Large Scale Ice Water Path and 3-D Ice Water Content

DOE Data Explorer

Liu, Guosheng

2008-01-15

Cloud ice water concentration is one of the most important, yet poorly observed, cloud properties. Developing physical parameterizations used in general circulation models through single-column modeling is one of the key foci of the ARM program. In addition to the vertical profiles of temperature, water vapor and condensed water at the model grids, large-scale horizontal advective tendencies of these variables are also required as forcing terms in the single-column models. Observed horizontal advection of condensed water has not been available because the radar/lidar/radiometer observations at the ARM site are single-point measurement, therefore, do not provide horizontal distribution of condensed water. The intention of this product is to provide large-scale distribution of cloud ice water by merging available surface and satellite measurements. The satellite cloud ice water algorithm uses ARM ground-based measurements as baseline, produces datasets for 3-D cloud ice water distributions in a 10 deg x 10 deg area near ARM site. The approach of the study is to expand a (surface) point measurement to an (satellite) areal measurement. That is, this study takes the advantage of the high quality cloud measurements at the point of ARM site. We use the cloud characteristics derived from the point measurement to guide/constrain satellite retrieval, then use the satellite algorithm to derive the cloud ice water distributions within an area, i.e., 10 deg x 10 deg centered at ARM site.

A comparison of single- and multi-site calibration and validation: a case study of SWAT in the Miyun Reservoir watershed, China

NASA Astrophysics Data System (ADS)

Bai, Jianwen; Shen, Zhenyao; Yan, Tiezhu

2017-09-01

An essential task in evaluating global water resource and pollution problems is to obtain the optimum set of parameters in hydrological models through calibration and validation. For a large-scale watershed, single-site calibration and validation may ignore spatial heterogeneity and may not meet the needs of the entire watershed. The goal of this study is to apply a multi-site calibration and validation of the Soil andWater Assessment Tool (SWAT), using the observed flow data at three monitoring sites within the Baihe watershed of the Miyun Reservoir watershed, China. Our results indicate that the multi-site calibration parameter values are more reasonable than those obtained from single-site calibrations. These results are mainly due to significant differences in the topographic factors over the large-scale area, human activities and climate variability. The multi-site method involves the division of the large watershed into smaller watersheds, and applying the calibrated parameters of the multi-site calibration to the entire watershed. It was anticipated that this case study could provide experience of multi-site calibration in a large-scale basin, and provide a good foundation for the simulation of other pollutants in followup work in the Miyun Reservoir watershed and other similar large areas.

Binding of pixantrone to DNA at CpA dinucleotide sequences and bulge structures.

PubMed

Konda, Shyam K; Wang, Haiqiang; Cutts, Suzanne M; Phillips, Don R; Collins, J Grant

2015-06-07

The binding of the anti-cancer drug pixantrone to three oligonucleotide sequences, d(TCATATGA)2, d(CCGAGAATTCCGG)2 {double bulge = DB} and the non-self complementary d(TACGATGAGTA) : d(TACCATCGTA) {single bulge = SB}, has been studied by NMR spectroscopy and molecular modelling. The upfield shifts observed for the aromatic resonances of pixantrone upon addition of the drug to each oligonucleotide confirmed the drug bound by intercalation. For the duplex sequence d(TCATATGA)2, NOEs were observed from the pixantrone aromatic H7/8 and aliphatic Ha/Hb protons to the H6/H8 and H1' protons of the C2, A3, T6 and G7 nucleotides, demonstrating that pixantrone preferentially binds at the symmetric CpA sites. However, weaker NOEs observed to various protons from the T4 and A5 residues indicated alternative minor binding sites. NOEs from the H7/H8 and Ha/Hb protons to both major (H6/H8) and minor groove (H1') protons indicated approximately equal proportions of intercalation was from the major and minor groove at the CpA sites. Intermolecular NOEs were observed between the H7/H8 and H4 protons of pixantrone and the A4H1' and G3H1' protons of the oligonucleotide that contains two symmetrically related bulge sites (DB), indicative of binding at the adenine bulge sites. For the oligonucleotide that only contains a single bulge site (SB), NOEs were observed from pixantrone protons to the SB G7H1', A8H1' and G9H1' protons, confirming that the drug bound selectively at the adenine bulge site. A molecular model of pixantrone-bound SB could be constructed with the drug bound from the minor groove at the A8pG9 site that was consistent with the observed NMR data. The results demonstrate that pixantrone preferentially intercalates at adenine bulge sites, compared to duplex DNA, and predominantly from the minor groove.

Single cell visualization of transcription kinetics variance of highly mobile identical genes using 3D nanoimaging

PubMed Central

Annibale, Paolo; Gratton, Enrico

2015-01-01

Multi-cell biochemical assays and single cell fluorescence measurements revealed that the elongation rate of Polymerase II (PolII) in eukaryotes varies largely across different cell types and genes. However, there is not yet a consensus whether intrinsic factors such as the position, local mobility or the engagement by an active molecular mechanism of a genetic locus could be the determinants of the observed heterogeneity. Here by employing high-speed 3D fluorescence nanoimaging techniques we resolve and track at the single cell level multiple, distinct regions of mRNA synthesis within the model system of a large transgene array. We demonstrate that these regions are active transcription sites that release mRNA molecules in the nucleoplasm. Using fluctuation spectroscopy and the phasor analysis approach we were able to extract the local PolII elongation rate at each site as a function of time. We measured a four-fold variation in the average elongation between identical copies of the same gene measured simultaneously within the same cell, demonstrating a correlation between local transcription kinetics and the movement of the transcription site. Together these observations demonstrate that local factors, such as chromatin local mobility and the microenvironment of the transcription site, are an important source of transcription kinetics variability. PMID:25788248

Testing Earth System Models with Earth System Data: using C isotopes in atmospheric CO2 to probe stomatal response to future climate change

NASA Astrophysics Data System (ADS)

Ballantyne, A. P.; Miller, J. B.; Bowling, D. R.; Tans, P. P.; Baker, I. T.

2013-12-01

The global cycles of water and carbon are inextricably linked through photosynthesis. This link is largely governed by stomatal conductance that regulates water loss to the atmosphere and carbon gain to the biosphere. Although extensive research has focused on the response of stomatal conductance to increased atmospheric CO2, much less research has focused on the response of stomatal conductance to concomitant climate change. Here we make use of intensive and extensive measurements of C isotopes in source CO2 to the atmosphere (del-bio) to make inferences about stomatal response to climatic factors at a single forest site and across a network of global observation sites. Based on intensive observations at the Niwot Ridge Ameriflux site we discover that del-bio is an excellent physical proxy of stomatal response during the growing season and this response is highly sensitive to atmospheric water vapor pressure deficit (VPD). We use these intensive single forest site observations to inform our analysis of the global observation network, focusing in on the growing season across an array of terrestrial sites. We find that stomatal response across most of these terrestrial sites is also highly sensitive to VPD. Lastly, we simulate the response of future climate change on stomatal response and discover that future increases in VPD may limit the biosphere's capacity to assimilate future CO2 emissions. These results have direct implications for the benchmarking of Earth System Models as stomatal conductance in many of these models does not vary as a function of VPD.

Vibrational Dynamics of Biological Molecules: Multi-quantum Contributions

PubMed Central

Leu, Bogdan M.; Timothy Sage, J.; Zgierski, Marek Z.; Wyllie, Graeme R. A.; Ellison, Mary K.; Robert Scheidt, W.; Sturhahn, Wolfgang; Ercan Alp, E.; Durbin, Stephen M.

2006-01-01

High-resolution X-ray measurements near a nuclear resonance reveal the complete vibrational spectrum of the probe nucleus. Because of this, nuclear resonance vibrational spectroscopy (NRVS) is a uniquely quantitative probe of the vibrational dynamics of reactive iron sites in proteins and other complex molecules. Our measurements of vibrational fundamentals have revealed both frequencies and amplitudes of 57Fe vibrations in proteins and model compounds. Information on the direction of Fe motion has also been obtained from measurements on oriented single crystals, and provides an essential test of normal mode predictions. Here, we report the observation of weaker two-quantum vibrational excitations (overtones and combinations) for compounds that mimic the active site of heme proteins. The predicted intensities depend strongly on the direction of Fe motion. We compare the observed features with predictions based on the observed fundamentals, using information on the direction of Fe motion obtained either from DFT predictions or from single crystal measurements. Two-quantum excitations may become a useful tool to identify the directions of the Fe oscillations when single crystals are not available. PMID:16894397

Aerosol Optical Properties in Southeast Asia From AERONET Observations

NASA Astrophysics Data System (ADS)

Eck, T. F.; Holben, B. N.; Boonjawat, J.; Le, H. V.; Schafer, J. S.; Reid, J. S.; Dubovik, O.; Smirnov, A.

2003-12-01

There is little published data available on measured optical properties of aerosols in the Southeast Asian region. The AERONET project and collaborators commenced monitoring of aerosol optical properties in February 2003 at four sites in Thailand and two sites in Viet Nam to measure the primarily anthropogenic aerosols generated by biomass burning and fossil fuel combustion/ industrial emissions. Automatic sun/sky radiometers at each site measured spectral aerosol optical depth in 7 wavelengths from 340 to 1020 nm and combined with directional radiances in the almucantar, retrievals were made of spectral single scattering albedo and aerosol size distributions. Angstrom exponents, size distributions and spectral single scattering albedo of primarily biomass burning aerosols at rural sites are compared to measurements made at AERONET sites in other major biomass burning regions in tropical southern Africa, South America, and in boreal forest regions. Additionally, the aerosol single scattering albedo and size distributions measured in Bangkok, Thailand are compared with those measured at other urban sites globally. The influences of aerosols originating from other regions outside of Southeast Asia are analyzed using trajectory analyses. Specifically, cases of aerosol transport and mixing from Southern China and from India are presented.

In vitro transcription in the presence of DNA oligonucleotides can generate strong anomalous initiation sites.

PubMed

Chow, C W; Clark, M P; Rinaldo, J E; Chalkley, R

1996-03-01

In the present study, we have explored an unexpected observation in transcription initiation that is mediated by single-stranded oligonucleotides. Initially, our goal was to understand the function of different upstream regulatory elements/initiation sites in the rat xanthine dehydrogenase/oxidase (XDH/XO) promoter. We performed in vitro transcription with HeLa nuclear extracts in the presence of different double-stranded oligonucleotides against upstream elements as competitors. A new and unusual transcription initiation site was detected by primer extension. This new initiation site maps to the downstream region of the corresponding competitor. Subsequent analyses have indicated that the induction of a new transcription initiation site is anomalous which is due to the presence of a small amount of single-stranded oligonucleotide in the competitor. We found that this anomalous initiation site is insensitive to the orientation of the promoter and requires only a small amount of single-stranded oligonucleotide (< 2-fold molar excess relative to template). We surmise that a complementary interaction between the single-stranded oligonucleotide and transiently denatured promoter template may be responsible for this sequence-specific transcription initiation artifact. To study the regulation of transcription initiation by in vitro transcription approaches, we propose that one should probe the effect of removing transacting factors by adding an excess of a cognate oligonucleotide which does not bear exact sequence identity to the template.

Characterization of recombinant monoclonal antibody variants detected by hydrophobic interaction chromatography and imaged capillary isoelectric focusing electrophoresis.

PubMed

King, Cory; Patel, Rekha; Ponniah, Gomathinayagam; Nowak, Christine; Neill, Alyssa; Gu, Zhenyu; Liu, Hongcheng

2018-05-15

In-depth characterization of the commonly observed variants is critical to the successful development of recombinant monoclonal antibody therapeutics. Multiple peaks of a recombinant monoclonal antibody were observed when analyzed by hydrophobic interaction chromatography and imaged capillary isoelectric focusing. The potential modification causing the heterogeneity was localized to F(ab')2 region by analyzing the antibody after IdeS digestion using hydrophobic interaction chromatography. LC-MS analysis identified asparagine deamidation as the root cause of the observed multiple variants. While the isoelectric focusing method is expected to separate deamidated species, the similar profile observed in hydrophobic interaction chromatography indicates that the single site deamidation caused differences in hydrophobicity. Forced degradation demonstrated that the susceptible asparagine residue is highly exposed, which is expected as it is located in the light chain complementarity determining region. Deamidation of this single site decreased the mAb binding affinity to its specific antigen. Copyright © 2018 Elsevier B.V. All rights reserved.

Site Variability in Regulatory Oversight for an International Study of Pediatric Sepsis.

PubMed

Michelson, Kelly N; Reubenson, Gary; Weiss, Scott L; Fitzgerald, Julie C; Ackerman, Kate K; Christie, LeeAnn; Bush, Jenny L; Nadkarni, Vinay M; Thomas, Neal J; Schreiner, Mark S

2018-04-01

Duplicative institutional review board/research ethics committee review for multicenter studies may impose administrative burdens and inefficiencies affecting study implementation and quality. Understanding variability in site-specific institutional review board/research ethics committee assessment and barriers to using a single review committee (an increasingly proposed solution) can inform a more efficient process. We provide needed data about the regulatory oversight process for the Sepsis PRevalence, OUtcomes, and Therapies multicenter point prevalence study. Survey. Sites invited to participate in Sepsis PRevalence, OUtcomes, and Therapies. Investigators at sites that expressed interest and/or participated in Sepsis PRevalence, OUtcomes, and Therapies. None. Using an electronic survey, we collected data about 1) logistics of protocol submission, 2) institutional review board/research ethics committee requested modifications, and 3) use of a single institutional review board (for U.S. sites). We collected surveys from 104 of 167 sites (62%). Of the 97 sites that submitted the protocol for institutional review board/research ethics committee review, 34% conducted full board review, 54% expedited review, and 4% considered the study exempt. Time to institutional review board/research ethics committee approval required a median of 34 (range 3-186) days, which took longer at sites that required protocol modifications (median [interquartile range] 50 d [35-131 d] vs 32 d [14-54 d)]; p = 0.02). Enrollment was delayed at eight sites due to prolonged (> 50 d) time to approval. Of 49 U.S. sites, 43% considered using a single institutional review board, but only 18% utilized this option. Time to final approval for U.S. sites using the single institutional review board was 62 days (interquartile range, 34-70 d) compared with 34 days (interquartile range, 15-54 d) for nonsingle institutional review board sites (p = 0.16). Variability in regulatory oversight was evident for this minimal-risk observational research study, most notably in the category of type of review conducted. Duplicative review prolonged time to protocol approval at some sites. Use of a single institutional review board for U.S. sites was rare and did not improve efficiency of protocol approval. Suggestions for minimizing these challenges are provided.

Single-particle speciation of alkylamines in ambient aerosol at five European sites.

PubMed

Healy, Robert M; Evans, Greg J; Murphy, Michael; Sierau, Berko; Arndt, Jovanna; McGillicuddy, Eoin; O'Connor, Ian P; Sodeau, John R; Wenger, John C

2015-08-01

Alkylamines are associated with both natural and anthropogenic sources and have been detected in ambient aerosol in a variety of environments. However, little is known about the ubiquity or relative abundance of these species in Europe. In this work, ambient single-particle mass spectra collected at five sampling sites across Europe have been analysed for their alkylamine content. The aerosol time-of-flight mass spectrometer (ATOFMS) data used were collected in Ireland (Cork), France (Paris, Dunkirk and Corsica) and Switzerland (Zurich) between 2008 and 2013. Each dataset was queried for mass spectral marker ions associated with the following ambient alkylamines: dimethylamine (DMA), trimethylamine (TMA), diethylamine (DEA), triethylamine (TEA), dipropylamine (DPA) and tripropylamine (TPA). The fraction of ambient particles that contained detectable alkylamines ranged from 1 to 17 % depending on location, with the highest fractions observed in Paris and Zurich in the winter months. The lowest fractions were observed at coastal sites, where the influence of animal husbandry-related alkylamine emissions is also expected to be lowest. TMA was the most ubiquitous particle phase alkylamine detected and was observed at all locations. Alkylamines were found to be internally mixed with both sulphate and nitrate for each dataset, suggesting that aminium salt formation may be important at all sites investigated. Interestingly, in Corsica, all alkylamine particles detected were also found to be internally mixed with methanesulphonic acid (MSA), indicating that aminium methanesulphonate salts may represent a component of marine ambient aerosol in the summer months. Internal mixing of alkylamines with sea salt was not observed, however. Alkylamine-containing particle composition was found to be reasonably homogeneous at each location, with the exception of the Corsica and Dunkirk sites, where two and four distinct mixing states were observed, respectively.

Cooperativity in Monomeric Enzymes with Single Ligand-Binding Sites

PubMed Central

Porter, Carol M.

2011-01-01

Cooperativity is widespread in biology. It empowers a variety of regulatory mechanisms and impacts both the kinetic and thermodynamic properties of macromolecular systems. Traditionally, cooperativity is viewed as requiring the participation of multiple, spatially distinct binding sites that communicate via ligand-induced structural rearrangements; however, cooperativity requires neither multiple ligand binding events nor multimeric assemblies. An underappreciated manifestation of cooperativity has been observed in the non-Michaelis-Menten kinetic response of certain monomeric enzymes that possess only a single ligand-binding site. In this review, we present an overview of kinetic cooperativity in monomeric enzymes. We discuss the primary mechanisms postulated to give rise to monomeric cooperativity and highlight modern experimental methods that could offer new insights into the nature of this phenomenon. We conclude with an updated list of single subunit enzymes that are suspected of displaying cooperativity, and a discussion of the biological significance of this unique kinetic response. PMID:22137502

Paired-pulse facilitation and depression at unitary synapses in rat hippocampus: quantal fluctuation affects subsequent release.

PubMed Central

Debanne, D; Guérineau, N C; Gähwiler, B H; Thompson, S M

1996-01-01

1. Excitatory synaptic transmission between pairs of monosynaptically coupled pyramidal cells was examined in rat hippocampal slice cultures. Action potentials were elicited in single CA3 pyramidal cells impaled with microelectrodes and unitary excitatory postsynaptic currents (EPSCs) were recorded in whole-cell voltage-clamped CA1 or CA3 cells. 2. The amplitude of successive unitary EPSCs in response to single action potentials varied. The amplitude of EPSCs was altered by adenosine or changes in the [Mg2+]/[CA2+] ratio. We conclude that single action potentials triggered the release of multiple quanta of glutamate. 3. When two action potentials were elicited in the presynaptic cell, the amplitude of the second EPSC was inversely related to the amplitude of the first. Paired-pulse facilitation (PPF) was observed when the first EPSC was small, i.e. the second EPSC was larger than the first, whereas paired-pulse depression (PPD) was observed when the first EPSC was large. 4. The number of trials displaying PPD was greater when release probability was increased, and smaller when release probability was decreased. 5. PPD was not postsynaptically mediated because it was unaffected by decreasing ionic flux with 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) or receptor desensitization with aniracetam. 6. PPF was maximal at an interstimulus interval of 70 ms and recovered within 500 ms. Recovery from PPD occurred within 5 s. 7. We propose that multiple release sites are formed by the axon of a CA3 pyramidal cell and a single postsynaptic CA1 or CA3 cell. PPF is observed if the first action potential fails to release transmitter at most release sites. PPD is observed if the first action potential successfully triggers release at most release sites. 8. Our observations of PPF are consistent with the residual calcium hypothesis. We conclude that PPD results from a decrease in quantal content, perhaps due to short-term depletion of readily releasable vesicles. PMID:9011608

Observation of sediment resuspension in Old Tampa Bay, Florida

USGS Publications Warehouse

Schoellhamer, David H.; ,

1990-01-01

Equipment and methodology have been developed to monitor sediment resuspension at two sites in Old Tampa Bay. Velocities are measured with electromagnetic current meters and suspended solids and turbidity are monitored with optical backscatterance sensors. In late November 1989, a vertical array of instrument pairs was deployed from a permanent platform at a deep-water site, and a submersible instrument package with a single pair of instruments was deployed at a shallow-water site. Wind waves caused resuspension at the shallow-water site, but not at the deeper platform site, and spring tidal currents did not cause resuspension at either site.

High ionic strength narrows the population of sites participating in protein ion-exchange adsorption: A single-molecule study

PubMed Central

Kisley, Lydia; Chen, Jixin; Mansur, Andrea P.; Dominguez-Medina, Sergio; Kulla, Eliona; Kang, Marci; Shuang, Bo; Kourentzi, Katerina; Poongavanam, Mohan-Vivekanandan; Dhamane, Sagar; Willson, Richard C.; Landes, Christy F.

2014-01-01

The retention and elution of proteins in ion-exchange chromatography is routinely controlled by adjusting the mobile phase salt concentration. It has repeatedly been observed, as judged from adsorption isotherms, that the apparent heterogeneity of adsorption is lower at more-eluting, higher ionic strength. Here, we present an investigation into the mechanism of this phenomenon using a single-molecule, super-resolution imaging technique called motion-blur Points Accumulation for Imaging in Nanoscale Topography (mbPAINT). We observed that the number of functional adsorption sites was smaller at high ionic strength and that these sites had reduced desorption kinetic heterogeneity, and thus narrower predicted elution profiles, for the anion-exchange adsorption of α-lactalbumin on an agarose-supported, clustered-charge ligand stationary phase. Explanations for the narrowing of the functional population such as inter-protein interactions and protein or support structural changes were investigated through kinetic analysis, circular dichroism spectroscopy, and microscopy of agarose microbeads, respectively. The results suggest the reduction of heterogeneity is due to both electrostatic screening between the protein and ligand and tuning the steric availability within the agarose support. Overall, we have shown that single molecule spectroscopy can aid in understanding the influence of ionic strength on the population of functional adsorbent sites participating in the ion-exchange chromatographic separation of proteins. PMID:24751557

Electron interactions, spin-orbit coupling, intersite correlations in pyrochlore iridates: a comparison of single-site and cluster calculations

NASA Astrophysics Data System (ADS)

Wang, Runzhi; Go, Ara; Millis, Andrew

Pyrochlore iridates (R2 Ir2O7) are studied using density functional theory plus single-site and cluster dynamical mean-field theory (DFT+DMFT). The calculations include spin-orbit coupling. Significant differences between the single-site and cluster calculations are found. The single-site approximation fails to account for the properties of the paramagnetic insulator phase, in particular predicting a larger gap than found in experiments, while cluster calculations yield gaps consistent with transport data. A ground-state phase diagram is computed. Paramagnetic metal, metallic all-in/all-out (AIAO) and insulating AIAO phases are found. Tilted Weyl cones are observed in the AIAO metallic phase for a relatively wide range of interaction strength. Our paramagnetic calculations predict almost identical behaviors for the Y and Eu compound, conflicting with the strong material dependence reported in experiments. Inclusion of magnetic order restores the material difference. The physical origin of the difference is discussed. The results indicate that intersite effects, most likely of antiferromagnetic origin, play an important role in studying the physics of pyrochlore iridates. This work is supported by DOE-ER046169.

Single-site neural tube closure in human embryos revisited.

PubMed

de Bakker, Bernadette S; Driessen, Stan; Boukens, Bastiaan J D; van den Hoff, Maurice J B; Oostra, Roelof-Jan

2017-10-01

Since the multi-site closure theory was first proposed in 1991 as explanation for the preferential localizations of neural tube defects, the closure of the neural tube has been debated. Although the multi-site closure theory is much cited in clinical literature, single-site closure is most apparent in literature concerning embryology. Inspired by Victor Hamburgers (1900-2001) statement that "our real teacher has been and still is the embryo, who is, incidentally, the only teacher who is always right", we decided to critically review both theories of neural tube closure. To verify the theories of closure, we studied serial histological sections of 10 mouse embryos between 8.5 and 9.5 days of gestation and 18 human embryos of the Carnegie collection between Carnegie stage 9 (19-21 days) and 13 (28-32 days). Neural tube closure was histologically defined by the neuroepithelial remodeling of the two adjoining neural fold tips in the midline. We did not observe multiple fusion sites in neither mouse nor human embryos. A meta-analysis of case reports on neural tube defects showed that defects can occur at any level of the neural axis. Our data indicate that the human neural tube fuses at a single site and, therefore, we propose to reinstate the single-site closure theory for neural tube closure. We showed that neural tube defects are not restricted to a specific location, thereby refuting the reasoning underlying the multi-site closure theory. Clin. Anat. 30:988-999, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

uvby photometry of theta Tucanae

NASA Astrophysics Data System (ADS)

Sterken, C.; Spoon, H.

2017-12-01

theta Tucanae (HR 139, V=6.11, A7 IV) is a binary with a delta Scuti primary that was the subject of several photometric monitoring campaigns during the 1970s and again in the 1990s. The data presented in this paper were collected during an observing campaign from mid-September to the end of October 1993 at ESO La Silla, Chile, using the simultaneous Stroemgren uvby photometer at the SAT telescope during 25 partial nights. We present a time series of 1432 four-colour extinction-corrected magnitudes in the SAT instrumental system. This collection of data forms a homogeneous and contiguous dataset, obtained in one single instrumental setup, at one single observing site using one single observing protocol, and with centralized data reduction.

Multi-Genetic Marker Approach and Spatio-Temporal Analysis Suggest There Is a Single Panmictic Population of Swordfish Xiphias gladius in the Indian Ocean

PubMed Central

Muths, Delphine; Le Couls, Sarah; Evano, Hugues; Grewe, Peter; Bourjea, Jerome

2013-01-01

Genetic population structure of swordfish Xiphias gladius was examined based on 2231 individual samples, collected mainly between 2009 and 2010, among three major sampling areas within the Indian Ocean (IO; twelve distinct sites), Atlantic (two sites) and Pacific (one site) Oceans using analysis of nineteen microsatellite loci (n = 2146) and mitochondrial ND2 sequences (n = 2001) data. Sample collection was stratified in time and space in order to investigate the stability of the genetic structure observed with a special focus on the South West Indian Ocean. Significant AMOVA variance was observed for both markers indicating genetic population subdivision was present between oceans. Overall value of F-statistics for ND2 sequences confirmed that Atlantic and Indian Oceans swordfish represent two distinct genetic stocks. Indo-Pacific differentiation was also significant but lower than that observed between Atlantic and Indian Oceans. However, microsatellite F-statistics failed to reveal structure even at the inter-oceanic scale, indicating that resolving power of our microsatellite loci was insufficient for detecting population subdivision. At the scale of the Indian Ocean, results obtained from both markers are consistent with swordfish belonging to a single unique panmictic population. Analyses partitioned by sampling area, season, or sex also failed to identify any clear structure within this ocean. Such large spatial and temporal homogeneity of genetic structure, observed for such a large highly mobile pelagic species, suggests as satisfactory to consider swordfish as a single panmictic population in the Indian Ocean. PMID:23717447

Structural characterization of framework-gas interactions in the metal-organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction.

PubMed

Gonzalez, Miguel I; Mason, Jarad A; Bloch, Eric D; Teat, Simon J; Gagnon, Kevin J; Morrison, Gregory Y; Queen, Wendy L; Long, Jeffrey R

2017-06-01

The crystallographic characterization of framework-guest interactions in metal-organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH 4 , N 2 , O 2 , Ar, and P 4 adsorption in Co 2 (dobdc) (dobdc 4- = 2,5-dioxido-1,4-benzenedicarboxylate), a metal-organic framework bearing coordinatively unsaturated cobalt(ii) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(ii) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal-organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co-CH 4 and Co-Ar interactions observed in Co 2 (dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal-CH 4 interaction and the first crystallographically characterized metal-Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(ii) sites in Co 2 (dobdc), with differential enthalpies of adsorption as weak as -17(1) kJ mol -1 (for Ar). Moreover, the structures of Co 2 (dobdc)·3.8N 2 , Co 2 (dobdc)·5.9O 2 , and Co 2 (dobdc)·2.0Ar reveal the location of secondary (N 2 , O 2 , and Ar) and tertiary (O 2 ) binding sites in Co 2 (dobdc), while high-pressure CO 2 , CO, CH 4 , N 2 , and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures.

Experimental study on bubble dynamics and wall heat transfer arising from a single nucleation site at subcooled flow boiling conditions – Part 2: Data analysis on sliding bubble characteristics and associated wall heat transfer

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

Yooa, Junsoo; Estrada-Perez, Carlos E.; Hassan, Yassin A.

In this second of two companion papers presents an analysis of sliding bubble and wall heat transfer parameters measured during subcooled boiling in a square, vertical, upward flow channel. Bubbles were generated only from a single nucleation site for better observation of both the sliding bubbles’ characteristics and their impact on wall heat transfer through optical measurement techniques. Specific interests include: (i) bubbles departure and subsequent growth while sliding, (ii) bubbles release frequency, (iii) coalescence of sliding bubbles, (iv) sliding bubbles velocity, (v) bubbles size distribution and (vi) wall heat transfer influenced by sliding bubbles. Our results showed that slidingmore » bubbles involve two distinct growth behaviors: (i) at low mass fluxes, sliding bubbles grew fast near the nucleation site, subsequently shrank, and then grew again, (ii) as mass flux increased, however, sliding bubbles grew more steadily. The bubbles originating from the single nucleation site coalesced frequently while sliding, which showed close relation with bubbles release frequency. The sliding bubble velocity near the nucleation site consistently decreased by increasing mass flux, while the observation often became reversed as the bubbles slid downstream due to the effect of interfacial drag. The sliding bubbles moved faster than the local liquid (i.e., ur<0) at low mass flux conditions, but it became reversed as the mass flux increased. The size distribution of sliding bubbles followed Gaussian distribution well both near and far from the nucleation site. The standard deviation of bubble size varied insignificantly through sliding compared to the changes in mean bubble size. Lastly, the sliding bubbles enhanced the wall heat transfer and the effect became more noticeable as inlet subcooling/mass flux decreased or wall heat flux increased. Particularly, the sliding bubble characteristics such as bubble growth behavior observed near the nucleation site played a dominant role in determining the ultimate level of wall heat transfer enhancement within the test channel.« less

Experimental study on bubble dynamics and wall heat transfer arising from a single nucleation site at subcooled flow boiling conditions – Part 2: Data analysis on sliding bubble characteristics and associated wall heat transfer

DOE PAGES

Yooa, Junsoo; Estrada-Perez, Carlos E.; Hassan, Yassin A.

2016-04-28

In this second of two companion papers presents an analysis of sliding bubble and wall heat transfer parameters measured during subcooled boiling in a square, vertical, upward flow channel. Bubbles were generated only from a single nucleation site for better observation of both the sliding bubbles’ characteristics and their impact on wall heat transfer through optical measurement techniques. Specific interests include: (i) bubbles departure and subsequent growth while sliding, (ii) bubbles release frequency, (iii) coalescence of sliding bubbles, (iv) sliding bubbles velocity, (v) bubbles size distribution and (vi) wall heat transfer influenced by sliding bubbles. Our results showed that slidingmore » bubbles involve two distinct growth behaviors: (i) at low mass fluxes, sliding bubbles grew fast near the nucleation site, subsequently shrank, and then grew again, (ii) as mass flux increased, however, sliding bubbles grew more steadily. The bubbles originating from the single nucleation site coalesced frequently while sliding, which showed close relation with bubbles release frequency. The sliding bubble velocity near the nucleation site consistently decreased by increasing mass flux, while the observation often became reversed as the bubbles slid downstream due to the effect of interfacial drag. The sliding bubbles moved faster than the local liquid (i.e., ur<0) at low mass flux conditions, but it became reversed as the mass flux increased. The size distribution of sliding bubbles followed Gaussian distribution well both near and far from the nucleation site. The standard deviation of bubble size varied insignificantly through sliding compared to the changes in mean bubble size. Lastly, the sliding bubbles enhanced the wall heat transfer and the effect became more noticeable as inlet subcooling/mass flux decreased or wall heat flux increased. Particularly, the sliding bubble characteristics such as bubble growth behavior observed near the nucleation site played a dominant role in determining the ultimate level of wall heat transfer enhancement within the test channel.« less

Stretching single atom contacts at multiple subatomic step-length.

PubMed

Wei, Yi-Min; Liang, Jing-Hong; Chen, Zhao-Bin; Zhou, Xiao-Shun; Mao, Bing-Wei; Oviedo, Oscar A; Leiva, Ezequiel P M

2013-08-14

This work describes jump-to-contact STM-break junction experiments leading to novel statistical distribution of last-step length associated with conductance of a single atom contact. Last-step length histograms are observed with up to five for Fe and three for Cu peaks at integral multiples close to 0.075 nm, a subatomic distance. A model is proposed in terms of gliding from a fcc hollow-site to a hcp hollow-site of adjacent atomic planes at 1/3 regular layer spacing along with tip stretching to account for the multiple subatomic step-length behavior.

Stereoscopically Observing Manipulative Actions

PubMed Central

Ferri, S.; Pauwels, K.; Rizzolatti, G.; Orban, G. A.

2016-01-01

The purpose of this study was to investigate the contribution of stereopsis to the processing of observed manipulative actions. To this end, we first combined the factors “stimulus type” (action, static control, and dynamic control), “stereopsis” (present, absent) and “viewpoint” (frontal, lateral) into a single design. Four sites in premotor, retro-insular (2) and parietal cortex operated specifically when actions were viewed stereoscopically and frontally. A second experiment clarified that the stereo-action-specific regions were driven by actions moving out of the frontoparallel plane, an effect amplified by frontal viewing in premotor cortex. Analysis of single voxels and their discriminatory power showed that the representation of action in the stereo-action-specific areas was more accurate when stereopsis was active. Further analyses showed that the 4 stereo-action-specific sites form a closed network converging onto the premotor node, which connects to parietal and occipitotemporal regions outside the network. Several of the specific sites are known to process vestibular signals, suggesting that the network combines observed actions in peripersonal space with gravitational signals. These findings have wider implications for the function of premotor cortex and the role of stereopsis in human behavior. PMID:27252350

Stereoscopically Observing Manipulative Actions.

PubMed

Ferri, S; Pauwels, K; Rizzolatti, G; Orban, G A

2016-08-01

The purpose of this study was to investigate the contribution of stereopsis to the processing of observed manipulative actions. To this end, we first combined the factors "stimulus type" (action, static control, and dynamic control), "stereopsis" (present, absent) and "viewpoint" (frontal, lateral) into a single design. Four sites in premotor, retro-insular (2) and parietal cortex operated specifically when actions were viewed stereoscopically and frontally. A second experiment clarified that the stereo-action-specific regions were driven by actions moving out of the frontoparallel plane, an effect amplified by frontal viewing in premotor cortex. Analysis of single voxels and their discriminatory power showed that the representation of action in the stereo-action-specific areas was more accurate when stereopsis was active. Further analyses showed that the 4 stereo-action-specific sites form a closed network converging onto the premotor node, which connects to parietal and occipitotemporal regions outside the network. Several of the specific sites are known to process vestibular signals, suggesting that the network combines observed actions in peripersonal space with gravitational signals. These findings have wider implications for the function of premotor cortex and the role of stereopsis in human behavior. © The Author 2016. Published by Oxford University Press.

Multisite rainfall downscaling and disaggregation in a tropical urban area

NASA Astrophysics Data System (ADS)

Lu, Y.; Qin, X. S.

2014-02-01

A systematic downscaling-disaggregation study was conducted over Singapore Island, with an aim to generate high spatial and temporal resolution rainfall data under future climate-change conditions. The study consisted of two major components. The first part was to perform an inter-comparison of various alternatives of downscaling and disaggregation methods based on observed data. This included (i) single-site generalized linear model (GLM) plus K-nearest neighbor (KNN) (S-G-K) vs. multisite GLM (M-G) for spatial downscaling, (ii) HYETOS vs. KNN for single-site disaggregation, and (iii) KNN vs. MuDRain (Multivariate Rainfall Disaggregation tool) for multisite disaggregation. The results revealed that, for multisite downscaling, M-G performs better than S-G-K in covering the observed data with a lower RMSE value; for single-site disaggregation, KNN could better keep the basic statistics (i.e. standard deviation, lag-1 autocorrelation and probability of wet hour) than HYETOS; for multisite disaggregation, MuDRain outperformed KNN in fitting interstation correlations. In the second part of the study, an integrated downscaling-disaggregation framework based on M-G, KNN, and MuDRain was used to generate hourly rainfall at multiple sites. The results indicated that the downscaled and disaggregated rainfall data based on multiple ensembles from HadCM3 for the period from 1980 to 2010 could well cover the observed mean rainfall amount and extreme data, and also reasonably keep the spatial correlations both at daily and hourly timescales. The framework was also used to project future rainfall conditions under HadCM3 SRES A2 and B2 scenarios. It was indicated that the annual rainfall amount could reduce up to 5% at the end of this century, but the rainfall of wet season and extreme hourly rainfall could notably increase.

Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

PubMed Central

Sheng, Gang; Gogakos, Tasos; Wang, Jiuyu; Zhao, Hongtu; Serganov, Artem; Juranek, Stefan

2017-01-01

Abstract We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6’U7’ and 6’A7’ on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6’N7’ bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson–Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction. PMID:28911094

Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites

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

Derebe, Mehabaw G.; Sauer, David B.; Zeng, Weizhong

2015-11-30

Selective ion conduction across ion channel pores is central to cellular physiology. To understand the underlying principles of ion selectivity in tetrameric cation channels, we engineered a set of cation channel pores based on the nonselective NaK channel and determined their structures to high resolution. These structures showcase an ensemble of selectivity filters with a various number of contiguous ion binding sites ranging from 2 to 4, with each individual site maintaining a geometry and ligand environment virtually identical to that of equivalent sites in K{sup +} channel selectivity filters. Combined with single channel electrophysiology, we show that only themore » channel with four ion binding sites is K{sup +} selective, whereas those with two or three are nonselective and permeate Na{sup +} and K{sup +} equally well. These observations strongly suggest that the number of contiguous ion binding sites in a single file is the key determinant of the channel's selectivity properties and the presence of four sites in K{sup +} channels is essential for highly selective and efficient permeation of K{sup +} ions.« less

Magnetic properties of single-phase MnBi grown from MnBi{sub 49} melt

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

Xiao, X. F.; Si, P. Z., E-mail: pzsi@cjlu.edu.cn; Feng, H.

2014-05-07

The single-phase NiAs-type MnBi, embedded in Bi matrix, was grown from homogeneous MnBi{sub 49} melt at low temperatures to prevent the formation of Mn{sub 1.08}Bi. An abrupt magnetization change was observed at ∼240 K. The origin of this change was ascribed to the movement of the Mn atoms between the regular sites and the interstitial sites in the MnBi lattices. The splitting of the x-ray photoelectron lines of MnBi indicates the presence of two binding states of Mn atoms, one of which was ascribed to interstitial Mn atoms. A large coercivity up to 1.79 T at 400 K was observed in the as-grownmore » bulk isotropic MnBi alloys.« less

Diffusion, capture and recycling of SCAR/WAVE and Arp2/3 complexes observed in cells by single-molecule imaging.

PubMed

Millius, Arthur; Watanabe, Naoki; Weiner, Orion D

2012-03-01

The SCAR/WAVE complex drives lamellipodium formation by enhancing actin nucleation by the Arp2/3 complex. Phosphoinositides and Rac activate the SCAR/WAVE complex, but how SCAR/WAVE and Arp2/3 complexes converge at sites of nucleation is unknown. We analyzed the single-molecule dynamics of WAVE2 and p40 (subunits of the SCAR/WAVE and Arp2/3 complexes, respectively) in XTC cells. We observed lateral diffusion of both proteins and captured the transition of p40 from diffusion to network incorporation. These results suggest that a diffusive 2D search facilitates binding of the Arp2/3 complex to actin filaments necessary for nucleation. After nucleation, the Arp2/3 complex integrates into the actin network and undergoes retrograde flow, which results in its broad distribution throughout the lamellipodium. By contrast, the SCAR/WAVE complex is more restricted to the cell periphery. However, with single-molecule imaging, we also observed WAVE2 molecules undergoing retrograde motion. WAVE2 and p40 have nearly identical speeds, lifetimes and sites of network incorporation. Inhibition of actin retrograde flow does not prevent WAVE2 association and disassociation with the membrane but does inhibit WAVE2 removal from the actin cortex. Our results suggest that membrane binding and diffusion expedites the recruitment of nucleation factors to a nucleation site independent of actin assembly, but after network incorporation, ongoing actin polymerization facilitates recycling of SCAR/WAVE and Arp2/3 complexes.

Diffusion, capture and recycling of SCAR/WAVE and Arp2/3 complexes observed in cells by single-molecule imaging

PubMed Central

Millius, Arthur; Watanabe, Naoki; Weiner, Orion D.

2012-01-01

The SCAR/WAVE complex drives lamellipodium formation by enhancing actin nucleation by the Arp2/3 complex. Phosphoinositides and Rac activate the SCAR/WAVE complex, but how SCAR/WAVE and Arp2/3 complexes converge at sites of nucleation is unknown. We analyzed the single-molecule dynamics of WAVE2 and p40 (subunits of the SCAR/WAVE and Arp2/3 complexes, respectively) in XTC cells. We observed lateral diffusion of both proteins and captured the transition of p40 from diffusion to network incorporation. These results suggest that a diffusive 2D search facilitates binding of the Arp2/3 complex to actin filaments necessary for nucleation. After nucleation, the Arp2/3 complex integrates into the actin network and undergoes retrograde flow, which results in its broad distribution throughout the lamellipodium. By contrast, the SCAR/WAVE complex is more restricted to the cell periphery. However, with single-molecule imaging, we also observed WAVE2 molecules undergoing retrograde motion. WAVE2 and p40 have nearly identical speeds, lifetimes and sites of network incorporation. Inhibition of actin retrograde flow does not prevent WAVE2 association and disassociation with the membrane but does inhibit WAVE2 removal from the actin cortex. Our results suggest that membrane binding and diffusion expedites the recruitment of nucleation factors to a nucleation site independent of actin assembly, but after network incorporation, ongoing actin polymerization facilitates recycling of SCAR/WAVE and Arp2/3 complexes. PMID:22349699

Single-Station Sigma for the Iranian Strong Motion Stations

NASA Astrophysics Data System (ADS)

Zafarani, H.; Soghrat, M. R.

2017-11-01

In development of ground motion prediction equations (GMPEs), the residuals are assumed to have a log-normal distribution with a zero mean and a standard deviation, designated as sigma. Sigma has significant effect on evaluation of seismic hazard for designing important infrastructures such as nuclear power plants and dams. Both aleatory and epistemic uncertainties are involved in the sigma parameter. However, ground-motion observations over long time periods are not available at specific sites and the GMPEs have been derived using observed data from multiple sites for a small number of well-recorded earthquakes. Therefore, sigma is dominantly related to the statistics of the spatial variability of ground motion instead of temporal variability at a single point (ergodic assumption). The main purpose of this study is to reduce the variability of the residuals so as to handle it as epistemic uncertainty. In this regard, it is tried to partially apply the non-ergodic assumption by removing repeatable site effects from total variability of six GMPEs driven from the local, Europe-Middle East and worldwide data. For this purpose, we used 1837 acceleration time histories from 374 shallow earthquakes with moment magnitudes ranging from M w 4.0 to 7.3 recorded at 370 stations with at least two recordings per station. According to estimated single-station sigma for the Iranian strong motion stations, the ratio of event-corrected single-station standard deviation ( Φ ss) to within-event standard deviation ( Φ) is about 0.75. In other words, removing the ergodic assumption on site response resulted in 25% reduction of the within-event standard deviation that reduced the total standard deviation by about 15%.

Characteristics of the first stage of constructing the Hoabinh Dam in Vietnam

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

Bogachenko, P.T.; Godunov, B.I.; Phunc Ne, T.

1985-06-01

As a result of an analysis of the data, investigations, and on-site observations at the Hoa-Binh Dam, Vietnam, the authors conclude: infilling of the rock mass with sand, successful for the Aswan dam, cannot be mechanically transferred to other dams; the possibility of using the energy of the river flow for removing low-quality soils in large amounts from the foundation of rock-fill dams by regulating the sequence of dumping the elements of the dam was confirmed in model investigations and successfully accomplished in the construction of the HoaBinh dam; at the site of the Hoa-Binh dam, observations of the dumpingmore » of the sand-gravel soil into water into a high shoulder did not reveal segregation of this soil, however, the data from investigations in a single borehole contradict the observations -- further on-site observation must therefore be made.« less

A Naturalistic Observational Study of Informal Segregation: Seating Patterns in Lectures

ERIC Educational Resources Information Center

Koen, Jennifer; Durrheim, Kevin

2010-01-01

In spite of the removal of legislated racial segregation, a number of observational studies in South Africa and elsewhere have shown that "informal," nonlegislated segregation persists in spaces of everyday interaction. Most of these have been case studies of segregation at single sites. The authors seek to quantify segregation in a…

Single α-particle irradiation permits real-time visualization of RNF8 accumulation at DNA damaged sites

NASA Astrophysics Data System (ADS)

Muggiolu, Giovanna; Pomorski, Michal; Claverie, Gérard; Berthet, Guillaume; Mer-Calfati, Christine; Saada, Samuel; Devès, Guillaume; Simon, Marina; Seznec, Hervé; Barberet, Philippe

2017-01-01

As well as being a significant source of environmental radiation exposure, α-particles are increasingly considered for use in targeted radiation therapy. A better understanding of α-particle induced damage at the DNA scale can be achieved by following their tracks in real-time in targeted living cells. Focused α-particle microbeams can facilitate this but, due to their low energy (up to a few MeV) and limited range, α-particles detection, delivery, and follow-up observations of radiation-induced damage remain difficult. In this study, we developed a thin Boron-doped Nano-Crystalline Diamond membrane that allows reliable single α-particles detection and single cell irradiation with negligible beam scattering. The radiation-induced responses of single 3 MeV α-particles delivered with focused microbeam are visualized in situ over thirty minutes after irradiation by the accumulation of the GFP-tagged RNF8 protein at DNA damaged sites.

ADP binding to TF1 and its subunits induces ultraviolet spectral changes.

PubMed

Hisabori, T; Yoshida, M; Sakurai, H

1986-09-01

Adenine nucleotide binding sites on the coupling factor ATPase of thermophilic bacterium PS3 (TF1) were investigated by UV spectroscopy and by equilibrium dialysis. When ADP was mixed with TF1 in the presence and in the absence of Mg2+, an UV absorbance change was induced (t1/2 approximately 1 min) with a peak at about 278 nm and a trough at about 250 nm. Similar spectral changes were induced by ADP with the isolated beta subunits in the presence and in the absence of Mg2+, and with the isolated alpha subunits in the presence of Mg2+ although the magnitudes of the changes were different. From equilibrium dialysis measurement we identified two classes of nucleotide binding sites in TF1 in the presence of Mg2+, three high-affinity sites (Kd = 61 nM) and three low-affinity sites (Kd = 87 microM). In the absence of Mg2+, TF1 has one high-affinity site (Kd less than 10 nM) and five low-affinity sites (Kd = 100 microM). Moreover, we found a single Mg2+-dependent ADP binding site on the isolated alpha subunit and a single Mg2+-independent ADP binding site on the isolated beta subunit. From the above observations, we concluded that the three Mg2+-dependent high-affinity sites for ADP are located on the alpha subunit in TF1 and that the single high-affinity site is located on one of the beta subunits in TF1 in the absence of Mg2+.

