelines. It sampled key stakeholders involved in two trials across five sites in South Africa, and reviewed relevant documentation. It concluded that sites were largely meeting guideline recommendations for addressing needs, with some exceeding these. Recommendations for writing protocols were only partially achieved. Recommendations for engaging participating community were mostly met, except for "moral negotiation" recommendations. Suggestions are made to strengthen practices, and to improve guidelines so they address empirical concerns.

A closer look at 40Ar/39Ar systematics of illite, recoil, retention ages, total gas ages, and a new correction method

NASA Astrophysics Data System (ADS)

Fitz-Diaz, E.; Hall, C. M.; van der Pluijm, B.

2013-12-01

One of the fundamentals of 40Ar-39Ar systematics of illite considers the effects of 39Ar recoil (ejection of 39Ar from tiny illite crystallites during the nuclear reaction 39K(n,p)39Ar), for which sample vacuum encapsulation prior to irradiation has been used since the 1990's. This technique separately measures the fraction of recoiled 39Ar and the Ar (39Ar and 40Ar) retained within illite crystals as they degas during step heating in vacuum. Total-gas ages (TGA) are calculated by using both recoiled and retained argon, while retention ages (RA) only involve retained Ar. Observations in numerous natural examples have shown that TGA fit stratigraphic constraints of geological processes when the average illite crystallite thickness (ICT) is smaller than 10nm, and that RA better matches these constrains for larger ICTs. Illite crystals with ICT >50nm show total gas and retention ages within a few My and they are identical, within analytical error, when ICT exceeds 150nm. We propose a new age correction that takes into account the average ICT and corresponding recoil for a sample , with such corrected ages (XCA) lying between the TGA and RA end-member ages. We apply this correction to samples containing one generation of illite and it particularly affects illite populations formed in the anchizone, with typical ICT values between 10-40nm. We analyzed bentonitic samples (S1, S2 and S3) from sites in Cretaceous carbonates in the front of the Monterrey salient in northern Mexico. Four size fractions (<0.05, 0.05-0.2, 0.2-1 & 1-2 μm) were separated, analyzed with XRD and dated by Ar-Ar. XRD analysis provides mineralogic characterization, illite polytype quantification, and illite crystallite thickness (ICT) determination using half-height peak width (illite crystallinity) and the Scherrer equation. All samples contain illite as the main mineral phase, ICT values between 8-27nm, from fine to coarser grain size fractions. Ages show a range in TGA among the different size fractions of S1, S2 and S3, respectively: 46-49, 36-43 and 40-52 My) and RA (54-64, 47-52 and 53-54 My. XCA calculations produce tighter constrained ranges (53-57, 45.5-48.5 and 49-52 My) with an overall average 51.1Ma×3.9 My. In the ICT vs. apparent age plot, authigenic illite grains show a greater slope that is in general slightly positive for TGA, slightly negative for RA, but close to zero for XCA. In the ICT vs. XCA plot thinner crystallites shows more dispersion than thicker ones. In order to test if such dispersion in the age of the finer/thinner illite is due to a different formation history in each site or the result of retention capability, degassing spectra were modeled for site XCA averages and overall XCA average. The modeling shows that local site ages best match the measured spectra, instead of a single age for the combined sites. The closeness between experimental and artificial degassing patterns also supports the hypothesis that each sample preserves a single age population. All illite grains in these samples grew progressively during folding in a time window that is constrained by the three sites. Small and large grains represent the same population in each sample, representing progressive degrees of grain growth (Ostwald ripening).

Plants and pixels: Comparing phenologies from the ground and from space (Invited)

NASA Astrophysics Data System (ADS)

Rutishauser, T.; Stoekli, R.; Jeanneret, F.; Peñuelas, J.