Crystal growth of carbonate apatite using a CaCO3 flux.

PubMed

Suetsugu, Y; Tanaka, J

1999-09-01

Single crystals of carbonate apatite were grown using a CaCO3 flux under an Ar gas pressure of 55 MPa. The crystals obtained were observed by scanning electron microscopy, optical microscopy and X-ray diffraction. Electron probe microanalyses and thermal analyses were performed. CO3 ions in planar triangle form replaced both OH sites and PO4 tetrahedral sites in the apatite structure: in particular, the OH sites were perfectly substituted by CO3 ions using this method.

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.

Subepidermal moisture surrounding pressure ulcers in persons with a spinal cord injury: A pilot study

PubMed Central

Harrow, Jeffrey John; Mayrovitz, Harvey N.

2014-01-01

Objective Characterization of a non-invasive method of quantifying subepidermal moisture (SEM) surrounding stages III and IV pressure ulcers (PrUs) in spinal cord injury (SCI). Design Prospective, single-visit, single-rater, observational study, using repeated-measures analysis. Method Setting-inpatient units of one VA SCI Center. Participants Convenience sample of 16 subjects with SCI with stage III or IV PrUs over sacrum or ischium. Interventions Measurement with the MoistureMeter-D, a hand-held device using 300 MHz electromagnetic waves. Outcome measures Dielectric constant, a dimensionless number which increases with the moisture content. Each subject had a PrU site and a control site. Measurements were made at each site, on intact skin, at four points spaced angularly around the site, in triplicate. Results (1) Short-term, single-rater relative error was 2.5%. (2) Order effect: first readings were higher than second readings in 55 of 64 measurement sets. Order effect was significant for control sites (P < 0.0001) but not for PrU sites. (3) Angular effect: SEM varied by angle at the PrU sites (P < 0.01); 12 o'clock position the highest and 6 o'clock the lowest. (4) Ability to differentiate PrUs from intact skin: SEM at PrU sites was greater by 9.0% than control sites (P < 0.05). (5) Site effect: SEM was higher at sacral locations than ischial at control sites by 20% (P < 0.005). Conclusions SEM differentiates PrUs from intact skin. Future study designs must take into account order, angular, and site effects on this measure. This information will inform designers of future studies of SEM in healing of PrUs. PMID:25398030

Disorder in KHCO3 as studied by EPR and DTA in Cu2+ doped and gamma-irradiated single crystals

NASA Astrophysics Data System (ADS)

Koksal, F.; Karabulut, B.; Demir, D.; Icbudak, H.; Koseoglu, R.

2005-08-01

Kalicinite (KHCO3) single crystals were investigated by the electron paramagnetric resonance (EPR) technique in their Cu2+ doped and gamma- irradiated states. It is observed that the behavior of the spectrum is the same at ambient and low temperatures down to 113 K in consistence with the monoclinic symmetry of the crystal. However, when the temperature is increased to 313 K, only one site signals were observed at all orientations of the magnetic field for the Cu2+ doped samples as the site splitted signals overlap at this temperature. Furthermore, for the gamma-irradiated crystals, two sites were observed for the induced H(C)over dot O-3 and (C)over dot O-2(-) radicals at ambient temperature for an arbitrary orientation of the magnetic field. However, when the temperature is increased to 348 K, the signals due to the H(C)over dot O-3 radical overlap indicating only one site, but the signals due to (C)over dot O-2(-) the radical do not and continue to indicate the presence of the two sites. Therefore, we conclude that this one site transition at 313 K is due to the disordering of the proton vacancies, as the charge compensation of Cu2+ is fulfilled by K+ and proton holes. This indicates that the proton vacancies come to disorder at 313 K and the protons get disordered at 348 K. The differential thermal analysis results show two small endothermic peaks for the Cu2+ doped and gamma-irradiated samples at 313 and 348 K that were attributed to the disorder of the proton vacancies and protons, in consistency with the EPR results.

Luminescent Li-based metal-organic framework tailored for the selective detection of explosive nitroaromatic compounds: direct observation of interaction sites.

PubMed

Kim, Tae Kyung; Lee, Jae Hwa; Moon, Dohyun; Moon, Hoi Ri

2013-01-18

A luminescent lithium metal-organic framework (MOF) is constructed from the solvothermal reaction of Li(+) and a well-designed organic ligand, bis(4-carboxyphenyl)-N-methylamine (H(2)CPMA). A Li-based MOF can detect an explosive aromatic compound containing nitro groups as an explosophore, by showing a dramatic color change with concurrent luminescence quenching in the solid state. The detection sites are proven directly through single-crystal-to-single-crystal transformations, which show strong interactions between the aromatic rings of the electron-rich CPMA(2-) molecules and the electron-deficient nitrobenzene.

Observing single protein binding by optical transmission through a double nanohole aperture in a metal film

PubMed Central

Al Balushi, Ahmed A.; Zehtabi-Oskuie, Ana; Gordon, Reuven

2013-01-01

We experimentally demonstrate protein binding at the single particle level. A double nanohole (DNH) optical trap was used to hold onto a 20 nm biotin-coated polystyrene (PS) particle which subsequently is bound to streptavidin. Biotin-streptavidin binding has been detected by an increase in the optical transmission through the DNH. Similar optical transmission behavior was not observed when streptavidin binding sites where blocked by mixing streptavidin with excess biotin. Furthermore, interaction of non-functionalized PS particles with streptavidin did not induce a change in the optical transmission through the DNH. These results are promising as the DNH trap can make an excellent single molecule resolution sensor which would enable studying biomolecular interactions and dynamics at a single particle/molecule level. PMID:24049672

Evidence of a Weakly Absorbing Intermediate Mode of Aerosols in AERONET Data from Saharan and Sahelian Sites

NASA Technical Reports Server (NTRS)

Gianelli, Scott M.; Lacis, Andrew A.; Carlson, Barbara E.; Hameed, Sultan

2013-01-01

Accurate retrievals of aerosol size distribution are necessary to estimate aerosols' impact on climate and human health. The inversions of the Aerosol Robotic Network (AERONET) usually retrieve bimodal distributions. However, when the inversion is applied to Saharan and Sahelian dust, an additional mode of intermediate size between the coarse and fine modes is sometimes seen. This mode explains peculiarities in the behavior of the Angstrom exponent, along with the fine mode fraction retrieved using the spectral deconvolution algorithm, observed in a March 2006 dust storm. For this study, 15 AERONET sites in northern Africa and on the Atlantic are examined to determine the frequency and properties of the intermediate mode. The mode is observed most frequently at Ilorin in Nigeria. It is also observed at Capo Verde and multiple sites located within the Sahel but much less frequently at sites in the northern Sahara and the Canary Islands. The presence of the intermediate mode coincides with increases in Angstrom exponent, fine mode fraction, single-scattering albedo, and to a lesser extent percent sphericity. The Angstrom exponent decreases with increasing optical depth at most sites when the intermediate mode is present, but the fine mode fraction does not. Single-scattering albedo does not steadily decrease with fine mode fraction when the intermediate mode is present, as it does in typical mixtures of dust and biomass-burning aerosols. Continued investigation is needed to further define the intermediate mode's properties, determine why it differs from most Saharan dust, and identify its climate and health effects.

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

Thein, Pyi Soe, E-mail: pyisoethein@yahoo.com; Geological Engineering Department, Gadjah Mada University, Yogyakarta; Pramumijoyo, Subagyo

In this study, we investigated the underground structure at Prambanan area, Yogyakarta. We performed single observations of microtremor at 124 sites in Prambanan area. The results enabled us to estimate the site-dependent shaking characteristics of earthquake ground motion. We also conducted 2-site bore holes investigation to gain a representative determination of the soil condition of subsurface structures in Prambanan. From the SPT of borehole observations, the prambanan area corresponds to relatively soil condition with Vs ≤ 298 m/s, the predominant periods due to horizontal vertical ratios (HVSRs) are in the range of 0.48 to 1.19 s and the frequency aremore » in the range of 0.95 to 1.92 Hz. By making these observations, we can obtain a relationship between the predominant periods, frequency and distribution of the first layer thickness of the sediment.« less

Microstructurally-sensitive fatigue crack nucleation in Ni-based single and oligo crystals

NASA Astrophysics Data System (ADS)

Chen, Bo; Jiang, Jun; Dunne, Fionn P. E.

2017-09-01

An integrated experimental, characterisation and computational crystal plasticity study of cyclic plastic beam loading has been carried out for nickel single crystal (CMSX4) and oligocrystal (MAR002) alloys in order to assess quantitatively the mechanistic drivers for fatigue crack nucleation. The experimentally validated modelling provides knowledge of key microstructural quantities (accumulated slip, stress and GND density) at experimentally observed fatigue crack nucleation sites and it is shown that while each of these quantities is potentially important in crack nucleation, none of them in its own right is sufficient to be predictive. However, the local (elastic) stored energy density, measured over a length scale determined by the density of SSDs and GNDs, has been shown to predict crack nucleation sites in the single and oligocrystals tests. In addition, once primary nucleated cracks develop and are represented in the crystal model using XFEM, the stored energy correctly identifies where secondary fatigue cracks are observed to nucleate in experiments. This (Griffith-Stroh type) quantity also correctly differentiates and explains intergranular and transgranular fatigue crack nucleation.

Molecular and kinetic determinants of local anaesthetic action on sodium channels.

PubMed

French, R J; Zamponi, G W; Sierralta, I E

1998-11-23

(1) Local anaesthetics (LA) rely for their clinical actions on state-dependent inhibition of voltage-dependent sodium channels. (2) Single, batrachoxin-modified sodium channels in planar lipid bilayers allow direct observation of drug-channel interactions. Two modes of inhibition of single-channel current are observed: fast block of the open channels and prolongation of a long-lived closed state, some of whose properties resemble those of the inactivated state of unmodified channels. (3) Analogues of different parts of the LA molecule separately mimic each blocking mode: amines--fast block, and water-soluble aromatics--closed state prolongation. (4) Interaction between a mu-conotoxin derivative and diethylammonium indicate an intrapore site of fast, open-state block. (5) Site-directed mutagenesis studies suggest that hydrophobic residues in transmembrane segment 6 of repeat domain 4 of sodium channels are critical for both LA binding and stabilization of the inactivated state.

CCl 4 chemistry on the magnetite selvedge of single-crystal hematite: competitive surface reactions

NASA Astrophysics Data System (ADS)

Adib, K.; Camillone, N., III; Fitts, J. P.; Rim, K. T.; Flynn, G. W.; Joyce, S. A.; Osgood, R. M., Jr.

2002-01-01

Temperature programmed reaction/desorption (TPR/D) studies were undertaken to characterize the surface chemistry which occurs between CCl 4 and the Fe 3O 4 (1 1 1) selvedge of single crystal α-Fe 2O 3 (0 0 0 1). Six separate desorption events are clearly observed and four desorbing species are identified: CCl 4, OCCl 2, C 2Cl 4 and FeCl 2. It is proposed that OCCl 2, CCl 4 and C 2Cl 4 are produced in reactions involving the same precursor, CCl 2. Three reaction paths compete for the CCl 2 precursor: oxygen atom abstraction (for OCCl 2), molecular recombinative desorption (for CCl 4) and associative desorption (for C 2Cl 4). During the TPR/D temperature ramp, the branching ratio is observed to depend upon temperature and the availability of reactive sites. The data are consistent with a rich site-dependent chemistry.

[Criteria of radical sector resection in mastopathy].

PubMed

Sidorenko, L N; Sokolovskiĭ, R M

1978-02-01

Statistical investigations of morphological structure in 2 groups of patients with localized forms of fibroadenomatosis (93 observations) have been carried out. Histological findings of the morphological picture have been received both within the localized fibroadenomatosis sites and beyond them. The character of the distribution of morphological forms has been shown to remain the same in all the sites of a single and in both mammary glands. Close relationship between the morphological picture in the localized sites and in so called "normal" sites of the mammae has been established. This proves the expedience of radical sectoral resection and the necessity of longlasting conservative treatment.

Early postoperative healing following buccal single flap approach to access intraosseous periodontal defects.

PubMed

Farina, Roberto; Simonelli, Anna; Rizzi, Alessandro; Pramstraller, Mattia; Cucchi, Alessandro; Trombelli, Leonardo

2013-07-01

This study aims to evaluate the early postoperative healing of papillary incision wounds and its association with (1) patient/site-related factors and technical (surgical) aspects as well as with (2) 6-month clinical outcomes following buccal single flap approach (SFA) in the treatment of intraosseous periodontal defects. Forty-three intraosseous defects in 35 patients were accessed with a buccal SFA alone or in combination with a reconstructive technology (graft, enamel matrix derivative (EMD), graft + EMD, or graft + membrane). Postoperative healing was evaluated at 2 weeks using the Early Wound-Healing Index (EHI). EHI ranged from score 1 (i.e., complete flap closure and optimal healing) to score 4 (i.e., loss of primary closure and partial tissue necrosis). SFA resulted in a complete wound closure at 2 weeks in the great majority of sites. A significantly more frequent presence of interdental contact point and interdental soft tissue crater, and narrower base of the interdental papilla were observed at sites with either EHI > 1 or EHI = 4 compared to sites with EHI = 1. No association between EHI and the 6-month clinical outcomes was observed. At 2 weeks, buccal SFA may result in highly predictable complete flap closure. Site-specific characteristics may influence the early postoperative healing of the papillary incision following SFA procedure. Two-week soft tissue healing, however, was not associated with the 6-month clinical outcomes.

Calibration of the Total Carbon Column Observing Network using Aircraft Profile Data

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

Wunch, Debra; Toon, Geoffrey C.; Wennberg, Paul O.

2010-03-26

The Total Carbon Column Observing Network (TCCON) produces precise measurements of the column average dry-air mole fractions of CO{sub 2}, CO, CH{sub 4}, N{sub 2}O and H{sub 2}O at a variety of sites worldwide. These observations rely on spectroscopic parameters that are not known with sufficient accuracy to compute total columns that can be used in combination with in situ measure ments. The TCCON must therefore be calibrated to World Meteorological Organization (WMO) in situ trace gas measurement scales. We present a calibration of TCCON data using WMO-scale instrumentation aboard aircraft that measured profiles over four TCCON stations during 2008more » and 2009. The aircraft campaigns are the Stratosphere-Troposphere Analyses of Regional Transport 2008 (START-08), which included a profile over the Park Falls site, the HIAPER Pole-to-Pole Observations (HIPPO-1) campaign, which included profiles over the Lamont and Lauder sites, a series of Learjet profiles over the Lamont site, and a Beechcraft King Air profile over the Tsukuba site. These calibrations are compared with similar observations made during the INTEX-NA (2004), COBRA-ME (2004) and TWP-ICE (2006) campaigns. A single, global calibration factor for each gas accurately captures the TCCON total column data within error.« less

Indentation recovery in GdPO 4 and observation of deformation twinning

DOE PAGES

Wilkinson, Taylor M.; Musselman, Matthew A.; Boatner, Lynn A.; ...

2016-09-30

A series of nanoindentation tests on both single and polycrystalline specimens of a monazite rare-earth orthophosphate, GdPO 4, revealed frequent observation of anomalous unloading behavior with a large degree of recovery, where previously this behavior had only been observed in xenotime-structure rare-earth orthophosphates. An indentation site in the polycrystalline sample was examined using TEM to identify the deformation mechanism responsible for recovery. Finally, the presence of a twin along the (100) orientation, along with a series of stacking faults contained within the deformation site, provide evidence that the mechanism of recovery in GdPO 4 is the collapse of deformation twinsmore » during unloading.« less

Indentation recovery in GdPO 4 and observation of deformation twinning

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

Wilkinson, Taylor M.; Musselman, Matthew A.; Boatner, Lynn A.

A series of nanoindentation tests on both single and polycrystalline specimens of a monazite rare-earth orthophosphate, GdPO 4, revealed frequent observation of anomalous unloading behavior with a large degree of recovery, where previously this behavior had only been observed in xenotime-structure rare-earth orthophosphates. An indentation site in the polycrystalline sample was examined using TEM to identify the deformation mechanism responsible for recovery. Finally, the presence of a twin along the (100) orientation, along with a series of stacking faults contained within the deformation site, provide evidence that the mechanism of recovery in GdPO 4 is the collapse of deformation twinsmore » during unloading.« less

Observation of seasonal variation of atmospheric multiple-muon events in the MINOS Near and Far Detectors

DOE PAGES

Adamson, P.; Bishai, M.; Diwan, M. V.; ...

2015-06-09

We report the first observation of seasonal modulations in the rates of cosmic ray multiple-muon events at two underground sites, the MINOS Near Detector with an overburden of 225 mwe, and the MINOS Far Detector site at 2100 mwe. At the deeper site, multiple-muon events with muons separated by more than 8 m exhibit a seasonal rate that peaks during the summer, similar to that of single-muon events. Conversely, the rate of multiple-muon events with muons separated by less than 5–8 m, and the rate of multiple-muon events in the smaller, shallower Near Detector, exhibit a seasonal rate modulation thatmore » peaks in the winter.« less

Atmospheric Radiation Measurement Program Facilities Newsletter - September 1999

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

Holdridge, D. J., ed

The Atmospheric Radiation Measurement Program September 1999 Facilities Newsletter discusses the several Intensive Observation Periods (IOPs) that the ARM SGP CART site will host in the near future. Two projects of note are the International Pyrgeometer Intercomparison and the Fall Single Column Model (SCM)/Nocturnal Boundary Layer (NBL) IOP. Both projects will bring many US and international scientists to the SGP CART site to participate in atmospheric research.

Re-evaluating the kinetics of ATP hydrolysis during initiation of DNA sliding by Type III restriction enzymes

PubMed Central

Tóth, Júlia; Bollins, Jack; Szczelkun, Mark D.

2015-01-01

DNA cleavage by the Type III restriction enzymes requires long-range protein communication between recognition sites facilitated by thermally-driven 1D diffusion. This ‘DNA sliding’ is initiated by hydrolysis of multiple ATPs catalysed by a helicase-like domain. Two distinct ATPase phases were observed using short oligoduplex substrates; the rapid consumption of ∼10 ATPs coupled to a protein conformation switch followed by a slower phase, the duration of which was dictated by the rate of dissociation from the recognition site. Here, we show that the second ATPase phase is both variable and only observable when DNA ends are proximal to the recognition site. On DNA with sites more distant from the ends, a single ATPase phase coupled to the conformation switch was observed and subsequent site dissociation required little or no further ATP hydrolysis. The overall DNA dissociation kinetics (encompassing site release, DNA sliding and escape via a DNA end) were not influenced by the second phase. Although the data simplifies the ATP hydrolysis scheme for Type III restriction enzymes, questions remain as to why multiple ATPs are hydrolysed to prepare for DNA sliding. PMID:26538601

Single-molecule resolution of protein dynamics on polymeric membrane surfaces: the roles of spatial and population heterogeneity.

PubMed

Langdon, Blake B; Mirhossaini, Roya B; Mabry, Joshua N; Sriram, Indira; Lajmi, Ajay; Zhang, Yanxia; Rojas, Orlando J; Schwartz, Daniel K

2015-02-18

Although polymeric membranes are widely used in the purification of protein pharmaceuticals, interactions between biomolecules and membrane surfaces can lead to reduced membrane performance and damage to the product. In this study, single-molecule fluorescence microscopy provided direct observation of bovine serum albumin (BSA) and human monoclonal antibody (IgG) dynamics at the interface between aqueous buffer and polymeric membrane materials including regenerated cellulose and unmodified poly(ether sulfone) (PES) blended with either polyvinylpyrrolidone (PVP), polyvinyl acetate-co-polyvinylpyrrolidone (PVAc-PVP), or polyethylene glycol methacrylate (PEGM) before casting. These polymer surfaces were compared with model surfaces composed of hydrophilic bare fused silica and hydrophobic trimethylsilane-coated fused silica. At extremely dilute protein concentrations (10(-3)-10(-7) mg/mL), protein surface exchange was highly dynamic with protein monomers desorbing from the surface within ∼1 s after adsorption. Protein oligomers (e.g., nonspecific dimers, trimers, or larger aggregates), although less common, remained on the surface for 5 times longer than monomers. Using newly developed super-resolution methods, we could localize adsorption sites with ∼50 nm resolution and quantify the spatial heterogeneity of the various surfaces. On a small anomalous subset of the adsorption sites, proteins adsorbed preferentially and tended to reside for significantly longer times (i.e., on "strong" sites). Proteins resided for shorter times overall on surfaces that were more homogeneous and exhibited fewer strong sites (e.g., PVAc-PVP/PES). We propose that strong surface sites may nucleate protein aggregation, initiated preferentially by protein oligomers, and accelerate ultrafiltration membrane fouling. At high protein concentrations (0.3-1.0 mg/mL), fewer strong adsorption sites were observed, and surface residence times were reduced. This suggests that at high concentrations, adsorbed proteins block strong sites from further protein adsorption. Importantly, this demonstrates that strong binding sites can be modified by changing solution conditions. Membrane surfaces are intrinsically heterogeneous; by employing single-molecule techniques, we have provided a new framework for understanding protein interactions with such surfaces.

Observation of quasiperiodic dynamics in a one-dimensional quantum walk of single photons in space

NASA Astrophysics Data System (ADS)

Xue, Peng; Qin, Hao; Tang, Bao; Sanders, Barry C.

2014-05-01

We realize the quasi-periodic dynamics of a quantum walker over 2.5 quasi-periods by realizing the walker as a single photon passing through a quantum-walk optical-interferometer network. We introduce fully controllable polarization-independent phase shifters in each optical path to realize arbitrary site-dependent phase shifts, and employ large clear-aperture beam displacers, while maintaining high-visibility interference, to enable 10 quantum-walk steps to be reached. By varying the half-wave-plate setting, we control the quantum-coin bias thereby observing a transition from quasi-periodic dynamics to ballistic diffusion.

Heat- and light-induced transformations of Yb trapping sites in an Ar matrix

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

Tao, L.-G.; Lambo, R., E-mail: lambo@mail.ustc.edu.cn; Zhou, X.-G.

2015-11-07

The low-lying electronic states of Yb isolated in a solid Ar matrix grown at 4.2 K are characterized through absorption and emission spectroscopy. Yb atoms are found to occupy three distinct thermally stable trapping sites labeled “red,” “blue,” and “violet” according to the relative positions of the absorption features they produce. Classical simulations of the site structure and relative stability broadly reproduced the experimentally observed matrix-induced frequency shifts and thus identified the red, blue, and violet sites as due to respective single substitutional (SS), tetravacancy (TV), and hexavacancy (HV) occupation. Prolonged excitation of the {sup 1}S → {sup 1}P transitionmore » was found to transfer the Yb population from HV sites into TV and SS sites. The process showed reversibility in that annealing to 24 K predominantly transferred the TV population back into HV sites. Population kinetics were used to deduce the effective rate parameters for the site transformation processes. Experimental observations indicate that the blue and violet sites lie close in energy, whereas the red one is much less stable. Classical simulations identify the blue site as the most stable one.« less

Structural characterization of framework–gas interactions in the metal–organic framework Co 2 (dobdc) by in situ single-crystal X-ray diffraction

DOE PAGES

Gonzalez, Miguel I.; Mason, Jarad A.; Bloch, Eric D.; ...

2017-04-19

The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH 4, N 2, O 2, Ar, and P 4 adsorption in Co2(dobdc) (dobdc 4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(II) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(II) sites in the framework that no analogous molecular structures exist,more » demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH 4 and Co–Ar interactions observed in Co 2(dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH 4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(II) sites in Co 2(dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol –1 (for Ar). Moreover, the structures of Co 2(dobdc)·3.8N 2, Co 2(dobdc)·5.9O 2, and Co 2(dobdc)·2.0Ar reveal the location of secondary (N 2, O 2, and Ar) and tertiary (O 2) binding sites in Co 2(dobdc), while high-pressure CO 2, CO, CH 4, N 2, and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures.« less

Research on Building Education & Workforce Capacity in Systems Engineering

DTIC Science & Technology

2011-02-07

manufacturing or design sites where students could observe engineering processes related to their projects Mentors with the highest level of student ... engagement interacted with students in every single activity area and with frequency, while others provided only intermittent correspondence. Note

3D near-surface soil response from H/V ambient-noise ratios

USGS Publications Warehouse

Wollery, E.W.; Street, R.

2002-01-01

The applicability of the horizontal-to-vertical (H/V) ambient-noise spectral ratio for characterizing earthquake site effects caused by nearsurface topography and velocity structures was evaluated at sites underlain by thick (i.e. >100 m) sediment deposits near the southern-end of the New Madrid seismic zone in the central United States. Three-component ambient-noise and velocity models derived from seismic (shearwave) refraction/reflection surveys showed that a relatively horizontal, sharp shear-wave velocity interface in the soil column resulted in an H/V spectral ratio with a single well-defined peak. Observations at sites with more than one sharp shear-wave velocity contrast and horizontally arranged soil layers resulted in at least two well-defined H/V spectral ratio peaks. Furthermore, at sites where there were sharp shear-wave velocity contrasts in nonhorizontal, near-surface soil layers, the H/V spectra exhibited a broad-bandwidth, relatively low amplitude signal instead of a single well-defined peak. ?? 2002 Elsevier Science Ltd. All rights reserved.

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.

An experimental study of symmetry lowering of analcime

NASA Astrophysics Data System (ADS)

Sugano, Neo; Kyono, Atsushi

2018-04-01

Single crystals of analcime were hydrothermally synthesized from a gel of analcime composition at 200 °C for 24 h. They were grown up to 100 μm in size with typical deltoidal icositetrahedron habit. The chemical composition determined by EPMA and TG analyses was Na0.84(Al0.89Si2.12)O6·1.04H2O. The single-crystal X-ray diffraction method was used to determine the symmetry and crystal structure of analcime. The analcime grown from a gel crystallized in cubic space group Ia3 d with lattice parameter a = 13.713(3) Å. In the cubic analcime, Si and Al cations were totally disordered over the framework T sites with site occupancy of Si:Al = 0.6871:0.3129(14). The single crystals of analcime with cubic symmetry were hydrothermally reheated at 200 °C in ultrapure water. After the hydrothermal treatment for 24 h, forbidden reflections for the cubic Ia3 d symmetry were observed. The reflection conditions led to an orthorhombic space group Ibca with lattice parameters a = 13.727(2) Å, b = 13.707(2) Å, and c = 13.707(2) Å. The unit-cell showed a slight distortion with ( a + b)/2 > c, yielding a flattened cell along c. In the orthorhombic analcime, Al exhibited a site preference for T11 site, which indicates that the Si/Al ordering over the framework T sites lowers the symmetry from cubic Ia3 d to orthorhombic Ibca. After the hydrothermal treatment for 48 h, reflections corresponding to orthorhombic space group Ibca were observed as well. The lattice parameters were a = 13.705(2) Å, b = 13.717(2) Å, and c = 13.706(2) Å, retaining the flattened cell shape with ( a + b)/2 > c. The Si and Al cations were further ordered among the framework T sites than the case of the hydrothermal treatment for 24 h. As a consequence, the Si/Al ordering was slightly but significantly accelerated with increasing the hydrothermal treatment time. During the hydrothermal reaction, however, chemical compositions were almost unchanged. The site occupancies of Na over the extra-framework sites remained unaffected with the heating time; thus, the hydrothermal heating influences the degree of ordering of Si and Al over the framework T sites rather than that of Na among the extra-framework sites.

Multispecies spawning sites for fishes on a low-latitude coral reef: spatial and temporal patterns.

PubMed

Claydon, J A B; McCormick, M I; Jones, G P

2014-04-01

Spawning sites used by one or more species were located by intensively searching nearshore coral reefs of Kimbe Bay (New Britain, Papua New Guinea). Once identified, the spawning sites were surveyed repeatedly within fixed 5 m radius circular areas, for  > 2000 h of observations ranging from before dawn to after dusk spanning 190 days between July 2001 and May 2004. A total of 38 spawning sites were identified on the seven study reefs distributed at an average of one site every 60 m of reef edge. Pelagic spawning was observed in 41 fish species from six families. On three intensively studied reefs, all 17 spawning sites identified were used by at least three species, with a maximum of 30 different species observed spawning at a single site. Spawning was observed during every month of the study, on all days of the lunar month, at all states of the tide and at most hours of the day studied. Nevertheless, the majority of species were observed spawning on proportionately more days from December to April, on more days around the new moon and in association with higher tides. The strongest temporal association, however, was with species-specific diel spawning times spanning < 3 h for most species. While dawn spawning, afternoon spawning and dusk spawning species were differentiated, the time of spawning for the striated surgeonfish Ctenochaetus striatus also differed significantly among sites. The large number of species spawning at the same restricted locations during predictable times suggests that these sites are extremely important on this low-latitude coral reef. © 2014 The Fisheries Society of the British Isles.

Evaluating species richness: biased ecological inference results from spatial heterogeneity in species detection probabilities

USGS Publications Warehouse

McNew, Lance B.; Handel, Colleen M.

2015-01-01

Accurate estimates of species richness are necessary to test predictions of ecological theory and evaluate biodiversity for conservation purposes. However, species richness is difficult to measure in the field because some species will almost always be overlooked due to their cryptic nature or the observer's failure to perceive their cues. Common measures of species richness that assume consistent observability across species are inviting because they may require only single counts of species at survey sites. Single-visit estimation methods ignore spatial and temporal variation in species detection probabilities related to survey or site conditions that may confound estimates of species richness. We used simulated and empirical data to evaluate the bias and precision of raw species counts, the limiting forms of jackknife and Chao estimators, and multi-species occupancy models when estimating species richness to evaluate whether the choice of estimator can affect inferences about the relationships between environmental conditions and community size under variable detection processes. Four simulated scenarios with realistic and variable detection processes were considered. Results of simulations indicated that (1) raw species counts were always biased low, (2) single-visit jackknife and Chao estimators were significantly biased regardless of detection process, (3) multispecies occupancy models were more precise and generally less biased than the jackknife and Chao estimators, and (4) spatial heterogeneity resulting from the effects of a site covariate on species detection probabilities had significant impacts on the inferred relationships between species richness and a spatially explicit environmental condition. For a real dataset of bird observations in northwestern Alaska, the four estimation methods produced different estimates of local species richness, which severely affected inferences about the effects of shrubs on local avian richness. Overall, our results indicate that neglecting the effects of site covariates on species detection probabilities may lead to significant bias in estimation of species richness, as well as the inferred relationships between community size and environmental covariates.

Assessing FPAR Source and Parameter Optimization Scheme in Application of a Diagnostic Carbon Flux Model

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

Turner, D P; Ritts, W D; Wharton, S

2009-02-26

The combination of satellite remote sensing and carbon cycle models provides an opportunity for regional to global scale monitoring of terrestrial gross primary production, ecosystem respiration, and net ecosystem production. FPAR (the fraction of photosynthetically active radiation absorbed by the plant canopy) is a critical input to diagnostic models, however little is known about the relative effectiveness of FPAR products from different satellite sensors nor about the sensitivity of flux estimates to different parameterization approaches. In this study, we used multiyear observations of carbon flux at four eddy covariance flux tower sites within the conifer biome to evaluate these factors.more » FPAR products from the MODIS and SeaWiFS sensors, and the effects of single site vs. cross-site parameter optimization were tested with the CFLUX model. The SeaWiFs FPAR product showed greater dynamic range across sites and resulted in slightly reduced flux estimation errors relative to the MODIS product when using cross-site optimization. With site-specific parameter optimization, the flux model was effective in capturing seasonal and interannual variation in the carbon fluxes at these sites. The cross-site prediction errors were lower when using parameters from a cross-site optimization compared to parameter sets from optimization at single sites. These results support the practice of multisite optimization within a biome for parameterization of diagnostic carbon flux models.« less

Identification of PM10 air pollution origins at a rural background site

NASA Astrophysics Data System (ADS)

Reizer, Magdalena; Orza, José A. G.

2018-01-01

Trajectory cluster analysis and concentration weighted trajectory (CWT) approach have been applied to investigate the origins of PM10 air pollution recorded at a rural background site in North-eastern Poland (Diabla Góra). Air mass back-trajectories used in this study have been computed with the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model for a 10-year period of 2006-2015. A cluster analysis grouped back-trajectories into 7 clusters. Most of the trajectories correspond to fast and moderately moving westerly and northerly flows (45% and 25% of the cases, respectively). However, significantly higher PM10 concentrations were observed for slow moving easterly (11%) and southerly (20%) air masses. The CWT analysis shows that high PM10 levels are observed at Diabla Góra site when air masses are originated and passed over the heavily industrialized areas in Central-Eastern Europe located to the south and south-east of the site.

Site-occupancy distribution modeling to correct population-trend estimates derived from opportunistic observations

USGS Publications Warehouse

Kery, M.; Royle, J. Andrew; Schmid, Hans; Schaub, M.; Volet, B.; Hafliger, G.; Zbinden, N.

2010-01-01

Species' assessments must frequently be derived from opportunistic observations made by volunteers (i.e., citizen scientists). Interpretation of the resulting data to estimate population trends is plagued with problems, including teasing apart genuine population trends from variations in observation effort. We devised a way to correct for annual variation in effort when estimating trends in occupancy (species distribution) from faunal or floral databases of opportunistic observations. First, for all surveyed sites, detection histories (i.e., strings of detection-nondetection records) are generated. Within-season replicate surveys provide information on the detectability of an occupied site. Detectability directly represents observation effort; hence, estimating detectablity means correcting for observation effort. Second, site-occupancy models are applied directly to the detection-history data set (i.e., without aggregation by site and year) to estimate detectability and species distribution (occupancy, i.e., the true proportion of sites where a species occurs). Site-occupancy models also provide unbiased estimators of components of distributional change (i.e., colonization and extinction rates). We illustrate our method with data from a large citizen-science project in Switzerland in which field ornithologists record opportunistic observations. We analyzed data collected on four species: the widespread Kingfisher (Alcedo atthis. ) and Sparrowhawk (Accipiter nisus. ) and the scarce Rock Thrush (Monticola saxatilis. ) and Wallcreeper (Tichodroma muraria. ). Our method requires that all observed species are recorded. Detectability was <1 and varied over the years. Simulations suggested some robustness, but we advocate recording complete species lists (checklists), rather than recording individual records of single species. The representation of observation effort with its effect on detectability provides a solution to the problem of differences in effort encountered when extracting trend information from haphazard observations. We expect our method is widely applicable for global biodiversity monitoring and modeling of species distributions. ?? 2010 Society for Conservation Biology.

Insertional Mutagenesis by CRISPR/Cas9 Ribonucleoprotein Gene Editing in Cells Targeted for Point Mutation Repair Directed by Short Single-Stranded DNA Oligonucleotides.

PubMed

Rivera-Torres, Natalia; Banas, Kelly; Bialk, Pawel; Bloh, Kevin M; Kmiec, Eric B

2017-01-01

CRISPR/Cas9 and single-stranded DNA oligonucleotides (ssODNs) have been used to direct the repair of a single base mutation in human genes. Here, we examine a method designed to increase the precision of RNA guided genome editing in human cells by utilizing a CRISPR/Cas9 ribonucleoprotein (RNP) complex to initiate DNA cleavage. The RNP is assembled in vitro and induces a double stranded break at a specific site surrounding the mutant base designated for correction by the ssODN. We use an integrated mutant eGFP gene, bearing a single base change rendering the expressed protein nonfunctional, as a single copy target in HCT 116 cells. We observe significant gene correction activity of the mutant base, promoted by the RNP and single-stranded DNA oligonucleotide with validation through genotypic and phenotypic readout. We demonstrate that all individual components must be present to obtain successful gene editing. Importantly, we examine the genotype of individually sorted corrected and uncorrected clonally expanded cell populations for the mutagenic footprint left by the action of these gene editing tools. While the DNA sequence of the corrected population is exact with no adjacent sequence modification, the uncorrected population exhibits heterogeneous mutagenicity with a wide variety of deletions and insertions surrounding the target site. We designate this type of DNA aberration as on-site mutagenicity. Analyses of two clonal populations bearing specific DNA insertions surrounding the target site, indicate that point mutation repair has occurred at the level of the gene. The phenotype, however, is not rescued because a section of the single-stranded oligonucleotide has been inserted altering the reading frame and generating truncated proteins. These data illustrate the importance of analysing mutagenicity in uncorrected cells. Our results also form the basis of a simple model for point mutation repair directed by a short single-stranded DNA oligonucleotides and CRISPR/Cas9 ribonucleoprotein complex.

Insertional Mutagenesis by CRISPR/Cas9 Ribonucleoprotein Gene Editing in Cells Targeted for Point Mutation Repair Directed by Short Single-Stranded DNA Oligonucleotides

PubMed Central

Rivera-Torres, Natalia; Bialk, Pawel; Bloh, Kevin M.; Kmiec, Eric B.

2017-01-01

CRISPR/Cas9 and single-stranded DNA oligonucleotides (ssODNs) have been used to direct the repair of a single base mutation in human genes. Here, we examine a method designed to increase the precision of RNA guided genome editing in human cells by utilizing a CRISPR/Cas9 ribonucleoprotein (RNP) complex to initiate DNA cleavage. The RNP is assembled in vitro and induces a double stranded break at a specific site surrounding the mutant base designated for correction by the ssODN. We use an integrated mutant eGFP gene, bearing a single base change rendering the expressed protein nonfunctional, as a single copy target in HCT 116 cells. We observe significant gene correction activity of the mutant base, promoted by the RNP and single-stranded DNA oligonucleotide with validation through genotypic and phenotypic readout. We demonstrate that all individual components must be present to obtain successful gene editing. Importantly, we examine the genotype of individually sorted corrected and uncorrected clonally expanded cell populations for the mutagenic footprint left by the action of these gene editing tools. While the DNA sequence of the corrected population is exact with no adjacent sequence modification, the uncorrected population exhibits heterogeneous mutagenicity with a wide variety of deletions and insertions surrounding the target site. We designate this type of DNA aberration as on-site mutagenicity. Analyses of two clonal populations bearing specific DNA insertions surrounding the target site, indicate that point mutation repair has occurred at the level of the gene. The phenotype, however, is not rescued because a section of the single-stranded oligonucleotide has been inserted altering the reading frame and generating truncated proteins. These data illustrate the importance of analysing mutagenicity in uncorrected cells. Our results also form the basis of a simple model for point mutation repair directed by a short single-stranded DNA oligonucleotides and CRISPR/Cas9 ribonucleoprotein complex. PMID:28052104

Substrate Shuttling Between Active Sites of Uroporphyrinogen Decarboxylase in Not Required to Generate Coproporphyrinogen

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

Phillips, J.; Warby, C; Whitby, F

2009-01-01

Uroporphyrinogen decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of four acetate side chains in the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer, with the active-site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single-chain protein (single-chain URO-D) in which the two subunits were connectedmore » by a flexible linker. The crystal structure of this protein was shown to be superimposable with wild-type activity and to have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of single-chain URO-D resulted in approximately half of wild-type activity. The distributions of reaction intermediates were the same for mutant and wild-type sequences and were unaltered in a competition experiment using I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function and suggest that the dimeric structure of URO-D is required to achieve conformational stability and to create a large active-site cleft.« less

E6 and E7 Gene Polymorphisms in Human Papillomavirus Types-58 and 33 Identified in Southwest China

PubMed Central

Wen, Qiang; Wang, Tao; Mu, Xuemei; Chenzhang, Yuwei; Cao, Man

2017-01-01

Cancer of the cervix is associated with infection by certain types of human papillomavirus (HPV). The gene variants differ in immune responses and oncogenic potential. The E6 and E7 proteins encoded by high-risk HPV play a key role in cellular transformation. HPV-33 and HPV-58 types are highly prevalent among Chinese women. To study the gene intratypic variations, polymorphisms and positive selections of HPV-33 and HPV-58 E6/E7 in southwest China, HPV-33 (E6, E7: n = 216) and HPV-58 (E6, E7: n = 405) E6 and E7 genes were sequenced and compared to others submitted to GenBank. Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0). The diversity of secondary structure was analyzed by PSIPred software. The selection pressures acting on the E6/E7 genes were estimated by PAML 4.8 (Phylogenetic Analyses by Maximun Likelihood version4.8) software. The positive sites of HPV-33 and HPV-58 E6/E7 were contrasted by ClustalX 2.1. Among 216 HPV-33 E6 sequences, 8 single nucleotide mutations were observed with 6/8 non-synonymous and 2/8 synonymous mutations. The 216 HPV-33 E7 sequences showed 3 single nucleotide mutations that were non-synonymous. The 405 HPV-58 E6 sequences revealed 8 single nucleotide mutations with 4/8 non-synonymous and 4/8 synonymous mutations. Among 405 HPV-58 E7 sequences, 13 single nucleotide mutations were observed with 10/13 non-synonymous mutations and 3/13 synonymous mutations. The selective pressure analysis showed that all HPV-33 and 4/6 HPV-58 E6/E7 major non-synonymous mutations were sites of positive selection. All variations were observed in sites belonging to major histocompatibility complex and/or B-cell predicted epitopes. K93N and R145 (I/N) were observed in both HPV-33 and HPV-58 E6. PMID:28141822

Desert Test Site Uniformity Analysis

NASA Technical Reports Server (NTRS)

Kerola, Dana X.; Bruegge, Carol J.

2009-01-01

Desert test sites such as Railroad Valley (RRV) Nevada, Egypt-1, and Libya-4 are commonly targeted to assess the on-orbit radiometric performance of sensors. Railroad Valley is used for vicarious calibration experiments, where a field-team makes ground measurements to produce accurate estimates of top-of-atmosphere (TOA) radiances. The Sahara desert test sites are not instrumented, but provide a stable target that can be used for sensor cross-comparisons, or for stability monitoring of a single sensor. These sites are of interest to NASA's Atmospheric Carbon Observation from Space (ACOS) and JAXA's Greenhouse Gas Observation SATellite (GOSAT) programs. This study assesses the utility of these three test sites to the ACOS and GOSAT calibration teams. To simulate errors in sensor-measured radiance with pointing errors, simulated data have been created using MODIS Aqua data. MODIS data are further utilized to validate the campaign data acquired from June 22 through July 5, 2009. The first GOSAT vicarious calibration experiment was conducted during this timeframe.

Monitoring the vernal advancement and retrogradation (green wave effect) of natural vegetation

NASA Technical Reports Server (NTRS)

Rouse, J. W., Jr. (Principal Investigator)

1973-01-01

The author has identified the following significant results. A comprehensive review of ERTS-1 MSS color composite imagery, obtained during the autumnal and vernal phases over the Great Plains Corridor test sites, shows that temporal changes in rangeland vegetation can be manually interpreted. The degree to which manual interpretations can be made from the MSS color composites appears to be limited primarily by variations in image reproduction quality. The vernal advancement and other phenophase related phenomena are observable from cycle to cycle and within a single frame for rangeland vegetation. Vegetation changes due to environmental conditions among the test sites and among grazing treatments within test sites are readily observable. An investigation has been initiated which will evaluate band-to-band ratios as an index of rangeland vegetation condition. Data currently available from August 1972 through April 1973 for the five southern test sites are being used to characterize band-to-band ratios as a function of quantity and quality of rangeland vegetation at each of the test sites.

Single-site Laparoscopic Colorectal Surgery Provides Similar Clinical Outcomes Compared to Standard Laparoscopic Surgery: An Analysis of 626 Patients

PubMed Central

Sangster, William; Messaris, Evangelos; Berg, Arthur S.; Stewart, David B.

2015-01-01

BACKGROUND Compared to standard laparoscopy, single-site laparoscopic colorectal surgerymay potentially offer advantages by creating fewer surgical incisions and providing a multi-functional trocar. Previous comparisons, however, have been limited by small sample sizes and selection bias. OBJECTIVE To compare 60-day outcomes between standard laparoscopic and single-site laparoscopic colorectal surgery patients undergoing elective and urgent surgeries. DESIGN This was an unselected retrospective cohort study comparing patients who underwent elective and unplanned standard laparoscopic or single-site laparoscopic colorectal resections for benign and malignant disease between 2008 and 2014. Outcomes were compared using univariate analyses. SETTING This study was conducted at a single institution. PATIENTS A total of 626 consecutive patients undergoing laparoscopic colorectal surgery were included. MAIN OUTCOME MEASURES Morbidity and mortality within 60 postoperative days. RESULTS 318 (51%) and 308 (49%) patients underwent standard laparoscopic and single-site laparoscopic procedures, respectively. No significant difference was noted in mean operative time (Standard laparoscopy 182.1 ± 81.3 vs. Single-site laparoscopy 177±86.5, p=0.30) and postoperative length of stay (Standard laparoscopy 4.8±3.4 vs. Single-site laparoscopy 5.5 ± 6.9, p=0.14). Conversions to laparotomy and 60-day readmissions were also similar for both cohorts across all procedures performed. A significant difference was identified in the number of patients who developed postoperative complications (Standard laparoscopy 19.2% vs. Single-site laparoscopy 10.7%, p=0.004), especially with respect to surgical-site infections (Standard laparoscopy 11.3% vs. Single-site laparoscopy 5.8%, p=0.02). LIMITATIONS This was a retrospective, single institution study. CONCLUSIONS Single-site laparoscopic colorectal surgery demonstrates similar results to standard laparoscopic colorectal surgery in regards to operative time, length of stay and readmissions. Single-site laparoscopic colorectal surgery may provide advantages in limiting the development of certain complications such as superficial surgical-site infections. PMID:26252848

Sliding movement of single actin filaments on one-headed myosin filaments

NASA Astrophysics Data System (ADS)

Harada, Yoshie; Noguchi, Akira; Kishino, Akiyoshi; Yanagida, Toshio

1987-04-01

The myosin molecule consists of two heads, each of which contains an enzymatic active site and an actin-binding site. The fundamental problem of whether the two heads function independently or cooperatively during muscle contraction has been studied by methods using an actomyosin thread1, superprecipitation2-4 and chemical modification of muscle fibres5. No clear conclusion has yet been reached. We have approached this question using an assay system in which sliding movements of fluorescently labelled single actin filaments along myosin filaments can be observed directly6,7. Here, we report direct measurement of the sliding of single actin filaments along one-headed myosin filaments in which the density of heads was varied over a wide range. Our results show that cooperative interaction between the two heads of myosin is not essential for inducing the sliding movement of actin filaments.

EPR study of gamma irradiated N-methyl taurine (C3H9NO3S) and sodium hydrogen sulphate monohydrate (NaHSO3·H2O) single crystals.

PubMed

Yıldırım, Ilkay; Karabulut, Bünyamin

2011-03-01

EPR study of gamma irradiated C(3)H(9)NO(3)S and NaHSO(3).H(2)O single crystals have been carried out at room temperature. There is one site for the radicals in C(3)H(9)NO(3)S and two magnetically distinct sites for the radicals in NaHSO(3). The observed lines in the EPR spectra have been attributed to the species of SO(3)(-) and RH radicals for N-methyl taurine, and to the SO(3)(-) and OH radicals for sodium hydrogen sulfate monohydrate single crystals. The principal values of the g for SO(3)(-), the hyperfine values of RH and OH proton splitting have been calculated and discussed. Copyright © 2010 Elsevier B.V. All rights reserved.

Simultaneous observation of chemomechanical coupling of a molecular motor.

PubMed

Nishizaka, Takayuki; Hasimoto, Yuh; Masaike, Tomoko

2011-01-01

F(1)-ATPase is the smallest rotary molecular motor ever found. Unidirectional rotation of the γ-shaft is driven by precisely coordinated sequential ATP hydrolysis reactions in three catalytic sites arranged 120° apart in the cylinder. Single-molecule observation allows us to directly watch the rotation of the shaft using micron-sized plastic beads. Additionally, an advanced version of "total internal reflection fluorescence microscope (TIRFM)" enables us to detect binding and release of energy currency through fluorescently labeled ATP. In this chapter, we describe how to set up the system for simultaneous observation of these two critical events. This specialized optical setup is applicable to a variety of research, not only molecular motors but also other single-molecule topics.

1.55 µm emission from a single III-nitride top-down and site-controlled nanowire quantum disk

NASA Astrophysics Data System (ADS)

Chen, Qiming; Yan, Changling; Qu, Yi

2017-07-01

InN/InGaN single quantum well (SQW) was fabricated on 100 nm GaN buffer layer which was deposited on GaN template by plasma assisted molecular beam epitaxy (PA-MBE). The In composition and the surface morphology were measured by x-ray diffusion (XRD) and atom force microscope (AFM), respectively. Afterwards, the sample was fabricated into site-controlled nanowires arrays by hot-embossing nano-imprint lithography (HE-NIL) and ultraviolet nanoimprint lithography (UV-NIL). The nanowires were uniform along the c-axis and aligned periodically as presented by scanning electron microscope (SEM). The single nanowire showed disk-in-a-wire structure by high angle annular dark field (HAADF) and an In-rich or Ga deficient region was observed by energy dispersive x-ray spectrum (EDXS). The optical properties of the SQW film and single nanowire were measured using micro photoluminescence (µ-PL) spectroscopy. The stimulating light wavelength was 632.8 nm which was emitted from a He-Ne laser and the detector was a liquid nitrogen cooled InGaAs detector. A blue peak shift from the film material to the nanowire was observed. This was due to the quantum confinement Stark Effect. More importantly, the 1.55 µm emission was given from the single disk-in-a-wire structure at room temperature. We believe the arrays of such nanowires may be useful for quantum communication in the future.

Contentious relationships in phylogenomic studies can be driven by a handful of genes

PubMed Central

Shen, Xing-Xing; Hittinger, Chris Todd; Rokas, Antonis

2017-01-01

Phylogenomic studies have resolved countless branches of the tree of life (ToL), but remain strongly contradictory on certain, contentious relationships. Here, we employ a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal, and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal of a single gene in concatenation analyses or a single site from every gene in coalescence-based analyses diminishes support and can alter the inferred topology. These results suggest that tiny subsets of very large data matrices drive the resolution of specific internodes, providing a dissection of the distribution of support and observed incongruence in phylogenomic analyses. We submit that quantifying the distribution of phylogenetic signal in phylogenomic data is essential for evaluating whether branches, especially contentious ones, are truly resolved. Finally, we offer one detailed example of such an evaluation for the controversy regarding the earliest-branching metazoan phylum, where examination of the distributions of gene-wise and site-wise phylogenetic signal across 8 data matrices consistently supports ctenophores as sister group to all other metazoans. PMID:28812701

Validation of TOMS Aerosol Products using AERONET Observations

NASA Technical Reports Server (NTRS)

Bhartia, P. K.; Torres, O.; Sinyuk, A.; Holben, B.

2002-01-01

The Total Ozone Mapping Spectrometer (TOMS) aerosol algorithm uses measurements of radiances at two near UV channels in the range 331-380 nm to derive aerosol optical depth and single scattering albedo. Because of the low near UV surface albedo of all terrestrial surfaces (between 0.02 and 0.08), the TOMS algorithm has the capability of retrieving aerosol properties over the oceans and the continents. The Aerosol Robotic Network (AERONET) routinely derives spectral aerosol optical depth and single scattering albedo at a large number of sites around the globe. We have performed comparisons of both aerosol optical depth and single scattering albedo derived from TOMS and AERONET. In general, the TOMS aerosol products agree well with the ground-based observations, Results of this validation will be discussed.

Design of Single-Site Photocatalyst using Metal-Organic Framework as Matrix.

PubMed

Wen, Meicheng; Mori, Kohsuke; Kuwahara, Yasutaka; An, Taicheng; Yamashita, Hiromi

2018-05-14

Single-site photocatalyst generally displays excellent photocatalytic activtiy and considerable high stability as compared to homogeneous catalytic system. A rational structural design of single-site photocatalyst with isolated, uniform and spatially separated active sites in a given solid is of prime importance to achieve high photocatalytic activity. Intense attentions have been focused on the engineering and fabrication of single-site photocatalys by using porous materials as platform. Metal-organic frameworks (MOFs) hold great potential for the design and fabrication of single-site photocatalysts due to their remarkable porosity, ultrahigh surface area, extraordinary tailorability and significant diversity. MOFs can provide abundant number of binding sites for anchoring active sites, result in significant enhancement of photocatalytic performance. In this focus review, the development of single-site MOF photocatalysts that perform in important and challenging chemical redox reaction such as photocatalytic water splitting, photocatalytic CO₂ conversion and organic transformations is summarized thoroughly. The successful strategies applied for the construction of single-site MOF photocatalysts and major challenge toward practical application was summarized and pointed out, respectively. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Changes in Nematode Communities in Different Physiographic Sites of the Condor Seamount (North-East Atlantic Ocean) and Adjacent Sediments

PubMed Central

Zeppilli, Daniela; Bongiorni, Lucia; Serrão Santos, Ricardo; Vanreusel, Ann

2014-01-01

Several seamounts are known as ‘oases’ of high abundances and biomass and hotspots of biodiversity in contrast to the surrounding deep-sea environments. Recent studies have indicated that each single seamount can exhibit a high intricate habitat turnover. Information on alpha and beta diversity of single seamount is needed in order to fully understand seamounts contribution to regional and global biodiversity. However, while most of the seamount research has been focused on summits, studies considering the whole seamount structure are still rather poor. In the present study we analysed abundance, biomass and diversity of nematodes collected in distinct physiographic sites and surrounding sediments of the Condor Seamount (Azores, North-East Atlantic Ocean). Our study revealed higher nematode biomass in the seamount bases and values 10 times higher in the Condor sediments than in the far-field site. Although biodiversity indices did not showed significant differences comparing seamount sites and far-field sites, significant differences were observed in term of nematode composition. The Condor summit harboured a completely different nematode community when compared to the other seamount sites, with a high number of exclusive species and important differences in term of nematode trophic diversity. The oceanographic conditions observed around the Condor Seamount and the associated sediment mixing, together with the high quality of food resources available in seamount base could explain the observed patterns. Our results support the hypothesis that seamounts maintain high biodiversity through heightened beta diversity and showed that not only summits but also seamount bases can support rich benthic community in terms of standing stocks and diversity. Furthermore functional diversity of nematodes strongly depends on environmental conditions link to the local setting and seamount structure. This finding should be considered in future studies on seamounts, especially in view of the potential impacts due to current and future anthropogenic threats. PMID:25541988

Prospective Observational Study of Single-Site Multiport Per-umbilical Laparoscopic Endosurgery versus Conventional Multiport Laparoscopic Cholecystectomy: Critical Appraisal of a Unique Umbilical Approach

PubMed Central

Jategaonkar, Priyadarshan Anand; Yadav, Sudeep Pradeep

2014-01-01

Purpose. This prospective observational study compares an innovative approach of Single-Site Multi-Port Per-umbilical Laparoscopic Endo-surgery (SSMPPLE) cholecystectomy with the gold standard—Conventional Multi-port Laparoscopic Cholecystectomy (CMLC)—to assess the feasibility and efficacy of the former. Methods. In all, 646 patients were studied. SSMPPLE cholecystectomy utilized three ports inserted through three independent mini-incisions at the umbilicus. Only the day-to-day rigid laparoscopic instruments were used in all cases. The SSMPPLE cholecystectomy group had 320 patients and the CMLC group had 326 patients. The outcomes were statistically compared. Results. SSMPPLE cholecystectomy had average operative time of 43.8 min and blood loss of 9.4 mL. Their duration of hospitalization was 1.3 days (range, 1–5). Six patients (1.9%) of this group were converted to CMLC. Eleven patients had controlled gallbladder perforations at dissection. The Visual Analogue Scores for pain on postoperative days 0 and 7, the operative time, and the scar grades were significantly better for SSMPPLE than CMLC. However, umbilical sepsis and seroma outcomes were similar. We had no bile-duct injuries or port-site hernias in this study. Conclusion. SSMPPLE cholecystectomy approach complies with the principles of laparoscopic triangulation; it seems feasible and safe method of minimally invasive cholecystectomy. Overall, it has a potential to emerge as an economically viable alternative to single-port surgery. PMID:24876955

Ce{sub 11}Ge{sub 3.73(2)}In{sub 6.27}: Solid-state synthesis, crystal structure and site-preference

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

Jeon, Beom-Yong; Nam, Gnu; Lee, Dong Woo

A novel intermetallic compound of Ce{sub 11}Ge{sub 3.73(2)}In{sub 6.27} has been synthesized through the high-temperature solid-state reaction using Nb-ampoules. A batch of well grown block-/short bar-shaped single-crystals has been obtained, and the crystal structure of the title compound has been characterized by single-crystal X-ray diffraction analyses. Ce{sub 11}Ge{sub 3.73(2)}In{sub 6.27} adopts the Ho{sub 11}Ge{sub 10}-type structure belonging to the tetragonal space group I4/mmm (Z=4, Pearson symbol tI84) with nine crystallographically unique atomic positions in the asymmetric unit. The lattice parameters are a=12.0163(1) Å and c=16.5396(2) Å. The overall crystal structure can simply be depicted as an assembly of three differentmore » types of co-facial cationic polyhedra centered by anions, which is further enclosed by the three-dimensional (3-D) cage-like anionic framework. The extra amount of In is observed in one of three isolated anionic sites resulting in introducing the Ge/In-mixed site at the Wyckoff 4e site. This unique site-preference of In substitution for Ge at the 4e site has been enlightened via the atomic size-aspect which was fully supported and rationalized by the site- and bond-energies analyses using tight-binding linear muffin-tin orbital (TB-LMTO) calculations. Energy-dispersive X-ray spectroscopy (EDS), density of states (DOS), crystal orbital Hamilton population (COHP), and electron localization function (ELF) analyses for the title compound are also presented. Magnetic susceptibility measurement proves that an antiferromagnetic ordering of Ce atoms at a low temperature with a paramagnetic Curie temperature of −23.2 K. - Graphical abstract: Reported is experimental and theoretical investigations for Ce{sub 11}Ge{sub 3.73(2)}In{sub 6.27}, which is the first reported example having the extra amounts of In substitution for Ge at one of three “isolated” anionic sites in the Ho{sub 11}Ge{sub 10}-type phase. The observed In site-preference toward the particular anionic site was rationalized via the atomic size-aspect supported by comprehensive analyses for the site-energies including the Wyckoff 4e and 8j sites. - Highlights: • Block or short-bar shaped single-crystals of Ce{sub 11}Ge{sub 3.73(2)}In{sub 6.27} were synthesized. • The first example of having the In/Ge mixture at the “isolated” anionic site. • The site-preference of In was rationalized by the site- and bond-energies.« less

How Single-site Mutation Affects HP Lattice Proteins

NASA Astrophysics Data System (ADS)

Shi, Guangjie; Landau, David P.; Vogel, Thomas; Wüst, Thomas; Li, Ying Wai

2014-03-01

We developed a heuristic method based on Wang-Landauand multicanonical sampling for determining the ground-state degeneracy of HP lattice proteins . Our algorithm allowed the most precise estimations of the (sometimes substantial) ground-state degeneracies of some widely studied HP sequences. We investigated the effects of single-site mutation on specific long HP lattice proteins comprehensively, including structural changes in ground-states, changes of ground-state degeneracy and thermodynamic properties of the systems. Both extremely sensitive and insensitive cases have been observed; consequently, properties such as specific heat, tortuosities etc. may be either largely unaffected or may change significantly due to mutation. More interestingly, mutation can even induce a lower ground-state energy in a few cases. Supported by NSF.

Honey bees can perform accurately directed waggle dances based solely on information from a homeward trip.

PubMed

Edrich, Wolfgang

2015-10-01

Honey bees were displaced several 100 m from their hive to an unfamiliar site and provisioned with honey. After feeding, almost two-thirds of the bees flew home to their hive within a 50 min observation time. About half of these returning, bees signalled the direction of the release site in waggle dances thus demonstrating that the dance can be guided entirely by information gathered on a single homeward trip. The likely reason for the bees' enthusiastic dancing on their initial return from this new site was the highly rewarding honeycomb that they were given there. The attractive nature of the site is confirmed by many of these bees revisiting the site and continuing to forage there.

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.

Cosmesis, patient satisfaction, and quality of life after da Vinci Single-Site cholecystectomy and multiport laparoscopic cholecystectomy: short-term results from a prospective, multicenter, randomized, controlled trial.

PubMed

Kudsi, Omar Yusef; Castellanos, Andres; Kaza, Srinivas; McCarty, Justin; Dickens, Eugene; Martin, David; Tiesenga, Frederick M; Konstantinidis, Konstantinos; Hirides, Petros; Mehendale, Shilpa; Gonzalez, Anthony

2017-08-01

Single-incision laparoscopic cholecystectomy evolved from the traditional multiport laparoscopic technique. Prior trials have demonstrated improved cosmesis with the single-incision technique. Robotic single-site surgery minimizes the technical difficulties associated with laparoscopic single-incision approach. This is the first prospective, randomized, controlled study comparing robotic single-site cholecystectomy (RSSC) and multiport laparoscopic cholecystectomy (MPLC) in terms of cosmesis and patient satisfaction. Patients with symptomatic benign gallbladder disease were randomized to RSSC or MPLC. Data included perioperative variables such as operative time, conversion and complications and cosmesis satisfaction, body image perception, quality of life using validated questionnaires, at postoperative visits of 2, 6 weeks and 3 months. One hundred thirty-six patients were randomized to RSSC (N = 83) and MPLC (N = 53) at 8 institutions. Both cohorts were dominated by higher enrollment of females (RSSC = 78%, MPLC = 92%). The RSSC and MPLC cohorts were otherwise statistically matched. Operative time was longer for RSSC (61 min vs. 44 min, P < 0.0001). There were no differences in complication rates. RSSC demonstrated a significant superiority in cosmesis satisfaction and body image perception (P value < 0.05 at every follow-up). There was no statistically significant difference in patient-reported quality of life. Multivariate analysis of female patients demonstrated significantly higher preference for RSSC over MPLC in cosmesis satisfaction and body image perception with no difference seen in overall quality of life. Results from this trial show that RSSC is associated with improved cosmesis satisfaction and body image perception without a difference in observed complication rate. The uncompromised safety and the improved cosmesis satisfaction and body image perception provided by RSSC for female patients support consideration of the robotic single-site approach. ClinicalTrials.gov identifier NCT01932216.

Defect Effects on TiO2 Nanosheets: Stabilizing Single Atomic Site Au and Promoting Catalytic Properties.

PubMed

Wan, Jiawei; Chen, Wenxing; Jia, Chuanyi; Zheng, Lirong; Dong, Juncai; Zheng, Xusheng; Wang, Yu; Yan, Wensheng; Chen, Chen; Peng, Qing; Wang, Dingsheng; Li, Yadong

2018-03-01

Isolated single atomic site catalysts have attracted great interest due to their remarkable catalytic properties. Because of their high surface energy, single atoms are highly mobile and tend to form aggregate during synthetic and catalytic processes. Therefore, it is a significant challenge to fabricate isolated single atomic site catalysts with good stability. Herein, a gentle method to stabilize single atomic site metal by constructing defects on the surface of supports is presented. As a proof of concept, single atomic site Au supported on defective TiO 2 nanosheets is prepared and it is discovered that (1) the surface defects on TiO 2 nanosheets can effectively stabilize Au single atomic sites through forming the Ti-Au-Ti structure; and (2) the Ti-Au-Ti structure can also promote the catalytic properties through reducing the energy barrier and relieving the competitive adsorption on isolated Au atomic sites. It is believed that this work paves a way to design stable and active single atomic site catalysts on oxide supports. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

7 CFR 1924.115 - Single Family Housing site evaluation.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 12 2011-01-01 2011-01-01 false Single Family Housing site evaluation. 1924.115 Section 1924.115 Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING... Work § 1924.115 Single Family Housing site evaluation. (a) Site review. The site approval official will...

7 CFR 1924.115 - Single Family Housing site evaluation.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 12 2010-01-01 2010-01-01 false Single Family Housing site evaluation. 1924.115... SERVICE, RURAL BUSINESS-COOPERATIVE SERVICE, RURAL UTILITIES SERVICE, AND FARM SERVICE AGENCY, DEPARTMENT... Work § 1924.115 Single Family Housing site evaluation. (a) Site review. The site approval official will...

Zr 2Ir 6B with an eightfold superstructure of the cubic perovskite-like boride ZrIr 3B 0.5: Synthesis, crystal structure and bonding analysis

NASA Astrophysics Data System (ADS)

Hermus, Martin; Fokwa, Boniface P. T.

2010-04-01

Single phase powder samples and single crystals of Zr 2Ir 6B were successfully synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere. Superstructure reflections were observed both on powder and on single crystal diffraction data, leading to an eightfold superstructure of ZrIr 3B x phase. The new phase, which has a metallic luster, crystallizes in space group Fm3¯m (no. 225) with the lattice parameters a=7.9903(4) Å, V=510.14(4) Å 3. Its crystal structure was refined on the basis of powder as well as single crystal data. The single crystal refinement converged to R1=0.0239 and w R2=0.0624 for all 88 unique reflections and 6 parameters. Zr 2Ir 6B is isotypic to Ti 2Rh 6B and its structure can be described as a defect double perovskite, A2BB' O6, where the A site is occupied by zirconium, the B site by boron, the O site by iridium but the B' site is vacant, leading to the formation of empty and boron-filled octahedral Ir 6 clusters. According to the result of tight-binding electronic structure calculations, Ir-B and Ir-Zr interactions are mainly responsible for the structural stability of the phase. According to COHP bonding analysis, the strongest bonding occurs for the Ir-B contacts, and the Ir-Ir bonding within the empty clusters is two times stronger than that in the BIr 6 octahedra.

Photoluminescence imaging of solitary dopant sites in covalently doped single-wall carbon nanotubes

DOE PAGES

Hartmann, Nicolai F.; Yalcin, Sibel Ebru; Adamska, Lyudmyla; ...

2015-11-11

Covalent dopants in semiconducting single wall carbon nanotubes (SWCNTs) are becoming important as routes for introducing new photoluminescent emitting states with potential for enhanced quantum yields, new functionality, and as species capable of near-IR room-temperature single photon emission. The origin and behavior of the dopant-induced emission is thus important to understand as a key requirement for successful room-T photonics and optoelectronics applications. Here, we use direct correlated two-color photoluminescence imaging to probe how the interplay between the SWCNT bright E 11 exciton and solitary dopant sites yields the dopant-induced emission for three different dopant species: oxygen, 4-methoxybenzene, and 4-bromobenzene. Wemore » introduce a route to control dopant functionalization to a low level as a means for introducing spatially well-separated solitary dopant sites. Resolution of emission from solitary dopant sites and correlation to their impact on E 11 emission allows confirmation of dopants as trapping sites for localization of E 11 excitons following their diffusive transport to the dopant site. Imaging of the dopant emission also reveals photoluminescence intermittency (blinking), with blinking dynamics being dependent on the specific dopant. Density functional theory calculations were performed to evaluate the stability of dopants and delineate the possible mechanisms of blinking. Furthermore, theoretical modeling suggests that the trapping of free charges in the potential well created by permanent dipoles introduced by dopant atoms/groups is likely responsible for the blinking, with the strongest effects being predicted and observed for oxygen-doped SWCNTs.« less

Entrapped Single Tungstate Site in Zeolite for Cooperative Catalysis of Olefin Metathesis with Brønsted Acid Site

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

Zhao, Pu; Ye, Lin; Sun, Zhenyu

Industrial olefin metathesis catalysts generally suffer from low reaction rates and require harsh reaction conditions for moderate activities. This is due to their inability to prevent metathesis active sites (MAS) from aggregation and their intrinsic poor adsorption and activation of olefin molecules. Here, isolated tungstate species as single molecular MAS is immobilized inside zeolite pores by Bronsted acid sites (BAS) on the inner surface. It is demonstrated for the first time that unoccupied BAS in atomic proximity to MAS enhance olefin adsorption and greatly facilitate the formation of metallocycle intermediates in a stereospecific manner. Thus, effective cooperative catalysis takes placemore » over the BAS-MAS pair. In consequence, for the cross-metathesis of ethene and trans-2-butene to propene, under the same mild reaction conditions, the propene production rate over WOx/USY is ca. 7,300 times that over the industrial WO3/SiO2 based catalyst. A propene yield up to 79% (80% selectivity) without observable deactivation was obtained over WOx/USY for a wide range of reaction conditions.« less

Homologous ligands accommodated by discrete conformations of a buried cavity

PubMed Central

Merski, Matthew; Fischer, Marcus; Balius, Trent E.; Eidam, Oliv; Shoichet, Brian K.

2015-01-01

Conformational change in protein–ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few substantial series of congeneric ligand complexes in the Protein Data Bank (PDB). Here we determine the structures of eight alkyl benzenes, in single-methylene increases from benzene to n-hexylbenzene, bound to an enclosed cavity in T4 lysozyme. The volume of the apo cavity suffices to accommodate benzene but, even with toluene, larger cavity conformations become observable in the electron density, and over the series two other major conformations are observed. These involve discrete changes in main-chain conformation, expanding the site; few continuous changes in the site are observed. In most structures, two discrete protein conformations are observed simultaneously, and energetic considerations suggest that these conformations are low in energy relative to the ground state. An analysis of 121 lysozyme cavity structures in the PDB finds that these three conformations dominate the previously determined structures, largely modeled in a single conformation. An investigation of the few congeneric series in the PDB suggests that discrete changes are common adaptations to a series of growing ligands. The discrete, but relatively few, conformational states observed here, and their energetic accessibility, may have implications for anticipating protein conformational change in ligand design. PMID:25847998

Homologous ligands accommodated by discrete conformations of a buried cavity.

PubMed

Merski, Matthew; Fischer, Marcus; Balius, Trent E; Eidam, Oliv; Shoichet, Brian K

2015-04-21

Conformational change in protein-ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few substantial series of congeneric ligand complexes in the Protein Data Bank (PDB). Here we determine the structures of eight alkyl benzenes, in single-methylene increases from benzene to n-hexylbenzene, bound to an enclosed cavity in T4 lysozyme. The volume of the apo cavity suffices to accommodate benzene but, even with toluene, larger cavity conformations become observable in the electron density, and over the series two other major conformations are observed. These involve discrete changes in main-chain conformation, expanding the site; few continuous changes in the site are observed. In most structures, two discrete protein conformations are observed simultaneously, and energetic considerations suggest that these conformations are low in energy relative to the ground state. An analysis of 121 lysozyme cavity structures in the PDB finds that these three conformations dominate the previously determined structures, largely modeled in a single conformation. An investigation of the few congeneric series in the PDB suggests that discrete changes are common adaptations to a series of growing ligands. The discrete, but relatively few, conformational states observed here, and their energetic accessibility, may have implications for anticipating protein conformational change in ligand design.

Urgent and Elective Robotic Single-Site Cholecystectomy: Analysis and Learning Curve of 150 Consecutive Cases.

PubMed

Kubat, Eric; Hansen, Nathan; Nguyen, Huy; Wren, Sherry M; Eisenberg, Dan

2016-03-01

The use of robotic single-site cholecystectomy has increased exponentially. There are few reports describing the safety, efficacy, and operative learning curve of robotic single-site cholecystectomy either in the community setting or with nonelective surgery. We performed a retrospective review of a prospective database of our initial experience with robotic single-site cholecystectomy. Demographics and perioperative outcomes were evaluated for both urgent and elective cholecystectomy. Cumulative sum analysis was performed to determine the surgeon's learning curve. One hundred fifty patients underwent robotic single-site cholecystectomy. Seventy-four (49.3%) patients underwent urgent robotic single-site cholecystectomy, and 76 (50.7%) underwent elective robotic single-site cholecystectomy. Mean total operative time for robotic single-site cholecystectomy was 83.3 ± 2.7 minutes. Mean operative time for the urgent cohort was significantly longer than for the elective cohort (95.0 ± 4.4 versus 71.9 ± 2.6 minutes; P < .001). There was one conversion in the urgent cohort and none in the elective cohort. There was one bile duct injury (0.7%) in the urgent cohort. Perioperative complications occurred in 8.7% of patients, and most consisted of superficial surgical-site infections. There were no incisional hernias detected. The surgeon's learning curve, inclusive of urgent and elective cases, was 48 operations. Robotic single-site cholecystectomy can be performed safely and effectively in both elective and urgent cholecystectomy with a reasonable learning curve and acceptable perioperative outcomes.

Evaluation of a Single-Beam Sonar System to Map Seagrass at Two Sites in Northern Puget Sound, Washington

USGS Publications Warehouse

Stevens, Andrew W.; Lacy, Jessica R.; Finlayson, David P.; Gelfenbaum, Guy

2008-01-01

Seagrass at two sites in northern Puget Sound, Possession Point and nearby Browns Bay, was mapped using both a single-beam sonar and underwater video camera. The acoustic and underwater video data were compared to evaluate the accuracy of acoustic estimates of seagrass cover. The accuracy of the acoustic method was calculated for three classifications of seagrass observed in underwater video: bare (no seagrass), patchy seagrass, and continuous seagrass. Acoustic and underwater video methods agreed in 92 percent and 74 percent of observations made in bare and continuous areas, respectively. However, in patchy seagrass, the agreement between acoustic and underwater video was poor (43 percent). The poor agreement between the two methods in areas with patchy seagrass is likely because the two instruments were not precisely colocated. The distribution of seagrass at the two sites differed both in overall percent vegetated and in the distribution of percent cover versus depth. On the basis of acoustic data, seagrass inhabited 0.29 km2 (19 percent of total area) at Possession Point and 0.043 km2 (5 percent of total area) at the Browns Bay study site. The depth distribution at the two sites was markedly different. Whereas the majority of seagrass at Possession Point occurred between -0.5 and -1.5 m MLLW, most seagrass at Browns Bay occurred at a greater depth, between -2.25 and -3.5 m MLLW. Further investigation of the anthropogenic and natural factors causing these differences in distribution is needed.

Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1.

PubMed

DeJong, Eric S; Chang, Chia-en; Gilson, Michael K; Marino, John P

2003-07-08

Rev is an essential regulatory HIV-1 protein that binds the Rev responsive element (RRE) within the env gene of the HIV-1 RNA genome, activating the switch between viral latency and active viral replication. Previously, we have shown that selective incorporation of the fluorescent probe 2-aminopurine (2-AP) into a truncated form of the RRE sequence (RRE-IIB) allowed the binding of an arginine-rich peptide derived from Rev and aminoglycosides to be characterized directly by fluorescence methods. Using these fluorescence and nuclear magnetic resonance (NMR) methods, proflavine has been identified, through a limited screen of selected small heterocyclic compounds, as a specific and high-affinity RRE-IIB binder which inhibits the interaction of the Rev peptide with RRE-IIB. Direct and competitive 2-AP fluorescence binding assays reveal that there are at least two classes of proflavine binding sites on RRE-IIB: a high-affinity site that competes with the Rev peptide for binding to RRE-IIB (K(D) approximately 0.1 +/- 0.05 microM) and a weaker binding site(s) (K(D) approximately 1.1 +/- 0.05 microM). Titrations of RRE-IIB with proflavine, monitored using (1)H NMR, demonstrate that the high-affinity proflavine binding interaction occurs with a 2:1 (proflavine:RRE-IIB) stoichiometry, and NOEs observed in the NOESY spectrum of the 2:1 proflavine.RRE-IIB complex indicate that the two proflavine molecules bind specifically and close to each other within a single binding site. NOESY data further indicate that formation of the 2:1 proflavine.RRE-IIB complex stabilizes base pairing and stacking within the internal purine-rich bulge of RRE-IIB in a manner analogous to what has been observed in the Rev peptide.RRE-IIB complex. The observation that proflavine competes with Rev for binding to RRE-IIB by binding as a dimer to a single high-affinity site opens the possibility for rational drug design based on linking and modifying it and related compounds.

Structural characterization of framework–gas interactions in the metal–organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction† †Electronic supplementary information (ESI) available: Supplementary figures, crystallographic information, adsorption isotherms and fits, CCDC 1530119–1530126. For ESI and crystallographic data in CIF or other electronic format. See DOI: 10.1039/c7sc00449d Click here for additional data file. Click here for additional data file.

PubMed Central

Gonzalez, Miguel I.; Mason, Jarad A.; Bloch, Eric D.; Teat, Simon J.; Gagnon, Kevin J.; Morrison, Gregory Y.; Queen, Wendy L.

2017-01-01

The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH4, N2, O2, Ar, and P4 adsorption in Co2(dobdc) (dobdc4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(ii) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(ii) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH4 and Co–Ar interactions observed in Co2(dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(ii) sites in Co2(dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol–1 (for Ar). Moreover, the structures of Co2(dobdc)·3.8N2, Co2(dobdc)·5.9O2, and Co2(dobdc)·2.0Ar reveal the location of secondary (N2, O2, and Ar) and tertiary (O2) binding sites in Co2(dobdc), while high-pressure CO2, CO, CH4, N2, and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures. PMID:28966783

Learning Spaces and Collaborative Work: Barriers or Supports?

ERIC Educational Resources Information Center

King, Hayley

2016-01-01

Drawing on 18 months of fieldwork, this article discusses the use of physical, virtual and social space to support collaborative work in translator education programs. The study adopted a contrastive ethnography approach that incorporated single- and multiple-case design rationales for site selection. Extended observation, informal chats and…

Hole pairing and thermodynamic properties of the two dimensional frustrated t-J model

NASA Astrophysics Data System (ADS)

Roy, K.; Pal, P.; Nath, S.; Ghosh, N. K.

2018-04-01

The frustrated t-J model is investigated by using the exact-diagonalization (ED) method on an 8-site cluster. The effect on next-nearest-neighbor (NNN) exchange interaction J' (frustration) on the hole pairing and the thermodynamic properties of the system is considered. Two holes initially remain unbound at smaller value of J'/t, but tend to bind at larger value. The maximum possibility of pair formation has been observed to be at NNN sites. Entropy calculation shows that the system goes to more disordered state with J'. The specific heat curves show a single peak structure. A decrease in effective exchange energy is observed due to the frustration.

Quantum Gas Microscope for Fermionic Atoms

NASA Astrophysics Data System (ADS)

Okan, Melih; Cheuk, Lawrence; Nichols, Matthew; Lawrence, Katherine; Zhang, Hao; Zwierlein, Martin

2016-05-01

Strongly interacting fermions define the properties of complex matter throughout nature, from atomic nuclei and modern solid state materials to neutron stars. Ultracold atomic Fermi gases have emerged as a pristine platform for the study of many-fermion systems. In this poster we demonstrate the realization of a quantum gas microscope for fermionic 40 K atoms trapped in an optical lattice and the recent experiments which allows one to probe strongly correlated fermions at the single atom level. We combine 3D Raman sideband cooling with high- resolution optics to simultaneously cool and image individual atoms with single lattice site resolution at a detection fidelity above 95%. The imaging process leaves the atoms predominantly in the 3D motional ground state of their respective lattice sites, inviting the implementation of a Maxwell's demon to assemble low-entropy many-body states. Single-site resolved imaging of fermions enables the direct observation of magnetic order, time resolved measurements of the spread of particle correlations, and the detection of many-fermion entanglement. NSF, AFOSR-PECASE, AFOSR-MURI on Exotic Phases of Matter, ARO-MURI on Atomtronics, ONR, a Grant from the Army Research Office with funding from the DARPA OLE program, and the David and Lucile Packard Foundation.

Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy.

PubMed

Baumann, Fabian; Bauer, Magnus S; Milles, Lukas F; Alexandrovich, Alexander; Gaub, Hermann E; Pippig, Diana A

2016-01-01

Strep-Tactin, an engineered form of streptavidin, binds avidly to the genetically encoded peptide Strep-tag II in a manner comparable to streptavidin binding to biotin. These interactions have been used in protein purification and detection applications. However, in single-molecule studies, for example using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), the tetravalency of these systems impedes the measurement of monodispersed data. Here, we introduce a monovalent form of Strep-Tactin that harbours a unique binding site for Strep-tag II and a single cysteine that allows Strep-Tactin to specifically attach to the atomic force microscope cantilever and form a consistent pulling geometry to obtain homogeneous rupture data. Using AFM-SMFS, the mechanical properties of the interaction between Strep-tag II and monovalent Strep-Tactin were characterized. Rupture forces comparable to biotin:streptavidin unbinding were observed. Using titin kinase and green fluorescent protein, we show that monovalent Strep-Tactin is generally applicable to protein unfolding experiments. We expect monovalent Strep-Tactin to be a reliable anchoring tool for a range of single-molecule studies.

Single crystal X-ray diffraction study of the HgBa2CuO4+δ superconducting compound

NASA Astrophysics Data System (ADS)

Bordet, P.; Duc, F.; Lefloch, S.; Capponi, J. J.; Alexandre, E.; Rosa-Nunes, M.; Antipov, E. V.; Putilin, S.

1996-02-01

A high precision X-ray diffraction analysis up to sin θ/λ = 1.15 of a HgBa2CuO4+δ single crystal having a Tc of ~ 90 K is presented. The cell parameters are a = 3.8815(4), c = 9.485 (7) Å. The refinements indicate the existence of a split barium site due to the presence of excess oxygen in the mercury layer. The position of this excess oxygen might be slightly displaced from the (1/2 1/2 0) position. A 6% mercury deficiency is observed. Models, including mercury defects, substitution by copper cations, or carbonate groups, are compared. However, we obtain no definite evidence for either of the three models. A possible disorder of the Hg position, due to the formation of chemical bonds with neighbouring extra oxygen anions, could correlate to the refinements of mixed species at the Hg site. A low temperature single crystal x-ray diffraction study, and comparison of refinements for the same single crystal with different extra oxygen contents, are in progress to help clarify this problem.

Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy

NASA Astrophysics Data System (ADS)

Baumann, Fabian; Bauer, Magnus S.; Milles, Lukas F.; Alexandrovich, Alexander; Gaub, Hermann E.; Pippig, Diana A.

2016-01-01

Strep-Tactin, an engineered form of streptavidin, binds avidly to the genetically encoded peptide Strep-tag II in a manner comparable to streptavidin binding to biotin. These interactions have been used in protein purification and detection applications. However, in single-molecule studies, for example using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), the tetravalency of these systems impedes the measurement of monodispersed data. Here, we introduce a monovalent form of Strep-Tactin that harbours a unique binding site for Strep-tag II and a single cysteine that allows Strep-Tactin to specifically attach to the atomic force microscope cantilever and form a consistent pulling geometry to obtain homogeneous rupture data. Using AFM-SMFS, the mechanical properties of the interaction between Strep-tag II and monovalent Strep-Tactin were characterized. Rupture forces comparable to biotin:streptavidin unbinding were observed. Using titin kinase and green fluorescent protein, we show that monovalent Strep-Tactin is generally applicable to protein unfolding experiments. We expect monovalent Strep-Tactin to be a reliable anchoring tool for a range of single-molecule studies.

Leveraging Oceanic and Surface Intensive Field Campaign Data Sets for Validation and Improvement of Recent Hyperspectral IR Satellite Data Products

NASA Astrophysics Data System (ADS)

Joseph, E.; Nalli, N. R.; Oyola, M. I.; Morris, V. R.; Sakai, R.

2014-12-01

An overview is given of research to validate or improve the retrieval of environmental data records (EDRs) from recently deployed hyperspectral IR satellite sensors such as Suomi NPP Cross-track Infrared Microwave Sounder Suite (CrIMSS). The effort centers around several surface field intensive campaigns that are designed or leveraged for EDR validation. These data include ship-based observations of upper air ozone, pressure, temperature and relative humidity soundings; aerosol and cloud properties; and sea surface temperature. Similar intensive data from two land-based sites are also utilized as well. One site, the Howard University Beltsville site, is at a single point location but has a comprehensive array of observations for an extended period of time. The other land site, presently being deployed by the University at Albany, is under development with limited upper air soundings but will have regionally distributed surface based microwave profiling of temperature and relative humidity on the scale of 10 - 50 km and other standard meteorological observations. Combined these observations provide data that are unique in their wide range including, a variety of meteorological conditions and atmospheric compositions over the ocean and urban-suburban environments. With the distributed surface sites the variability of atmospheric conditions are captured concurrently across a regional spatial scale. Some specific examples are given of comparisons of moisture and temperature correlative EDRs from the satellite sensors and surface based observations. An additional example is given of the use of this data to correct sea surface temperature (SST) retrieval biases from the hyperspectral IR satellite observations due to aerosol contamination.

Mechanisms for Ductile Rupture - FY16 ESC Progress Report

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

Boyce, Brad L.; Carroll, Jay D.; Noell, Phillip

2017-01-01

Ductile rupture in metals is generally a multi-step process of void nucleation, growth, and coalescence. Particle decohesion and particle fracture are generally invoked as the primary microstructural mechanisms for room-temperature void nucleation. However, because high-purity materials also fail by void nucleation and coalescence, other microstructural features must also act as sites for void nucleation. Early studies of void initiation in high-purity materials, which included post-mortem fracture surface characterization using scanning electron microscopy (SEM) and high-voltage electron microscopy (HVEM) and in-situ HVEM observations of fracture, established the presence of dislocation cell walls as void initiation sites in high-purity materials. Direct experimentalmore » evidence for this contention was obtained during in-situ HVEM tensile tests of Be single crystals. Voids between 0.2 and 1 μm long appeared suddenly along dislocation cell walls during tensile straining. However, subsequent attempts to replicate these results in other materials, particularly α -Fe single crystals, were unsuccessful because of the small size of the dislocation cells, and these remain the only published in-situ HVEM observations of void nucleation at dislocation cell walls in the absence of a growing macrocrack. Despite this challenge, other approaches to studying void nucleation in high-purity metals also indicate that dislocation cell walls are nucleation sites for voids.« less

A varying T cell subtype explains apparent tobacco smoking induced single CpG hypomethylation in whole blood.

PubMed

Bauer, Mario; Linsel, Gunter; Fink, Beate; Offenberg, Kirsten; Hahn, Anne Maria; Sack, Ulrich; Knaack, Heike; Eszlinger, Markus; Herberth, Gunda

2015-01-01

Many recent epigenetic studies report that cigarette smoking reduces DNA methylation in whole blood at the single CpG site cg19859270 within the GPR15 gene. Within two independent cohorts, we confirmed the differentially expression of the GPR15 gene when smokers and non-smokers subjects are compared. By validating the GPR15 protein expression at the cellular level, we found that the observed decreased methylation at this site in white blood cells (WBC) of smokers is mainly caused by the high proportion of CD3+GPR15+ expressing T cells in peripheral blood. In current smokers, the percentage of GPR15+ cells among CD3+ T cells in peripheral blood is significantly higher (15.5 ± 7.2 %, mean ± standard deviation) compared to non-smokers (3.7 ± 1.6 %). Treatment of peripheral blood mononuclear cell (PBMC) cultures with aqueous cigarette smoke extract did not induce a higher proportion of this T cell subtype. Our results underline that DNA hypomethylation at cg19859270 site, observed in WBCs of smokers, did not arise by direct effect of tobacco smoking compounds on methylation of DNA but rather by the enrichment of a tobacco-smoking-induced lymphocyte population in the peripheral blood.

Three-stage nucleation and growth of Ge self-assembled quantum dots grown on partially relaxed SiGe buffer layers

NASA Astrophysics Data System (ADS)

Kim, H. J.; Zhao, Z. M.; Xie, Y. H.

2003-11-01

Three-stage nucleation and growth of Ge self-assembled quantum dots (SAQDs) on a relaxed SiGe buffer layer has been studied. Plastic relaxation of the SiGe buffer layer is associated with a network of buried 60° dislocations leading to an undulating strain field. As a result, the surface possesses three different types of sites for the nucleation and growth of Ge SAQDs: over the intersection of two perpendicular buried dislocations, over a single dislocation line, and in the region beyond one diffusion length away from any dislocation. Ge SAQDs are observed to nucleate exclusively over the dislocation intersections first, followed by over single dislocation lines, and finally in the region far away from dislocations. By increasing the Ge coverage at a slow rate, the prenucleation stage at the various sites is observed. It appears that the varying strain field has a significant effect on both the diffusion of Ge adatoms before SAQD nucleation, as well as the shape evolution of the SAQDs after they form. Moreover, two distinctly different self-assembly mechanisms are observed at different sites. There exist denuded zones free of Ge SAQDs adjacent to dislocation lines. The width of the denuded zone can be used to make direct determination of the Ge adatom diffusion lengths. The partially relaxed substrate provides a useful experimental vehicle for the in-depth understanding of the formation mechanism of SAQDs grown epitaxially in the Stranski-Krastanov growth mode.

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

Adamson, P.; Bishai, M.; Diwan, M. V.

We report the first observation of seasonal modulations in the rates of cosmic ray multiple-muon events at two underground sites, the MINOS Near Detector with an overburden of 225 mwe, and the MINOS Far Detector site at 2100 mwe. At the deeper site, multiple-muon events with muons separated by more than 8 m exhibit a seasonal rate that peaks during the summer, similar to that of single-muon events. Conversely, the rate of multiple-muon events with muons separated by less than 5–8 m, and the rate of multiple-muon events in the smaller, shallower Near Detector, exhibit a seasonal rate modulation thatmore » peaks in the winter.« less

Site occupation of indium and jump frequencies of cadmium in FeGa 3

NASA Astrophysics Data System (ADS)

Newhouse, Randal; Collins, Gary S.; Zacate, Matthew O.

2016-12-01

Perturbed angular correlation (PAC) measurements using the In-111 probe were carried out on FeGa3 as part of a broader investigation of indium site occupation and cadmium diffusion in intermetallic compounds. One PAC signal was observed with hyperfine parameters ω 1= 513.8(1) Mrad/s and η= 0.939(2) at room temperature. By comparison with quadrupole frequencies observed in PAC measurements on isostructural RuIn3, it was determined that indium occupies only the 8j site in the FeGa3 structure, denoted Ga(2) below because two out of the three Ga sites have this point symmetry. PAC spectra at elevated temperature exhibited damping characteristic of electric field gradients (EFGs) that fluctuate as Cd probes jump among Ga(2) sites within the lifetime of the excited PAC level. A stochastic model for the EFG fluctuations based on four conceivable, single-step jump-pathways connecting one Ga(2) site to neighboring Ga(2) sites was developed and used to fit PAC spectra. The four pathways lead to two observable EFG reorientation rates, and these reorientation rates were found to be strongly dependent on EFG orientation. Calculations using density functional theory were used to reduce the number of unknowns in the model with respect to EFG orientation. This made it possible to determine with reasonable precision the total jump rate of Cd among Ga(2) sites that correspond to a change in mirror plane orientation of site-symmetry. This total jump rate was found to be thermally activated with an activation enthalpy of 1.8 ±0.1 eV.

Satellite Ephemeris Correction via Remote Site Observation for Star Tracker Navigation Performance Improvement

DTIC Science & Technology

2016-03-01

squared RMS root mean squared GCRF Geocentric Celestial Reference Frame xi List of Figures Figure Page 1 Geometry of single observation...RA and DEC in the celestial sphere. The Geocentric Celestial Reference Frame (GCRF) is the standard geocentric frame that measures the RA east in the...Figure 2. Right ascension (α) and declination (δ) in the celestial sphere[6] 7 made between geocentric and topocentric angles. Geocentric is referred to

Deciphering the complexation process of a fluoroquinolone antibiotic, levofloxacin, with bovine serum albumin in the presence of additives

NASA Astrophysics Data System (ADS)

Kaur, Amandeep; Khan, Imran Ahmd; Banipal, Parampaul Kaur; Banipal, Tarlok Singh

2018-02-01

The current work aims to explore the thermodynamic and conformational aspects for the binding of fluoroquinolone antibacterial drug, levofloxacin (LFC), with bovine serum albumin (BSA) using calorimetric, spectroscopic (UV-visible, fluorescence, circular dichroism, and 1H NMR), dynamic light scattering (DLS) and computational methods (molecular docking). The binding of LFC with BSA at two sequential sites with higher affinity ( 103 M- 1) at the first site has been explored by calorimetry whereas the binding at a single site with affinity of the order of 104 M- 1 has been observed from fluorescence spectroscopy. The calorimetric study in the presence of additives along with docking analysis reveals the significant role of electrostatic, hydrogen bonding, and hydrophobic interactions in the association process. The slight conformational changes in protein as well as the changes in the water network structure around the binding cavity of protein have been observed from spectroscopic and DLS measurements. The LFC induced quenching of BSA fluorescence was observed to be initiated mainly through the static quenching process and this suggests the formation of ground state LFC-BSA association complex. The stronger interactions of LFC in the cavity of Sudlow site I (subdomain IIA) of protein have been explored from site marker calorimetric and molecular docking study.