2010-12-01

Changes in the seasonality of life cycles of plants as recorded in phenological observations have been widely analysed at the species level with data available for many decades back in time. At the same time, seasonality changes in satellite-based observations and prognostic phenology models comprise information at the pixel-size or landscape scale. Change analysis of satellite-based records is restricted due to relatively short satellite records that further include gaps while model-based analyses are biased due to current model deficiencies. At 30 selected sites across Europe, we analysed three different sources of plant seasonality during the 1971-2000 period. Data consisted of (1) species-specific development stages of flowering and leave-out with different species observed at each site. (2) We used a synthetic phenological metric that integrates the common interannual phenological signal across all species at one site. (3) We estimated daily Leaf Area Index with a prognostic phenology model. The prior uncertainties of the model’s empirical parameter space are constrained by assimilating the Fraction of Photosynthetically Active Radiation absorbed by vegetation (FPAR) and Leaf Area Index (LAI) from the MODerate Resolution Imaging Spectroradiometer (MODIS). We extracted the day of year when the 25%, 50% and 75% thresholds were passed each spring. The question arises how the three phenological signals compare and correlate across climate zones in Europe. Is there a match between single species observations, species-based ground-observed metrics and the landscape-scale prognostic model? Are there single key-species across Europe that best represent a landscape scale measure from the prognostic model? Can one source substitute another and serve as proxy-data? What can we learn from potential mismatches? Focusing on changes in spring this contribution presents first results of an ongoing comparison study from a number of European test sites that will be extended to the pan-European phenological database Cost725 and PEP725.

Match and mismatch - comparing plant phenological metrics from ground-observations and from a prognostic model

NASA Astrophysics Data System (ADS)

Rutishauser, This; Stöckli, Reto; Jeanneret, François; Peñuelas, Josep

2010-05-01

Changes in the seasonality of life cycles of plants as recorded in phenological observations have been widely analysed at the species level with data available for many decades back in time. At the same time, seasonality changes in satellite-based observations and prognostic phenology models comprise information at the pixel-size or landscape scale. Change analysis of satellite-based records is restricted due to relatively short satellite records that further include gaps while model-based analyses are biased due to current model deficiencies., At 30 selected sites across Europe, we analysed three different sources of plant seasonality during the 1971-2000 period. Data consisted of (1) species-specific development stages of flowering and leave-out with different species observed at each site. (2) We used a synthetic phenological metric that integrates the common interannual phenological signal across all species at one site. (3) We estimated daily Leaf Area Index with a prognostic phenology model. The prior uncertainties of the model's empirical parameter space are constrained by assimilating the Fraction of Photosynthetically Active Radiation absorbed by vegetation (FPAR) and Leaf Area Index (LAI) from the MODerate Resolution Imaging Spectroradiometer (MODIS). We extracted the day of year when the 25%, 50% and 75% thresholds were passed each spring. The question arises how the three phenological signals compare and correlate across climate zones in Europe. Is there a match between single species observations, species-based ground-observed metrics and the landscape-scale prognostic model? Are there single key-species across Europe that best represent a landscape scale measure from the prognostic model? Can one source substitute another and serve as proxy-data? What can we learn from potential mismatches? Focusing on changes in spring this contribution presents first results of an ongoing comparison study from a number of European test sites that will be extended to the pan-European phenological database Cost725 and PEP725.

Cation ordering and effect of biaxial strain in double perovskite CsRbCaZnCl 6

DOE PAGES

Pilania, G.; Uberuaga, B. P.

2015-03-19

Here, we investigate the electronic structure, energetics of cation ordering, and effect of biaxial strain on double perovskite CsRbCaZnCl 6 using first-principles calculations based on density functional theory. The two constituents (i.e., CsCaCl 3 and RbZnCl 3) forming the double perovskite exhibit a stark contrast. While CsCaCl 3 is known to exist in a cubic perovskite structure and does not show any epitaxial strain induced phase transitions within an experimentally accessible range of compressive strains, RbZnCl 3 is thermodynamically unstable in the perovskite phase and exhibits ultra-sensitive response at small epitaxial strains if constrained in the perovskite phase. We showmore » that combining the two compositions in a double perovskite structure not only improves overall stability but also the strain-polarization coupling of the material. Our calculations predict a ground state with P4/nmm space group for the double perovskite, where A-site cations (i.e., Cs and Rb) are layer-ordered and B-site cations (i.e., Ca and Zn) prefer a rocksalt type ordering. The electronic structure and bandgap in this system are shown to be quite sensitive to the B-site cation ordering and is minimally affected by the ordering of A-site cations. We find that at experimentally accessible compressive strains CsRbCaZnCl 6 can be phase transformed from its paraelectric ground state to an antiferroelectric state, where Zn atoms contribute predominantly to the polarization. Furthermore, both energy difference and activation barrier for a transformation between this antiferroelectric state and the corresponding ferroelectric configuration are predicted to be small. As a result, the computational approach presented here opens a new pathway towards a rational design of novel double perovskites with improved strain response and functionalities.« less

An ecosystem-scale perspective of the net land methanol flux. Synthesis of micrometeorological flux measurements

DOE PAGES

Wohlfahrt, G.; Amelynck, C.; Ammann, C.; ...