On the dynamical nature of the active center in a single-site photocatalyst visualized by 4D ultrafast electron microscopy

PubMed Central

Yoo, Byung-Kuk; Su, Zixue; Thomas, John Meurig; Zewail, Ahmed H.

2016-01-01

Understanding the dynamical nature of the catalytic active site embedded in complex systems at the atomic level is critical to developing efficient photocatalytic materials. Here, we report, using 4D ultrafast electron microscopy, the spatiotemporal behaviors of titanium and oxygen in a titanosilicate catalytic material. The observed changes in Bragg diffraction intensity with time at the specific lattice planes, and with a tilted geometry, provide the relaxation pathway: the Ti4+=O2− double bond transformation to a Ti3+−O1− single bond via the individual atomic displacements of the titanium and the apical oxygen. The dilation of the double bond is up to 0.8 Å and occurs on the femtosecond time scale. These findings suggest the direct catalytic involvement of the Ti3+−O1− local structure, the significance of nonthermal processes at the reactive site, and the efficient photo-induced electron transfer that plays a pivotal role in many photocatalytic reactions. PMID:26729878

Seismic Anisotropy Beneath Eastern North America: Results from Multi-Event Inversion

NASA Astrophysics Data System (ADS)

Li, Y.; Levin, V. L.; Chen, X.

2017-12-01

Seismic anisotropy observed from the split core-refracted shear phases reflects upper mantle deformation. To characterize anisotropic signatures beneath eastern North America, we collected observations along a 1300 km long array from James Bay to the Fundy Basin. The averaged splitting parameters of individual sites show uniform fast polarization orientation of 80° and delay times linearly decreasing from 1.0 s in the Appalachians to 0.5 s in the Superior Province. We also see directional variation of fast polarizations at most sites, which is a likely effect of vertical changes in anisotropic properties. For sites with 10 or more observations, we used a multi-event inversion technique to solve for the underlying anisotropic structure. The technique considers the NULL observations from single-event analysis that are excluded from the averaged splitting parameters. For models with a single 100 km thick anisotropic layer with a horizontal fast axis, we find up to 6% of anisotropy in the Appalachian Orogen, equivalent to a splitting delay time of 1.5 s. Anisotropy strength reduces to 1.8% in the Superior Province, equivalent to delay times under 0.5 s. The overall decrease in anisotropic strength is modified by local changes of up to 2%, suggesting small-scale local variations near the surface. Orientations of the fast axes change from 60° in the Appalachian Orogen to 90° in the Superior Province, and are also modulated by local deviations. In the Appalachian Orogen the fast axes are close to the absolute plate motion in a hot-spot reference frame, while those in the Superior Province differ from it by almost 30°. Average values of splitting delays agree well with results of inversions in the Superior Province, and diverge in the Appalachians. Conversely, averaged fast polarizations match inversion results in the Appalachians, and are systematically different in the Superior Province. For an set of sites with recording periods exceeding 5 years, we will test more complicated models of anisotropy, including dipping fast axes and multiple layers. Figure 1. The best fit anisotropic parameters, orientations of fast axes (top) and strength of anisotropy (bottom), assuming a single 100 km thick horizontal layer with a horizontal fast axis. The red line in top represents the absolute plate motion in a hot spot reference frame.

Characteristics of chronic pain associated with sleep difficulty in the older population: The MOBILIZE Boston Study

PubMed Central

Chen, Qian; Hayman, Laura L.; Shmerling, Robert H.; Bean, Jonathan F.; Leveille, Suzanne G.

2012-01-01

Objectivers To evaluate pain severity and distribution in relation to sleep difficulty in older adults. Design Population-based cross-sectional study Setting Community within a 5-mile radius of the study center at the Institute for Aging Research, Hebrew SeniorLife (HSL) in Boston Participants 765 participants of the Maintenance of Balance, Independent Living, Intellect, and Zest in the Elderly (MOBILIZE) Boston Study, aged 64 and older. Measurements Pain severity was measured using the Brief Pain Inventory (BPI), Pain Severity Subscale. Musculoskeletal pain distribution was grouped according to no pain, single site, ≥2 sites, and widespread pain (upper and lower extremities and back pain). We measured 3 aspects of sleep difficulty using items from the CESD-R (trouble getting to sleep, sleep more than usual, and restless sleep). Results Prevalence of trouble getting to sleep according to BPI severity was 17.8%, 19.7%, 32.0%, and 37.0% for the lowest to highest pain severity quartiles, respectively. Similar relationships between pain and sleep were observed across sleep measures according to pain severity and distribution. Adjusted for sociodemographic characteristics, chronic conditions and health behaviors, chronic pain was strongly associated with trouble sleeping (≥1d/week), (single site pain, OR=1.77, 95%CI, 1.10–2.87; multisite pain OR=2.38, 95% CI, 1.48–3.83; and widespread pain, OR=2.55, 95% CI, 1.43–4.54, each compared with no pain). Similar associations were observed for restless sleep and sleeping more than usual. With specific pain sites alone or in combination with other sites of pain, only modest associations were observed with sleep problems. Conclusion Widespread or other multisite pain and moderate to severe pain are strongly associated with sleep difficulty in older adults. Further research is needed to better understand the burden and consequences of pain-related sleep problems in the older population. PMID:21806564

Cooperative communication within and between single nanocatalysts

NASA Astrophysics Data System (ADS)

Zou, Ningmu; Zhou, Xiaochun; Chen, Guanqun; Andoy, Nesha May; Jung, Won; Liu, Guokun; Chen, Peng

2018-06-01

Enzymes often show catalytic allostery in which reactions occurring at different sites communicate cooperatively over distances of up to a few nanometres. Whether such effects can occur with non-biological nanocatalysts remains unclear, even though these nanocatalysts can undergo restructuring and molecules can diffuse over catalyst surfaces. Here we report that phenomenologically similar, but mechanistically distinct, cooperative effects indeed exist for nanocatalysts. Using spatiotemporally resolved single-molecule catalysis imaging, we find that catalytic reactions on a single Pd or Au nanocatalyst can communicate with each other, probably via hopping of positively charged holes on the catalyst surface, over 102 nanometres and with a temporal memory of 101 to 102 seconds, giving rise to positive cooperativity among its surface active sites. Similar communication is also observed between individual nanocatalysts, however it operates via a molecular diffusion mechanism involving negatively charged product molecules, and its communication distance is many micrometres. Generalization of these long-range intra- and interparticle catalytic communication mechanisms may introduce a novel conceptual framework for understanding nanoscale catalysis.

Point defects in crystalline zircon (zirconium silicate), ZrSiO4: electron paramagnetic resonance studies

NASA Astrophysics Data System (ADS)

Tennant, W. C.; Claridge, R. F. C.; Walsby, C. J.; Lees, N. S.

This article outlines the present state of knowledge of paramagnetic defects in crystalline zircon as obtained mainly, but not exclusively, from electron paramagnetic resonance (EPR) studies in crystalline zircon (zirconium silicate, ZrSiO4). The emphasis is on single-crystal studies where, in principle, unambiguous analysis is possible. Firstly, the crystallography of zircon is presented. Secondly, the relationships between available crystal-site symmetries and the symmetries of observed paramagnetic species in zircon, and how these observations lead to unambiguous assignments of point-group symmetries for particular paramagnetic species are detailed. Next, spin-Hamiltonian (SH) analysis is discussed with emphasis on the symmetry relationships that necessarily exist amongst the Laue classes of the crystal sites in zircon, the paramagnetic species occupying those sites and the SH itself. The final sections of the article then survey the results of EPR studies on zircon over the period 1960-2002.

Anisotropic magnetic susceptibility of erbium and ytterbium in zircon, ZrSiO4

USGS Publications Warehouse

Thorpe, A.N.; Briggs, Charles; Tsang, T.; Senftle, F.; Alexander, Corrine

1977-01-01

Magnetic susceptibility measurements have been made for both Er- and Yb-doped (1̃03ppm) zircon single crystals with the magnetic field perpendicular and parallel to the [001] axis. Large susceptibility anisotropies were found in both cases. Our observed anisotropies of ZrSiO4: Yb indicate small populations (1̃9%) of Yb ions at the axial (tetragonal) sites, as the susceptibility of ZrSiO4: Yb would be nearly isotropic if the Yb ions only occupied the orthorhombic sites. For Er3+ in orthorhombic sites of zircon, our data indicate that the first excited state is paramagnetic with gx = 9 and gy 5̃ at 20 cm-1 above the ground state (gx 0̃, gy 1̃5). The first excited state is quite similar to the ground states observed for Er3+ in many host lattices. ?? 1977.

Tips on robotic single-site surgery suture technique: Screwing and clockwise direction suture technique for Robotic single-site surgery.

PubMed

Moon, Hye-Sung

2018-06-01

Using the da Vinci single-site platform, surgeons can perform more minimally invasive surgery. However, surgical challenges exist due to the limitations of single-site instrumental movements. To aid in the performance of successful robotic single-site hysterectomy, a new suturing technique using the current set of limited instruments is introduced in this study. New vaginal cuff suturing techniques have been used in 55 robotic single-site hysterectomies in our institute over the past 2 years. A needle driver approach utilizing screwing and advancing the needle driver in the correct direction at an increasing angle from the transverse cuff margin with dragging and formation of an adequate loop of thread was used when suturing the vaginal cuff. Using the new vaginal suturing techniques, easy and firm vaginal cuff closure with reduced operative time relative to previous hysterectomies was achieved. The new vaginal cuff suturing techniques may convince more surgeons to perform robotic single-site hysterectomies more frequently and with greater ease. Copyright © 2018. Published by Elsevier B.V.

Growth and structural characterization of single crystals of the magnetic superconductor Ru1-xSr2-yGd1+yCu2+xO8-δ (RuGd-1212) obtained by the partial melting technique

NASA Astrophysics Data System (ADS)

Yamaki, K.; Bamba, Y.; Mochiku, T.; Funahashi, S.; Matsushita, Y.; Irie, A.

2018-05-01

In this study, cubic single crystals of the magnetic superconductor Ru1-xSr2-yGd1+yCu2+xO8-δ (RuGd-1212) with typical dimensions of 100-150 μm in length were grown by the partial melting technique. Multiple 00l reflections were first observed by XRD measurements of the bulk RuGd-1212 single crystals. The resistivity of the obtained crystals was roughly estimated to be ∼24-80 mΩ cm and no superconducting transition was observed down to 4.2 K. From the XRD measurements and refinement of the crystal structure, it was apparent that the Ru and Sr sites of the single-crystal RuGd-1212 were partially substituted by Cu and Gd, respectively. Oxygen defects were found to be minor (δ ≈ 0.1). The lattice parameters a and c of the single crystals were found to be larger and smaller, respectively, than those of a polycrystalline sample.

Evaluating the utility of hexapod species for calculating a confidence interval about a succession based postmortem interval estimate.

PubMed

Perez, Anne E; Haskell, Neal H; Wells, Jeffrey D

2014-08-01

Carrion insect succession patterns have long been used to estimate the postmortem interval (PMI) during a death investigation. However, no published carrion succession study included sufficient replication to calculate a confidence interval about a PMI estimate based on occurrence data. We exposed 53 pig carcasses (16±2.5 kg), near the likely minimum needed for such statistical analysis, at a site in north-central Indiana, USA, over three consecutive summer seasons. Insects and Collembola were sampled daily from each carcass for a total of 14 days, by this time each was skeletonized. The criteria for judging a life stage of a given species to be potentially useful for succession-based PMI estimation were (1) nonreoccurrence (observed during a single period of presence on a corpse), and (2) found in a sufficiently large proportion of carcasses to support a PMI confidence interval. For this data set that proportion threshold is 45/53. Of the 266 species collected and identified, none was nonreoccuring in that each showed at least a gap of one day on a single carcass. If the definition of nonreoccurrence is relaxed to include such a single one-day gap the larval forms of Necrophilaamericana, Fanniascalaris, Cochliomyia macellaria, Phormiaregina, and Luciliaillustris satisfied these two criteria. Adults of Creophilus maxillosus, Necrobiaruficollis, and Necrodessurinamensis were common and showed only a few, single-day gaps in occurrence. C.maxillosus, P.regina, and L.illustris displayed exceptional forensic utility in that they were observed on every carcass. Although these observations were made at a single site during one season of the year, the species we found to be useful have large geographic ranges. We suggest that future carrion insect succession research focus only on a limited set of species with high potential forensic utility so as to reduce sample effort per carcass and thereby enable increased experimental replication. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Transport properties of carbon dioxide and methane from molecular dynamics simulations.

PubMed

Aimoli, C G; Maginn, E J; Abreu, C R A

2014-10-07

Transport properties of carbon dioxide and methane are predicted for temperatures between (273.15 and 573.15) K and pressures up to 800 MPa by molecular dynamics simulations. Viscosities and thermal conductivities were obtained through the Green-Kubo formalism, whereas the Einstein relation was used to provide self-diffusion coefficient estimates. The differences in property predictions due to the force field nature and parametrization were investigated by the comparison of seven different CO2 models (two single-site models, three rigid three-site models, and two fully flexible three-site models) and three different CH4 models (two single-site models and one fully flexible five-site model). The simulation results show good agreement with experimental data, except for thermal conductivities at low densities. The molecular structure and force field parameters play an important role in the accuracy of the simulations, which is within the experimental deviations reported for viscosities and self-diffusion coefficients considering the most accurate CO2 and CH4 models studied. On the other hand, the molecular flexibility does not seem to improve accuracy, since the explicit account of vibrational and bending degrees of freedom in the CO2 flexible models leads to slightly less accurate results. Nonetheless, the use of a correctional term to account for vibrational modes in rigid models generally improves estimations of thermal conductivity values. At extreme densities, the caging effect observed with single-site representations of the molecules restrains mobility and leads to an unphysical overestimation of viscosities and, conversely, to the underestimation of self-diffusion coefficients. This result may help to better understand the limits of applicability of such force fields concerning structural and transport properties of dense systems.

Gingival abrasion and recession in manual and oscillating-rotating power brush users.

PubMed

Rosema, N A M; Adam, R; Grender, J M; Van der Sluijs, E; Supranoto, S C; Van der Weijden, G A

2014-11-01

To assess gingival recession (GR) in manual and power toothbrush users and evaluate the relationship between GR and gingival abrasion scores (GA). This was an observational (cross-sectional), single-centre, examiner-blind study involving a single-brushing exercise, with 181 young adult participants: 90 manual brush users and 91 oscillating-rotating power brush users. Participants were assessed for GR and GA as primary response variables. Secondary response variables were the level of gingival inflammation, plaque score reduction and brushing duration. Pearson correlation was used to describe the relationship between number of recession sites and number of abrasions. Prebrushing (baseline) and post-brushing GA and plaque scores were assessed and differences analysed using paired tests. Two-sample t-test was used to analyse group differences; ancova was used for analyses of post-brushing changes with baseline as covariate. Overall, 97.8% of the study population had at least one site of ≥1 mm of gingival recession. For the manual group, this percentage was 98.9%, and for the power group, this percentage was 96.7% (P = 0.621). Post-brushing, the power group showed a significantly smaller GA increase than the manual group (P = 0.004); however, there was no significant correlation between number of recession sites and number of abrasions for either group (P ≥ 0.327). Little gingival recession was observed in either toothbrush user group; the observed GR levels were comparable. Lower post-brushing gingival abrasion levels were seen in the power group. There was no correlation between gingival abrasion as a result of brushing and the observed gingival recession following use of either toothbrush. © 2014 The Authors International Journal of Dental Hygiene Published by John Wiley & Sons Ltd.

Gingival abrasion and recession in manual and oscillating–rotating power brush users

PubMed Central

Rosema, NAM; Adam, R; Grender, JM; Van der Sluijs, E; Supranoto, SC; Van der Weijden, GA

2014-01-01

Objective To assess gingival recession (GR) in manual and power toothbrush users and evaluate the relationship between GR and gingival abrasion scores (GA). Methods This was an observational (cross-sectional), single-centre, examiner-blind study involving a single-brushing exercise, with 181 young adult participants: 90 manual brush users and 91 oscillating–rotating power brush users. Participants were assessed for GR and GA as primary response variables. Secondary response variables were the level of gingival inflammation, plaque score reduction and brushing duration. Pearson correlation was used to describe the relationship between number of recession sites and number of abrasions. Prebrushing (baseline) and post-brushing GA and plaque scores were assessed and differences analysed using paired tests. Two-sample t-test was used to analyse group differences; ancova was used for analyses of post-brushing changes with baseline as covariate. Results Overall, 97.8% of the study population had at least one site of ≥1 mm of gingival recession. For the manual group, this percentage was 98.9%, and for the power group, this percentage was 96.7% (P = 0.621). Post-brushing, the power group showed a significantly smaller GA increase than the manual group (P = 0.004); however, there was no significant correlation between number of recession sites and number of abrasions for either group (P ≥ 0.327). Conclusions Little gingival recession was observed in either toothbrush user group; the observed GR levels were comparable. Lower post-brushing gingival abrasion levels were seen in the power group. There was no correlation between gingival abrasion as a result of brushing and the observed gingival recession following use of either toothbrush. PMID:24871587

Metal–organic and covalent organic frameworks as single-site catalysts

PubMed Central

Rogge, S. M. J.; Bavykina, A.; Hajek, J.; Garcia, H.; Olivos-Suarez, A. I.; Sepúlveda-Escribano, A.; Vimont, A.; Clet, G.; Bazin, P.; Kapteijn, F.

2017-01-01

Heterogeneous single-site catalysts consist of isolated, well-defined, active sites that are spatially separated in a given solid and, ideally, structurally identical. In this review, the potential of metal–organic frameworks (MOFs) and covalent organic frameworks (COFs) as platforms for the development of heterogeneous single-site catalysts is reviewed thoroughly. In the first part of this article, synthetic strategies and progress in the implementation of such sites in these two classes of materials are discussed. Because these solids are excellent playgrounds to allow a better understanding of catalytic functions, we highlight the most important recent advances in the modelling and spectroscopic characterization of single-site catalysts based on these materials. Finally, we discuss the potential of MOFs as materials in which several single-site catalytic functions can be combined within one framework along with their potential as powerful enzyme-mimicking materials. The review is wrapped up with our personal vision on future research directions. PMID:28338128

Monomolecular Siloxane Film as a Model of Single Site Catalysts

DOE PAGES

Martynowycz, Michael W.; Hu, Bo; Kuzmenko, Ivan; ...

2016-09-06

Achieving structurally well-defined catalytic species requires a fundamental understanding of surface chemistry. Detailed structural characterization of the catalyst binding sites in situ, such as single site catalysts on silica supports, is technically challenging or even unattainable. Octadecyltrioxysilane (OTOS) monolayers formed from octadecyltrimethoxysilane (OTMS) at the air-liquid interface after hydrolysis and condensation at low pH were chosen as a model system of surface binding sites in silica-supported Zn 2+ catalysts. We characterize the system by grazing incidence X-ray diffraction, X-ray reflectivity (XR), and X-ray fluorescence spectroscopy (XFS). Previous X-ray and infrared surface studies of OTMS/OTOS films at the airliquid interface proposedmore » the formation of polymer OTOS structures. According to our analysis, polymer formation is inconsistent with the X-ray observations and structural properties of siloxanes; it is energetically unfavorable and thus highly unlikely. We suggest an alternative mechanism of hydrolysis/condensation in OTMS leading to the formation of structurally allowed cyclic trimers with the six-membered siloxane rings, which explain well both the X-ray and infrared results. XR and XFS consistently demonstrate that tetrahedral [Zn(NH 3) 4] 2+ ions bind to hydroxyl groups of the film at a stoichiometric ratio of OTOS:Zn ~ 2:1. The high binding affinity of zinc ions to OTOS trimers suggests that the six-membered siloxane rings are binding locations for single site Zn/SiO 2 catalysts. Finally, our results show that OTOS monolayers may serve as a platform for studying silica surface chemistry or hydroxyl-mediated reactions.« less

Differentiation between Shallow and Deep Charge Trap States on Single Poly(3-hexylthiophene) Chains through Fluorescence Photon Statistics.

PubMed

Grußmayer, Kristin S; Steiner, Florian; Lupton, John M; Herten, Dirk-Peter; Vogelsang, Jan

2015-12-01

Blinking of the photoluminescence (PL) emitted from individual conjugated polymer chains is one of the central observations made by single-molecule spectroscopy (SMS). Important information, for example regarding excitation energy transfer, can be extracted by evaluating dynamic quenching. However, the nature of trap states, which are responsible for PL quenching, often remains obscured. We present a detailed investigation of the photon statistics of single poly(3-hexylthiophene) (P3HT) chains obtained by SMS. The photon statistics provide a measure of the number and brightness of independently emitting areas on a single chain. These observables can be followed during blinking. A decrease in PL intensity is shown to be correlated with either 1) a decrease in the average brightness of the emitting sites; or 2) a decrease in the number of emitting regions. We attribute these phenomena to the formation of 1) shallow charge traps, which can weakly affect all emitting areas of a single chain at once; and 2) deep traps, which have a strong effect on small regions within the single chains. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single-strand breakage of DNA in UV-irradiated uvrA, uvrB, and uvrC mutants of Escherichia coli.

PubMed Central

Tang, M S; Ross, L

1985-01-01

We transduced the uvrA6, uvrB5, uvrC34, and uvrC56 markers from the original mutagenized strains into an HF4714 background. Although in the original mutagenized strains uvrA6 cells are more UV sensitive than uvrB5 and uvrC34 cells, in the new background no significant difference in UV sensitivity is observed among uvrA6, uvrB5, and uvrC34 cells. No DNA single-strand breaks are detected in UV-irradiated uvrA6 or uvrB5 cells, whereas in contrast a significant number of single-strand breaks are detected in both UV-irradiated uvrC34 and uvrC56 cells. The number of single-strand breaks in these cells reaches a plateau at 20-J/m2 irradiation. Since these single-strand breaks can be detected by both alkaline sucrose and neutral formamide-sucrose gradient sedimentation, we concluded that the single-strand breaks observed in UV-irradiated uvrC cells are due to phosphodiester bond interruptions in DNA and are not due to apurinic/apyrimidinic sites. PMID:3882671

Untangling the effects of multiple human stressors and their impacts on fish assemblages in European running waters.

PubMed

Schinegger, Rafaela; Palt, Martin; Segurado, Pedro; Schmutz, Stefan

2016-12-15

This work addresses human stressors and their impacts on fish assemblages at pan-European scale by analysing single and multiple stressors and their interactions. Based on an extensive dataset with 3105 fish sampling sites, patterns of stressors, their combination and nature of interactions, i.e. synergistic, antagonistic and additive were investigated. Geographical distribution and patterns of seven human stressor variables, belonging to four stressor groups (hydrological-, morphological-, water quality- and connectivity stressors), were examined, considering both single and multiple stressor combinations. To quantify the stressors' ecological impact, a set of 22 fish metrics for various fish assemblage types (headwaters, medium gradient rivers, lowland rivers and Mediterranean streams) was analysed by comparing their observed and expected response to different stressors, both acting individually and in combination. Overall, investigated fish sampling sites are affected by 15 different stressor combinations, including 4 stressors acting individually and 11 combinations of two or more stressors; up to 4 stressor groups per fish sampling site occur. Stressor-response analysis shows divergent results among different stressor categories, even though a general trend of decreasing ecological integrity with increasing stressor quantity can be observed. Fish metrics based on density of species 'intolerant to water quality degradation' and 'intolerant to oxygen depletion" responded best to single and multiple stressors and their interactions. Interactions of stressors were additive (40%), synergistic (30%) or antagonistic (30%), emphasizing the importance to consider interactions in multi-stressor analyses. While antagonistic effects are only observed in headwaters and medium-gradient rivers, synergistic effects increase from headwaters over medium gradient rivers and Mediterranean streams to large lowland rivers. The knowledge gained in this work provides a basis for advanced investigations in European river basins and helps prioritizing further restoration and management actions. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Polarization Observations with the Cosmic Background Imager

NASA Astrophysics Data System (ADS)

Cartwright, J. K.; Padin, S.; Pearson, T. J.; Readhead, A. C. S.; Shepherd, M. C.; Taylor, G. B.

2001-05-01

We describe polarization observations of the CMBR with the Cosmic Background Imager, a 13 element interferometer which operates in the 26-36 GHz band from a site at 5000m in northern Chile. The array consists of 90-cm Cassegrain antennas mounted on a single, fully steerable platform; this platform can be rotated about the optical axis to facilitate polarization observations. The CBI employs single mode circularly polarized receivers, of which 12 are configured for LCP and one is configured for RCP. The 12 cross polarized baselines sample multipoles from l 600 to l 3500. The instrumental polarization of the CBI was calibrated with observations of 3C279, a bright polarized source which is unresolved by the CBI. Because the centimeter flux of 3C279 is variable, it was monitored twice per month for 8 months in 2000 with the VLA at 22 and 43 GHz. These observations also established the stability of the polarization characteristics of the CBI. This work was made possible by NSF grant AST-9802989

Association of CA 15-3 and CEA with clinicopathological parameters in patients with metastatic breast cancer.

PubMed

Geng, Biao; Liang, Man-Man; Ye, Xiao-Bing; Zhao, Wen-Ying

2015-01-01

The objective of this study was to investigate the association of serum cancer antigen 15-3 (CA 15-3) and carcinoembryonic antigen (CEA) levels with clinicopathological parameters in patients diagnosed with metastatic breast cancer (MBC). We retrospectively evaluated the medical records of 284 patients diagnosed with MBC between January, 2007 and December, 2012 who fulfilled the specified criteria and the association between the levels of the two tumor marker and clinicopathological parameters was analyzed. Of the 284 patients, elevated CA 15-3 and CEA levels at initial diagnosis of recurrence were identified in 163 (57.4%) and 97 (34.2%) patients, respectively. Elevated CA 15-3 and CEA levels were significantly associated with breast cancer molecular subtypes (P<0.001 and P=0.032, respectively). Cases with luminal subtypes exhibited a higher percentage of elevated CA 15-3 and CEA levels compared to non-luminal subtypes. Elevated CA 15-3 level was correlated with bone metastasis (P=0.017). However, elevation of CEA was observed regardless of the site of metastasis. Elevation of CA 15-3 was significantly more common in MBC with multiple metastatic sites compared to MBC with a single metastasis (P=0.001). However, the incidence of elevated CEA levels did not differ between patients with a single and those with multiple metastatic sites. In conclusion, elevated CA 15-3 and CEA levels at initial diagnosis of recurrence were found to be associated with breast cancer molecular subtypes, whereas an elevated CA 15-3 level was significantly correlated with bone metastasis and an elevated CEA level was observed regardless of metastatic site. The proportion of MBC cases with elevated CA 15-3 levels differed according to the number of metastatic sites.

Clearing the waters: Evaluating the need for site-specific field fluorescence corrections based on turbidity measurements

USGS Publications Warehouse

Saraceno, John F.; Shanley, James B.; Downing, Bryan D.; Pellerin, Brian A.

2017-01-01

In situ fluorescent dissolved organic matter (fDOM) measurements have gained increasing popularity as a proxy for dissolved organic carbon (DOC) concentrations in streams. One challenge to accurate fDOM measurements in many streams is light attenuation due to suspended particles. Downing et al. (2012) evaluated the need for corrections to compensate for particle interference on fDOM measurements using a single sediment standard in a laboratory study. The application of those results to a large river improved unfiltered field fDOM accuracy. We tested the same correction equation in a headwater tropical stream and found that it overcompensated fDOM when turbidity exceeded ∼300 formazin nephelometric units (FNU). Therefore, we developed a site-specific, field-based fDOM correction equation through paired in situ fDOM measurements of filtered and unfiltered streamwater. The site-specific correction increased fDOM accuracy up to a turbidity as high as 700 FNU, the maximum observed in this study. The difference in performance between the laboratory-based correction equation of Downing et al. (2012) and our site-specific, field-based correction equation likely arises from differences in particle size distribution between the sediment standard used in the lab (silt) and that observed in our study (fine to medium sand), particularly during high flows. Therefore, a particle interference correction equation based on a single sediment type may not be ideal when field sediment size is significantly different. Given that field fDOM corrections for particle interference under turbid conditions are a critical component in generating accurate DOC estimates, we describe a way to develop site-specific corrections.

H 2 Adsorbed Site-to-Site Electronic Delocalization within IRMOF-1: Understanding Non-Negligible Interactions at High Pressure

DOE PAGES

Wu, Jian; Kucukkal, Mustafa U.; Clark, Aurora E.

2016-07-15

Isoreticular metal organic frameworks (IRMOFs) have shown high uptake capabilities for storage of H 2 (11.5 wt % at 77 K and 170 bar). A significant literature has employed fragment models and a single adsorbed H 2 to identify adsorption sites within IRMOFs, as well as the necessary adsorbate–adsorbent interactions needed to reach sufficient adsorption enthalpy for practical usage, however at high pressures it remains to be seen if H 2···H 2 intermolecular interactions may influence the energetics. This study focuses upon IRMOF-1 (also known as MOF-5), and examines the individual H 2 stabilization energies at different sites using Möller–Plessetmore » perturbation theory and density functional theory alongside chemical models that consist of isolated fragment models and a cubic super cell cluster consisting of both the face- and edge-cube’s of IRMOF-1. Optimization of twenty stable configurations of singly adsorbed H 2 in the super-cell cluster is observed to be essential to obtain energy ordering of the five primary sites consistent with experiment and prior benchmark calculations (α >> β > γ > δ ≈ ε). To examine site-to-site interactions that may occur in the high-pressure regime, 64 co-adsorbed H2 within a super-cell cluster have been studied (a theoretical maximum of all adsorption sites, 14 wt %). There, delocalization and/or charge transfer of electrons is observed from the σ orbitals of the H 2 bound at the γ positions into the σ* orbitals of H 2 bound at the α sites leads to stabilization of the interaction of H 2 at the γ, by 1.4 kJ/mol, respectively (using M06-2X/LANL2DZ). Furthermore, this effect has been confirmed to be charge transfer, and not a manifestation of enhanced dispersion at high loading, through natural bond order (NBO) analysis and by comparisons of the square of off-diagonal NBO Fock matrix elements for both density functionals that account for dispersion interactions and Hartree–Fock calculations that ignore dispersion.« less

Factors associated with biopsy site identification, postponement of surgery, and patient confidence in a dermatologic surgery practice.

PubMed

Zhang, Junqian; Rosen, Alex; Orenstein, Lauren; Van Voorhees, Abby; Miller, Christopher J; Sobanko, Joseph F; Shin, Thuzar M; Etzkorn, Jeremy R

2016-06-01

Biopsy site identification is critical to avoid wrong-site surgery and may impact patient-centered outcomes. We sought to evaluate risk factors for biopsy site misidentification, postponement of surgery, and patient confidence in surgical site selection and to assess the near-miss rate for wrong-site surgeries. This was a prospective observational cohort study. Near-miss wrong-site surgeries were detected and averted in 1.3% (3 of 239) of patients with biopsy site photographs. Risk factors for biopsy site misidentification by patients were 6 weeks or longer between biopsy and surgery (odds ratio [OR] 2.19, 95% confidence interval [CI] 1.12-4.27; P = .028) and patient inability to see biopsy site (OR 3.95, 95% CI 1.50-10.37; P = .002). Risk factors for physician misidentification were 6 or more weeks between biopsy and surgery (OR 3.68, 95% CI 1.40-9.66; P = .007) and biopsy specimens from multiple sites (OR 4.39, 95% CI 1.67-11.54; P = .003). Postponement of surgery was associated with absence of a biopsy site photograph (OR 12.5, 95% CI 2.79-62.21; P < .001). Patient confidence in surgical site identification was associated with the presence of a biopsy site photograph (OR 5.48, 95% CI 1.96-15.30; P = .001). This was a single-site observational study. Biopsy site photography is associated with reduced rates of postponed surgeries and improved rates of patient confidence in surgical site selection. Risk factors for biopsy site misidentification should be considered before definitive treatment. Copyright © 2015 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

Superposition model analysis of the magnetocrystalline anisotropy of Ba-ferrite

NASA Astrophysics Data System (ADS)

Novák, Pavel

1994-06-01

Theoretical analysis of the first magnetocrystalline anisotropy constantK 1 of BaFe12O19 is performed. Two contributions toK 1 are considered — single ion anisotropy and dipolar anisotropy. ParameterD which determines the magnitude of the single ion contribution is calculated on the basis of the superposition model. It is argued that the disagreement between calculated and observed values ofK 1 is most likely connected with the contribution of Fe3+ ions on bipyramidal sites, for which the value ofD is uncertain.

Distributed query plan generation using multiobjective genetic algorithm.

PubMed

Panicker, Shina; Kumar, T V Vijay

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability.

Distributed Query Plan Generation Using Multiobjective Genetic Algorithm

PubMed Central

Panicker, Shina; Vijay Kumar, T. V.

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability. PMID:24963513

Determination of Large-Scale Cloud Ice Water Concentration by Combining Surface Radar and Satellite Data in Support of ARM SCM Activities

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

Liu, Guosheng

2013-03-15

Single-column modeling (SCM) is one of the key elements of Atmospheric Radiation Measurement (ARM) research initiatives for the development and testing of various physical parameterizations to be used in general circulation models (GCMs). The data required for use with an SCM include observed vertical profiles of temperature, water vapor, and condensed water, as well as the large-scale vertical motion and tendencies of temperature, water vapor, and condensed water due to horizontal advection. Surface-based measurements operated at ARM sites and upper-air sounding networks supply most of the required variables for model inputs, but do not provide the horizontal advection term ofmore » condensed water. Since surface cloud radar and microwave radiometer observations at ARM sites are single-point measurements, they can provide the amount of condensed water at the location of observation sites, but not a horizontal distribution of condensed water contents. Consequently, observational data for the large-scale advection tendencies of condensed water have not been available to the ARM cloud modeling community based on surface observations alone. This lack of advection data of water condensate could cause large uncertainties in SCM simulations. Additionally, to evaluate GCMs cloud physical parameterization, we need to compare GCM results with observed cloud water amounts over a scale that is large enough to be comparable to what a GCM grid represents. To this end, the point-measurements at ARM surface sites are again not adequate. Therefore, cloud water observations over a large area are needed. The main goal of this project is to retrieve ice water contents over an area of 10 x 10 deg. surrounding the ARM sites by combining surface and satellite observations. Built on the progress made during previous ARM research, we have conducted the retrievals of 3-dimensional ice water content by combining surface radar/radiometer and satellite measurements, and have produced 3-D cloud ice water contents in support of cloud modeling activities. The approach of the study is to expand a (surface) point measurement to an (satellite) area measurement. That is, the study takes the advantage of the high quality cloud measurements (particularly cloud radar and microwave radiometer measurements) at the point of the ARM sites. We use the cloud ice water characteristics derived from the point measurement to guide/constrain a satellite retrieval algorithm, then use the satellite algorithm to derive the 3-D cloud ice water distributions within an 10° (latitude) x 10° (longitude) area. During the research period, we have developed, validated and improved our cloud ice water retrievals, and have produced and archived at ARM website as a PI-product of the 3-D cloud ice water contents using combined satellite high-frequency microwave and surface radar observations for SGP March 2000 IOP and TWP-ICE 2006 IOP over 10 deg. x 10 deg. area centered at ARM SGP central facility and Darwin sites. We have also worked on validation of the 3-D ice water product by CloudSat data, synergy with visible/infrared cloud ice water retrievals for better results at low ice water conditions, and created a long-term (several years) of ice water climatology in 10 x 10 deg. area of ARM SGP and TWP sites and then compared it with GCMs.« less

Atomic Bose-Hubbard Systems with Single-Particle Control

NASA Astrophysics Data System (ADS)

Preiss, Philipp Moritz

Experiments with ultracold atoms in optical lattices provide outstanding opportunities to realize exotic quantum states due to a high degree of tunability and control. In this thesis, I present experiments that extend this control from global parameters to the level of individual particles. Using a quantum gas microscope for 87Rb, we have developed a single-site addressing scheme based on digital amplitude holograms. The system self-corrects for aberrations in the imaging setup and creates arbitrary beam profiles. We are thus able to shape optical potentials on the scale of single lattice sites and control the dynamics of individual atoms. We study the role of quantum statistics and interactions in the Bose-Hubbard model on the fundamental level of two particles. Bosonic quantum statistics are apparent in the Hong-Ou-Mandel interference of massive particles, which we observe in tailored double-well potentials. These underlying statistics, in combination with tunable repulsive interactions, dominate the dynamics in single- and two-particle quantum walks. We observe highly coherent position-space Bloch oscillations, bosonic bunching in Hanbury Brown-Twiss interference and the fermionization of strongly interacting bosons. Many-body states of indistinguishable quantum particles are characterized by large-scale spatial entanglement, which is difficult to detect in itinerant systems. Here, we extend the concept of Hong-Ou-Mandel interference from individual particles to many-body states to directly quantify entanglement entropy. We perform collective measurements on two copies of a quantum state and detect entanglement entropy through many-body interference. We measure the second order Renyi entropy in small Bose-Hubbard systems and detect the buildup of spatial entanglement across the superfluid-insulator transition. Our experiments open new opportunities for the single-particle-resolved preparation and characterization of many-body quantum states.

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

Adamson, P.

We report the first observation of seasonal modulations in the rates of cosmic ray multiple-muon events at two underground sites, the MINOS Near Detector with an overburden of 225 mwe, and the MINOS Far Detector site at 2100 mwe. Thus, at the deeper site, multiple-muon events with muons separated by more than 8 m exhibit a seasonal rate that peaks during the summer, similar to that of single-muon events. In contrast and unexpectedly, the rate of multiple-muon events with muons separated by less than 5–8 m, and the rate of multiple-muon events in the smaller, shallower Near Detector, exhibit amore » seasonal rate modulation that peaks in the winter.« less

Methane mobility in carbon nanotubes

NASA Astrophysics Data System (ADS)

Bienfait, M.; Asmussen, B.; Johnson, M.; Zeppenfeld, P.

2000-07-01

Quasi-elastic neutron scattering has been used to characterize the diffusivity of CH 4 molecules condensed in single-wall carbon nanotubes. It is shown that the two sites of adsorption, previously observed by adsorption volumetry and calorimetry measurements, correspond to a solid-like phase for the more strongly bound site at T<120 K and to a liquid-like component for the more weakly bound site at 70< T<120 K. The diffusion coefficients of the mobile molecules range between 3×10 -7 to 15×10 -7 cm 2 s -1. The fraction of this viscous liquid diminishes as the temperature is decreased; the adsorbate is fully solidified at 50 K and below.

Linking terrestrial and marine conservation planning and threats analysis.

PubMed

Tallis, Heather; Ferdaña, Zach; Gray, Elizabeth

2008-02-01

The existence of the Gulf of Mexico dead zone makes it clear that marine ecosystems can be damaged by terrestrial inputs. Marine and terrestrial conservation planning need to be aligned in an explicit fashion to fully represent threats to marine systems. To integrate conservation planning for terrestrial and marine systems, we used a novel threats assessment that included 5 cross-system threats in a site-prioritization exercise for the Pacific Northwest coast ecoregion (U.S.A.). Cross-system threats are actions or features in one ecological realm that have effects on species in another realm. We considered bulkheads and other forms of shoreline hardening threats to terrestrial systems and roads, logging, agriculture, and urban areas threats to marine systems. We used 2 proxies of freshwater influence on marine environments, validated against a mechanistic model and field observations, to propagate land-based threats into marine sites. We evaluated the influence of cross-system threats on conservation priorities by comparing MARXAN outputs for 3 scenarios that identified terrestrial and marine priorities simultaneously: (1) no threats, (2) single-system threats, and (3) single- and cross-system threats. Including cross-system threats changed the threat landscape dramatically. As a result the best plan that included only single-system threats identified 323 sites (161,500 ha) at risk from cross-system threats. Including these threats changed the location of best sites. By comparing the best and sum solutions of the single- and cross-system scenarios, we identified areas ideal for preservation or restoration through integrated management. Our findings lend quantitative support to the call for explicitly integrated decision making and management action in terrestrial and marine ecosystems.

A full-potential approach to the relativistic single-site Green's function

DOE PAGES

Liu, Xianglin; Wang, Yang; Eisenbach, Markus; ...

2016-07-07

One major purpose of studying the single-site scattering problem is to obtain the scattering matrices and differential equation solutions indispensable to multiple scattering theory (MST) calculations. On the other hand, the single-site scattering itself is also appealing because it reveals the physical environment experienced by electrons around the scattering center. In this study, we demonstrate a new formalism to calculate the relativistic full-potential single-site Green's function. We implement this method to calculate the single-site density of states and electron charge densities. Lastly, the code is rigorously tested and with the help of Krein's theorem, the relativistic effects and full potentialmore » effects in group V elements and noble metals are thoroughly investigated.« less

Robotic single-site pelvic lymphadenectomy.

PubMed

Tateo, Saverio; Nozza, Arrigo; Del Pezzo, Chiara; Mereu, Liliana

2014-09-01

To examine the feasibility of performing pelvic lymphadenectomy with robotic single site approach. Recent papers described the feasibility of robotic-single site hysterectomy [1-3] for benign and malign pathologies but only with the development of new single site 5mm instruments as the bipolar forceps, robotic single site platform can be safely utilized also for lymphadenectomy. A 65 year-old, multiparous patient with a body mass index of 22.5 and diagnosed with well differentiated adenocarcinoma of the endometrium underwent a robotic single-site peritoneal washing, total hysterectomy, bilateral adnexectomy and pelvic lymphadenectomy. The procedure was performed using the da Vinci Si Surgical System (Intuitive Surgical, Sunnyvale, CA) through a single 2,5 cm umbilical incision, with a multi-channel system and two single site robotic 5mm instruments. A 3-dimensional, HD 8.5mm endoscope and a 5mm accessory instrument were also utilized. Type I lymphonodes dissection for external iliac and obturator regions was performed [4]. Total operative time was 210 min; incision, trocar placement and docking time occurring in 12 min. Total console time was 183 min, estimated blood loss was 50 ml, no intra-operative or post-operative complications occurred. Hospital discharge occurred on post operative day 2 and total number of lymphnodes removed was 33. Difficulties in term of instrument's clashing and awkward motions have been encountered. Robotic single-site pelvic lymphadenectomy using bipolar forceps and monopolar hook is feasible. New developments are needed to improve surgical ergonomics and additional studies should be performed to explore possible benefits of this procedure. Copyright © 2014 Elsevier Inc. All rights reserved.

Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

PubMed

Roston, Daniel; Demapan, Darren; Cui, Qiang

2016-06-15

A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.

Suicidal single gunshot injury to the head: differences in site of entrance wound and direction of the bullet path between right- and left-handed--an autopsy study.

PubMed

Nikolić, Slobodan; Zivković, Vladimir; Babić, Dragan; Juković, Fehim

2012-03-01

The aim of this study was to determine the differences in the anatomical site of a gunshot entrance wound and the direction of the bullet path between right- and left-handed subjects who committed a suicide by a single gunshot injury to the head. The retrospective autopsy study was performed for a 10-year period, and it included selected cases of single suicidal gunshot head injury, committed by handguns. We considered only contact or near-contact wounds. The sample included 479 deceased, with average age 47.1 ± 19.1 years (range, 12-89 years): 432 males and 47 females, with 317 right-handed, 25 left-handed, and 137 subjects with unknown dominant hand. In our observed sample, most cases involved the right temple as the site of entrance gunshot wound (about 67%), followed by the mouth (16%), forehead (7%), left temple (6%), submental (2%), and parietal region (1%). The left temple, right temple, and forehead were the sites of the gunshot entrance wounds, which were the best predictors of the handedness of the deceased (Spearman ρ = 0.149, P = 0.006). Our study showed that the direction of the bullet intracranial path in cases of suicide was even a more potent predictor of the handedness of the deceased (Spearman ρ = 0.263, P = 0.000; Wald = 149.503, P = 0.000).

Toxicity of Single-dose Intramuscular Injection of Samjeong Pharmacopuncture in Sprague-Dawley Rats.

PubMed

Kwon, Kang; Kim, Chul-Yun; Kim, Nam-Kwen; Sun, Seung-Ho; Seo, Hyung-Sik

2015-06-01

This study was carried out in order to find both the single-dose intramuscular injection toxicity and the approximate lethal dose of samjeong pharmacopuncture (SP) in Sprague-Dawley (SD) rats. The SD rats in this study were divided into four groups, one control group (1.0 mL/animal, normal saline) and three experimental groups (0.25, 0.5, and 1.0 mL/animal, SP). All groups consisted of five male and five female rats. SP was injected as a single-dose intramuscularly at the thigh. After the injection, general symptoms and weight were observed for 14 days. After the observations had ended, hematologic and serum biochemical examinations, necropsy and a local tolerance test at the injection site were performed. The experiments were carried out at the Good Laboratory Practice firm, Biotoxtech Co. (Cheongwon, Chungbuk). Animal experiments were approved by the Ethics Committee (Approval Number: 130379). No deaths occurred in any of the three experimental groups. The injection of SP had no effects on the general symptoms, body weights, results of the hematologic, and serum biochemical examinations, and necropsy findings. In local tolerance tests at the injection sites, mild inflammation was observed in the experimental group, but it did not appear to be a treatment related effect. Under the conditions of this test, the results from the injection of SP suggest that the approximate lethal dose of SP is above 1.0 mL/animal for both male and female SD rats. Therefore, the clinical use of SP is thought to be safe.

Mobile Platforms for Continuous Spatial Measurements of Urban Trace Gases and Criteria Pollutants

NASA Astrophysics Data System (ADS)

Fasoli, B.; Mitchell, L.; Bares, R.; Crosman, E.; Bush, S. E.; Horel, J.; Lin, J. C.; Bowling, D. R.; Ehleringer, J. R.

2015-12-01

Surface-based observations of atmospheric trace gases and criteria pollutants provide critical data on how emissions and pollutant concentrations vary over time. However, traditional stationary measurement sites only quantify concentrations at a single point in space, limiting our ability to understand spatial patterns. Using trace gas instrumentation capable of making continuous high-frequency (~1s) measurements, we have developed mobile platforms to complement stationary observation sites in order to better constrain the heterogeneity and complexities of urban emissions. These compact trace gas and criteria pollutant measurement systems are capable of precisely measuring CO2, CH4 PM2.5, O3, NOx, and several meteorological parameters on TRAX, Salt Lake City's light-rail system, and in a van-based mobile laboratory. Using case study observations, we discuss mobile measurement methodologies and the practical applications of mobile trace gas sampling platforms.

High-Frequency Orographically Forced Variability in a Single-Layer Model of the Martian Atmosphere

NASA Technical Reports Server (NTRS)

Keppenne, C. L.; Ingersoll, A. P.

1993-01-01

A shallow water model with realistic topography and idealized zonal wind forcing is used toinvestigate orographically forced modes in the Martian atmosphere. Locally, the model reproduceswell the climatology at the sites of Viking Lander I and II (VL1 and VL2) as inferred from theViking Lander fall and spring observations. Its variability at those sites is dominated by a 3-sol(Martian solar day) oscillation in the region of VL1 and by a 6-sol oscillation in that of VL2. Theseoscillations are forced by the zonal asymmetries of the Martian mountain field. It is suggested thatthey contribute to the observed variability by reinforcing the baroclinic oscillations with nearbyperiods identified in observational studies. The spatial variability associated with the orographicallyforced oscillations is studied by means of extended empirical orthogonal function analysis. The 3-solVL1 oscillation corresponds to a tropical, eastward-traveling, zonal-wavenumber one pattern...

Elucidating energy and electron transfer dynamics within molecular assemblies for solar energy conversion

NASA Astrophysics Data System (ADS)

Morseth, Zachary Aaron

The use of sunlight to make chemical fuels (i.e. solar fuels) is an attractive approach in the quest to develop sustainable energy sources. Using nature as a guide, assemblies for artificial photosynthesis will need to perform multiple functions. They will need to be able to harvest light across a broad region of the solar spectrum, transport excited-state energy to charge-separation sites, and then transport and store redox equivalents for use in the catalytic reactions that produce chemical fuels. This multifunctional behavior will require the assimilation of multiple components into a single macromolecular system. A wide variety of different architectures including porphyrin arrays, peptides, dendrimers, and polymers have been explored, with each design posing unique challenges. Polymer assemblies are attractive due to their relative ease of production and facile synthetic modification. However, their disordered nature gives rise to stochastic dynamics not present in more ordered assemblies. The rational design of assemblies requires a detailed understanding of the energy and electron transfer events that follow light absorption, which can occur on timescales ranging from femtoseconds to hundreds of microseconds, necessitating the use of sophisticated techniques. We have used a combination of time-resolved absorption and emission spectroscopies with observation times that span nine orders of magnitude to follow the excited-state evolution within single-site and polymer-based molecular assemblies. We complement experimental observations with electronic structure calculations, molecular dynamics simulations, and kinetic modeling to develop a microscopic view of these dynamics. This thesis provides an overview of work on single-site molecular assemblies and polymers decorated with pendant chromophores, both in solution and on surfaces. This work was made possible through extensive collaboration with Dr. Kirk Schanze's and Dr. John Reynolds' research groups who synthesized the samples for study.

Relationship between soft stratum thickness and predominant frequency of ground based on microtremor observation data

NASA Astrophysics Data System (ADS)

Chia, Kenny; Lau, Tze Liang

2017-07-01

Despite categorized as low seismicity group, until being affected by distant earthquake ground motion from Sumatra and the recent 2015 Sabah Earthquake, Malaysia has come to realize that seismic hazard in the country is real and has the potential to threaten the public safety and welfare. The major concern in this paper is to study the effect of local site condition, where it could amplify the magnitude of ground vibration at sites. The aim for this study is to correlate the thickness of soft stratum with the predominant frequency of soil. Single point microtremor measurements were carried out at 24 selected points where the site investigation reports are available. Predominant period and frequency at each site are determined by Nakamura's method. The predominant period varies from 0.22 s to 0.98 s. Generally, the predominant period increases when getting closer to the shoreline which has thicker sediments. As far as the thickness of the soft stratum could influence the amplification of seismic wave, the advancement of micotremor observation to predict the thickness of soft stratum (h) from predominant frequency (fr) is of the concern. Thus an empirical relationship h =54.917 fr-1.314 is developed based on the microtremor observation data. The empirical relationship will be benefited in the prediction of thickness of soft stratum based on microtremor observation for seismic design with minimal cost compared to conventional boring method.

Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease.

PubMed

Ragland, Debra A; Nalivaika, Ellen A; Nalam, Madhavi N L; Prachanronarong, Kristina L; Cao, Hong; Bandaranayake, Rajintha M; Cai, Yufeng; Kurt-Yilmaz, Nese; Schiffer, Celia A

2014-08-27

HIV-1 protease inhibitors are part of the highly active antiretroviral therapy effectively used in the treatment of HIV infection and AIDS. Darunavir (DRV) is the most potent of these inhibitors, soliciting drug resistance only when a complex combination of mutations occur both inside and outside the protease active site. With few exceptions, the role of mutations outside the active site in conferring resistance remains largely elusive. Through a series of DRV-protease complex crystal structures, inhibition assays, and molecular dynamics simulations, we find that single and double site mutations outside the active site often associated with DRV resistance alter the structure and dynamic ensemble of HIV-1 protease active site. These alterations correlate with the observed inhibitor binding affinities for the mutants, and suggest a network hypothesis on how the effect of distal mutations are propagated to pivotal residues at the active site and may contribute to conferring drug resistance.

The implementation of a mobile problem-specific electronic CEX for assessing directly observed student-patient encounters.

PubMed

Ferenchick, Gary S; Foreback, Jami; Towfiq, Basim; Kavanaugh, Kevin; Solomon, David; Mohmand, Asad

2010-01-29

Facilitating direct observation of medical students' clinical competencies is a pressing need. We developed an electronic problem-specific Clinical Evaluation Exercise (eCEX) based on a national curriculum. We assessed its feasibility in monitoring and recording students' competencies and the impact of a grading incentive on the frequency of direct observations in an internal medicine clerkship. Students (n = 56) at three clinical sites used the eCEX and comparison students (n = 56) at three other clinical sites did not. Students in the eCEX group were required to arrange 10 evaluations with faculty preceptors. Students in the second group were required to document a single, faculty observed 'Full History and Physical' encounter with a patient. Students and preceptors were surveyed at the end of each rotation. eCEX increased students' and evaluators' understanding of direct-observation objectives and had a positive impact on the evaluators' ability to provide feedback and assessments. The grading incentive increased the number of times a student reported direct observation by a resident preceptor. eCEX appears to be an effective means of enhancing student evaluation.

Basic cytogenetics and physical mapping of ribosomal genes in four Astyanax species (Characiformes, Characidae) collected in Middle Paraná River, Iguassu National Park: considerations on taxonomy and systematics of the genus

PubMed Central

Paiz, Leonardo Marcel; Baumgärtner, Lucas; da Graça, Weferson Júnio; Margarido, Vladimir Pavan

2015-01-01

Abstract Karyotypes and chromosomal characteristics of both minor and major rDNAs in four fish species known popularly as “lambaris”, namely Astyanax abramis (Jenyns, 1842), Astyanax asuncionensis Géry, 1972, Astyanax correntinus (Holmberg, 1891) and Astyanax sp. collected from downstream of the Iguassu Falls (Middle Paraná River basin), preservation area of the Iguassu National Park, were analyzed by conventional and molecular protocols. Astyanax abramis had diploid chromosome number 2n=50 (4m+30sm+8st+8a) and single AgNORs (pair 22), Astyanax asuncionensis had 2n=50 (8m+24sm+6st+12a) and single AgNORs (pair 20), Astyanax sp. had 2n=50 (4m+26sm+8st+12a) and single AgNORs (pair 25), and Astyanax correntinus had 2n=36 (12m+16sm+2st+6a) and multiple AgNORs (pairs 12, 15, 16, 17). FISH with 18S rDNA showed a single site for Astyanax abramis, Astyanax asuncionensis and Astyanax sp. and multiple for Astyanax correntinus (14 sites). FISH with 5S rDNA showed single 5S-bearing loci chromosome pair only for Astyanax asuncionensis and multiple for Astyanax abramis (four sites), Astyanax correntinus (five sites) and Astyanax sp. (four sites). Distinct distribution patterns of heterochromatin were observed for karyotypes of all species, with the exception of the first acrocentric chromosome pair characterized by centromeric, interstitial-proximal and telomeric blocks of heterochromatin on the long arm, which may represent homeology between karyotypes of Astyanax abramis and Astyanax asuncionensis. Our study showed species-specific characteristics which can serve in diagnosis and differentiation between Astyanax abramis and Astyanax asuncionensis, considered cryptic species, as well as strengthening the occurrence of a species of Astyanax not yet described taxonomically. In addition, the data obtained from first cytogenetic studies in Astyanax correntinus suggest a high similarity with Astyanax schubarti Britski, 1964, suggesting that these species may belong to the same morphological group and that can be phylogenetically related. PMID:25893074

View From a Megacity: Aerosol Light Absorption and Scattering at Four Sites in and Near Mexico City.

NASA Astrophysics Data System (ADS)

Paredes-Miranda, G.; Arnott, W. P.; Gaffney, J. S.; Marley, N. A.

2006-12-01

As part of the Megacity Impacts on Regional and Global Environments, MIRAGE-Mex deployment to Mexico City in the period of 30 days, March 2006, a suite of photoacoustic spectrometers (PAS) were installed to measure at ground level the light absorption and scattering by aerosols at four sites: an urban site at Instituto Mexicano del Petroleo (Mexican Oil Institute, denoted by IMP), a suburban site at the Technological University of Tecamac, a rural site at "La Biznaga" ranch, and a site at the Paseo de Cortes (altitude 3,810 meters ASL) in the rural area above Amecameca in the State of Mexico, on the saddle between the volcanoes Popocatepetl and Iztaccihuatl. The IMP site gave in-situ characterization of the Mexico City plume under favorable wind conditions while the other sites provided characterization of the plume, mixed in with any local sources. The second and third sites are north of Mexico City, and the fourth site is south. The PAS used at IMP operates at 532 nm, and conveniently allowed for characterization of gaseous absorption at this wavelength as well. Instruments at the second and third sites operate at 870 nm, and the one at the fourth site at 780 nm. Light scattering measurements are accomplished within the PAS by the reciprocal nephelometery method. In the urban site the aerosol absorption coefficient typically varies between 40 and 250 Mm-1 during the course of the day and significant diurnal variation of the aerosol single scattering albedo was observed. Comparisons with TSI nephelometer scattering and Aetholemeter absorption measurements at the T0 site will be presented. We will present a broad overview of the diurnal variation of the scattering and absorption as well as the single scattering albedo and fraction of absorption due to gases at the IMP site. Insight on the dynamical connections will be discussed.

Microscopic observation of magnon bound states and their dynamics.

PubMed

Fukuhara, Takeshi; Schauß, Peter; Endres, Manuel; Hild, Sebastian; Cheneau, Marc; Bloch, Immanuel; Gross, Christian

2013-10-03

The existence of bound states of elementary spin waves (magnons) in one-dimensional quantum magnets was predicted almost 80 years ago. Identifying signatures of magnon bound states has so far remained the subject of intense theoretical research, and their detection has proved challenging for experiments. Ultracold atoms offer an ideal setting in which to find such bound states by tracking the spin dynamics with single-spin and single-site resolution following a local excitation. Here we use in situ correlation measurements to observe two-magnon bound states directly in a one-dimensional Heisenberg spin chain comprising ultracold bosonic atoms in an optical lattice. We observe the quantum dynamics of free and bound magnon states through time-resolved measurements of two spin impurities. The increased effective mass of the compound magnon state results in slower spin dynamics as compared to single-magnon excitations. We also determine the decay time of bound magnons, which is probably limited by scattering on thermal fluctuations in the system. Our results provide a new way of studying fundamental properties of quantum magnets and, more generally, properties of interacting impurities in quantum many-body systems.

Single crystal EPR, optical absorption and superposition model study of Cr3+ doped ammonium dihydrogen phosphate.

PubMed

Kripal, Ram; Pandey, Sangita

2010-06-01

The electron paramagnetic resonance (EPR) studies are carried out on Cr(3+) ion doped ammonium dihydrogen phosphate (ADP) single crystals at room temperature. Four magnetically inequivalent sites for chromium are observed. No hyperfine structure is obtained. The crystal-field and spin Hamiltonian parameters are calculated from the resonance lines obtained at different angular rotations. The zero field and spin Hamiltonian parameters of Cr(3+) ion in ADP are calculated as: |D|=(257+/-2) x 10(-4) cm(-1), |E|=(79+/-2) x 10(-4) cm(-1), g=1.9724+/-0.0002 for site I; |D|=(257+/-2) x 10(-4) cm(-1), |E|=(77+/-2) x 10(-4) cm(-1), g=1.9727+/-0.0002 for site II; |D|=(259+/-2) x 10(-4) cm(-1), |E|=(78+/-2) x 10(-4) cm(-1), g=1.9733+/-0.0002 for site III; |D|=(259+/-2) x 10(-4) cm(-1), |E|=(77+/-2) x 10(-4) cm(-1), g=1.973+/-0.0002 for site IV, respectively. The site symmetry of Cr(3+) doped single crystal is discussed on the basis of EPR data. The Cr(3+) ion enters the lattice substitutionally replacing the NH(4)(+) sites. The optical absorption spectra are recorded in 195-925 nm wavelength range at room temperature. The energy values of different orbital levels are determined. On the basis of EPR and optical data, the nature of bonding in the crystal is discussed. The calculated values of Racah interelectronic repulsion parameters (B and C), cubic crystal-field splitting parameter (D(q)) and nephelauxetic parameters (h and k) are: B=640, C=3070, D(q)=2067 cm(-1), h=1.44 and k=0.21, respectively. ZFS parameters are also determined using B(kq) parameters from superposition model. Copyright 2010 Elsevier B.V. All rights reserved.

Robotic single-access splenectomy using the Da Vinci Single-Site® platform: a case report.

PubMed

Corcione, Francesco; Bracale, Umberto; Pirozzi, Felice; Cuccurullo, Diego; Angelini, Pier Luigi

2014-03-01

Single-access laparoscopic splenectomy can offer patients some advantages. It has many difficulties, such as instrument clashing, lack of triangulation, odd angles and lack of space. The Da Vinci Single-Site® robotic surgery platform could decrease these difficulties. We present a case of single-access robotic splenectomy using this device. A 37 year-old female with idiopathic thrombocytopenic purpura was operated on with a single-site approach, using the Da Vinci Single-Site robotic surgery device. The procedure was successfully completed in 140 min. No intraoperative and postoperative complications occurred. The patient was discharged from hospital on day 3. Single-access robotic splenectomy seems to be feasible and safe using the new robotic single-access platform, which seems to overcome certain limits of previous robotic or conventional single-access laparoscopy. We think that additional studies should also be performed to explore the real cost-effectiveness of the platform. Copyright © 2013 John Wiley & Sons, Ltd.

Single-Site Laparoscopic Surgery for Inflammatory Bowel Disease

PubMed Central

Bedros, Nicole; Hakiman, Hekmat; Araghizadeh, Farshid Y.

2014-01-01

Background and Objectives: Single-site laparoscopic colorectal surgery has been firmly established; however, few reports addressing this technique in the inflammatory bowel disease population exist. Methods: We conducted a case-matched retrospective review of 20 patients who underwent single-site laparoscopic procedures for inflammatory bowel disease compared with 20 matched patients undergoing multiport laparoscopic procedures. Data regarding these patients were tabulated in the following categories: demographic characteristics, operative parameters, and perioperative outcomes. Results: A wide range of cases were completed: 9 ileocolic resections, 7 cases of proctocolectomy with end ileostomy or ileal pouch anal anastomosis, 2 cases of proctectomy with ileal pouch anal anastomosis, and 2 total abdominal colectomies with end ileostomy were all matched to equivalent multiport laparoscopic cases. No single-incision cases were converted to multiport laparoscopy, and 2 single-incision cases (10%) were converted to an open approach. For single-incision cases, the mean length of stay was 7.7 days, the mean time to oral intake was 3.3 days, and the mean period of intravenous analgesic use was 5.0 days. There were no statistically significant differences between single-site and multiport cases. Conclusions: Single-site laparoscopic surgery is technically feasible in inflammatory bowel disease. The length of stay and period of intravenous analgesic use (in days) appear to be higher than those in comparable series examining outcomes of single-site laparoscopic colorectal surgery, and the outcomes are comparable with those of multiport laparoscopy. This may be because of the nature of inflammatory bowel disease, limiting the benefits of a single-site approach in this population. PMID:24960490

Describing Site Amplification for Surface Waves in Realistic Basins

NASA Astrophysics Data System (ADS)

Bowden, D. C.; Tsai, V. C.

2017-12-01

Standard characterizations of site-specific site response assume a vertically-incident shear wave; given a 1D velocity profile, amplification and resonances can be calculated based on conservation of energy. A similar approach can be applied to surface waves, resulting in an estimate of amplification relative to a hard rock site that is different in terms of both amount of amplification and frequency. This prediction of surface-wave site amplification has been well validated through simple simulations, and in this presentation we explore the extent to which a 1D profile can explain observed amplifications in more realistic scenarios. Comparisons of various simple 2D and 3D simulations, for example, allow us to explore the effect of different basin shapes and the relative importance of effects such as focusing, conversion of wave-types and lateral surface wave resonances. Additionally, the 1D estimates for vertically-incident shear waves and for surface waves are compared to spectral ratios of historic events in deep sedimentary basins to demonstrate the appropriateness of the two different predictions. This difference in amplification responses between the wave types implies that a single measurement of site response, whether analytically calculated from 1D models or empirically observed, is insufficient for regions where surface waves play a strong role.

Evolution of wavelength-dependent mass absorption cross sections of carbonaceous aerosols during the 2010 DOE CARES campaign

NASA Astrophysics Data System (ADS)

Flowers, B. A.; Dubey, M. K.; Subramanian, R.; Sedlacek, A. J.; Kelley, P.; Luke, W. T.; Jobson, B. T.; Zaveri, R. A.

2011-12-01

Predictions of aerosol radiative forcing require process level optical property models that are built on precise and accurate field observations. Evolution of aerosol optical properties for urban influenced carbonaceous aerosol undergoing transport and mixing with rural air masses was a focal point of the DOE Carbonaceous Aerosol and Radiative Effects (CARES) campaign near Sacramento, CA in summer 2010. Urban aerosol was transported from Sacramento, CA (T0) to the foothills of the Sierra Nevada Mountains to a rural site located near Cool, CA (T1). Aerosol absorption and scattering coefficients were measured at the T0 and T1 sites using integrated photoacoustic acoustic/nephelometer instruments (PASS-3 and PASS-UV) at 781, 532, 405, and 375 nm. Single particle soot photometry (SP2) instrumentation was used to monitor black carbon (BC) mass at both sites. Combining data from these sensors allows estimate of the wavelength-dependent mass absorption coefficient (MAC(λ)) and partitioning of MAC(λ) into contributions from the BC core and from enhancements from coating of BC cores. MAC(λ) measured in this way is free of artifacts associated with filter-based aerosol absorption measurements and takes advantage of the single particle sensitivity of the SP2 instrument, allowing observation of MAC(λ) on 10 minute and faster time scales. Coating was observed to enhance MAC(λ) by 20 - 30 % and different wavelength dependence for MAC(λ) was observed for urban and biomass burning aerosol. Further, T0 - T1 evolution of MAC(λ) was correlated with separately measured NO/NOy ratios and CO/CO2 ratios to understand the effects of aging & transport on MAC(λ) and the implications of aerosol processing that links air quality to radiative forcing on a regional scale. Aircraft observations made from the Gulfstream-1 during CARES are also analyzed to enhance process level understanding of the optical properties of fresh and aged carbonaceous aerosol in the urban-rural interface.

Robotic Single-Site Surgery for Female-to-Male Transsexuals: Preliminary Experience

PubMed Central

Bogliolo, Stefano; Cassani, Chiara; Babilonti, Luciana; Gardella, Barbara; Zanellini, Francesca; Santamaria, Valentina; Nappi, Rossella Elena; Spinillo, Arsenio

2014-01-01

Hysterectomy with bilateral salpingo-oophorectomy is a part of gender reassignment surgery for the treatment of female-to-male transsexualism. Over the last years many efforts were made in order to reduce invasiveness of laparoscopic and robotic surgery such as the introduction of single-site approach. We report our preliminary experience on single-site robotic hysterectomy for cross-sex reassignment surgery. Our data suggest that single-site robotic hysterectomy is feasible and safe in female-to-male transsexualism with some benefits in terms of postoperative pain and aesthetic results. PMID:24982976

Single-Site Laparoscopic Management of a Large Adnexal Mass

PubMed Central

Scribner, Dennis R.; Weiss, Patrice M.

2013-01-01

Introduction: Single-site laparoscopy is gaining acceptance in many surgical fields including gynecology. The purpose of this report is to demonstrate the technique and outcome for removing a large adnexal mass through a single site. Case Description: A 41-y-old female was referred to gynecology oncology for increased abdominal girth for 3 mo. An ultrasound confirmed a benign-appearing, 37-cm left adnexal mass. The mass was removed through a single-site laparoscopic incision with the aid of drainage and a morcellator. The operating time was 84 min. The patient was discharged 2 h and 35 min later with full return to normal activity in 5 d. Conclusion: Large, benign-appearing adnexal masses can be managed safely with superior cosmetic results using single-site laparoscopy. PMID:23925036

Large-Strain Monitoring Above a Longwall Coal Mine With GPS and Seismic Measurements

NASA Astrophysics Data System (ADS)

Swanson, P. L.; Andreatta, V.; Meertens, C. M.; Krahenbuhl, T.; Kenner, B.

2001-12-01

As part of an effort to evaluate continuous GPS measurements for use in mine safety studies, a joint GPS-seismic experiment was conducted at an underground longwall coal mine near Paonia, Colorado in June, 2001. Seismic and deformation signals were measured using prototype low-cost monitoring systems as a longwall panel was excavated 150 m beneath the site. Data from both seismic and GPS instruments were logged onto low-power PC-104 Linux computers which were networked using a wireless LAN. The seismic system under development at NIOSH/SRL is based on multiple distributed 8-channel 24-bit A/D converters. The GPS system uses a serial single-frequency (L1) receiver and UNAVCO's "Jstream" Java data logging software. For this experiment, a continuously operating dual-frequency GPS receiver was installed 2.4 km away to serve as a reference site. In addition to the continuously operating sites, 10 benchmarks were surveyed daily with short "rapid-static" occupations in order to provide greater spatial sampling. Two single-frequency sites were located 35 meters apart on a relatively steep north-facing slope. As mining progressed from the east, net displacements of 1.2 meters to the north and 1.65 meters of subsidence were observed over a period of 6 days. The east component exhibited up to 0.45 meters of eastward displacement (toward the excavation) followed by reverse movement to the west. This cycle, observed approximately two days earlier at the eastern L1 site, is consistent with a change in surface strain from tension to compression as the excavation front passed underneath. As this strain "wave" propagated across the field site, surface deformation underwent a cycle of tension crack nucleation, crack opening (up to 15 cm normal displacements), subsequent crack closure, and production of low-angle-thrust compressional deformation features. Analysis of seismic results, surface deformation, and additional survey results are presented.

Methane Seeps in the Gulf of Mexico: repeat acoustic surveying shows highly temporally and spatially variable venting

NASA Astrophysics Data System (ADS)

Beaumont, B. C.; Raineault, N.

2016-02-01

Scientists have recognized that natural seeps account for a large amount of methane emissions. Despite their widespread occurrence in areas like the Gulf of Mexico, little is known about the temporal variability and site-scale spatial variability of venting over time. We used repeat acoustic surveys to compare multiple days of seep activity and determine the changes in the locus of methane emission and plume height. The Sleeping Dragon site was surveyed with an EM302 multibeam sonar on three consecutive days in 2014 and 4 days within one week in 2015. The data revealed three distinctive plume regions. The locus of venting varied by 10-60 meters at each site. The plume that exhibited the least spatial variability in venting, was also the most temporally variable. This seep was present in one-third of survey dates in 2014 and three quarters of survey dates in 2015, showing high day-to-day variability. The plume height was very consistent for this plume, whereas the other plumes were more consistent temporally, but varied in maximum plume height detection by 25-85 m. The single locus of emission at the site that had high day-to-day variability may be due to a single conduit for methane release, which is sometimes closed off by carbonate or clathrate hydrate formation. In addition to day-to-day temporal variability, the locus of emission at one site was observed to shift from a point-source in 2014 to a diffuse source in 2015 at a nearby location. ROV observations showed that one of the seep sites that closed off temporarily, experienced an explosive breakthrough of gas, releasing confined methane and blowing out rock. The mechanism that causes on/off behavior of certain plumes, combined with the spatial variability of the locus of methane release shown in this study may point to carbonate or hydrate formation in the seep plumbing system and should be further investigated.

Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3), and comparison of the closely related E. coli B and K-12 genomes

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

Studier, F.W.; Daegelen, P.; Lenski, R. E.

2009-12-01

Each difference between the genome sequences of Escherichia coli B strains REL606 and BL21(DE3) can be interpreted in light of known laboratory manipulations plus a gene conversion between ribosomal RNA operons. Two treatments with 1-methyl-3-nitro-1-nitrosoguanidine in the REL606 lineage produced at least 93 single-base-pair mutations ({approx} 90% GC-to-AT transitions) and 3 single-base-pair GC deletions. Two UV treatments in the BL21(DE3) lineage produced only 4 single-base-pair mutations but 16 large deletions. P1 transductions from K-12 into the two B lineages produced 317 single-base-pair differences and 9 insertions or deletions, reflecting differences between B DNA in BL21(DE3) and integrated restriction fragments ofmore » K-12 DNA inherited by REL606. Two sites showed selective enrichment of spontaneous mutations. No unselected spontaneous single-base-pair mutations were evident. The genome sequences revealed that a progenitor of REL606 had been misidentified, explaining initially perplexing differences. Limited sequencing of other B strains defined characteristic properties of B and allowed assembly of the inferred genome of the ancestral B of Delbrueck and Luria. Comparison of the B and K-12 genomes shows that more than half of the 3793 proteins of their basic genomes are predicted to be identical, although {approx} 310 appear to be functional in either B or K-12 but not in both. The ancestral basic genome appears to have had {approx} 4039 coding sequences occupying {approx} 4.0 Mbp. Repeated horizontal transfer from diverged Escherichia coli genomes and homologous recombination may explain the observed variable distribution of single-base-pair differences. Fifteen sites are occupied by phage-related elements, but only six by comparable elements at the same site. More than 50 sites are occupied by IS elements in both B and K, 16 in common, and likely founding IS elements are identified. A signature of widespread cryptic phage P4-type mobile elements was identified. Complex deletions (dense clusters of small deletions and substitutions) apparently removed nonessential genes from {approx} 30 sites in the basic genomes.« less

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

Zukin, R.S.; Eghbali, M.; Olive, D.

{kappa} opioid receptors ({kappa} receptors) have been characterized in homogenates of guinea pig and rat brain under in vitro binding conditions. {kappa} receptors were labeled by using the tritiated prototypic {kappa} opioid ethylketocyclazocine under conditions in which {mu} and {delta} opioid binding was suppressed. In the case of guinea pig brain membranes, a single population of high-affinity {kappa} opioid receptor sites was observed. In contrast, in the case of rat brain, two populations of {kappa} sites were observed. To test the hypothesis that the high- and low-affinity {kappa} sites represent two distinct {kappa} receptor subtypes, a series of opioids weremore » tested for their abilities to compete for binding to the two sites. U-69,593 and Cambridge 20 selectively displaced the high-affinity {kappa} site in both guinea pig and rat tissue, but were inactive at the rat-brain low-affinity site. Other {kappa} opioid drugs competed for binding to both sites, but with different rank orders of potency. Quantitative light microscopy in vitro autoradiography was used to visualize the neuroanatomical pattern of {kappa} receptors in rat and guinea pig brain. The distribution patterns of the two {kappa} receptor subtypes of rat brain were clearly different. Collectively, these data provide direct evidence for the presence of two {kappa} receptor subtypes; the U-69,593-sensitive, high-affinity {kappa}{sub 1} site predominates in guinea pig brain, and the U-69,593-insensitive, low-affinity {kappa}{sub 2} site predominates in rat brain.« less

Investigating the Surface Structure of γ-Al 2 O 3 Supported WO X Catalysts by High Field 27 Al MAS NMR and Electronic Structure Calculations

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

Wan, Chuan; Hu, Mary Y.; Jaegers, Nicholas R.

The metal-support interaction in γ-Al2O3 supported WOX catalysts is investigated by a combination of high field quantitative single pulse (SP) 27Al MAS NMR spectroscopy, 2D MQMAS, 1H-27Al CP/MAS, and electronic structure calculations. NMR allows the observation of at least seven different Al sites, including a pentahedral Al site, three different tetrahedral Al sites, and three octahedral Al sites. It is found that the penta-coordinated Al (AlP) site density decreases monotonically with an increased WOX loading while the octahedral Al (AlO) site density increases concurrently. This suggests that the Alp sites are the preferred surface anchoring positions for the WOX species.more » Importantly, the AlP site isotropic chemical shift observed for the unsupported γ-Al2O3 at about 38 ppm migrates into the octahedral region with a new isotropic chemical shift value appearing near 7 ppm when the Alp site is anchored by WOX species. Density functional theory (DFT) computational modeling of the NMR parameters on proposed cluster models is carried out to accurately interpret the dramatic chemical shift changes from which the detailed anchoring mechanisms are obtained. It is found that tungsten dimers and monomers are the preferred supported surface species on γ-Al2O3, wherein one monomeric and several dimeric structures are identified as the most likely surface anchoring structures.« less

Site-Selection in Single-Molecule Junction for Highly Reproducible Molecular Electronics.

PubMed

Kaneko, Satoshi; Murai, Daigo; Marqués-González, Santiago; Nakamura, Hisao; Komoto, Yuki; Fujii, Shintaro; Nishino, Tomoaki; Ikeda, Katsuyoshi; Tsukagoshi, Kazuhito; Kiguchi, Manabu

2016-02-03

Adsorption sites of molecules critically determine the electric/photonic properties and the stability of heterogeneous molecule-metal interfaces. Then, selectivity of adsorption site is essential for development of the fields including organic electronics, catalysis, and biology. However, due to current technical limitations, site-selectivity, i.e., precise determination of the molecular adsorption site, remains a major challenge because of difficulty in precise selection of meaningful one among the sites. We have succeeded the single site-selection at a single-molecule junction by performing newly developed hybrid technique: simultaneous characterization of surface enhanced Raman scattering (SERS) and current-voltage (I-V) measurements. The I-V response of 1,4-benzenedithiol junctions reveals the existence of three metastable states arising from different adsorption sites. Notably, correlated SERS measurements show selectivity toward one of the adsorption sites: "bridge sites". This site-selectivity represents an essential step toward the reliable integration of individual molecules on metallic surfaces. Furthermore, the hybrid spectro-electric technique reveals the dependence of the SERS intensity on the strength of the molecule-metal interaction, showing the interdependence between the optical and electronic properties in single-molecule junctions.

Evaluation of Single-Doppler Radar Wind Retrievals in Flat and Complex Terrain

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

Newsom, Rob K.; Berg, Larry K.; Pekour, Mikhail S.

2014-08-01

The accuracy of winds derived from NEXRAD level II data is assessed by comparison with independent observations from 915 MHz radar wind profilers. The evaluation is carried out at two locations with very different terrain characteristics. One site is located in an area of complex terrain within the State Line Wind Energy Center in northeast Oregon. The other site is located in an area of flat terrain on the east-central Florida coast. The National Severe Storm Laboratory’s 2DVar algorithm is used to retrieve wind fields from the KPDT (Pendleton OR) and KMLB (Melbourne FL) NEXRAD radars. Comparisons between the 2DVarmore » retrievals and the radar profilers were conducted over a period of about 6 months and at multiple height levels at each of the profiler sites. Wind speed correlations at most observation height levels fell in the range from 0.7 to 0.8, indicating that the retrieved winds followed temporal fluctuations in the profiler-observed winds reasonably well. The retrieved winds, however, consistently exhibited slow biases in the range of1 to 2 ms-1. Wind speed difference distributions were broad with standard deviations in the range from 3 to 4 ms-1. Results from the Florida site showed little change in the wind speed correlations and difference standard deviations with altitude between about 300 and 1400 m AGL. Over this same height range, results from the Oregon site showed a monotonic increase in the wind speed correlation and a monotonic decrease in the wind speed difference standard deviation with increasing altitude. The poorest overall agreement occurred at the lowest observable level (~300 m AGL) at the Oregon site, where the effects of the complex terrain were greatest.« less

Electric currents and coronal heating in NOAA active region 6952

NASA Technical Reports Server (NTRS)

Metcalf, T. R.; Canfield, R. C.; Hudson, H. S.; Mickey, D. L.; Wulser, J. -P.; Martens, P. C. H.; Tsuneta, S.

1994-01-01

We examine the spatial and temporal relationship between coronal structures observed with the soft X-ray telescope (SXT) on board the Yohkoh spacecraft and the vertical electric current density derived from photospheric vector magnetograms obtained using the Stokes Polarimeter at the Mees Solar Observatory. We focus on a single active region: AR 6952 which we observed on 7 days during 1991 December. For 11 independent maps of the vertical electric current density co-aligned with non-flaring X-ray images, we search for a morphological relationship between sites of high vertical current density in the photosphere and enhanced X-ray emission in the overlying corona. We find no compelling spatial or temporal correlation between the sites of vertical current and the bright X-ray structures in this active region.

Measuring and computing natural ground-water recharge at sites in south-central Kansas

USGS Publications Warehouse

Sophocleous, M.A.; Perry, C.A.

1987-01-01

To measure the natural groundwater recharge process, two sites in south-central Kansas were instrumented with sensors and data microloggers. The atmospheric-boundary layer and the unsaturated and saturated soil zones were monitored as a single regime. Direct observations also were used to evaluate the measurements. Atmospheric sensors included an anemometer, a tipping-bucket rain gage, an air-temperature thermistor, a relative-humidity probe, a net radiometer, and a barometric-pressure transducer. Sensors in the unsaturated zone consisted of soil-temperature thermocouples, tensiometers coupled with pressure transducers and dial gages, gypsum blocks, and a neutron-moisture probe. The saturated-zone sensors consisted of a water-level pressure transducer, a conventional float gage connected to a variable potentiometer, soil thermocouples, and a number of multiple-depth piezometers. Evaluation of the operation of these sensors and recorders indicates that certain types of equipment, such as pressure transducers, are very sensitive to environmental conditions. A number of suggestions aimed at improving instrumentation of recharge investigations are outlined. Precipitation and evapotranspiration data, taken together with soil moisture profiles and storage changes, water fluxes in the unsaturated zone and hydraulic gradients in the saturated zone at various depths, soil temperature, water table hydrographs, and water level changes in nearby wells, describe the recharge process. Although the two instrumented sites are located in sand-dune environments in area characterized by a shallow water table and a sub-humid continental climate, a significant difference was observed in the estimated total recharge. The estimates ranged from less than 2.5 mm at the Zenith site to approximately 154 mm at the Burrton site from February to June 1983. The principal reasons that the Burrton site had more recharge than the Zenith site were more precipitation, less evapotranspiration, and a shallower depth to the water table. Effective recharge took place only during late winter and spring. No summer or fall recharge was observed at either site during the observation period of this study. (Author 's abstract)

Entanglement entropy and fidelity susceptibility in the one-dimensional spin-1 XXZ chains with alternating single-site anisotropy.

PubMed

Ren, Jie; Liu, Guang-Hua; You, Wen-Long

2015-03-18

We study the fidelity susceptibility in an antiferromagnetic spin-1 XXZ chain numerically. By using the density-matrix renormalization group method, the effects of the alternating single-site anisotropy D on fidelity susceptibility are investigated. Its relation with the quantum phase transition is analyzed. It is found that the quantum phase transition from the Haldane spin liquid to periodic Néel spin solid can be well characterized by the fidelity. Finite size scaling of fidelity susceptibility shows a power-law divergence at criticality, which indicates the quantum phase transition is of second order. The results are confirmed by the second derivative of the ground-state energy. We also study the relationship between the entanglement entropy, the Schmidt gap and quantum phase transitions. Conclusions drawn from these quantum information observables agree well with each other.

Debye screening in single-molecule carbon nanotube field-effect sensors.

PubMed

Sorgenfrei, Sebastian; Chiu, Chien-Yang; Johnston, Matthew; Nuckolls, Colin; Shepard, Kenneth L

2011-09-14

Point-functionalized carbon nanotube field-effect transistors can serve as highly sensitive detectors for biomolecules. With a probe molecule covalently bound to a defect in the nanotube sidewall, two-level random telegraph noise (RTN) in the conductance of the device is observed as a result of a charged target biomolecule binding and unbinding at the defect site. Charge in proximity to the defect modulates the potential (and transmission) of the conductance-limiting barrier created by the defect. In this Letter, we study how these single-molecule electronic sensors are affected by ionic screening. Both charge in proximity to the defect site and buffer concentration are found to affect RTN amplitude in a manner that follows from simple Debye length considerations. RTN amplitude is also dependent on the potential of the electrolyte gate as applied to the reference electrode; at high enough gate potentials, the target DNA is completely repelled and RTN is suppressed.

Scientific Benefit of Enlarging Gravitational Wave Detector Networks

NASA Astrophysics Data System (ADS)

Chu, Qi; Wen, Linqing; Blair, David

2012-06-01

Localising the sources of gravitational waves (GWs) in the sky is crucial to observing the electromagnetic counterparts of GW sources. The localisation capability is poor by a single GW detector yet can be improved by adding more detectors to the detector network. In this paper we review recent studies on scientific benefits of global detector networks and focus on their localisation capability. We employ Wen-Chen's formula to compare this merit of current and future detector networks for localising gravitational wave bursts. We find that the addition of a new detector located in Japan, or India, or Australia will increase angular resolution 3~5 fold with respect to current LIGO-Virgo network, and that the angular resolution improvement by adding a single detector in Australia is comparable to that achieved by adding detectors in both India and Japan. A six-site network achieves a 11-fold improvement in angular resolution compared with the existing three-site network.

Debye screening in single-molecule carbon nanotube field-effect transistors

PubMed Central

Sorgenfrei, Sebastian; Chiu, Chien-yang; Johnston, Matthew; Nuckolls, Colin; Shepard, Kenneth L.

2013-01-01

Point-functionalized carbon nanotube field-effect transistors can serve as highly sensitive detectors for biomolecules. With a probe molecule covalently bound to a defect in the nanotube sidewall, two-level random telegraph noise (RTN) in the conductance of the device is observed as a result of a charged target biomolecule binding and unbinding at the defect site. Charge in proximity to the defect modulates the potential (and transmission) of the conductance-limiting barrier created by the defect. In this Letter, we study how these single-molecule electronic sensors are affected by ionic screening. Both charge in proximity to the defect site and buffer concentration are found to affect RTN amplitude in a manner that follows from simple Debye length considerations. RTN amplitude is also dependent on the potential of the electrolyte gate as applied to the reference electrode; at high enough repulsive potentials, the target DNA is completely repelled and RTN is suppressed. PMID:21806018

Local Optical Closure Using Single Particle Mixing State Observations during the 2010 DOE CARES Campaign

NASA Astrophysics Data System (ADS)

Zaveri, R. A.; Arnott, W. P.; Atkinson, D. B.; Barnard, J.; Beranek, J.; Cappa, C. D.; Chand, D.; Dubey, M. K.; Easter, R. C.; Flowers, B. A.; Gyawali, M. S.; Jobson, B. T.; Pekour, M. S.; Riemer, N. S.; Subramanian, R.; Song, C.; Zelenyuk, A.

2011-12-01

Atmospheric black carbon (BC) particles readily absorb both upwelling and downwelling broadband radiation and are thought to be second only to CO2 in contributing to global warming. However large uncertainties still exist in the global estimates of BC radiative forcing, which depend not only on our ability to accurately simulate the global loading and distribution of BC, but also on the precise knowledge of the mixing state and morphology of BC particles due to aging. To this end, one of the objectives of the Carbonaceous Aerosols and Radiative Effects Study (CARES) conducted in Sacramento, CA, during June 2010 was to investigate the evolution of urban BC particles and the associated optical properties, with the overarching goal of improving their process-level model representations. The daytime Sacramento urban plume was routinely transported to the northeast into the Sierra Nevada foothills area rich in biogenic emissions, and the aged aerosols were often recirculated back into the urban area the next morning. The CARES campaign observational strategy was designed to take advantage of this flow pattern by setting up two observation supersites - one located within the Sacramento urban area, referred to as the "T0 site," and another located about 24 km to the northeast in Cool, CA, a small town in the rural foothills area, referred to as the "T1 site." BC size distribution and mixing state were measured at both the sites with single particle soot photometry (SP2). The single particle mass spectrometer SPLAT II was also deployed at the T0 site to characterize the size, composition (mixing state), density, and morphology of BC and non-BC containing particles. Non-refractory aerosol species were measured by Aerodyne aerosol mass spectrometer (AMS). Aerosol light absorption and scattering (or extinction) at multiple wavelengths were measured using several techniques, including photoacoustic, cavity ring-down, nephelometer as well as the filter-based particle/soot absorption photometer (PSAP). Other supporting measurements include aerosol size distribution and key trace gases (NOx, NOy, O3, and volatile organic compounds). The combined data thus provides a unique opportunity to characterize BC aging and its effect on optical properties. In this paper, we will present results from a local optical closure study for selected 10-minute samples at the T0 urban site using the particle-resolved version of the comprehensive aerosol model MOSAIC coupled to a shell/core Mie code. Sensitivity of the predicted optical properties to various measurements and model representations of particle composition, mixing state, size bin resolution, and refractive indices will be examined.

Single-Molecule Localization Microscopy allows for the analysis of cancer metastasis-specific miRNA distribution on the nanoscale

PubMed Central

Tezcan, Kerem Can; Schaufler, Wladimir; Bestvater, Felix; Patil, Nitin; Birk, Udo; Hafner, Mathias; Altevogt, Peter; Cremer, Christoph; Allgayer, Heike

2015-01-01

We describe a novel approach for the detection of small non-coding RNAs in single cells by Single-Molecule Localization Microscopy (SMLM). We used a modified SMLM–setup and applied this instrument in a first proof-of-principle concept to human cancer cell lines. Our method is able to visualize single microRNA (miR)-molecules in fixed cells with a localization accuracy of 10–15 nm, and is able to quantify and analyse clustering and localization in particular subcellular sites, including exosomes. We compared the metastasis-site derived (SW620) and primary site derived (SW480) human colorectal cancer (CRC) cell lines, and (as a proof of principle) evaluated the metastasis relevant miR-31 as a first example. We observed that the subcellular distribution of miR-31 molecules in both cell lines was very heterogeneous with the largest subpopulation of optically acquired weakly metastatic cells characterized by a low number of miR-31 molecules, as opposed to a significantly higher number in the majority of the highly metastatic cells. Furthermore, the highly metastatic cells had significantly more miR-31-molecules in the extracellular space, which were visualized to co-localize with exosomes in significantly higher numbers. From this study, we conclude that miRs are not only aberrantly expressed and regulated, but also differentially compartmentalized in cells with different metastatic potential. Taken together, this novel approach, by providing single molecule images of miRNAs in cellulo can be used as a powerful supplementary tool in the analysis of miRNA function and behaviour and has far reaching potential in defining metastasis-critical subpopulations within a given heterogeneous cancer cell population. PMID:26561203

Unusual binding of ursodeoxycholic acid to ileal bile acid binding protein: role in activation of FXRα.

PubMed

Fang, Changming; Filipp, Fabian V; Smith, Jeffrey W

2012-04-01

Ursodeoxycholic acid (UDCA, ursodiol) is used to prevent damage to the liver in patients with primary biliary cirrhosis. The drug also prevents the progression of colorectal cancer and the recurrence of high-grade colonic dysplasia. However, the molecular mechanism by which UDCA elicits its beneficial effects is not entirely understood. The aim of this study was to determine whether ileal bile acid binding protein (IBABP) has a role in mediating the effects of UDCA. We find that UDCA binds to a single site on IBABP and increases the affinity for major human bile acids at a second binding site. As UDCA occupies one of the bile acid binding sites on IBABP, it reduces the cooperative binding that is often observed for the major human bile acids. Furthermore, IBABP is necessary for the full activation of farnesoid X receptor α (FXRα) by bile acids, including UDCA. These observations suggest that IBABP may have a role in mediating some of the intestinal effects of UDCA.

Multiple sites of extinction for a single learned response

PubMed Central

Mauk, Michael D.

2012-01-01

Most learned responses can be diminished by extinction, a process that can be engaged when a conditioned stimulus (CS) is presented but not reinforced. We present evidence that plasticity in at least two brain regions can mediate extinction of responses produced by trace eyelid conditioning, where the CS and the reinforcing stimulus are separated by a stimulus-free interval. We observed individual differences in the effects of blocking extinction mechanisms in the cerebellum, the structure that, along with several forebrain structures, mediates acquisition of trace eyelid responses; in some rabbits extinction was prevented, whereas in others it was largely unaffected. We also show that cerebellar mechanisms can mediate extinction when noncerebellar mechanisms are bypassed. Together, these observations indicate that trace eyelid responses can be extinguished via processes operating at more than one site, one in the cerebellum and one upstream in forebrain. The relative contributions of these sites may vary from animal to animal and situation to situation. PMID:21940608

Unusual binding of ursodeoxycholic acid to ileal bile acid binding protein: role in activation of FXRα[S

PubMed Central

Fang, Changming; Filipp, Fabian V.; Smith, Jeffrey W.

2012-01-01

Ursodeoxycholic acid (UDCA, ursodiol) is used to prevent damage to the liver in patients with primary biliary cirrhosis. The drug also prevents the progression of colorectal cancer and the recurrence of high-grade colonic dysplasia. However, the molecular mechanism by which UDCA elicits its beneficial effects is not entirely understood. The aim of this study was to determine whether ileal bile acid binding protein (IBABP) has a role in mediating the effects of UDCA. We find that UDCA binds to a single site on IBABP and increases the affinity for major human bile acids at a second binding site. As UDCA occupies one of the bile acid binding sites on IBABP, it reduces the cooperative binding that is often observed for the major human bile acids. Furthermore, IBABP is necessary for the full activation of farnesoid X receptor α (FXRα) by bile acids, including UDCA. These observations suggest that IBABP may have a role in mediating some of the intestinal effects of UDCA. PMID:22223860

Computational active site analysis of molecular pathways to improve functional classification of enzymes.