2015-07-09

Methanol is the second most abundant volatile organic compound in the troposphere and plays a significant role in atmospheric chemistry. While there is consensus about the dominant role of living plants as the major source and the reaction with OH as the major sink of methanol, global methanol budgets diverge considerably in terms of source/sink estimates, reflecting uncertainties in the approaches used to model and the empirical data used to separately constrain these terms. Here we compiled micrometeorological methanol flux data from eight different study sites and reviewed the corresponding literature in order to provide a first cross-site synthesis ofmore » the terrestrial ecosystem-scale methanol exchange and present an independent data-driven view of the land–atmosphere methanol exchange. Our study shows that the controls of plant growth on production, and thus the methanol emission magnitude, as well as stomatal conductance on the hourly methanol emission variability, established at the leaf level, hold across sites at the ecosystem level. Unequivocal evidence for bi-directional methanol exchange at the ecosystem scale is presented. Deposition, which at some sites even exceeds methanol emissions, represents an emerging feature of ecosystem-scale measurements and is likely related to environmental factors favouring the formation of surface wetness. Methanol may adsorb to or dissolve in this surface water and eventually be chemically or biologically removed from it. Management activities in agriculture and forestry are shown to increase local methanol emission by orders of magnitude; however, they are neglected at present in global budgets. While contemporary net land methanol budgets are overall consistent with the grand mean of the micrometeorological methanol flux measurements, we caution that the present approach of simulating methanol emission and deposition separately is prone to opposing systematic errors and does not allow for full advantage to be taken of the rich information content of micrometeorological flux measurements.« less

An ecosystem-scale perspective of the net land methanol flux: synthesis of micrometeorological flux measurements

PubMed Central

Wohlfahrt, G.; Amelynck, C.; Ammann, C.; Arneth, A.; Bamberger, I.; Goldstein, A. H.; Gu, L.; Guenther, A.; Hansel, A.; Heinesch, B.; Holst, T.; Hörtnagl, L.; Karl, T.; Laffineur, Q.; Neftel, A.; McKinney, K.; Munger, J. W.; Pallardy, S. G.; Schade, G. W.; Seco, R.; Schoon, N.

2015-01-01

Methanol is the second most abundant volatile organic compound in the troposphere and plays a significant role in atmospheric chemistry. While there is consensus about the dominant role of living plants as the major source and the reaction with OH as the major sink of methanol, global methanol budgets diverge considerably in terms of source/sink estimates reflecting uncertainties in the approaches used to model, and the empirical data used to separately constrain these terms. Here we compiled micrometeorological methanol flux data from eight different study sites and reviewed the corresponding literature in order to provide a first cross-site synthesis of the terrestrial ecosystem-scale methanol exchange and present an independent data-driven view of the land–atmosphere methanol exchange. Our study shows that the controls of plant growth on the production, and thus the methanol emission magnitude, and stomatal conductance on the hourly methanol emission variability, established at the leaf level, hold across sites at the ecosystem-level. Unequivocal evidence for bi-directional methanol exchange at the ecosystem scale is presented. Deposition, which at some sites even exceeds methanol emissions, represents an emerging feature of ecosystem-scale measurements and is likely related to environmental factors favouring the formation of surface wetness. Methanol may adsorb to or dissolve in this surface water and eventually be chemically or biologically removed from it. Management activities in agriculture and forestry are shown to increase local methanol emission by orders of magnitude; they are however neglected at present in global budgets. While contemporary net land methanol budgets are overall consistent with the grand mean of the micrometeorological methanol flux measurements, we caution that the present approach of simulating methanol emission and deposition separately is prone to opposing systematic errors and does not allow taking full advantage of the rich information content of micrometeorological flux measurements. PMID:25983744