PubMed

Ozyurt, A Sinem; Selby, Thomas L

2008-07-01

This study describes a method to computationally assess the function of homologous enzymes through small molecule binding interaction energy. Three experimentally determined X-ray structures and four enzyme models from ornithine cyclo-deaminase, alanine dehydrogenase, and mu-crystallin were used in combination with nine small molecules to derive a function score (FS) for each enzyme-model combination. While energy values varied for a single molecule-enzyme combination due to differences in the active sites, we observe that the binding energies for the entire pathway were proportional for each set of small molecules investigated. This proportionality of energies for a reaction pathway appears to be dependent on the amino acids in the active site and their direct interactions with the small molecules, which allows a function score (FS) to be calculated to assess the specificity of each enzyme. Potential of mean force (PMF) calculations were used to obtain the energies, and the resulting FS values demonstrate that a measurement of function may be obtained using differences between these PMF values. Additionally, limitations of this method are discussed based on: (a) larger substrates with significant conformational flexibility; (b) low homology enzymes; and (c) open active sites. This method should be useful in accurately predicting specificity for single enzymes that have multiple steps in their reactions and in high throughput computational methods to accurately annotate uncharacterized proteins based on active site interaction analysis. 2008 Wiley-Liss, Inc.

Local protein dynamics during microvesicle exocytosis in neuroendocrine cells.

PubMed

Somasundaram, Agila; Taraska, Justin

2018-06-06

Calcium triggered exocytosis is key to many physiological processes, including neurotransmitter and hormone release by neurons and endocrine cells. Dozens of proteins regulate exocytosis, yet the temporal and spatial dynamics of these factors during vesicle fusion remain unclear. Here we use total internal reflection fluorescence microscopy to visualize local protein dynamics at single sites of exocytosis of small synaptic-like microvesicles in live cultured neuroendocrine PC12 cells. We employ two-color imaging to simultaneously observe membrane fusion (using vesicular acetylcholine transporter (VAChT) tagged to pHluorin) and the dynamics of associated proteins at the moments surrounding exocytosis. Our experiments show that many proteins, including the SNAREs syntaxin1 and VAMP2, the SNARE modulator tomosyn, and Rab proteins, are pre-clustered at fusion sites and rapidly lost at fusion. The ATPase NSF is locally recruited at fusion. Interestingly, the endocytic BAR domain-containing proteins amphiphysin1, syndapin2, and endophilins are dynamically recruited to fusion sites, and slow the loss of vesicle membrane-bound cargo from fusion sites. A similar effect on vesicle membrane protein dynamics was seen with the over-expression of the GTPases dynamin1 and dynamin2. These results suggest that proteins involved in classical clathrin-mediated endocytosis can regulate exocytosis of synaptic-like microvesicles. Our findings provide insights into the dynamics, assembly, and mechanistic roles of many key factors of exocytosis and endocytosis at single sites of microvesicle fusion in live cells.

Free terminal amines in DNA-binding peptides alter the product distribution from guanine radicals produced by single electron oxidation.

PubMed

Konigsfeld, Katie M; Lee, Melissa; Urata, Sarah M; Aguilera, Joe A; Milligan, Jamie R

2012-03-01

Electron deficient guanine radical species are major intermediates produced in DNA by the direct effect of ionizing irradiation. There is evidence that they react with amine groups in closely bound ligands to form covalent crosslinks. Crosslink formation is very poorly characterized in terms of quantitative rate and yield data. We sought to address this issue by using oligo-arginine ligands to model the close association of DNA and its binding proteins in chromatin. Guanine radicals were prepared in plasmid DNA by single electron oxidation. The product distribution derived from them was assayed by strand break formation after four different post-irradiation incubations. We compared the yields of DNA damage produced in the presence of four ligands in which neither, one, or both of the amino and carboxylate termini were blocked with amides. Free carboxylate groups were unreactive. Significantly higher yields of heat labile sites were observed when the amino terminus was unblocked. The rate of the reaction was characterized by diluting the unblocked amino group with its amide blocked derivative. These observations provide a means to develop quantitative estimates for the yields in which these labile sites are formed in chromatin by exposure to ionizing irradiation.

New 50-M-Class Single Dish Telescope: Large Submillimeter Telescope (LST)

NASA Astrophysics Data System (ADS)

Kawabe, Ryohei

2018-01-01

We report on the plan to construct a 50 m class millimeter (mm) and sub-mm single dish telescope, the Large Submillimeter Telescope (LST). The telescope is optimized for wide-area imaging and spectroscopic surveys in the 70 to 420 GHz main frequency range, which just covers main atmospheric windows at millimeter and submillimeter wavelengths for good observing sites such as the ALMA site in Chile. We also target observations at higher frequencies of up to 1 THz, using an inner part high-precision surface. Active surface control is required in order to correct gravitational and thermal deformations of the surface. The LST will facilitate new discovery spaces such as wide-field imaging with both continuum and spectral lines, along with new developments for time domain science. With exploiting synergy with ALMA and other telescopes, LST can contribute to a wide range of topics in astronomy and astrophysics, e.g., astrochemistry, star formation in the Galaxy and galaxies, evolution of galaxy clusters via SZ effect. We also report the recent progress on the technical study, e.g., the tentative study of the surface error budget and challenges to correction for the wind-load effect.

Reversing the Outcome of Synapse Elimination at Developing Neuromuscular Junctions In Vivo: Evidence for Synaptic Competition and Its Mechanism

PubMed Central

Turney, Stephen G.; Lichtman, Jeff W.

2012-01-01

During mammalian development, neuromuscular junctions and some other postsynaptic cells transition from multiple- to single-innervation as synaptic sites are exchanged between different axons. It is unclear whether one axon invades synaptic sites to drive off other inputs or alternatively axons expand their territory in response to sites vacated by other axons. Here we show that soon-to-be-eliminated axons rapidly reverse fate and grow to occupy vacant sites at a neuromuscular junction after laser removal of a stronger input. This reversal supports the idea that axons take over sites that were previously vacated. Indeed, during normal development we observed withdrawal followed by takeover. The stimulus for axon growth is not postsynaptic cell inactivity because axons grow into unoccupied sites even when target cells are functionally innervated. These results demonstrate competition at the synaptic level and enable us to provide a conceptual framework for understanding this form of synaptic plasticity. PMID:22745601

Constraints on core-collapse supernova progenitors from explosion site integral field spectroscopy

NASA Astrophysics Data System (ADS)

Kuncarayakti, H.; Anderson, J. P.; Galbany, L.; Maeda, K.; Hamuy, M.; Aldering, G.; Arimoto, N.; Doi, M.; Morokuma, T.; Usuda, T.

2018-05-01

Context. Observationally, supernovae (SNe) are divided into subclasses according to their distinct characteristics. This diversity naturally reflects the diversity in the progenitor stars. It is not entirely clear, however, how different evolutionary paths leading massive stars to become an SN are governed by fundamental parameters such as progenitor initial mass and metallicity. Aims: This paper places constraints on progenitor initial mass and metallicity in distinct core-collapse SN subclasses through a study of the parent stellar populations at the explosion sites. Methods: Integral field spectroscopy (IFS) of 83 nearby SN explosion sites with a median distance of 18 Mpc has been collected and analysed, enabling detection and spectral extraction of the parent stellar population of SN progenitors. From the parent stellar population spectrum, the initial mass and metallicity of the coeval progenitor are derived by means of comparison to simple stellar population models and strong-line methods. Additionally, near-infrared IFS was employed to characterise the star formation history at the explosion sites. Results: No significant metallicity differences are observed among distinct SN types. The typical progenitor mass is found to be highest for SN type Ic, followed by type Ib, then types IIb and II. Type IIn is the least associated with young stellar populations and thus massive progenitors. However, statistically significant differences in progenitor initial mass are observed only when comparing SNe IIn with other subclasses. Stripped-envelope SN progenitors with initial mass estimates lower than 25 M⊙ are found; they are thought to be the result of binary progenitors. Confirming previous studies, these results support the notion that core-collapse SN progenitors cannot arise from single-star channels only, and both single and binary channels are at play in the production of core-collapse SNe. Near-infrared IFS suggests that multiple stellar populations with different ages may be present in some of the SN sites. As a consequence, there could be a non-negligible amount of contamination from old populations, and therefore the individual age estimates are effectively lower limits. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 089.D-0367, 091.D-0482, 093.D-0318, 094.D-0290, and 095.D-0172

Toxin MqsR Cleaves Single-Stranded mRNA with Various 5 Ends

DTIC Science & Technology

2016-08-24

either protein ORIGINAL RESEARCH Toxin MqsR cleaves single- stranded mRNA with various 5’ ends Nityananda Chowdhury1,*, Brian W. Kwan1,*, Louise C...in which a single 5′- GCU site was predicted to be single- stranded (ssRNA), double- stranded (dsRNA), in the loop of a stem - loop (slRNA), or in a...single- stranded 5′- GCU sites since cleavage was approximately 20- fold higher than cleavage seen with the 5′- GCU site in the stem - loop and

Robotic right colectomy using the Da Vinci Single-Site® platform: case report.

PubMed

Morelli, Luca; Guadagni, Simone; Caprili, Giovanni; Di Candio, Giulio; Boggi, Ugo; Mosca, Franco

2013-09-01

While single-port laparoscopy for abdominal surgery is technically challenging, the Da Vinci Single-Site® robotic surgery platform may help to overcome some of the difficulties of this rapidly evolving technique. The authors of this article present a case of single-incision, robotic right colectomy using this device. A 74-year-old female with malignant polyp of caecum was operated on with a single-site approach using the Da Vinci Single-Site® robotic surgery device. Resection and anastomosis were performed extra-corporeally after undocking the robot. The procedure was successfully completed in 200 min. No surgical complications occurred during the intervention and the post-operative stay and no conversion to laparotomy or additional trocars were required. To the best of our knowledge, this is the first case of right colectomy using the Da Vinci Single-Site® robotic surgery platform to be reported. The procedure is feasible and safe and its main advantages are restoration of triangulation and reduced instrument clashes. Copyright © 2013 John Wiley & Sons, Ltd.

Site-Specific N-Glycosylation of Recombinant Pentameric and Hexameric Human IgM

NASA Astrophysics Data System (ADS)

Moh, Edward S. X.; Lin, Chi-Hung; Thaysen-Andersen, Morten; Packer, Nicolle H.

2016-07-01

Glycosylation is known to play an important role in IgG antibody structure and function. Polymeric IgM, the largest known antibody in humans, displays five potential N-glycosylation sites on each heavy chain monomer. IgM can exist as a pentamer with a connecting singly N-glycosylated J-chain (with a total of 51 glycosylation sites) or as a hexamer (60 glycosylation sites). In this study, the N-glycosylation of recombinant pentameric and hexameric IgM produced by the same human cell type and culture conditions was site-specifically profiled by RP-LC-CID/ETD-MS/MS using HILIC-enriched tryptic and GluC glycopeptides. The occupancy of all putative N-glycosylation sites on the pentameric and hexameric IgM were able to be determined. Distinct glycosylation differences were observed between each of the five N-linked sites on the IgM heavy chains. While Asn171, Asn332, and Asn395 all had predominantly complex type glycans, differences in glycan branching and sialylation were observed between the sites. Asn563, a high mannose-rich glycosylation site that locates in the center of the IgM polymer, was only approximately 60% occupied in both the pentameric and hexameric IgM forms, with a difference in relative abundance of the glycan structures between the pentamer and hexamer. This study highlights the information obtained by characterization of the site-heterogeneity of a highly glycosylated protein of high molecular mass with quaternary structure, revealing differences that would not be seen by global glycan or deglycosylated peptide profiling.

A Tale of two Cities: Photoacoustic and Aethalometer Measurements Comparisons of Light Absorption in Mexico City and Las Vegas, NV, USA

NASA Astrophysics Data System (ADS)

Paredes-Miranda, G.; Arnott, W. P.; Marley, N. A.; Gaffney, J. S.

2007-05-01

As part of the Megacity Impacts on Regional and Global Environments, MIRAGE-Mex deployment to Mexico City in the period of 30 days, March 2006, a suite of photoacoustic spectrometers (PAS; W. Arnott & G. Paredes), nephelometer scattering, and aetholemeter absorption instruments (N. Marley & J.Gaffney) were installed to measure at ground level the light absorption and scattering by aerosols at the urban site at Instituto Mexicano del Petroleo (Mexican Oil Institute, denoted by IMP). This IMP site gave in-situ characterization of the Mexico City plume under favorable wind conditions. The PAS used at IMP operates at 532 nm, and conveniently allowed for characterization of gaseous absorption at this wavelength as well. Light scattering measurements are accomplished within the PAS by the reciprocal nephelometery method. In the urban site the aerosol absorption coefficient typically varies between 20 and 180 Mm-1 during the course of the day and significant diurnal variation of the aerosol single scattering albedo was observed. The Las Vegas, NV site was located at East Charleston Street on January-February, 2003. In east Las Vegas typical westerly winds carry the city plume across the site. Comparisons of PAS aerosol light absorption and aetholemeter absorption measurements at 521 nm at both Las Vegas NV and Mexico City sites will be presented. We will also present a broad overview of the diurnal variation of the scattering and absorption as well as the single scattering albedo and fraction of absorption due to gases at the sites in relation to secondary aerosol formation.

Layer speciation and electronic structure investigation of freestanding hexagonal boron nitride nanosheets

NASA Astrophysics Data System (ADS)

WangEqual Contribution To This Work., Jian; Wang, Zhiqiang; Cho, Hyunjin; Kim, Myung Jong; Sham, T. K.; Sun, Xuhui

2015-01-01

Chemical imaging, thickness mapping, layer speciation and polarization dependence have been performed on single and multilayered (up to three layers and trilayered nanosheets overlapping to form 6 and 9 layers) hexagonal boron nitride (hBN) nanosheets by scanning transmission X-ray microscopy. Spatially-resolved XANES directly from freestanding regions of different layers has been extracted and compared with sample normal and 30° tilted configurations. Notably a double feature σ* excitonic state and a stable high energy σ* state were observed at the boron site in addition to the intense π* excitonic state. The boron projected σ* DOS, especially the first σ* exciton, is sensitive to surface modification, particularly in the single layered hBN nanosheet which shows more significant detectable contaminants and defects such as tri-coordinated boron/nitrogen oxide. The nitrogen site has shown very weak or no excitonic character. The distinct excitonic effect on boron and nitrogen was interpreted to the partly ionic state of hBN. Bulk XANES of hBN nanosheets was also measured to confirm the spectro-microscopic STXM result. Finally, the unoccupied electronic structures of hBN and graphene were compared.Chemical imaging, thickness mapping, layer speciation and polarization dependence have been performed on single and multilayered (up to three layers and trilayered nanosheets overlapping to form 6 and 9 layers) hexagonal boron nitride (hBN) nanosheets by scanning transmission X-ray microscopy. Spatially-resolved XANES directly from freestanding regions of different layers has been extracted and compared with sample normal and 30° tilted configurations. Notably a double feature σ* excitonic state and a stable high energy σ* state were observed at the boron site in addition to the intense π* excitonic state. The boron projected σ* DOS, especially the first σ* exciton, is sensitive to surface modification, particularly in the single layered hBN nanosheet which shows more significant detectable contaminants and defects such as tri-coordinated boron/nitrogen oxide. The nitrogen site has shown very weak or no excitonic character. The distinct excitonic effect on boron and nitrogen was interpreted to the partly ionic state of hBN. Bulk XANES of hBN nanosheets was also measured to confirm the spectro-microscopic STXM result. Finally, the unoccupied electronic structures of hBN and graphene were compared. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr04445b

Detection and plant monitoring programs: lessons from an intensive survey of Asclepias meadii with five observers.

PubMed

Alexander, Helen M; Reed, Aaron W; Kettle, W Dean; Slade, Norman A; Bodbyl Roels, Sarah A; Collins, Cathy D; Salisbury, Vaughn

2012-01-01

Monitoring programs, where numbers of individuals are followed through time, are central to conservation. Although incomplete detection is expected with wildlife surveys, this topic is rarely considered with plants. However, if plants are missed in surveys, raw count data can lead to biased estimates of population abundance and vital rates. To illustrate, we had five independent observers survey patches of the rare plant Asclepias meadii at two prairie sites. We analyzed data with two mark-recapture approaches. Using the program CAPTURE, the estimated number of patches equaled the detected number for a burned site, but exceeded detected numbers by 28% for an unburned site. Analyses of detected patches using Huggins models revealed important effects of observer, patch state (flowering/nonflowering), and patch size (number of stems) on probabilities of detection. Although some results were expected (i.e. greater detection of flowering than nonflowering patches), the importance of our approach is the ability to quantify the magnitude of detection problems. We also evaluated the degree to which increased observer numbers improved detection: smaller groups (3-4 observers) generally found 90 - 99% of the patches found by all five people, but pairs of observers or single observers had high error and detection depended on which individuals were involved. We conclude that an intensive study at the start of a long-term monitoring study provides essential information about probabilities of detection and what factors cause plants to be missed. This information can guide development of monitoring programs.

An additional substrate binding site in a bacterial phenylalanine hydroxylase

PubMed Central

Ronau, Judith A.; Paul, Lake N.; Fuchs, Julian E.; Corn, Isaac R.; Wagner, Kyle T.; Liedl, Klaus R.; Abu-Omar, Mahdi M.; Das, Chittaranjan

2014-01-01

Phenylalanine hydroxylase (PAH) is a non-heme iron enzyme that catalyzes phenylalanine oxidation to tyrosine, a reaction that must be kept under tight regulatory control. Mammalian PAH features a regulatory domain where binding of the substrate leads to allosteric activation of the enzyme. However, existence of PAH regulation in evolutionarily distant organisms, such as certain bacteria in which it occurs, has so far been underappreciated. In an attempt to crystallographically characterize substrate binding by PAH from Chromobacterium violaceum (cPAH), a single-domain monomeric enzyme, electron density for phenylalanine was observed at a distal site, 15.7Å from the active site. Isothermal titration calorimetry (ITC) experiments revealed a dissociation constant of 24 ± 1.1 µM for phenylalanine. Under the same conditions, no detectable binding was observed in ITC for alanine, tyrosine, or isoleucine, indicating the distal site may be selective for phenylalanine. Point mutations of residues in the distal site that contact phenylalanine (F258A, Y155A, T254A) lead to impaired binding, consistent with the presence of distal site binding in solution. Kinetic analysis reveals that the distal site mutants suffer a discernible loss in their catalytic activity. However, x-ray structures of Y155A and F258A, two of the mutants showing more noticeable defect in their activity, show no discernible change in their active site structure, suggesting that the effect of distal binding may transpire through protein dynamics in solution. PMID:23860686

Orientation independence of single-vacancy and single-ion permeability ratios.

PubMed Central

McGill, P; Schumaker, M F

1995-01-01

Single-vacancy models have been proposed as open channel permeation mechanisms for K+ channels. Single-ion models have been used to describe permeation through Na+ channels. This paper demonstrates that these models have a distinctive symmetry property. Their permeability ratios, measured under biionic conditions, are independent of channel orientation when the reversal potential is zero. This symmetry is a property of general m-site single-vacancy channels, m-site shaking-stack channels, as well as m-site single-ion channels. An experimental finding that the permeability ratios of a channel did not have this symmetry would provide evidence that a single-vacancy or single-ion model is an incorrect or incomplete description of permeation. Images FIGURE 1 PMID:7669913

Detection of quantum well induced single degenerate-transition-dipoles in ZnO nanorods.

PubMed

Ghosh, Siddharth; Ghosh, Moumita; Seibt, Michael; Rao, G Mohan

2016-02-07

Quantifying and characterising atomic defects in nanocrystals is difficult and low-throughput using the existing methods such as high resolution transmission electron microscopy (HRTEM). In this article, using a defocused wide-field optical imaging technique, we demonstrate that a single ultrahigh-piezoelectric ZnO nanorod contains a single defect site. We model the observed dipole-emission patterns from optical imaging with a multi-dimensional dipole and find that the experimentally observed dipole pattern and model-calculated patterns are in excellent agreement. This agreement suggests the presence of vertically oriented degenerate-transition-dipoles in vertically aligned ZnO nanorods. The HRTEM of the ZnO nanorod shows the presence of a stacking fault, which generates a localised quantum well induced degenerate-transition-dipole. Finally, we elucidate that defocused wide-field imaging can be widely used to characterise defects in nanomaterials to answer many difficult questions concerning the performance of low-dimensional devices, such as in energy harvesting, advanced metal-oxide-semiconductor storage, and nanoelectromechanical and nanophotonic devices.

Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication.

PubMed

Feng, Wenyi; Collingwood, David; Boeck, Max E; Fox, Lindsay A; Alvino, Gina M; Fangman, Walton L; Raghuraman, Mosur K; Brewer, Bonita J

2006-02-01

During DNA replication one or both strands transiently become single stranded: first at the sites where initiation of DNA synthesis occurs (known as origins of replication) and subsequently on the lagging strands of replication forks as discontinuous Okazaki fragments are generated. We report a genome-wide analysis of single-stranded DNA (ssDNA) formation in the presence of hydroxyurea during DNA replication in wild-type and checkpoint-deficient rad53 Saccharomyces cerevisiae cells. In wild-type cells, ssDNA was first observed at a subset of replication origins and later 'migrated' bi-directionally, suggesting that ssDNA formation is associated with continuously moving replication forks. In rad53 cells, ssDNA was observed at virtually every known origin, but remained there over time, suggesting that replication forks stall. Telomeric regions seemed to be particularly sensitive to the loss of Rad53 checkpoint function. Replication origins in Schizosaccharomyces pombe were also mapped using our method.

Surface-modified CMOS IC electrochemical sensor array targeting single chromaffin cells for highly parallel amperometry measurements.

PubMed

Huang, Meng; Delacruz, Joannalyn B; Ruelas, John C; Rathore, Shailendra S; Lindau, Manfred

2018-01-01

Amperometry is a powerful method to record quantal release events from chromaffin cells and is widely used to assess how specific drugs modify quantal size, kinetics of release, and early fusion pore properties. Surface-modified CMOS-based electrochemical sensor arrays allow simultaneous recordings from multiple cells. A reliable, low-cost technique is presented here for efficient targeting of single cells specifically to the electrode sites. An SU-8 microwell structure is patterned on the chip surface to provide insulation for the circuitry as well as cell trapping at the electrode sites. A shifted electrode design is also incorporated to increase the flexibility of the dimension and shape of the microwells. The sensitivity of the electrodes is validated by a dopamine injection experiment. Microwells with dimensions slightly larger than the cells to be trapped ensure excellent single-cell targeting efficiency, increasing the reliability and efficiency for on-chip single-cell amperometry measurements. The surface-modified device was validated with parallel recordings of live chromaffin cells trapped in the microwells. Rapid amperometric spikes with no diffusional broadening were observed, indicating that the trapped and recorded cells were in very close contact with the electrodes. The live cell recording confirms in a single experiment that spike parameters vary significantly from cell to cell but the large number of cells recorded simultaneously provides the statistical significance.

Average structure and M2 site configurations in C2/c clinopyroxenes along the Di-En join

NASA Astrophysics Data System (ADS)

Tribaudino, M.; Benna, P.; Bruno, E.

1989-12-01

In order to clarify the structural configurations observed in Diss in the Ca-rich region of the Di-En join (in which TEM observations show neither exsolution microstructures nor evidence of spinodal decomposition) single crystals large enough for X-ray diffraction analyses, with composition (Ca0.66Mg0.34)MgSi2O6, have been equilibrated close to the solvus at T=1350° C for 317 h, and quenched at room temperature. The refinement in C2/c space group shows that in the M2 site Ca and Mg are fully ‘ordered’ in two split positions (M2occ: 0.66 Ca; M2'occ: 0.34 Mg). Since the average structure shows a relevant elongation of anisotropic thermal ellipsoids of the O2 and O3 oxygen atoms, the refinement has been carried out according to a split model for O2 and O3 atoms: Ca appears 8-coordinated (as in diopside) and Mg shows a sixfold coordination similar to that of high-pigeonite. This coordination for Mg is significantly different from the fourfold coordination (Zn-like in Zn-cpx) proposed previously and it is a more probable coordination for Mg from a crystalchemical point of view. The same results were obtained refining a Di80En20 cpx, equilibrated at T=1230° C, according to the same O-split model. The data support the coexistence of a Di-like configuration for Ca and of a highPig-like configuration for Mg away from the solvus also. At T very near to T solidus the different configurations, observed at room temperature in the quenched samples, should converge and Ca and Mg should retain a single disordered configuration in the M2 site.

Understanding rapid changes in phase partitioning between cloud liquid and ice in an Arctic stratiform mixed-phase cloud

NASA Astrophysics Data System (ADS)

Kalesse, Heike; de Boer, Gijs; Solomon, Amy; Oue, Mariko; Ahlgrimm, Maike; Zhang, Damao; Shupe, Matthew; Luke, Edward; Protat, Alain

2016-04-01

In the Arctic, a region particularly sensitive to climate change, mixed-phase clouds occur as persistent single or multiple stratiform layers. For many climate models, the correct partitioning of hydrometeor phase (liquid vs. ice) remains a challenge. However, this phase partitioning plays an important role for precipitation processes and the radiation budget. To better understand the partitioning of phase in Arctic clouds, observations using a combination of surface-based remote sensors are useful. In this study, the focus is on a persistent low-level single-layer stratiform Arctic mixed-phase cloud observed during March 11-12, 2013 at the US Department of Energy's (DOE) Atmospheric Radiation Measurement (ARM) North Slope of Alaska (NSA) permanent site in Barrow, Alaska. This case is of particular interest due to two significant shifts in observed precipitation intensity over a 36 hour period. For the first 12 hours of this case, the observed liquid portion of the cloud cover featured a stable cloud top height with a gradually descending liquid cloud base and continuous ice precipitation. Then the ice precipitation intensity significantly decreased. A second decrease in ice precipitation intensity was observed a few hours later coinciding with the advection of a cirrus over the site. Through analysis of the data collected by extensive ground-based remote-sensing and in-situ observing systems as well as Nested Weather Research and Forecasting (WRF) simulations and ECMWF radiation scheme simulations, we try to shed light on the processes responsible for these rapid changes in precipitation rates. A variety of parameters such as the evolution of the internal dynamics and microphysics of the low-level mixed-phase cloud and the influence of the cirrus cloud are evaluated.

Scaling for Robust Empirical Modeling and Predictions of Net Ecosystem Exchange (NEE) from Diverse Wetland Ecosystems

NASA Astrophysics Data System (ADS)

Ishtiaq, K. S.; Abdul-Aziz, O. I.

2014-12-01

We developed a scaling-based, simple empirical model for spatio-temporally robust prediction of the diurnal cycles of wetland net ecosystem exchange (NEE) by using an extended stochastic harmonic algorithm (ESHA). A reference-time observation from each diurnal cycle was utilized as the scaling parameter to normalize and collapse hourly observed NEE of different days into a single, dimensionless diurnal curve. The modeling concept was tested by parameterizing the unique diurnal curve and predicting hourly NEE of May to October (summer growing and fall seasons) between 2002-12 for diverse wetland ecosystems, as available in the U.S. AmeriFLUX network. As an example, the Taylor Slough short hydroperiod marsh site in the Florida Everglades had data for four consecutive growing seasons from 2009-12; results showed impressive modeling efficiency (coefficient of determination, R2 = 0.66) and accuracy (ratio of root-mean-square-error to the standard deviation of observations, RSR = 0.58). Model validation was performed with an independent year of NEE data, indicating equally impressive performance (R2 = 0.68, RSR = 0.57). The model included a parsimonious set of estimated parameters, which exhibited spatio-temporal robustness by collapsing onto narrow ranges. Model robustness was further investigated by analytically deriving and quantifying parameter sensitivity coefficients and a first-order uncertainty measure. The relatively robust, empirical NEE model can be applied for simulating continuous (e.g., hourly) NEE time-series from a single reference observation (or a set of limited observations) at different wetland sites of comparable hydro-climatology, biogeochemistry, and ecology. The method can also be used for a robust gap-filling of missing data in observed time-series of periodic ecohydrological variables for wetland or other ecosystems.

Radiation damage in Tb-implanted CaF 2 observed by channeling and luminescence measurements

NASA Astrophysics Data System (ADS)

Aono, K.; Kumagai, M.; Iwaki, M.; Aoyagi, Y.; Namba, S.

1993-06-01

The effects of 100 keV Tb ion implantation in CaF 2 single crystals have been investigated using Rutherford backscattering/channeling technique and luminescence spectra during ion implantation, depending on ion doses. Terbium ions were implanted into (111)-cut CaF 2 single crystals in random directions with doses ranging from 1 × 10 13 to 1 × 10 17 Tb +/cm 2 at -100°C, 25°C and 100°C. The luminescence signals were measured by 100 keV Ar ion beam irradiation at room temperature to Tb-implanted specimens in order to detect the ionic state of Tb. Two broad emission peaks (near 380 and 545 nm) in visible regions were observed, originating from Tb 3+ in CaF 2. The same luminescence was also observed even during Tb implantation to CaF 2. The luminescence near 380 nm is identified as an emission of 5D 3→ 7F 6 and that near 545 nm is 5D 4→ 7F 5. The emission peak intensities depend on ion dose. Channeling measurements suggest that most of the Tb atoms occupy substitutional lattice sites. Intensities of luminescence and Tb depth profiles depend on the target temperature. In conclusion, implanted Tb atoms occupy Ca lattice sites and emit green luminescence light.

Mössbauer properties of the diferric cluster and the differential iron(II)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study.

PubMed

Han, Wen-Ge; Sandala, Gregory M; Giammona, Debra Ann; Bashford, Donald; Noodleman, Louis

2011-11-14

The R2 subunit of class-Ia ribonucleotide reductase (RNR) from Escherichia coli (E. coli) contains a diiron active site. Starting from the apo-protein and Fe(II) in solution at low Fe(II)/apoR2 ratios, mononuclear Fe(II) binding is observed indicating possible different Fe(II) binding affinities for the two alternative sites. Further, based on their Mössbauer spectroscopy and two-iron-isotope reaction experiments, Bollinger et al. (J. Am. Chem. Soc., 1997, 119, 5976-5977) proposed that the site Fe1, which bonds to Asp84, should be associated with the higher observed (57)Fe Mössbauer quadrupole splitting (2.41 mm s(-1)) and lower isomer shift (0.45 mm s(-1)) in the Fe(III)Fe(III) state, site Fe2, which is further from Tyr122, should have a greater affinity for Fe(II) binding than site Fe1, and Fe(IV) in the intermediate X state should reside at site Fe2. In this paper, using density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) methodologies, we have demonstrated that the observed large quadrupole splitting for the diferric state R2 does come from site Fe1(III) and it is mainly caused by the binding position of the carboxylate group of the Asp84 sidechain. Further, a series of active site clusters with mononuclear Fe(II) binding at either site Fe1 or Fe2 have been studied, which show that with a single dielectric medium outside the active site quantum region, there is no energetic preference for Fe(II) binding at one site over another. However, when including the explicit extended protein environment in the PB-SCRF model, the reaction field favors the Fe(II) binding at site Fe2 rather than at site Fe1 by ~9 kcal mol(-1). Therefore our calculations support the proposal of the previous Mössbauer spectroscopy and two-iron-isotope reaction experiments by Bollinger et al.

Giant Acceleration of Diffusion Observed in a Single-Molecule Experiment on F(1)-ATPase.

PubMed

Hayashi, Ryunosuke; Sasaki, Kazuo; Nakamura, Shuichi; Kudo, Seishi; Inoue, Yuichi; Noji, Hiroyuki; Hayashi, Kumiko

2015-06-19

The giant acceleration (GA) of diffusion is a universal phenomenon predicted by the theoretical analysis given by Reimann et al. [Phys. Rev. Lett. 87, 010602 (2001)]. Here we apply the theory of the GA of diffusion to a single-molecule experiment on a rotary motor protein, F(1), which is a component of F(o)F(1) adenosine triphosphate synthase. We discuss the energetic properties of F(1) and identify a high energy barrier of the rotary potential to be 20k(B)T, with the condition that the adenosine diphosphates are tightly bound to the F(1) catalytic sites. To conclude, the GA of diffusion is useful for measuring energy barriers in nonequilibrium and single-molecule experiments.

Observation of Single-Protein and DNA Macromolecule Collisions on Ultramicroelectrodes.

PubMed

Dick, Jeffrey E; Renault, Christophe; Bard, Allen J

2015-07-08

Single-molecule detection is the ultimate sensitivity in analytical chemistry and has been largely unavailable in electrochemical analysis. Here, we demonstrate the feasibility of detecting electrochemically inactive single biomacromolecules, such as enzymes, antibodies, and DNA, by blocking a solution redox reaction when molecules adsorb and block electrode sites. By oxidizing a large concentration of potassium ferrocyanide on an ultramicroelectrode (UME, radius ≤150 nm), time-resolved, discrete adsorption events of antibodies, enzymes, DNA, and polystyrene nanospheres can be differentiated from the background by their "footprint". Further, by assuming that the mass transport of proteins to the electrode surface is controlled mainly by diffusion, a size estimate using the Stokes-Einstein relationship shows good agreement of electrochemical data with known protein sizes.

Giant Acceleration of Diffusion Observed in a Single-Molecule Experiment on F1-ATPase

NASA Astrophysics Data System (ADS)

Hayashi, Ryunosuke; Sasaki, Kazuo; Nakamura, Shuichi; Kudo, Seishi; Inoue, Yuichi; Noji, Hiroyuki; Hayashi, Kumiko

2015-06-01

The giant acceleration (GA) of diffusion is a universal phenomenon predicted by the theoretical analysis given by Reimann et al. [Phys. Rev. Lett. 87, 010602 (2001)]. Here we apply the theory of the GA of diffusion to a single-molecule experiment on a rotary motor protein, F1 , which is a component of Fo F1 adenosine triphosphate synthase. We discuss the energetic properties of F1 and identify a high energy barrier of the rotary potential to be 20 kBT , with the condition that the adenosine diphosphates are tightly bound to the F1 catalytic sites. To conclude, the GA of diffusion is useful for measuring energy barriers in nonequilibrium and single-molecule experiments.

Ambient lead measurements in Cairo, Egypt

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

Howes, J.E. Jr.; Labib, M.; Samaha, N.

1999-07-01

The Cairo Air Improvement Project (CAIP) has established a network of 36 stations to monitor airborne lead levels in the Greater Cairo Area. Data obtained during the first 4 months of the monitoring program indicates that lead levels in ambient air significantly exceed the Government of Egypt's (GOE) Law Number 4 (1994) limit of 1 {micro} g/m{sup 3} (annual mean) in areas downwind of secondary lead smelters and in heavily trafficked areas. The highest mean and single sampling event lead levels were observed in the heavily industrialized areas of Shoubra el-Kheima and Tebbin. At two sites in Shoubra el-Kheima, meanmore » and maximum lead levels were determined to be approximately 20 {micro} g/m{sup 3} and 79 {micro} g/m{sup 3}, respectively. At three sites located in areas of high motor vehicle traffic in the central part of the city, the mean lead level was about 4 {micro} g/m{sup 3} and the maximum levels ranged from approximately 10 x 20 {micro} g/m{sup 3}. Of the remainder of the sites, the mean lead concentrations were 2fd3 {micro} g/m{sup 3} at three sites, 1 P2 {mu} g/m{sup 3} at 16 sites, and below 1 {micro} g/m{sup 3} at eight sites. Lead levels in areas devoted primarily to residential use were generally less than 2 {micro} g/m{sup 3}. The maximum mean monthly PM{sub 10} lead value measured at fugitive emission monitoring sites near lead smelters was approximately 73 {micro} g/m{sup 3}. The maximum lead concentration measured during a single sampling event was 180 {micro} g/m{sup 3}. Generally lower lead levels were observed in December due to regulation action that resulted in some suspension of smelting operations and to approximately 180-degree wind direction shifts that typically occur during this period of the year. The GOE is working vigorously to eliminate the lead problem in Egypt through implementation of the Lead Exposure Action Plan (LEAP). A major component of LEAP is the Lead Smelter Action Plan (LSAP).« less

An open prospective single cohort multicenter study evaluating the novel, tapered, conical connection implants supporting single crowns in the anterior and premolar maxilla: interim 1-year results.

PubMed

Fügl, Alexander; Zechner, Werner; Pozzi, Alessandro; Heydecke, Guido; Mirzakhanian, Christine; Behneke, Nikolaus; Behneke, Alexandra; Baer, Russell A; Nölken, Robert; Gottesman, Edward; Colic, Snjezana

2017-07-01

The aim of this multicenter prospective clinical study was to evaluate anodized tapered implants with a conical connection and integrated platform shifting placed in the anterior and premolar maxilla. The study enrolled patients requiring single-tooth restorations in healed sites of maxillary anterior and premolar teeth. All implants were immediately temporized. Clinical and radiographic evaluations were conducted at implant insertion, 6 months, and 1 year. Outcome measures included bone remodeling, cumulative survival rate (CSR), success rate, soft-tissue health and esthetics, and patient satisfaction. Bone remodeling and pink esthetic score were analyzed using Wilcoxon signed-rank tests. CSR was calculated using life table analysis. Other soft-tissue outcomes were analyzed using sign tests. Out of 97 enrolled patients (102 implants), 87 patients (91 implants) completed the 1-year visit. Marginal bone remodeling was -0.85 ± 1.36 mm. After the expected initial bone loss, a mean bone gain of 0.11 ± 1.05 mm was observed between 6 months and 1 year. The CSR was 99.0%, and the cumulative success rate was 97.0%. Partial or full papilla was observed at 30.8% of sites at baseline, 87.2% at 6 months, and 90.5% at 1 year. Soft-tissue response, esthetics, and patient satisfaction all improved during the study period. Bone gain was observed following the expected initial bone loss, and soft-tissue outcomes improved suggesting favorable tissue response using anodized tapered conical connection implants. Rapid stabilization of bone remodeling and robust papilla regeneration indicate favorable tissue healing promoted by the conical connection, platform-shift design. clinicaltrials.gov NCT02175550.

Asymmetry of the three catalytic sites on beta subunits of TF1 from a thermophilic Bacillus strain PS3.

PubMed

Hisabori, T; Kobayashi, H; Kaibara, C; Yoshida, M

1994-03-01

F1-ATPase isolated from plasma membrane of a thermophilic Bacillus strain PS3 (TF1) has very little or no endogenously bound adenine nucleotides. However, it can bind one ADP per mol of the enzyme on one of three beta subunits to form a stable TF1.ADP complex when incubated with a high concentration of ADP [Yoshida, M. & Allison, W.S. (1986) J. Biol. Chem. 261, 5714-5721]. The same TF1.ADP complex was recovered after filling all ADP binding sites with [3H]ADP and repeated gel filtration. Direct binding assay revealed that the TF1.ADP complex had lost the highest affinity site for TNP-ADP. When a substoichiometric amount of TNP-ATP was added, the complex hydrolyzed TNP-ATP slowly (single site hydrolysis), like native TF1. However, this hydrolysis was not promoted by chase-addition of excess ATP. The optimal pH of the ATPase activity of TF1 or the TF1.ADP complex measured with a short reaction period, 6.5, was lower than the reported value, 9.0, under the steady-state condition. Although the bound ADP was released from the complex only when the enzyme underwent multiple catalytic turnover, the rate of this release was much slower than the turnover. These results suggest that when one ADP binds to a site on one of the beta subunits and stays there for a long time, the enzyme will change form and the bound ADP will become a special species which is not able to be directly involved in the enzyme catalysis. This binding site for ADP appears to be the first site responsible for the single-site catalysis reaction observed for native TF1.

Uncertainty, variability, and earthquake physics in ground‐motion prediction equations

USGS Publications Warehouse

Baltay, Annemarie S.; Hanks, Thomas C.; Abrahamson, Norm A.

2017-01-01

Residuals between ground‐motion data and ground‐motion prediction equations (GMPEs) can be decomposed into terms representing earthquake source, path, and site effects. These terms can be cast in terms of repeatable (epistemic) residuals and the random (aleatory) components. Identifying the repeatable residuals leads to a GMPE with reduced uncertainty for a specific source, site, or path location, which in turn can yield a lower hazard level at small probabilities of exceedance. We illustrate a schematic framework for this residual partitioning with a dataset from the ANZA network, which straddles the central San Jacinto fault in southern California. The dataset consists of more than 3200 1.15≤M≤3 earthquakes and their peak ground accelerations (PGAs), recorded at close distances (R≤20  km). We construct a small‐magnitude GMPE for these PGA data, incorporating VS30 site conditions and geometrical spreading. Identification and removal of the repeatable source, path, and site terms yield an overall reduction in the standard deviation from 0.97 (in ln units) to 0.44, for a nonergodic assumption, that is, for a single‐source location, single site, and single path. We give examples of relationships between independent seismological observables and the repeatable terms. We find a correlation between location‐based source terms and stress drops in the San Jacinto fault zone region; an explanation of the site term as a function of kappa, the near‐site attenuation parameter; and a suggestion that the path component can be related directly to elastic structure. These correlations allow the repeatable source location, site, and path terms to be determined a priori using independent geophysical relationships. Those terms could be incorporated into location‐specific GMPEs for more accurate and precise ground‐motion prediction.

Neuronal growth cones respond to laser-induced axonal damage

PubMed Central

Wu, Tao; Mohanty, Samarendra; Gomez-Godinez, Veronica; Shi, Linda Z.; Liaw, Lih-Huei; Miotke, Jill; Meyer, Ronald L.; Berns, Michael W.

2012-01-01

Although it is well known that damage to neurons results in release of substances that inhibit axonal growth, release of chemical signals from damaged axons that attract axon growth cones has not been observed. In this study, a 532 nm 12 ns laser was focused to a diffraction-limited spot to produce site-specific damage to single goldfish axons in vitro. The axons underwent a localized decrease in thickness (‘thinning’) within seconds. Analysis by fluorescence and transmission electron microscopy indicated that there was no gross rupture of the cell membrane. Mitochondrial transport along the axonal cytoskeleton immediately stopped at the damage site, but recovered over several minutes. Within seconds of damage nearby growth cones extended filopodia towards the injury and were often observed to contact the damaged site. Turning of the growth cone towards the injured axon also was observed. Repair of the laser-induced damage was evidenced by recovery of the axon thickness as well as restoration of mitochondrial movement. We describe a new process of growth cone response to damaged axons. This has been possible through the interface of optics (laser subcellular surgery), fluorescence and electron microscopy, and a goldfish retinal ganglion cell culture model. PMID:21831892

Acute toxicity of subcutaneously administered vitamin E isomers delta- and gamma-tocotrienol in mice.

PubMed

Swift, Sibyl N; Pessu, Roli L; Chakraborty, Kushal; Villa, Vilmar; Lombardini, Eric; Ghosh, Sanchita P

2014-01-01

The toxicity of parenterally administered vitamin E isomers, delta-tocotrienol (DT3) and gamma-tocotrienol (GT3), was evaluated in male and female CD2F1 mice. In an acute toxicity study, a single dose of DT3 or GT3 was administered subcutaneously in a dose range of 200 to 800 mg/kg. A mild to moderately severe dermatitis was observed clinically and microscopically in animals at the injection site at doses above 200 mg/kg. The severity of the reaction was reduced when the drug concentration was lowered. Neither drug produced detectable toxic effects in any other tissue at the doses tested. Based on histopathological analysis for both DT3 and GT3, and macroscopic observations of inflammation at the injection site, a dose of 300 mg/kg was selected as the lowest toxic dose in a 30-day toxicity study performed in male mice. At this dose, a mild skin irritation occurred at the injection site that recovered completely by the end of the experimental period. At a dose of 300 mg/kg of DT3 or GT3, no adverse effects were observed in any tissues or organs. © The Author(s) 2014.

A structurally based analytic model of growth and biomass dynamics in single species stands of conifers

Treesearch

Robin J. Tausch

2015-01-01

A theoretically based analytic model of plant growth in single species conifer communities based on the species fully occupying a site and fully using the site resources is introduced. Model derivations result in a single equation simultaneously describes changes over both, different site conditions (or resources available), and over time for each variable for each...

High performance platinum single atom electrocatalyst for oxygen reduction reaction

NASA Astrophysics Data System (ADS)

Liu, Jing; Jiao, Menggai; Lu, Lanlu; Barkholtz, Heather M.; Li, Yuping; Wang, Ying; Jiang, Luhua; Wu, Zhijian; Liu, Di-Jia; Zhuang, Lin; Ma, Chao; Zeng, Jie; Zhang, Bingsen; Su, Dangsheng; Song, Ping; Xing, Wei; Xu, Weilin; Wang, Ying; Jiang, Zheng; Sun, Gongquan

2017-07-01

For the large-scale sustainable implementation of polymer electrolyte membrane fuel cells in vehicles, high-performance electrocatalysts with low platinum consumption are desirable for use as cathode material during the oxygen reduction reaction in fuel cells. Here we report a carbon black-supported cost-effective, efficient and durable platinum single-atom electrocatalyst with carbon monoxide/methanol tolerance for the cathodic oxygen reduction reaction. The acidic single-cell with such a catalyst as cathode delivers high performance, with power density up to 680 mW cm-2 at 80 °C with a low platinum loading of 0.09 mgPt cm-2, corresponding to a platinum utilization of 0.13 gPt kW-1 in the fuel cell. Good fuel cell durability is also observed. Theoretical calculations reveal that the main effective sites on such platinum single-atom electrocatalysts are single-pyridinic-nitrogen-atom-anchored single-platinum-atom centres, which are tolerant to carbon monoxide/methanol, but highly active for the oxygen reduction reaction.

High performance platinum single atom electrocatalyst for oxygen reduction reaction

PubMed Central

Liu, Jing; Jiao, Menggai; Lu, Lanlu; Barkholtz, Heather M.; Li, Yuping; Wang, Ying; Jiang, Luhua; Wu, Zhijian; Liu, Di-jia; Zhuang, Lin; Ma, Chao; Zeng, Jie; Zhang, Bingsen; Su, Dangsheng; Song, Ping; Xing, Wei; Xu, Weilin; Wang, Ying; Jiang, Zheng; Sun, Gongquan

2017-01-01

For the large-scale sustainable implementation of polymer electrolyte membrane fuel cells in vehicles, high-performance electrocatalysts with low platinum consumption are desirable for use as cathode material during the oxygen reduction reaction in fuel cells. Here we report a carbon black-supported cost-effective, efficient and durable platinum single-atom electrocatalyst with carbon monoxide/methanol tolerance for the cathodic oxygen reduction reaction. The acidic single-cell with such a catalyst as cathode delivers high performance, with power density up to 680 mW cm−2 at 80 °C with a low platinum loading of 0.09 mgPt cm−2, corresponding to a platinum utilization of 0.13 gPt kW−1 in the fuel cell. Good fuel cell durability is also observed. Theoretical calculations reveal that the main effective sites on such platinum single-atom electrocatalysts are single-pyridinic-nitrogen-atom-anchored single-platinum-atom centres, which are tolerant to carbon monoxide/methanol, but highly active for the oxygen reduction reaction. PMID:28737170

Atom-scale covalent electrochemical modification of single-layer graphene on SiC substrates by diaryliodonium salts

DOE PAGES

Gearba, Raluca I.; Mueller, Kory M.; Veneman, Peter A.; ...

2015-05-09

Owing to its high conductivity, graphene holds promise as an electrode for energy devices such as batteries and photovoltaics. However, to this end, the work function and doping levels in graphene need to be precisely tuned. One promising route for modifying graphene’s electronic properties is via controlled covalent electrochemical grafting of molecules. We show that by employing diaryliodonium salts instead of the commonly used diazonium salts, spontaneous functionalization is avoided. This then allows for precise tuning of the grafting density. Moreover, by employing bis(4-nitrophenyl)iodonium(III) tetrafluoroborate (DNP) salt calibration curves, the surface functionalization density (coverage) of glassy carbon was controlled usingmore » cyclic voltammetry in varying salt concentrations. These electro-grafting conditions and calibration curves translated directly over to modifying single layer epitaxial graphene substrates (grown on insulating 6H-SiC (0 0 0 1)). In addition to quantifying the functionalization densities using electrochemical methods, samples with low grafting densities were characterized by low-temperature scanning tunneling microscopy (LT-STM). We show that the use of buffer-layer free graphene substrates is required for clear observation of the nitrophenyl modifications. Furthermore, atomically-resolved STM images of single site modifications were obtained, showing no preferential grafting at defect sites or SiC step edges as supposed previously in the literature. Most of the grafts exhibit threefold symmetry, but occasional extended modifications (larger than 4 nm) were observed as well.« less

Oxygen chemisorption on copper (110)

NASA Astrophysics Data System (ADS)

Mundenar, J. M.; Baddorf, A. P.; Plummer, E. W.; Sneddon, L. G.; Didio, R. A.; Zehner, D. M.

1987-09-01

High resolution electron energy loss spectroscopy (EELS) and angle-resolved ultra-violet photoelectron spectroscopy (UPS) have been used: (1) to study a surface phonon of Cu(110) as a function of oxygen coverage, (2) to identify oxygen adsorption site(s) in the p(2×1)O, c(6×2)O, and disordered oxygen overlayer (formed by O 2 exposure at 100 K), and (3) to determine whether molecular adsorption or dissociation of O 2 followed by atomic adsorption occurs after oxygen exposure at 100 K. With EELS, a continuous shift in energy of the surface phonon as a function of oxygen exposure at 300 K is observed. Our EELS data for the p(2×1)O overlayer support previous reports of a single long-bridge adsorption site, while indicating two sites are populated in the c(6×2)O overlayer: a long-bridge site and a four-coordinated site. The long-bridge site is populated at all coverages while the four-coordinated sites is occupied only after high exposures (≥2×10 4 L) at room temperature, or after exposures >2 L at low temperature (100 K). For both conditions the oxygen coverages are greater than 0.5 monolayer. Also, EELS and complementary UPS data clearly show that oxygen adsorbs dissociatively on Cu(110) after O 2 exposure at 100 K. At this temperature, LEED results indicate that the oxygen atoms are adsorbed without long-range order; however, local adsorption sites, which are similar to those in the c(6×2)O surface, are observed.

Robotic-assisted single-port donor nephrectomy using the da Vinci single-site platform.

PubMed

LaMattina, John C; Alvarez-Casas, Josue; Lu, Irene; Powell, Jessica M; Sultan, Samuel; Phelan, Michael W; Barth, Rolf N

2018-02-01

Although single-port donor nephrectomy offers improved cosmetic outcomes, technical challenges have limited its application to selected centers. Our center has performed over 400 single-port donor nephrectomies. The da Vinci single-site robotic platform was utilized in an effort to overcome the steric, visualization, ergonomic, and other technical limitations associated with the single-port approach. Food and Drug Administration device exemption was obtained. Selection criteria for kidney donation included body mass index <35, left kidney donors, and ≤2 renal arteries. After colonic mobilization using standard single-port techniques, the robotic approach was utilized for ureteral complex and hilar dissection. Three cases were performed using the robotic single-site platform. Average total operative time was 262 ± 42 min including 82 ± 16 min of robotic use. Docking time took 20 ± 10 min. Blood loss averaged 77 ± 64 mL. No intraoperative complications occurred, and all procedures were completed with our standard laparoscopic single-port approach. This is the first clinical experience of robotic-assisted donor nephrectomy utilizing the da Vinci single-site platform. Our experience supported the safety of this approach but found that the technology added cost and complexity without tangible benefit. Development of articulating instruments, energy, and stapling devices will be necessary for increased application of robotic single-site surgery for donor nephrectomy. Copyright © 2017 Elsevier Inc. All rights reserved.

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

Modeling of microclimatic characteristics of highland area

NASA Astrophysics Data System (ADS)

Sitdikova, Iuliia; Rusin, Igor

2013-04-01

Microclimatic characteristics of highlands may vary considerably over distances of a few meters depending on slope and aspect. There is a problem of estimation of components of surface energy balance based on observation of single stations for description of microclimate highlands. The aim of this paper is to develop a method that would restore microclimatic characteristics of terrain, based on observations of the single station, by physical extrapolation. The input parameters to obtain the microclimatic characteristics are as follows: air temperature, relative humidity, and wind speed on two vertical levels, air pressure, surface temperature, direct and diffused solar radiation and surface albedo. The recent version of the Meteorological Radiation Model (MRM) has been used to calculate a solar radiation over the area and to estimate an influence of cloudiness amounts. The height, slope and aspect were accounted at each point with using a digital elevation model. Have been supposed that air temperature and specific humidity vary with altitude only. Net radiation was calculated at all points of the area. Supposed that the difference between the surface temperature and the air temperature is a linear function of net radiation. The empirical coefficient, which depends on wind speed with adjustment of given area. Latent and sensible fluxes are calculated by using the modified Bowen ratio, which varies on the area. Method was tested on field research in Krasnodar region (RF). The meteorological observations were made every three hour on actinometric and gradient sites. The editional gradient site with different orientation of the slope was organized from 400 meters of the main site. Topographic survey of area was made 1x1,3 km in size for a digital elevation model constructing. At all points of the area of radiation and heat balance were calculated. The results of researches are the maps of surface temperature, net radiation, latent and sensible fluxes. The calculations showed that the average value of components of heat balance by area differ significantly from the data observed on meteorological station.

Spectrophotometric properties of materials observed by Pancam on the Mars Exploration Rovers: 1. Spirit

USGS Publications Warehouse

Johnson, J. R.; Grundy, W.M.; Lemmon, M.T.; Bell, J.F.; Johnson, M.J.; Deen, R.G.; Arvidson, R. E.; Farrand, W. H.; Guinness, E.A.; Hayes, A.G.; Herkenhoff, K. E.; Seelos, F.; Soderblom, J.; Squyres, S.

2006-01-01

Multispectral observations of rocks and soils were acquired under varying illumination and viewing geometries in visible/near-infrared wavelengths by the Panoramic Camera (Pancam) on the Spirit Mars Exploration Rover to provide constraints on the physical and mineralogical nature of geologic materials in Gusev Crater. Data sets were acquired at six sites located near the landing site, in the surrounding plains, and in the West Spur and Husband Hill regions of the Columbia Hills. From these ???600 images, over 10,000 regions of interest were selected of rocks and soils over a wide range of phase angles (0-130??). Corrections for diffuse skylight incorporated sky models based on observations of atmospheric opacity throughout the mission. Disparity maps created from Pancam stereo images allowed inclusion of estimates of local facet orientations in the sky models. Single-term and two-term phase functions derived from Hapke scattering models exhibit a dominantly broad backscattering trend for soils and "Red" rocks inferred to be covered with variable amounts of dust and other coatings, consistent with the results from the Viking Lander and Imager for Mars Pathfinder cameras. Darker "Gray" rock surfaces (inferred to be relatively less dust covered) display more narrow, forward scattering behaviors, consistent with particles exhibiting little internal scattering. Gray and Red rocks are macroscopically rougher than most soil units, although a "dust-cleaning" event observed near the Paso Robles site caused an increase in soil surface roughness in addition to a substantial decrease in surface single scattering albedo. Gray rocks near the rim of Bonneville Crater exhibit the largest macroscopic roughness (????) among all units, as well as the greatest backscattering among Gray rocks. Photometric properties of coated Red rocks vary in the West Spur region, possibly as a result of weathering differences related to elevation-dependent aeolian regimes. Copyright 2006 by the American Geophysical Union.

Tracking plant physiological properties from multi-angular tower-based remote sensing.

PubMed

Hilker, Thomas; Gitelson, Anatoly; Coops, Nicholas C; Hall, Forrest G; Black, T Andrew

2011-04-01

Imaging spectroscopy is a powerful technique for monitoring the biochemical constituents of vegetation and is critical for understanding the fluxes of carbon and water between the land surface and the atmosphere. However, spectral observations are subject to the sun-observer geometry and canopy structure which impose confounding effects on spectral estimates of leaf pigments. For instance, the sun-observer geometry influences the spectral brightness measured by the sensor. Likewise, when considering pigment distribution at the stand level scale, the pigment content observed from single view angles may not necessarily be representative of stand-level conditions as some constituents vary as a function of the degree of leaf illumination and are therefore not isotropic. As an alternative to mono-angle observations, multi-angular remote sensing can describe the anisotropy of surface reflectance and yield accurate information on canopy structure. These observations can also be used to describe the bi-directional reflectance distribution which then allows the modeling of reflectance independently of the observation geometry. In this paper, we demonstrate a method for estimating pigment contents of chlorophyll and carotenoids continuously over a year from tower-based, multi-angular spectro-radiometer observations. Estimates of chlorophyll and carotenoid content were derived at two flux-tower sites in western Canada. Pigment contents derived from inversion of a CR model (PROSAIL) compared well to those estimated using a semi-analytical approach (r(2) = 0.90 and r(2) = 0.69, P < 0.05 for both sites, respectively). Analysis of the seasonal dynamics indicated that net ecosystem productivity was strongly related to total canopy chlorophyll content at the deciduous site (r(2) = 0.70, P < 0.001), but not at the coniferous site. Similarly, spectral estimates of photosynthetic light-use efficiency showed strong seasonal patterns in the deciduous stand, but not in conifers. We conclude that multi-angular, spectral observations can play a key role in explaining seasonal dynamics of fluxes of carbon and water and provide a valuable addition to flux-tower-based networks.

Artificial Metalloproteins Containing Co 4O 4Cubane Active Sites

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

Olshansky, Lisa; Huerta-Lavorie, Raul; Nguyen, Andy I.

Artificial metalloproteins (ArMs) containing Co 4O 4 cubane active sites were constructed via biotin-streptavidin technology. Stabilized by hydrogen bonds (H-bonds), terminal and cofacial Co III-OH 2 moieties are observed crystallographically in a series of immobilized cubane sites. Solution electrochemistry provided correlations of oxidation potential and pH. For variants containing Ser and Phe adjacent to the metallocofactor, 1e -/1H + chemistry predominates until pH 8, above which the oxidation becomes pH-independent. Installation of Tyr proximal to the Co 4O 4 active site provided a single H-bond to one of a set of cofacial Co III-OH 2 groups. With this variant, multi-emore » - /multi-H + chemistry is observed, along with a change in mechanism at pH 9.5 that is consistent with Tyr deprotonation. Finally, with structural similarities to both the oxygen-evolving complex of photosystem II (H-bonded Tyr) and to thin film water oxidation catalysts (Co 4O 4 core), these findings bridge synthetic and biological systems for water oxidation, highlighting the importance of secondary sphere interactions in mediating multi-e - /multi-H + reactivity.« less

Artificial Metalloproteins Containing Co 4O 4Cubane Active Sites

DOE PAGES

Olshansky, Lisa; Huerta-Lavorie, Raul; Nguyen, Andy I.; ...

2018-02-05

Artificial metalloproteins (ArMs) containing Co 4O 4 cubane active sites were constructed via biotin-streptavidin technology. Stabilized by hydrogen bonds (H-bonds), terminal and cofacial Co III-OH 2 moieties are observed crystallographically in a series of immobilized cubane sites. Solution electrochemistry provided correlations of oxidation potential and pH. For variants containing Ser and Phe adjacent to the metallocofactor, 1e -/1H + chemistry predominates until pH 8, above which the oxidation becomes pH-independent. Installation of Tyr proximal to the Co 4O 4 active site provided a single H-bond to one of a set of cofacial Co III-OH 2 groups. With this variant, multi-emore » - /multi-H + chemistry is observed, along with a change in mechanism at pH 9.5 that is consistent with Tyr deprotonation. Finally, with structural similarities to both the oxygen-evolving complex of photosystem II (H-bonded Tyr) and to thin film water oxidation catalysts (Co 4O 4 core), these findings bridge synthetic and biological systems for water oxidation, highlighting the importance of secondary sphere interactions in mediating multi-e - /multi-H + reactivity.« less

Design of the aerosol sampling manifold for the Southern Great Plains site

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

Leifer, R.; Knuth, R.H.; Guggenheim, S.F.

1995-04-01

To meet the needs of the ARM program, the Environmental Measurements Laboratory (EML) has the responsibility to establish a surface aerosol measurements program at the Southern Great Plains (SGP) site in Lamont, OK. At the present time, EML has scheduled installation of five instruments at SGP: a single wavelength nephelometer, an optical particle counter (OPC), a condensation particle counter (CPC), an optical absorption monitor (OAM), and an ozone monitor. ARM`s operating protocol requires that all the observational data be placed online and sent to the main computer facility in real time. EML currently maintains a computer file containing back trajectorymore » (BT) analyses for the SGP site. These trajectories are used to characterize air mass types as they pass over the site. EML is continuing to calculate and store the resulting trajectory analyses for future use by the ARM science team.« less

Ground Motion Uncertainty and Variability (single-station sigma): Insights from Euroseistest, Greece

NASA Astrophysics Data System (ADS)

Ktenidou, O. J.; Roumelioti, Z.; Abrahamson, N. A.; Cotton, F.; Pitilakis, K.

2014-12-01

Despite recent improvements in networks and data, the global aleatory uncertainty (sigma) in GMPEs is still large. One reason is the ergodic approach, where we combine data in space to make up for lack of data in time. By estimating the systematic site response, we can make site-specific GMPEs and use a lower, site-specific uncertainty: single-station sigma. In this study we use the EUROSEISTEST database (http://euroseisdb.civil.auth.gr), which has two distinct advantages: good existing knowledge of site conditions at all stations, and careful relocation of the recorded events. Constraining the site and source parameters as best we can, we minimise the within- and between-events components of the global, ergodic sigma. Following that, knowledge of the site response from empirical and theoretical approaches permits us to move on to single-station sigma. The variability per site is not clearly correlated to the site class. We show that in some cases knowledge of Vs30 is not sufficient, and that site-specific data are needed to capture the response, possibly due to 2D/3D effects from complex geometry. Our values of single-station sigma are low compared to the literature. This may be due to the good ray coverage we have in all directions for small, nearby records. Indeed, our single-station sigma values are similar to published single-path values, which means that they may correspond to a fully -rather than partially- non-ergodic approach. We find larger ground motion variability for short distances and small magnitudes. This may be related to the uncertainty in the depth affecting nearby records more, or to stress drop and causing trade-offs between the source and site terms for small magnitudes.

Carbon isotope evidence for a magmatic origin for Archaean gold-quartz vein ore deposits

NASA Technical Reports Server (NTRS)

Burrows, D. R.; Wood, P. C.; Spooner, E. T. C.

1986-01-01

Sediments from three sites in the Santa Barbara Basin were examined with a 160X power light microscope and TEM equipment to characterize the magnetostatic bacteria (MB) in the samples. Both the free magnetite and the crystals in the MB in the samples had lengths from 40-60 nm in length and increased in size from one end to the next. An intact magnetosome was also observed. Scanning the sediments with saturation isothermal remanent magnetization (SIRM) and altering field demagnetization techniques using a SQUID magnetometer yielded coercivity spectra which showed that the primary remanence carrier in the sediments was single domain magnetite. Although it is expected that the predominance of the bacterial magnetite component will decrease with depth in the open ocean basin, single-domain bacteria as old as 50 Myr have been observed in oceanic sediments.

Single-dose Intramuscular-injection Toxicology Test of Water-soluble Carthami-flos and Cervi cornu parvum Pharmacopuncture in a Rat Model.

PubMed

Park, Sunju; Sun, Seung-Ho

2015-09-01

The aim of the study is to investigate both the single-dose intramuscular injection toxicity and the approximate lethal dose of water-soluble Carthami-flos and Cervi cornu parvum pharmacopuncture (WCFC) in male and female Sprague-Dawley (SD) rats. The study was conducted at Biotoxtech Co. according to the Good Laboratory Practice (GLP) regulation and the toxicity test guidelines of the Ministry of Food and Drug Safety (MFDS) after approval of the Institutional Animal Care and Use Committee. Dosages for the control, high dose, middle dose and low dose groups were 0.5 mL/animal of saline and 0.5, 0.25 and 0.125 mL/animal of WCFC, respectively. WCFC was injected into the muscle of the left femoral region by using a disposable syringe (1 mL, 26 gauge). The general symptoms and mortality were observed 30 minutes, 1, 2, 4, and 6 hours after the first injection and then daily for 14 days after the injection. The body weights of the SD rats were measured on the day of the injection (before injection) and on the third, seventh, and fourteenth days after the injection. Serum biochemical and hematologic tests, necropsy examinations, and histopathologic examinations at the injection site were performed after the observation period. No deaths, abnormal clinical symptoms, or significant weight changes were observed in either male or female SD rats in the control or the test (0.125, 0.25, and 0.5 mL/animal) groups during the observation period. No significant differences in hematology and serum biochemistry and no macroscopic abnormalities at necropsy were found. No abnormal reactions at injection sites were noted on the topical tolerance tests. The results of this single-dose toxicity study show that WCFC is safe, its lethal doses in male and female SD rats being estimated to be higher than 0.5 mL/animal.

Da Vinci single site© surgical platform in clinical practice: a systematic review.

PubMed

Morelli, Luca; Guadagni, Simone; Di Franco, Gregorio; Palmeri, Matteo; Di Candio, Giulio; Mosca, Franco

2016-12-01

The Da Vinci single-site© surgical platform (DVSSP) is a set of single-site instruments and accessories specifically dedicated to robot-assisted single-site surgery. The PubMed database from inception to June 2015 was searched for English literature on the clinical use of DVSSP in general surgery, urology and gynecology. Twenty-nine articles involving the clinical application of DVSSP were identified; 15 articles on general surgery (561 procedures), four articles on urology (48 procedures) and 10 articles on gynecology (212 procedures). All studies have proven the safety and feasibility of the use of DVSSP. The principal reported advantage is the restoration of intra-abdominal triangulation, while the main reported limitation is the lack of the endowrist. Da Vinci systems have proven to be valuable assets in single-site surgery, owing to the combination of robot use with the dedicated single-incision platform. However, case-control or prospective trials are warranted to draw more definitive conc lusions. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

A 10-Year Climatology of Cloud Cover and Vertical Distribution Derived from Both Surface and GOES Observations Over the DOE ARM SGP Site

NASA Technical Reports Server (NTRS)

Xi, Baike; Dong, Xiquan; Minnis, P.; Khaiyer, M.

2010-01-01

Analysis of a decade of ARM radar-lidar and GOES observations at the SGP site reveal that 0.5 and 4-hr averages of the surface cloud fraction correspond closely to 0.5deg and 2.5deg averages of GOES cloudiness, respectively. The long-term averaged surface and GOES cloud fractions agree to within 0.5%. Cloud frequency increases and cloud amount decreases as the temporal and spatial averaging scales increase. Clouds occurred most often during winter and spring. Single-layered clouds account for 61.5% of the total cloud frequency. There are distinct bimodal vertical distributions of clouds with a lower peak around 1 km and an upper one that varies from 7.5 to 10.8 km between winter and summer, respectively. The frequency of occurrence for nighttime GOES high-cloud tops agree well with the surface observations, but are underestimated during the day.

Aerosol Light Absorption and Scattering at Four Sites in and Near Mexico City: Comparison with Las Vegas, Nevada, USA

NASA Astrophysics Data System (ADS)

Arnott, W. P.; Miranda, G. P.; Gaffney, J. S.; Marley, N. A.

2007-05-01

Four photoacoustic spectrometers (PAS) for aerosol light scattering and absorption measurements were deployed in and near Mexico City in March 2006 as part of the Megacity Impacts on Regional and Global Environments (MIRAGE). The four sites included: an urban site at Instituto Mexicano del Petroleo (Mexican Oil Institute, denoted by IMP); a suburban site at the Technological University of Tecamac; a rural site at "La Biznaga" ranch; and a site at the Paseo de Cortes (altitude 3,810 meters ASL) in the rural area above Amecameca in the State of Mexico, on the saddle between the volcanoes Popocatepetl and Iztaccihuatl. A similar campaign was held in Las Vegas, Nevada, USA in January-February, 2003. The IMP site gave in-situ characterization of the Mexico City plume under favorable wind conditions while the other sites provided characterization of the plume, mixed in with any local sources. The second and third sites are north of Mexico City, and the fourth site is south. The PAS used at IMP operates at 532 nm, and conveniently allowed for characterization of gaseous absorption at this wavelength as well. Instruments at the second and third sites operate at 870 nm, and the one at the fourth site at 780 nm. Light scattering measurements are accomplished within the PAS by the reciprocal nephelometery method. In the urban site the aerosol absorption coefficient typically varies between 20 and 180 Mm-1 during the course of the day and significant diurnal variation of the aerosol single scattering albedo was observed probably as a consequence of secondary aerosol formation. Comparisons with TSI nephelometer scattering at the T0 site will be presented. We will present the diurnal variation of the scattering and absorption as well as the single scattering albedo and fraction of absorption due to gases at the IMP site and compare with Las Vegas diurnal variation. Mexico City 'breaths' more during the course of the day than Las Vegas, Nevada in part because the latitude of Mexico City resulted in more direct solar radiation. Further insight on the meteorological connections will be discussed.

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

Liu, Xianglin; Wang, Yang; Eisenbach, Markus

One major purpose of studying the single-site scattering problem is to obtain the scattering matrices and differential equation solutions indispensable to multiple scattering theory (MST) calculations. On the other hand, the single-site scattering itself is also appealing because it reveals the physical environment experienced by electrons around the scattering center. In this study, we demonstrate a new formalism to calculate the relativistic full-potential single-site Green's function. We implement this method to calculate the single-site density of states and electron charge densities. Lastly, the code is rigorously tested and with the help of Krein's theorem, the relativistic effects and full potentialmore » effects in group V elements and noble metals are thoroughly investigated.« less

Prognostic effect of liver metastasis in lung cancer patients with distant metastasis.

PubMed

Ren, Yijiu; Dai, Chenyang; Zheng, Hui; Zhou, Fangyu; She, Yunlang; Jiang, Gening; Fei, Ke; Yang, Ping; Xie, Dong; Chen, Chang

2016-08-16

Because the need of clinical prognostic evaluation by specific metastatic organ, we aim to analyze the prognostic factors in lung cancer patients with M1b disease with Surveillance Epidemiology and End-Results database (SEER). This retrospective study evaluated lung cancer patients of adenocarcinoma (AD), squamous cell carcinoma (SQCC), and small cell lung cancer (SCLC) selected from SEER. We provided the prognostic correlates of overall survival (OS) and lung cancer-specific survival (LCSS) in this population. 23,679 eligible patients were included. Bone was the most common metastatic site in AD (63.1%) and SQCC (61.1%), while liver was the most prevalent site (61.9%) in SCLC. Single site metastasis was significantly associated with better outcome compared to multiple sites metastases in all patients. Among patients with single site metastasis, OS and LCSS were longer for AD and SCLC if involving brain or bone, with median survival time of 5 to 7 months, comparing to 3 months if invloving liver (all p-values < 0.001). Similarly, among patients with multiple metastases, better outcomes were observed in AD patients (4 vs 3 months; OS and LCSS, p < 0.001) and SCLC patients (6 vs 4 months; OS, p = 0.017; LCSS, p = 0.023) without liver metastasis compared to those with liver metastasis. In conclusion, we estimated multiple survival outcomes by histology of primary tumor and sites of metastasis. Liver metastasis is found to be the worst prognostic factor for AD and SCLC patients with distant metastasis. More in-depth research is warranted to identify patients who are prone to develop distance metastasis, especially to liver.

Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level

PubMed Central

Koslover, Daniel J.; Fazal, Furqan M.; Mooney, Rachel A.; Landick, Robert; Block, Steven M.

2012-01-01

Rho termination factor is an essential hexameric helicase responsible for terminating 20–50% of all mRNA synthesis in E. coli. We used single- molecule force spectroscopy to investigate Rho-RNA binding interactions at the Rho- utilization (rut) site of the ? tR1 terminator. Our results are consistent with Rho complexes adopting two states, one that binds 57 ±2 nucleotides of RNA across all six of the Rho primary binding sites, and another that binds 85 ±2 nucleotides at the six primary sites plus a single secondary site situated at the center of the hexamer. The single-molecule data serve to establish that Rho translocates 5′-to-3′ towards RNA polymerase (RNAP) by a tethered-tracking mechanism, looping out the intervening RNA between the rut site and RNAP. These findings lead to a general model for Rho binding and translocation, and establish a novel experimental approach that should facilitate additional single- molecule studies of RNA-binding proteins. PMID:22885804

The atmospheric boundary layer in the CSIRO global climate model: simulations versus observations

NASA Astrophysics Data System (ADS)

Garratt, J. R.; Rotstayn, L. D.; Krummel, P. B.

2002-07-01

A 5-year simulation of the atmospheric boundary layer in the CSIRO global climate model (GCM) is compared with detailed boundary-layer observations at six locations, two over the ocean and four over land. Field observations, in the form of surface fluxes and vertical profiles of wind, temperature and humidity, are generally available for each hour over periods of one month or more in a single year. GCM simulations are for specific months corresponding to the field observations, for each of five years. At three of the four land sites (two in Australia, one in south-eastern France), modelled rainfall was close to the observed climatological values, but was significantly in deficit at the fourth (Kansas, USA). Observed rainfall during the field expeditions was close to climatology at all four sites. At the Kansas site, modelled screen temperatures (Tsc), diurnal temperature amplitude and sensible heat flux (H) were significantly higher than observed, with modelled evaporation (E) much lower. At the other three land sites, there is excellent correspondence between the diurnal amplitude and phase and absolute values of each variable (Tsc, H, E). Mean monthly vertical profiles for specific times of the day show strong similarities: over land and ocean in vertical shape and absolute values of variables, and in the mixed-layer and nocturnal-inversion depths (over land) and the height of the elevated inversion or height of the cloud layer (over the sea). Of special interest is the presence climatologically of early morning humidity inversions related to dewfall and of nocturnal low-level jets; such features are found in the GCM simulations. The observed day-to-day variability in vertical structure is captured well in the model for most sites, including, over a whole month, the temperature range at all levels in the boundary layer, and the mix of shallow and deep mixed layers. Weaknesses or unrealistic structure include the following, (a) unrealistic model mixed-layer temperature profiles over land in clear skies, related to use of a simple local first-order turbulence closure, (b) a tendency to overpredict cloud liquid water near the surface.

Omega 3 (peripheral type benzodiazepine binding) site distribution in the rat immune system: an autoradiographic study with the photoaffinity ligand (/sup 3/H)PK 14105

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

Benavides, J.; Dubois, A.; Dennis, T.

1989-04-01

The anatomical distribution of omega 3 (peripheral type benzodiazepine binding) sites in the immune system organs of the rat has been studied autoradiographically at both macroscopic and microscopic levels of resolution using either reversible or irreversible (UV irradiation) labeling with (/sup 3/H)PK 14105. In thymus sections, (/sup 3/H)PK 14105 labeled with high affinity (Kd, derived from saturation experiments = 10.8 nM) a single population of sites which possessed the pharmacological characteristics of omega 3 sites. In the thymus gland, higher omega 3 site densities were detected in the cortex than in the medulla; in these subregions, silver grains were associatedmore » to small (10-18 microns diameter) cells. In the spleen, omega 3 sites were more abundant in the white than in the red pulp. In the white pulp, silver grains were denser in the marginal zone than in the vicinity of the central artery and labeling was, as in the thymus, associated to small cytoplasm-poor cells. In the red pulp, omega 3 site associated silver grains were observed mainly in the Bilroth cords. In the lymph nodes, the medullary region showed a higher labeling than the surrounding follicles and paracortex. A significant accumulation of silver grains was observed in the lymph node medullary cords. In the intestine, Peyer patches were particularly enriched in omega 3 sites (especially in the periphery of the follicles). The distribution of omega 3 sites in the immune system organs suggests a preferential labeling of cells of T and monocytic lineages. This is consistent with the proposed immunoregulatory properties of some omega 3 site ligands.« less

HIV integration sites in latently infected cell lines: evidence of ongoing replication.

PubMed

Symons, Jori; Chopra, Abha; Malatinkova, Eva; De Spiegelaere, Ward; Leary, Shay; Cooper, Don; Abana, Chike O; Rhodes, Ajantha; Rezaei, Simin D; Vandekerckhove, Linos; Mallal, Simon; Lewin, Sharon R; Cameron, Paul U

2017-01-13

Assessing the location and frequency of HIV integration sites in latently infected cells can potentially inform our understanding of how HIV persists during combination antiretroviral therapy. We developed a novel high throughput sequencing method to evaluate HIV integration sites in latently infected cell lines to determine whether there was virus replication or clonal expansion in these cell lines observed as multiple integration events at the same position. We modified a previously reported method using random DNA shearing and PCR to allow for high throughput robotic processing to identify the site and frequency of HIV integration in latently infected cell lines. Latently infected cell lines infected with intact virus demonstrated multiple distinct HIV integration sites (28 different sites in U1, 110 in ACH-2 and 117 in J1.1 per 150,000 cells). In contrast, cell lines infected with replication-incompetent viruses (J-Lat cells) demonstrated single integration sites. Following in vitro passaging of the ACH-2 cell line, we observed a significant increase in the frequency of unique HIV integration sites and there were multiple mutations and large deletions in the proviral DNA. When the ACH-2 cell line was cultured with the integrase inhibitor raltegravir, there was a significant decrease in the number of unique HIV integration sites and a transient increase in the frequency of 2-LTR circles consistent with virus replication in these cells. Cell lines latently infected with intact HIV demonstrated multiple unique HIV integration sites indicating that these cell lines are not clonal and in the ACH-2 cell line there was evidence of low level virus replication. These findings have implications for the use of latently infected cell lines as models of HIV latency and for the use of these cells as standards.

Evaluation of postoperative antibiotics after non-perforated appendectomy.

PubMed

Rafiq, Muhammad Salman; Khan, Mah Muneer; Khan, Attaullah; Jan, Hizbullah

2015-08-01

To evaluate the role of postoperative antibiotics in reducing surgical site infections after appendectomy for non-perforated appendicitis. The randomised controlled trial was conducted at Khyber Teaching Hospital, Peshawar, Pakistan, from November 11, 2012, to May 30, 2014, and comprised patients of emergency appendectomy for non-perforated appendicitis who were divided into groups A and B. Group A received a single dose of cefuroxime sodium and metronidazole half-an-hour before induction, while Group B received one more dose of the same antibiotics postoperatively. Both groups were followed for 6 weeks. SPSS 20 was used for statistical analysis. Of the 390 patients in the study, 192(49.2%) were in Group A and 198(50.7%) in Group B. Number of surgical site infections was 15(7.8%) in Group A and 18(9.1%) in Group B (p=0.65). Mean hospital stay of 3.32±0.4 days and 3.59±0.46 days was observed for Group A and B, respectively, (p<0.001). A single pre-operative dose of cefuroxime and metronidazole had the same efficacy in preventing surgical site infections in cases of non-perforated appendicitis as when the same regimen was repeated post-operatively.

Crossovers are associated with mutation and biased gene conversion at recombination hotspots.

PubMed

Arbeithuber, Barbara; Betancourt, Andrea J; Ebner, Thomas; Tiemann-Boege, Irene

2015-02-17

Meiosis is a potentially important source of germline mutations, as sites of meiotic recombination experience recurrent double-strand breaks (DSBs). However, evidence for a local mutagenic effect of recombination from population sequence data has been equivocal, likely because mutation is only one of several forces shaping sequence variation. By sequencing large numbers of single crossover molecules obtained from human sperm for two recombination hotspots, we find direct evidence that recombination is mutagenic: Crossovers carry more de novo mutations than nonrecombinant DNA molecules analyzed for the same donors and hotspots. The observed mutations were primarily CG to TA transitions, with a higher frequency of transitions at CpG than non-CpGs sites. This enrichment of mutations at CpG sites at hotspots could predominate in methylated regions involving frequent single-stranded DNA processing as part of DSB repair. In addition, our data set provides evidence that GC alleles are preferentially transmitted during crossing over, opposing mutation, and shows that GC-biased gene conversion (gBGC) predominates over mutation in the sequence evolution of hotspots. These findings are consistent with the idea that gBGC could be an adaptation to counteract the mutational load of recombination.

Crossovers are associated with mutation and biased gene conversion at recombination hotspots

PubMed Central

Arbeithuber, Barbara; Betancourt, Andrea J.; Ebner, Thomas; Tiemann-Boege, Irene

2015-01-01

Meiosis is a potentially important source of germline mutations, as sites of meiotic recombination experience recurrent double-strand breaks (DSBs). However, evidence for a local mutagenic effect of recombination from population sequence data has been equivocal, likely because mutation is only one of several forces shaping sequence variation. By sequencing large numbers of single crossover molecules obtained from human sperm for two recombination hotspots, we find direct evidence that recombination is mutagenic: Crossovers carry more de novo mutations than nonrecombinant DNA molecules analyzed for the same donors and hotspots. The observed mutations were primarily CG to TA transitions, with a higher frequency of transitions at CpG than non-CpGs sites. This enrichment of mutations at CpG sites at hotspots could predominate in methylated regions involving frequent single-stranded DNA processing as part of DSB repair. In addition, our data set provides evidence that GC alleles are preferentially transmitted during crossing over, opposing mutation, and shows that GC-biased gene conversion (gBGC) predominates over mutation in the sequence evolution of hotspots. These findings are consistent with the idea that gBGC could be an adaptation to counteract the mutational load of recombination. PMID:25646453

Direct Single-Molecule Observation of Mode and Geometry of RecA-Mediated Homology Search.

PubMed

Lee, Andrew J; Endo, Masayuki; Hobbs, Jamie K; Wälti, Christoph

2018-01-23

Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single-molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging. We show that RecA nucleoprotein filaments move along DNA substrates via short-distance facilitated diffusions, or slides, interspersed with longer-distance random moves, or hops. Importantly, from the specific interaction geometry, we find that the double-stranded substrate DNA resides in the secondary DNA binding-site within the RecA nucleoprotein filament helical groove during the homology search. This work demonstrates that tailored DNA origami, in conjunction with HS-AFM, can be employed to reveal directly conformational and geometrical information on dynamic protein-DNA interactions which was previously inaccessible at an individual single-molecule level.

Description of borehole geophysical and geologist logs, Berks Sand Pit Superfund Site, Longswamp Township, Berks County, Pennsylvania

USGS Publications Warehouse

Low, Dennis J.; Conger, Randall W.

2003-01-01

Between October 2002 and January 2003, geophysical logging was conducted in six boreholes at the Berks Sand Pit Superfund Site, Longswamp Township, Berks County, Pa., to determine (1) the waterproducing zones, water-receiving zones, zones of vertical borehole flow, orientation of fractures, and borehole and casing depth; and (2) the hydraulic interconnection between the six boreholes and the site extraction well. The boreholes range in depth from 61 to 270 feet. Geophysical logging included collection of caliper, natural-gamma, single-point-resistance, fluid-temperature, fluid-flow, and acoustic-televiewer logs. Caliper and acoustic-televiewer logs were used to locate fractures, joints, and weathered zones. Inflections on fluid-temperature and single-point-resistance logs indicated possible water-bearing fractures, and flowmeter measurements verified these locations. Single-point-resistance, natural-gamma, and geologist logs provided information on stratigraphy. Flowmeter measurements were conducted while the site extraction well was pumping and when it was inactive to determine the hydraulic connections between the extraction well and the boreholes.Borehole geophysical logging and heatpulse flowmetering indicate active flow in the boreholes. Two of the boreholes are in ground-water discharge areas, two boreholes are in ground-water recharge areas, and one borehole is in an intermediate regime. Flow was not determined in one borehole. Heatpulse flowmetering, in conjunction with the geologist logs, indicates highly weathered zones in the granitic gneiss can be permeable and effective transmitters of water, confirming the presence of a two-tiered ground-water-flow system. The effort to determine a hydraulic connection between the site extraction well and six logged boreholes was not conclusive. Three boreholes showed decreases in depth to water after pumping of the site extraction well; in two boreholes, the depth to water increased. One borehole was cased its entire depth and was not revisited after it was logged by the caliper log. Substantial change in flow rates or direction of borehole flow was not observed in any of the three wells logged with the heatpulse flowmeter when the site extraction well was pumping and when it was inactive.

Dynamic and dual-site atrial pacing in the prevention of atrial fibrillation: The STimolazione Atrial DInamica Multisito (STADIM) Study.

PubMed

De Simone, Antonio; Senatore, Gaetano; Donnici, Giovanni; Turco, Pietro; Romano, Enrico; Gazzola, Carlo; Stabile, G

2007-01-01

The impact of new algorithms to consistently pace the atrium on the prevention of atrial fibrillation (AF) remains unclear. Our randomized, crossover study compared the efficacy of single- and dual-site atrial pacing, with versus without dynamic atrial overdrive pacing in preventing AF. We studied 72 patients (mean age = 69.6 +/- 6.5 years, 34 men) with sick sinus syndrome (SSS) and paroxysmal or persistent AF, who received dual-chamber pacemakers (PM) equipped with an AF prevention algorithm and two atrial leads placed in the right atrial appendage (RAA), by passive fixation, and in the coronary sinus ostium (CS), by active fixation, respectively. At implant, the patients were randomly assigned to unipolar CS versus RAA pacing. The PM was programmed in DDDR mode 1 month after implant. Each patient underwent four study phases of equal duration: (1) unipolar, single site (CS or RAA) pacing with the AF algorithm ON (atrial lower rate = 0 ppm); (2) unipolar, single site pacing with the AF algorithm OFF (atrial lower rate = 70 bpm); (3) bipolar, dual-site pacing with AF algorithm ON; (4) bipolar, dual-site pacing with the AF algorithm OFF. Among 40 patients (56%), who completed the follow-up (15 +/- 4 months) no difference was observed in the mean number of automatic mode switch (AMS) corrected for the duration of follow-up, in unipolar (5.6 +/- 22.8 vs 2.6 +/- 5.5) or bipolar mode (3.3 +/- 12.7 vs 2.1 +/- 4.9) with, respectively, the algorithm OFF or ON. With the AF prevention algorithm ON, the percentage of atrial pacing increased significantly from 78.7 +/- 22.1% to 92.4 +/- 4.9% (P < 0.001), while the average ventricular heart rate was significantly lower with the algorithm ON (62.4 +/- 17.5 vs 79.9 +/- 3 bpm (P < 0.001). The AF prevention algorithm increased the percentage of atrial pacing significantly, regardless of the atrial pulse configuration and pacing site, while maintaining a slower ventricular heart rate. It had no impact on the number of AMS in the unipolar and bipolar modes in patients with SSS.

Relation between physico-chemical limnology and crustacean community in Wular Lake of Kashmir Himalaya.

PubMed

Shah, Javaid Ahmad; Pandit, Ashok K

2013-10-01

The present study scrutinizes the seasonal variation in the distribution of crustacean zooplankton in relation to physico-chemical liminology of Wular lake. Water samples were collected from five study sites during September 2010-August 2011. Remarkable spatial and temporal variations were observed among the different study sites. Among the parameters recorded water temperature showed positive correlation with pH (p<0.01) and orthophosphate (p<0.05).Transparency showed a significant negative correlation with total alkalinity (p<0.01), free carbon dioxide (p<0.01) and ammonical nitrogen (p<0.01). Crustacean zooplankton were collected by filtering 100 L lake water through a 30 microm nytal mesh and preserved in 4% formalin. A total of 42 taxa of crustacean were recorded, among them 23 species belonged to Cladocera, 16 to Copepoda and only 3 to Ostracoda. Species diversity and density depicted an abrupt up surge on the advent of warmer period (extending from March). Among the various sites a maximum of 40 species were recorded from a single biotope (site III) against the minimum of only 17 species being recorded from site I. Bray-Curtis cluster analysis showed close similarity (0.928-0.944%) between summer and autumn in terms of species diversity. Pearson correlation coefficient of the various physico-chemical parameters of water with crustacean zooplankton depicted that not only a single but multiple factors govern over the distribution and diversity of crustacean in the lake.

Aerosol Light Absorption and Scattering in Mexico City: Comparison With Las Vegas, NV, and Los Angeles, CA.

NASA Astrophysics Data System (ADS)

Paredes-Miranda, G.; Arnott, W. P.; Gaffney, J. S.; Marley, N. A.; Campbell, D.; Fujita, E.

2007-12-01

Aerosol light scattering and absorption measurements were deployed in and near Mexico City in March 2006 as part of the Megacity Impacts on Regional and Global Environments (MIRAGE). The primary site in Mexico City was an urban site at Instituto Mexicano del Petroleo (Mexican Oil Institute, denoted by IMP). Similar campaigns were held in Las Vegas, NV in January-February, 2003; and Los Angeles, CA at numerous sites during all seasons from 2003 through 2007. The IMP site gave in-situ characterization of the Mexico City plume under favorable wind conditions. The photoacoustic instrument (PAS) used at IMP operates at 532 nm, and conveniently allowed for characterization of gaseous absorption at this wavelength as well. Light scattering measurements are accomplished within the PAS by the reciprocal nephelometery method. In Mexico City the aerosol absorption coefficient typically varies between 20 and 180 Mm-1 during the course of the day and significant diurnal variation of the aerosol single scattering albedo was observed probably as a consequence of secondary aerosol formation. We will present the diurnal variation of the scattering and absorption as well as the single scattering albedo and fraction of absorption due to gases at the IMP site and compare with Las Vegas diurnal variation. Mexico City 'breaths' more during the course of the day than Las Vegas, Nevada in part because the latitude of Mexico City resulted in more direct solar radiation. Further insight on the meteorological connections and population dynamics will be discussed.

Experimental Infrasound Studies in Nevada

NASA Astrophysics Data System (ADS)

Herrin, E. T.; Negraru, P. T.; Golden, P.; Williams, A.

2009-12-01

An experimental propagation study was carried out in Nevada in June 2009 on Julian days 173-177. During this field experiment we deployed 16 single channel digital infrasound recorders to monitor the munitions disposal activities near Hawthorne, NV. The sensors were deployed in a single line and placed approximately 12 km apart at distances ranging from 2 to 177 km. A four element semi-permanent infrasound array named FNIAR was installed approximately 154 km north of the detonation site in line with the individual temporary recorders. Tropospheric arrivals were observed during all days of the experiment, but during day 176 the observed arrivals had very large amplitudes. A large signal was observed at 58 km from the detonation site with amplitude as large as 4 Pascals, while at 94 km no signal was observed. At FNIAR the amplitude of the tropospheric arrival was 1 Pascal. During this day meteorological data acquired in the propagation path showed a strong jet stream to the north. On day 177 we were not able to identify tropospheric arrivals beyond 34 km, but at stations beyond 152 km we observed stratospheric arrivals. Continuous monitoring of these signals at FNIAR shows that stratospheric arrivals are the most numerous. In a two month period, from 06/15/2009 to 08/15/2009 there were 35 operational days at the Hawthorne disposal facility resulting in 212 explosions with known origin times. Based on the celerity values there were 115 explosions that have only stratospheric arrivals (celerities of 300-275 m/s), 72 explosions with both tropospheric (celerities above 330 m/s) and stratospheric arrivals, 20 explosions that were not detected and five explosions that have only tropospheric arrivals.

Magnetic relaxation pathways in lanthanide single-molecule magnets.

PubMed

Blagg, Robin J; Ungur, Liviu; Tuna, Floriana; Speak, James; Comar, Priyanka; Collison, David; Wernsdorfer, Wolfgang; McInnes, Eric J L; Chibotaru, Liviu F; Winpenny, Richard E P

2013-08-01

Single-molecule magnets are compounds that exhibit magnetic bistability caused by an energy barrier for the reversal of magnetization (relaxation). Lanthanide compounds are proving promising as single-molecule magnets: recent studies show that terbium phthalocyanine complexes possess large energy barriers, and dysprosium and terbium complexes bridged by an N2(3-) radical ligand exhibit magnetic hysteresis up to 13 K. Magnetic relaxation is typically controlled by single-ion factors rather than magnetic exchange (whether one or more 4f ions are present) and proceeds through thermal relaxation of the lowest excited states. Here we report polylanthanide alkoxide cage complexes, and their doped diamagnetic yttrium analogues, in which competing relaxation pathways are observed and relaxation through the first excited state can be quenched. This leads to energy barriers for relaxation of magnetization that exceed 800 K. We investigated the factors at the lanthanide sites that govern this behaviour.

Excel Spreadsheet Tools for Analyzing Groundwater Level Records and Displaying Information in ArcMap

USGS Publications Warehouse

Tillman, Fred D.

2009-01-01

When beginning hydrologic investigations, a first action is often to gather existing sources of well information, compile this information into a single dataset, and visualize this information in a geographic information system (GIS) environment. This report presents tools (macros) developed using Visual Basic for Applications (VBA) for Microsoft Excel 2007 to assist in these tasks. One tool combines multiple datasets into a single worksheet and formats the resulting data for use by the other tools. A second tool produces summary information about the dataset, such as a list of unique site identification numbers, the number of water-level observations for each, and a table of the number of sites with a listed number of water-level observations. A third tool creates subsets of the original dataset based on user-specified options and produces a worksheet with water-level information for each well in the subset, including the average and standard deviation of water-level observations and maximum decline and rise in water levels between any two observations, among other information. This water-level information worksheet can be imported directly into ESRI ArcMap as an 'XY Data' file, and each of the fields of summary well information can be used for custom display. A separate set of VBA tools distributed in an additional Excel workbook creates hydrograph charts of each of the wells in the data subset produced by the aforementioned tools and produces portable document format (PDF) versions of the hydrograph charts. These PDF hydrographs can be hyperlinked to well locations in ArcMap or other GIS applications.

Tuberculosis screening among homeless persons with AIDS living in single-room-occupancy hotels.

PubMed

Layton, M C; Cantwell, M F; Dorsinville, G J; Valway, S E; Onorato, I M; Frieden, T R

1995-11-01

Congregate facilities for homeless persons with the acquired immunodeficiency syndrome (AIDS) are often endemic for tuberculosis. We evaluated tuberculosis screening methods at single-room-occupancy hotels housing persons with AIDS. Residents were screened by cross matching the New York City Tuberculosis Registry, interviewing for tuberculosis history, skin testing, and chest radiography. Cases were classified as either previously or newly diagnosed. Among the 106 participants, 16 (15%) previously diagnosed tuberculosis cases were identified. Participants' tuberculosis histories were identified by the questionnaire (100%) or by registry match (69%). Eight participants (50%) were noncompliant with therapy. These findings prompted the establishment of a directly observed therapy program on site.

Polarization entangled photons from quantum dots embedded in nanowires.

PubMed

Huber, Tobias; Predojević, Ana; Khoshnegar, Milad; Dalacu, Dan; Poole, Philip J; Majedi, Hamed; Weihs, Gregor

2014-12-10

In this Letter, we present entanglement generated from a novel structure: a single InAsP quantum dot embedded in an InP nanowire. These structures can grow in a site-controlled way and exhibit high collection efficiency; we detect 0.5 million biexciton counts per second coupled into a single mode fiber with a standard commercial avalanche photo diode. If we correct for the known setup losses and detector efficiency, we get an extraction efficiency of 15(3) %. For the measured polarization entanglement, we observe a fidelity of 0.76(2) to a reference maximally entangled state as well as a concurrence of 0.57(6).

Defect chemistry and characterization of (Hg, Cd)Te

NASA Technical Reports Server (NTRS)

Vydyanath, H. R.

1981-01-01

Single crystal samples of phosphorus doped Hg sub 0.8 Cd sub 0.2 Te were anneald at temperatures varying from 450 C to 600 C in various Hg atmospheres. The samples were quenched to room temperature from the annealing temperatures. Hall effect and mobility measurements were performed at 77 K on all these samples. The results indicate the crystals to be p type for a total phosphorus concentration of 10 to the 19th power/cu cm in all the samples. The hole concentration at 77 K increases with increasing Hg pressures at 450 C and 500 C contrary to the observation in undoped crystals. Also, at low Hg pressures the concentration of holes in the phosphorus doped crystals is lower than in the undoped crystals. The hole concentration in all the samples is lower than the intrinsic carrier concentration at the annealing temperatures. The hole mobility in the doped crystals is similar to that in the undoped crystals. A defect model according to which phosphorus behaves as a single acceptor interstitially, occupying Te lattice sites while it acts as a single donor occupying Hg lattice sites was established. Equilibrum constants established for the incorporation of all the phosphorus species explain the experimental results

Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology.

PubMed

Liu, Ying; Lu, Zheming; Xu, Ruiping; Ke, Yang

2016-02-02

Integration of human papillomavirus (HPV) DNA into the host genome can be a driver mutation in cervical carcinoma. Identification of HPV integration at base resolution has been a longstanding technical challenge, largely due to sensitivity masking by HPV in episomes or concatenated forms. The aim was to enhance the understanding of the precise localization of HPV integration sites using an innovative strategy. Using HPV capture technology combined with next generation sequencing, HPV prevalence and the exact integration sites of the HPV DNA in 47 primary cervical cancer samples and 2 cell lines were investigated. A total of 117 unique HPV integration sites were identified, including HPV16 (n = 101), HPV18 (n = 7), and HPV58 (n = 9). We observed that the HPV16 integration sites were broadly located across the whole viral genome. In addition, either single or multiple integration events could occur frequently for HPV16, ranging from 1 to 19 per sample. The viral integration sites were distributed across almost all the chromosomes, except chromosome 22. All the cervical cancer cases harboring more than four HPV16 integration sites showed clinical diagnosis of stage III carcinoma. A significant enrichment of overlapping nucleotides shared between the human genome and HPV genome at integration breakpoints was observed, indicating that it may play an important role in the HPV integration process. The results expand on knowledge from previous findings on HPV16 and HPV18 integration sites and allow a better understanding of the molecular basis of the pathogenesis of cervical carcinoma.

Face, content, and construct validity of four, inanimate training exercises using the da Vinci ® Si surgical system configured with Single-Site ™ instrumentation.

PubMed

Jarc, Anthony M; Curet, Myriam

2015-08-01

Validated training exercises are essential tools for surgeons as they develop technical skills to use robot-assisted minimally invasive surgical systems. The purpose of this study was to show face, content, and construct validity of four, inanimate training exercises using the da Vinci (®) Si surgical system configured with Single-Site (™) instrumentation. New (N = 21) and experienced (N = 6) surgeons participated in the study. New surgeons (11 Gynecology [GYN] and 10 General Surgery [GEN]) had not completed any da Vinci Single-Site cases but may have completed multiport cases using the da Vinci system. They participated in this study prior to attending a certification course focused on da Vinci Single-Site instrumentation. Experienced surgeons (5 GYN and 1 GEN) had completed at least 25 da Vinci Single-Site cases. The surgeons completed four inanimate training exercises and then rated them with a questionnaire. Raw metrics and overall normalized scores were computed using both video recordings and kinematic data collected from the surgical system. The experienced surgeons significantly outperformed new surgeons for many raw metrics and the overall normalized scores derived from video review (p < 0.05). Only one exercise did not achieve a significant difference between new and experienced surgeons (p = 0.08) when calculating an overall normalized score using both video and advanced metrics derived from kinematic data. Both new and experienced surgeons rated the training exercises as appearing, to train and measure technical skills used during da Vinci Single-Site surgery and actually testing the technical skills used during da Vinci Single-Site surgery. In summary, the four training exercises showed face, content, and construct validity. Improved overall scores could be developed using additional metrics not included in this study. The results suggest that the training exercises could be used in an overall training curriculum aimed at developing proficiency in technical skills for surgeons new to da Vinci Single-Site instrumentation.

New Technique for Retrieving Liquid Water Path over Land using Satellite Microwave Observations

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

Deeter, M.N.; Vivekanandan, J.

2005-03-18

We present a new methodology for retrieving liquid water path over land using satellite microwave observations. As input, the technique exploits the Advanced Microwave Scanning Radiometer for earth observing plan (EOS) (AMSR-E) polarization-difference signals at 37 and 89 GHz. Regression analysis performed on model simulations indicates that over variable atmospheric and surface conditions the polarization-difference signals can be simply parameterized in terms of the surface emissivity polarization difference ({Delta}{var_epsilon}), surface temperature, liquid water path (LWP), and precipitable water vapor (PWV). The resulting polarization-difference parameterization (PDP) enables fast and direct (noniterative) retrievals of LWP with minimal requirements for ancillary data. Single-more » and dual-channel retrieval methods are described and demonstrated. Data gridding is used to reduce the effects of instrumental noise. The methodology is demonstrated using AMSR-E observations over the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) site during a six day period in November and December, 2003. Single- and dual-channel retrieval results mostly agree with ground-based microwave retrievals of LWP to within approximately 0.04 mm.« less

Protostellar Outflows Mapped with ALMA and Techniques to Include Short Spacings

NASA Astrophysics Data System (ADS)

Plunkett, Adele

2018-01-01

Protostellar outflows are early signs of star formation, yet in cluster environments - common sites of star formation - their role and interaction with surrounding gas are complicated. Protostellar outflows are interesting and complex because they connect protostars (scales 10s au) to the surrounding gas environment (few pc), and their morphology constrains launching and/or accretion modes. A complete outflow study must use observing methods that recover several orders of magnitude of spatial scales, ideally with sub-arcsecond resolution and mapping over a few parsecs. ALMA provides high-resolution observations of outflows, and in some cases outflows have been mapped in clusters. Combining with observations using the Total Power array is possible, but challenging, and a large single dish telescope providing more overlap in uv space is advantageous. In this presentation I show protostellar outflows observed with ALMA using 12m, 7m, and To tal Power arrays. With a new CASA tool TP2VIS we create total power ``visibility'' data and perform joint imaging and deconvolution of interferometry and single dish data. TP2VIS will ultimately provide synergy between ALMA and AtLAST data.

Improved simulation of group averaged CO2 surface concentrations using GEOS-Chem and fluxes from VEGAS

NASA Astrophysics Data System (ADS)

Chen, Z. H.; Zhu, J.; Zeng, N.

2013-01-01

CO2 measurements have been combined with simulated CO2 distributions from a transport model in order to produce the optimal estimates of CO2 surface fluxes in inverse modeling. However one persistent problem in using model-observation comparisons for this goal relates to the issue of compatibility. Observations at a single site reflect all underlying processes of various scales that usually cannot be fully resolved by model simulations at the grid points nearest the site due to lack of spatial or temporal resolution or missing processes in models. In this article we group site observations of multiple stations according to atmospheric mixing regimes and surface characteristics. The group averaged values of CO2 concentration from model simulations and observations are used to evaluate the regional model results. Using the group averaged measurements of CO2 reduces the noise of individual stations. The difference of group averaged values between observation and modeled results reflects the uncertainties of the large scale flux in the region where the grouped stations are. We compared the group averaged values between model results with two biospheric fluxes from the model Carnegie-Ames-Stanford-Approach (CASA) and VEgetation-Global-Atmosphere-Soil (VEGAS) and observations to evaluate the regional model results. Results show that the modeling group averaged values of CO2 concentrations in all regions with fluxes from VEGAS have significant improvements for most regions. There is still large difference between two model results and observations for grouped average values in North Atlantic, Indian Ocean, and South Pacific Tropics. This implies possible large uncertainties in the fluxes there.

Detection and Plant Monitoring Programs: Lessons from an Intensive Survey of Asclepias meadii with Five Observers

PubMed Central

Alexander, Helen M.; Reed, Aaron W.; Kettle, W. Dean; Slade, Norman A.; Bodbyl Roels, Sarah A.; Collins, Cathy D.; Salisbury, Vaughn

2012-01-01

Monitoring programs, where numbers of individuals are followed through time, are central to conservation. Although incomplete detection is expected with wildlife surveys, this topic is rarely considered with plants. However, if plants are missed in surveys, raw count data can lead to biased estimates of population abundance and vital rates. To illustrate, we had five independent observers survey patches of the rare plant Asclepias meadii at two prairie sites. We analyzed data with two mark-recapture approaches. Using the program CAPTURE, the estimated number of patches equaled the detected number for a burned site, but exceeded detected numbers by 28% for an unburned site. Analyses of detected patches using Huggins models revealed important effects of observer, patch state (flowering/nonflowering), and patch size (number of stems) on probabilities of detection. Although some results were expected (i.e. greater detection of flowering than nonflowering patches), the importance of our approach is the ability to quantify the magnitude of detection problems. We also evaluated the degree to which increased observer numbers improved detection: smaller groups (3–4 observers) generally found 90 – 99% of the patches found by all five people, but pairs of observers or single observers had high error and detection depended on which individuals were involved. We conclude that an intensive study at the start of a long-term monitoring study provides essential information about probabilities of detection and what factors cause plants to be missed. This information can guide development of monitoring programs. PMID:23285179

A single-dose regimen for antimicrobial prophylaxis to prevent perioperative infection in urological clean and clean-contaminated surgery.

PubMed

Higuchi, Yoshihide; Takesue, Yoshio; Yamada, Yusuke; Ueda, Yasuo; Suzuki, Toru; Aihara, Kinue; Maruyama, Takuo; Kondoh, Nobuyuki; Nojima, Michio; Yamamoto, Shingo

2011-04-01

A single dose of antimicrobial prophylaxis (AMP) was administered parenterally for the prevention of perioperative infection in a total of 788 patients undergoing urological surgery, including 380 endoscopic-instrumental, 328 clean, and 80 clean-contaminated operations performed at our institute between January 2007 and December 2009. Surgical site infections (SSIs), urinary tract infections (UTIs), and remote infections (RIs) were prospectively surveyed. The definition for a single dose of AMP allowed for the administration of an additional dose of an antimicrobial during surgery if the procedure was longer than 3 h, but not for the parenteral or oral administration at the end of the procedure in the recovery room, or at a later time over a period of more than 24 h. UTI was observed in 12 (3.2%) patients after endoscopic-instrumental operation, 1 (0.3%) after clean operation, and 1 (0.9%) after clean-contaminated operation. SSI was observed in 2 (0.6%) patients after clean operation but in none after clean-contaminated operations. RI was observed in 1 (0.3%) patient after endoscopic-instrumental operation, 3 (0.9%) after clean operation, and none after clean-contaminated operations. A single-dose regimen of AMP was effective and feasible for the prevention of perioperative infections, including SSIs, UTIs, and RIs, in endoscopic-instrumental, clean, and clean-contaminated urological surgical procedures.

Gold nanoparticle enhanced fluorescence anisotropy for the assay of single nucleotide polymorphisms (SNPs) based on toehold-mediated strand-displacement reaction.

PubMed

Wang, Xinyi; Zou, Mingjian; Huang, Hongduan; Ren, Yuqian; Li, Limei; Yang, Xiaoda; Li, Na

2013-03-15

We developed a highly differentiating, homogeneous gold nanoparticle (AuNP) enhanced fluorescence anisotropic method for single nucleotide polymorphism (SNP) detection at nanomolar level using toehold-mediated strand-displacement reaction. The template strand, containing a toehold domain with an allele-specific site, was immobilized on the surface of AuNPs, and the solution fluorescence anisotropy was markedly enhanced when the fluorescein-labeled blocking DNA was attached to the AuNP via hybridization. Strand-displacement by the target ssDNA strand resulted in detachment of fluorescein-labeled DNA from AuNPs, and thus decreased fluorescence anisotropy. The drastic kinetic difference in strand-displacement from toehold design was used to distinguish between the perfectly matched and the single-base mismatched strands. Free energy changes were calculated to elucidate the dependence of the differentiation ability on the mutation site in the toehold region. A solid negative signal change can be obtained for single-base mismatched strand in the dynamic range of the calibration curve, and a more than 10-fold signal difference can still be observed in a mixed solution containing 100 times the single-base mismatched strand, indicating the good specificity of the method. This proposed method can be performed with a standard spectrofluorimeter in a homogeneous and cost-effective manner, and has the potential to be extended to the application of fluorescence anisotropy method of SNP detection. Copyright © 2012 Elsevier B.V. All rights reserved.

Risk of surgical site infection in paediatric herniotomies without any prophylactic antibiotics: A preliminary experience.

PubMed

Vaze, Dhananjay; Samujh, Ram; Narasimha Rao, Katragadda Lakshmi

2014-01-01

Different studies underline the use of pre-operative antibiotic prophylaxis in clean surgeries like herniotomy and inguinal orchiopexy. But, the meta-analyses do not recommend nor discard the use of prophylactic pre-operative antibiotics. The scarcity of controlled clinical trials in paediatric population further vitiates the matter. This study assessed the difference in the rate of early post-operative wound infection cases in children who received single dose of pre-operative antibiotics and children who did not receive antibiotics after inguinal herniotomy and orchiopexy. This randomised prospective study was conducted in Paediatric Surgery department of PGIMER Chandigarh. Out of 251 patients, 112 patients were randomised to the case group and 139 were ascribed to the control group. The patients in control group were given a standard regimen of single dose of intravenous antibiotic at the time of induction followed by 3-4 days of oral antibiotic. Case group patients underwent the surgical procedure in similar manner with no antibiotic either at the time of induction or post-operatively. The incidence of surgical site infection in case group was 3.73 % and that in control group was 2.22%. The observed difference in the incidence of surgical site infection was statistically insignificant (P value = 0.7027). The overall infection rate in case and control group was 2.89%. Our preliminary experience suggests that there is no statistically significant difference in the proportion of early post-operative wound infection between the patients who received single dose of pre-operative antibiotics and the patients who received no antibiotics after inguinal herniotomy and orchiopexy. The risk of surgical site infection in paediatric heriotomies does not increase even if the child's weight is less than his/her expected weight for age.

Spontaneous regeneration of the corticospinal tract after transection in young rats: a key role of reactive astrocytes in making favorable and unfavorable conditions for regeneration.

PubMed

Iseda, T; Nishio, T; Kawaguchi, S; Yamanoto, M; Kawasaki, T; Wakisaka, S

2004-01-01

We demonstrated the occurrence of marked regeneration of the corticospinal tract (CST) after a single transection and failure of regeneration after a repeated transection in young rats. To provide convincing evidence for the complete transection and regeneration we used retrograde neuronal double labeling. Double-labeled neurons that took up the first tracer from the transection site and the second tracer from the injection site caudal to the transection site were observed in the sensorimotor cortex. The anterograde tracing method revealed various patterns of regeneration. In the most successful cases the vast majority of regenerated fibers descended in the normal tract and terminated normally whereas a trace amount of fibers coursed aberrantly. In the less successful cases fibers descended partly normally and partly aberrantly or totally aberrantly. To clarify the role of astrocytes in determining the success or failure of regeneration we compared expression of glial fibrillary acidic protein (GFAP), vimentin and neurofilament (NF) immunoreactivity (IR) in the lesion between single and repeated transections. In either transection, astrocytes disappeared from the CST near the lesion site as early as 3 h after lesioning. However, by 24 h after a single transection, immature astrocytes coexpressing GFAP- and vimentin-IR appeared in the former astrocyte-free area and NF-positive axons crossed the lesion. By contrast, after a repeated transection the astrocyte-free area spread and NF-positive axons never crossed the lesion. It appears likely that the major sign, and possibly cause of failure of regeneration is the prolonged disappearance of astrocytes in the lesioned tract area. Copyright 2004 IBRO

Catalyst and Fuel Interactions to Optimize Endothermic Cooling

DTIC Science & Technology

2016-08-30

research , special, group study, etc. 3. DATES COVERED. Indicate the time during which the work was performed and the report was written, e.g., Jun 1997...information from the experimental measurements. In close collaboration with experimental group of Anderson, we completed theoretical studies on the effect...observed shifts. 3. Methane Activation by Controlling s- and d-states in Iron-based Single Site Catalysts In a recent experimental finding Guo et

Single microfilaments mediate the early steps of microtubule bundling during preprophase band formation in onion cotyledon epidermal cells

PubMed Central

Takeuchi, Miyuki; Karahara, Ichirou; Kajimura, Naoko; Takaoka, Akio; Murata, Kazuyoshi; Misaki, Kazuyo; Yonemura, Shigenobu; Staehelin, L. Andrew; Mineyuki, Yoshinobu

2016-01-01

The preprophase band (PPB) is a cytokinetic apparatus that determines the site of cell division in plants. It originates as a broad band of microtubules (MTs) in G2 and narrows to demarcate the future division site during late prophase. Studies with fluorescent probes have shown that PPBs contain F-actin during early stages of their development but become actin depleted in late prophase. Although this suggests that actins contribute to the early stages of PPB formation, how actins contribute to PPB-MT organization remains unsolved. To address this question, we used electron tomography to investigate the spatial relationship between microfilaments (MFs) and MTs at different stages of PPB assembly in onion cotyledon epidermal cells. We demonstrate that the PPB actins observed by fluorescence microscopy correspond to short, single MFs. A majority of the MFs are bound to MTs, with a subset forming MT-MF-MT bridging structures. During the later stages of PPB assembly, the MF-mediated links between MTs are displaced by MT-MT linkers as the PPB MT arrays mature into tightly packed MT bundles. On the basis of these observations, we propose that the primary function of actins during PPB formation is to mediate the initial bundling of the PPB MTs. PMID:27053663

Local spin structure of the α -RuCl3 honeycomb-lattice magnet observed via muon spin rotation/relaxation

NASA Astrophysics Data System (ADS)

Yamauchi, Ichihiro; Hiraishi, Masatoshi; Okabe, Hirotaka; Takeshita, Soshi; Koda, Akihiro; Kojima, Kenji M.; Kadono, Ryosuke; Tanaka, Hidekazu

2018-04-01

We report a muon spin rotation/relaxation (μ SR ) study of single-crystalline samples of the α -RuCl3 honeycomb magnet, which is presumed to be a model compound for the Kitaev-Heisenberg interaction. It is inferred from magnetic susceptibility and specific-heat measurements that the present samples exhibit successive magnetic transitions at different critical temperatures TN with decreasing temperature, eventually falling into the TN=7 K antiferromagnetic (7 K) phase that has been observed in only single-crystalline specimens with the least stacking fault. Via μ SR measurements conducted under a zero external field, we show that such behavior originates from a phase separation induced by the honeycomb plane stacking fault, yielding multiple domains with different TN's. We also perform μ SR measurements under a transverse field in the paramagnetic phase to identify the muon site from the muon-Ru hyperfine parameters. Based on a comparison of the experimental and calculated internal fields at the muon site for the two possible spin structures inferred from neutron diffraction data, we suggest a modulated zigzag spin structure for the 7 K phase, with the amplitude of the ordered magnetic moment being significantly reduced from that expected for the orbital quenched spin-1/2 state.

Antibiotic interactions with the hammerhead ribozyme:tetracyclines as a new class of hammerhead inhibitor.

PubMed Central

Murray, J B; Arnold, J R

1996-01-01

A screening of a range of common laboratory antibiotics for inhibition of the hammerhead ribozyme has shown that in addition to certain aminoglycosides (most notably neomycin B) the tetracyclines are also effective inhibitors, with chlorotetracycline being more effective than tetracycline. Inhibition by chlorotetracycline is not as strong as that by neomycin B but is more complicated, with at least two binding sites apparent. As with hammerhead inhibition by neomycin B, chlorotetracycline inhibition can be overcome by raising the concentration of the Mg2+ ion cofactor. We find that around six Mg2+ ions will displace neomycin B, compared with twelve for chlorotetracycline. Inhibition observed in the presence of mixtures of neomycin B and chlorotetracycline is consistent with separate binding sites on the hammerhead for these two classes of antibiotic. Under certain conditions of the mixing order and low concentration of chlorotetracycline, enhancement of single-turnover hammerhead cleavage by up to 20% is observed, with higher concentrations of antibiotic being inhibitory. We have also found that the presence of 2.5% (v/v) DMSO causes a 30% enhancement of the single-turnover cleavage. These results thus extend the range of known inhibitors of hammerhead cleavage, and also demonstrate how the cleavage can be accelerated. PMID:8760373

A thermal desorption spectroscopy study of hydrogen trapping in polycrystalline α-uranium

DOE PAGES

Lillard, R. S.; Forsyth, R. T.

2015-03-14

The kinetics of hydrogen desorption from polycrystalline α-uranium (α-U) was examined using thermal desorption spectroscopy (TDS). The goal was to identify the major trap sites for hydrogen and their associated trap energies. In polycrystalline α-U six TDS adsorption peaks were observed at temperatures of 521 K, 556 K, 607 K, 681 K, 793 K and 905 K. In addition, the desorption was determined to be second order based on peak shape. The position of the first three peaks was consistent with desorption from UH3. To identify the trap site corresponding to the high temperature peaks the data were compared tomore » a plastically deformed sample and a high purity single crystal sample. The plastically deformed sample allowed the identification of trapping at dislocations while the single crystal sample allow for the identification of high angle boundaries and impurities. Thus, with respect to the desorption energy associated with each peak, values between 12.9 and 26.5 kJ/mole were measured.« less

Karyotype divergence and spreading of 5S rDNA sequences between genomes of two species: darter and emerald gobies ( Ctenogobius , Gobiidae).

PubMed

Lima-Filho, P A; Bertollo, L A C; Cioffi, M B; Costa, G W W F; Molina, W F

2014-01-01

Karyotype analyses of the cryptobenthic marine species Ctenogobius boleosoma and C. smaragdus were performed by means of classical and molecular cytogenetics, including physical mapping of the multigene 18S and 5S rDNA families. C. boleosoma has 2n = 44 chromosomes (2 submetacentrics + 42 acrocentrics; FN = 46) with a single chromosome pair each carrying 18S and 5S ribosomal sites; whereas C. smaragdus has 2n = 48 chromosomes (2 submetacentrics + 46 acrocentrics; FN = 50), also with a single pair bearing 18S rDNA, but an extensive increase in the number of GC-rich 5S rDNA sites in 21 chromosome pairs. The highly divergent karyotypes among Ctenogobius species contrast with observations in several other marine fish groups, demonstrating an accelerated rate of chromosomal evolution mediated by both chromosomal rearrangements and the extensive dispersion of 5S rDNA sequences in the genome. © 2014 S. Karger AG, Basel.

Fis protein induced λF-DNA bending observed by single-pair fluorescence resonance energy transfer

NASA Astrophysics Data System (ADS)

Chi-Cheng, Fu; Wunshain, Fann; Yuan Hanna, S.

2006-03-01

Fis, a site-specific DNA binding protein, regulates many biological processes including recombination, transcription, and replication in E.coli. Fis induced DNA bending plays an important role in regulating these functions and bending angle range from ˜50 to 95 dependent on the DNA sequence. For instance, the average bending angle of λF-DNA (26 bp, 8.8nm long, contained λF binding site on the center) measured by gel mobility shift assays was ˜ 94 . But the traditional method cannot provide information about the dynamics and the angle distribution. In this study, λF-DNA was labeled with donor (Alexa Fluor 546) and acceptor (Alexa Fluor 647) dyes on its two 5' ends and the donor-acceptor distances were measured using single-pair fluorescence resonance energy transfer (sp-FRET) with and without the present of Fis protein. Combing with structure information of Fis-DNA complex, the sp-FRET results are used to estimate the protein induced DNA bending angle distribution and dynamics.

On multi-site damage identification using single-site training data

NASA Astrophysics Data System (ADS)

Barthorpe, R. J.; Manson, G.; Worden, K.

2017-11-01

This paper proposes a methodology for developing multi-site damage location systems for engineering structures that can be trained using single-site damaged state data only. The methodology involves training a sequence of binary classifiers based upon single-site damage data and combining the developed classifiers into a robust multi-class damage locator. In this way, the multi-site damage identification problem may be decomposed into a sequence of binary decisions. In this paper Support Vector Classifiers are adopted as the means of making these binary decisions. The proposed methodology represents an advancement on the state of the art in the field of multi-site damage identification which require either: (1) full damaged state data from single- and multi-site damage cases or (2) the development of a physics-based model to make multi-site model predictions. The potential benefit of the proposed methodology is that a significantly reduced number of recorded damage states may be required in order to train a multi-site damage locator without recourse to physics-based model predictions. In this paper it is first demonstrated that Support Vector Classification represents an appropriate approach to the multi-site damage location problem, with methods for combining binary classifiers discussed. Next, the proposed methodology is demonstrated and evaluated through application to a real engineering structure - a Piper Tomahawk trainer aircraft wing - with its performance compared to classifiers trained using the full damaged-state dataset.

Estimating Terra MODIS Polarization Effect Using Ocean Data

NASA Technical Reports Server (NTRS)

Wald, Andrew E.; Brinkmann, Jake; Wu, Aisheng; Xiong, Jack

2016-01-01

Terra MODIS has been known since pre-launch to have polarization sensitivity, particularly in shortest-wavelength bands 8 and 9. On-orbit reflectance trending of pseudo-invariant sites show a variation in reflectance as a function of band and scan mirror angle of incidence consistent with time-dependent polarization effects from the rotating double-sided scan mirror. The MODIS Characterization Support Team [MCST] estimates the Mueller matrix trending from this variation as observed from a single desert site, but this effect is not included in Collection 6 [C6] calibration. Here we extend the MCSTs current polarization sensitivity monitoring to two ocean sites distributed over latitude to helpestimate the uncertainties in the derived Mueller matrix. The Mueller matrix elements derived for polarization-sensitive Band 8 for a given site are found to be fairly insensitive to surface brdf modeling. The site-to-site variation is a measure of the uncertainty in the Mueller estimation.Results for band 8 show that the polarization correction reduces mirror-side striping by up to 50% and reduces the instrument polarization effect on reflectance time series of an ocean target.

Breakdown of single spin-fluid model in the heavily hole-doped superconductor CsFe2As2

NASA Astrophysics Data System (ADS)

Zhao, D.; Li, S. J.; Wang, N. Z.; Li, J.; Song, D. W.; Zheng, L. X.; Nie, L. P.; Luo, X. G.; Wu, T.; Chen, X. H.

2018-01-01

Although Fe-based superconductors are correlated electronic systems with multiorbital, previous nuclear magnetic resonance (NMR) measurement suggests that a single spin-fluid model is sufficient to describe its spin behavior. Here, we first observed the breakdown of single spin-fluid model in a heavily hole-doped Fe-based superconductor CsFe2As2 by site-selective NMR measurement. At high-temperature regime, both Knight shift and nuclear spin-lattice relaxation at 133Cs and 75As nuclei exhibit distinct temperature-dependent behavior, suggesting the breakdown of the single spin-fluid model in CsFe2As2 . This is ascribed to the coexistence of both localized and itinerant spin degree of freedom at 3 d orbitals, which is consistent with the orbital-selective Mott phase. With decreasing temperature, the single spin-fluid behavior is recovered below T*˜75 K due to a coherent state among 3 d orbitals. The Kondo liquid scenario is proposed to understand the low-temperature coherent state.

Effect of single and mixed polycyclic aromatic hydrocarbon contamination on plant biomass yield and PAH dissipation during phytoremediation.

PubMed

Afegbua, Seniyat Larai; Batty, Lesley Claire

2018-04-27

Polycyclic aromatic hydrocarbon (PAH)-contaminated sites have a mixture of PAH of varying concentration which may affect PAH dissipation differently to contamination with a single PAH. In this study, pot experiments investigated the impact of PAH contamination on Medicago sativa, Lolium perenne, and Festuca arundinacea biomass and PAH dissipation from soils spiked with phenanthrene (Phe), fluoranthene (Flu), and benzo[a]pyrene (B[a]P) in single and mixed treatments. Stimulatory or inhibitory effects of PAH contamination on plant biomass yields were not different for the single and mixed PAH treatments. Results showed significant effect of PAH treatments on plant growth with an increased root biomass yield for F. arundinacea in the Phe (175%) and Flu (86%) treatments and a root biomass decrease in the mixed treatment (4%). The mean residual PAHs in the planted treatments and unplanted control for the single treatments were not significantly different. B[a]P dissipation was enhanced for single and mixed treatments (71-72%) with F. arundinacea compared to the unplanted control (24-50%). On the other hand, B[a]P dissipation was inhibited with L. perenne (6%) in the single treatment and M. sativa (11%) and L. perenne (29%) in the mixed treatment. Abiotic processes had greater contribution to PAH dissipation compared to rhizodegradation in both treatments. In most cases, a stimulatory effect of PAH contamination on plant biomass yield without an enhancement of PAH dissipation was observed. Plant species among other factors affect the relative contribution of PAH dissipation mechanisms during phytoremediation. These factors determine the effectiveness and suitability of phytoremediation as a remedial strategy for PAH-contaminated sites. Further studies on impact of PAH contamination, plant selection, and rhizosphere activities on soil microbial community structure and remediation outcome are required.

Analysis of spatial patterns informs community assembly and sampling requirements for Collembola in forest soils

NASA Astrophysics Data System (ADS)

Dirilgen, Tara; Juceviča, Edite; Melecis, Viesturs; Querner, Pascal; Bolger, Thomas

2018-01-01

The relative importance of niche separation, non-equilibrial and neutral models of community assembly has been a theme in community ecology for many decades with none appearing to be applicable under all circumstances. In this study, Collembola species abundances were recorded over eleven consecutive years in a spatially explicit grid and used to examine (i) whether observed beta diversity differed from that expected under conditions of neutrality, (ii) whether sampling points differed in their relative contributions to overall beta diversity, and (iii) the number of samples required to provide comparable estimates of species richness across three forest sites. Neutrality could not be rejected for 26 of the forest by year combinations. However, there is a trend toward greater structure in the oldest forest, where beta diversity was greater than predicted by neutrality on five of the eleven sampling dates. The lack of difference in individual- and sample-based rarefaction curves also suggests randomness in the system at this particular scale of investigation. It seems that Collembola communities are not spatially aggregated and assembly is driven primarily by neutral processes particularly in the younger two sites. Whether this finding is due to small sample size or unaccounted for environmental variables cannot be determined. Variability between dates and sites illustrates the potential of drawing incorrect conclusions if data are collected at a single site and a single point in time.

Sodium Binding Sites and Permeation Mechanism in the NaChBac Channel: A Molecular Dynamics Study.

PubMed

Guardiani, Carlo; Rodger, P Mark; Fedorenko, Olena A; Roberts, Stephen K; Khovanov, Igor A

2017-03-14

NaChBac was the first discovered bacterial sodium voltage-dependent channel, yet computational studies are still limited due to the lack of a crystal structure. In this work, a pore-only construct built using the NavMs template was investigated using unbiased molecular dynamics and metadynamics. The potential of mean force (PMF) from the unbiased run features four minima, three of which correspond to sites IN, CEN, and HFS discovered in NavAb. During the run, the selectivity filter (SF) is spontaneously occupied by two ions, and frequent access of a third one is often observed. In the innermost sites IN and CEN, Na + is fully hydrated by six water molecules and occupies an on-axis position. In site HFS sodium interacts with a glutamate and a serine from the same subunit and is forced to adopt an off-axis placement. Metadynamics simulations biasing one and two ions show an energy barrier in the SF that prevents single-ion permeation. An analysis of the permeation mechanism was performed both computing minimum energy paths in the axial-axial PMF and through a combination of Markov state modeling and transition path theory. Both approaches reveal a knock-on mechanism involving at least two but possibly three ions. The currents predicted from the unbiased simulation using linear response theory are in excellent agreement with single-channel patch-clamp recordings.

First records of tool-set use for ant-dipping by Eastern chimpanzees (Pan troglodytes schweinfurthii) in the Kalinzu Forest Reserve, Uganda.

PubMed

Hashimoto, Chie; Isaji, Mina; Koops, Kathelijne; Furuichi, Takeshi

2015-10-01

Chimpanzees at numerous study sites are known to prey on army ants by using a single wand to dip into the ant nest or column. However, in Goualougo (Republic of Congo) in Central Africa, chimpanzees use a different technique, use of a woody sapling to perforate the ant nest, then use of a herb stem as dipping tool to harvest the army ants. Use of a tool set has also been found in Guinea, West Africa: at Seringbara in the Nimba Mountains and at nearby Bossou. There are, however, no reports for chimpanzees in East Africa. We observed use of such a tool set in Kalinzu, Uganda, for the first time by Eastern chimpanzees. This behavior was observed among one group of chimpanzees at Kalinzu (S-group) but not among the adjacent group (M-group) with partly overlapping ranging areas despite the fact that the latter group has been under intensive observation since 1997. In Uganda, ant-dipping has not been observed in the northern three sites (Budongo, Semliki, and Kibale) but has been observed or seems to occur in the southern sites (Kalinzu and Bwindi), which suggests that ant-dipping was invented by and spread from the southern region after the northern and southern forest blocks became separated. Use of a tool-set by only one group at Kalinzu further suggests that this behavior was recently invented and has not yet spread to the other group via migrating females.

Single-molecule electrocatalysis by single-walled carbon nanotubes.

PubMed

Xu, Weilin; Shen, Hao; Kim, Yoon Ji; Zhou, Xiaochun; Liu, Guokun; Park, Jiwoong; Chen, Peng

2009-12-01

We report a single-molecule fluorescence study of electrocatalysis by single-walled carbon nanotubes (SWNTs) at single-reaction resolution. Applying super-resolution optical imaging, we find that the electrocatalysis occurs at discrete, nanometer-dimension sites on SWNTs. Single-molecule kinetic analysis leads to an electrocatalytic mechanism, allowing quantification of the reactivity and heterogeneity of individual reactive sites. Combined with conductivity measurements, this approach will be powerful to interrogate how the electronic structure of SWNTs affects the electrocatalytic interfacial charge transfer, a process fundamental to photoelectrochemical cells.

Useful Bicistronic Reporter System for Studying Poly(A) Site-Defining cis Elements and Regulation of Alternative Polyadenylation.

PubMed

Deng, Zhongyuan; Zhang, Shen; Gu, Shaohua; Ni, Xinzhi; Zeng, Wenxian; Li, Xianchun

2018-01-17

The link between polyadenylation (pA) and various biological, behavioral, and pathological events of eukaryotes underlines the need to develop in vivo polyadenylation assay methods for characterization of the cis -acting elements, trans -acting factors and environmental stimuli that affect polyadenylation efficiency and/or relative usage of two alternative polyadenylation (APA) sites. The current protein-based CAT or luciferase reporter systems can measure the polyadenylation efficiency of a single pA site or candidate cis element but not the choice of two APA sites. To address this issue, we developed a set of four new bicistronic reporter vectors that harbor either two luciferase or fluorescence protein open reading frames connected with one Internal Ribosome Entry Site (IRES). Transfection of single or dual insertion constructs of these vectors into mammalian cells demonstrated that they could be utilized not only to quantify the strength of a single candidate pA site or cis element, but also to accurately measure the relative usage of two APA sites at both the mRNA (qRT-PCR) and protein levels. This represents the first reporter system that can study polyadenylation efficiency of a single pA site or element and regulation of two APA sites at both the mRNA and protein levels.

Dynamics of HIV-1 Assembly and Release

PubMed Central

Ivanchenko, Sergey; Godinez, William J.; Lampe, Marko; Kräusslich, Hans-Georg; Eils, Roland; Rohr, Karl; Bräuchle, Christoph; Müller, Barbara; Lamb, Don C.

2009-01-01

Assembly and release of human immunodeficiency virus (HIV) occur at the plasma membrane of infected cells and are driven by the Gag polyprotein. Previous studies analyzed viral morphogenesis using biochemical methods and static images, while dynamic and kinetic information has been lacking until very recently. Using a combination of wide-field and total internal reflection fluorescence microscopy, we have investigated the assembly and release of fluorescently labeled HIV-1 at the plasma membrane of living cells with high time resolution. Gag assembled into discrete clusters corresponding to single virions. Formation of multiple particles from the same site was rarely observed. Using a photoconvertible fluorescent protein fused to Gag, we determined that assembly was nucleated preferentially by Gag molecules that had recently attached to the plasma membrane or arrived directly from the cytosol. Both membrane-bound and cytosol derived Gag polyproteins contributed to the growing bud. After their initial appearance, assembly sites accumulated at the plasma membrane of individual cells over 1–2 hours. Assembly kinetics were rapid: the number of Gag molecules at a budding site increased, following a saturating exponential with a rate constant of ∼5×10−3 s−1, corresponding to 8–9 min for 90% completion of assembly for a single virion. Release of extracellular particles was observed at ∼1,500±700 s after the onset of assembly. The ability of the virus to recruit components of the cellular ESCRT machinery or to undergo proteolytic maturation, or the absence of Vpu did not significantly alter the assembly kinetics. PMID:19893629

Ultrashort Carbon Nanotubes That Fluoresce Brightly in the Near-Infrared.

PubMed

Danné, Noémie; Kim, Mijin; Godin, Antoine G; Kwon, Hyejin; Gao, Zhenghong; Wu, Xiaojian; Hartmann, Nicolai F; Doorn, Stephen K; Lounis, Brahim; Wang, YuHuang; Cognet, Laurent

2018-06-14

The intrinsic near-infrared photoluminescence observed in long single-walled carbon nanotubes is known to be quenched in ultrashort nanotubes due to their tiny size as compared to the exciton diffusion length in these materials (>100 nm). Here, we show that intense photoluminescence can be created in ultrashort nanotubes (∼40 nm length) upon incorporation of exciton-trapping sp 3 defect sites. Using super-resolution photoluminescence imaging at <25 nm resolution, we directly show the preferential localization of excitons at the nanotube ends, which separate by less than 40 nm and behave as independent emitters. This unexpected observation opens the possibility to synthesize fluorescent ultrashort nanotubes-a goal that has been long thought impossible-for bioimaging applications, where bright near-infrared photoluminescence and small size are highly desirable, and for quantum information science, where high quality and well-controlled near-infrared single photon emitters are needed.

A Family of A-Site Cation-Deficient Double-Perovskite-Related Iridates: Ln9Sr2Ir4O24 (Ln = La, Pr, Nd, Sm).

PubMed

Ferreira, Timothy; Smith, Mark D; Zur Loye, Hans-Conrad

2018-06-21

The compositions of the general formula Ln 11- x Sr x Ir 4 O 24 (Ln = La, Pr, Nd, Sm; 1.37 ≥ x ≥ 2) belonging to a family of A-site cation-deficient double-perovskite-related oxide iridates were grown as highly faceted single crystals from a molten strontium chloride flux. Their structures were determined by single-crystal X-ray diffraction. On the basis of the single-crystal results, additional compositions, Ln 9 Sr 2 Ir 4 O 24 (Ln = La, Pr, Nd, Sm), were prepared as polycrystalline powders via solid-state reactions and structurally characterized by Rietveld refinement. The compositions Ln 9 Sr 2 Ir 4 O 24 (Ln = La, Pr, Nd, Sm) contain Ir(V) and Ir(IV) in a 1:3 ratio with an average iridium oxidation state of 4.25. The single-crystal compositions La 9.15 Sr 1.85 Ir 4 O 24 and Pr 9.63 Sr 1.37 Ir 4 O 24 contain relatively less Ir(V), with the average iridium oxidation states being 4.21 and 4.09, respectively. The magnetic properties of Ln 9 Sr 2 Ir 4 O 24 (Ln = La, Pr, Nd, Sm) were measured, and complex magnetic behavior was observed in all cases at temperatures below 30 K.

SEM-induced shrinkage and site-selective modification of single-crystal silicon nanopores

NASA Astrophysics Data System (ADS)

Chen, Qi; Wang, Yifan; Deng, Tao; Liu, Zewen

2017-07-01

Solid-state nanopores with feature sizes around 5 nm play a critical role in bio-sensing fields, especially in single molecule detection and sequencing of DNA, RNA and proteins. In this paper we present a systematic study on shrinkage and site-selective modification of single-crystal silicon nanopores with a conventional scanning electron microscope (SEM). Square nanopores with measurable sizes as small as 8 nm × 8 nm and rectangle nanopores with feature sizes (the smaller one between length and width) down to 5 nm have been obtained, using the SEM-induced shrinkage technique. The analysis of energy dispersive x-ray spectroscopy and the recovery of the pore size and morphology reveal that the grown material along with the edge of the nanopore is the result of deposition of hydrocarbon compounds, without structural damage during the shrinking process. A simplified model for pore shrinkage has been developed based on observation of the cross-sectional morphology of the shrunk nanopore. The main factors impacting on the task of controllably shrinking the nanopores, such as the accelerating voltage, spot size, scanned area of e-beam, and the initial pore size have been discussed. It is found that single-crystal silicon nanopores shrink linearly with time under localized irradiation by SEM e-beam in all cases, and the pore shrinkage rate is inversely proportional to the initial equivalent diameter of the pore under the same e-beam conditions.

Charge carrier trapping and acoustic phonon modes in single CdTe nanowires.

PubMed

Lo, Shun Shang; Major, Todd A; Petchsang, Nattasamon; Huang, Libai; Kuno, Masaru K; Hartland, Gregory V

2012-06-26

Semiconductor nanostructures produced by wet chemical synthesis are extremely heterogeneous, which makes single particle techniques a useful way to interrogate their properties. In this paper the ultrafast dynamics of single CdTe nanowires are studied by transient absorption microscopy. The wires have lengths of several micrometers and lateral dimensions on the order of 30 nm. The transient absorption traces show very fast decays, which are assigned to charge carrier trapping into surface defects. The time constants vary for different wires due to differences in the energetics and/or density of surface trap sites. Measurements performed at the band edge compared to the near-IR give slightly different time constants, implying that the dynamics for electron and hole trapping are different. The rate of charge carrier trapping was observed to slow down at high carrier densities, which was attributed to trap-state filling. Modulations due to the fundamental and first overtone of the acoustic breathing mode were also observed in the transient absorption traces. The quality factors for these modes were similar to those measured for metal nanostructures, and indicate a complex interaction with the environment.

Predicting ecological flow regime at ungaged sites: A comparison of methods

USGS Publications Warehouse

Murphy, Jennifer C.; Knight, Rodney R.; Wolfe, William J.; Gain, W. Scott

2012-01-01

Nineteen ecologically relevant streamflow characteristics were estimated using published rainfall–runoff and regional regression models for six sites with observed daily streamflow records in Kentucky. The regional regression model produced median estimates closer to the observed median for all but two characteristics. The variability of predictions from both models was generally less than the observed variability. The variability of the predictions from the rainfall–runoff model was greater than that from the regional regression model for all but three characteristics. Eight characteristics predicted by the rainfall–runoff model display positive or negative bias across all six sites; biases are not as pronounced for the regional regression model. Results suggest that a rainfall–runoff model calibrated on a single characteristic is less likely to perform well as a predictor of a range of other characteristics (flow regime) when compared with a regional regression model calibrated individually on multiple characteristics used to represent the flow regime. Poor model performance may misrepresent hydrologic conditions, potentially distorting the perceived risk of ecological degradation. Without prior selection of streamflow characteristics, targeted calibration, and error quantification, the widespread application of general hydrologic models to ecological flow studies is problematic. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

New suturing technique for robotic-assisted vaginal cuff closure during single-site hysterectomy.

PubMed

Shin, So-Jin; Chung, Hyewon; Kwon, Sang-Hoon; Cha, Soon-Do; Cho, Chi-Heum

2017-06-01

To describe a simple and efficient technique for suturing the vaginal cuff in robotic-assisted single-site hysterectomy using barbed suture and a straight needle. Consecutive patients undergoing robotic-assisted single-site hysterectomy from February 2014 to August 2015 at Dong San Hospital, Keimyung University were included. Surgeons used two barbed sutures in a running fashion to close the vaginal cuff. A barbed suture was exclusively used with a straightened needle in upward direction from posterior vaginal cuff to anterior vaginal cuff which played a pivotal role for closure. A total of 100 patients underwent robotic-assisted single-site hysterectomy. The total operation time was 132.5 min and vaginal cuff closure time was 12.0 min. There were no postoperative complications; vaginal cuff dehiscence, vaginal cuff infection, and vaginal bleeding that require surgical intervention or admission. The use of barbed suture with straightened needle to close the vaginal cuff in robotic-assisted single-site hysterectomy is easy to perform and demonstrates safety and efficacy. This technique offers secure, fast, and effective incision closure.

EPR study of a gamma-irradiated (2-hydroxyethyl)triphenylphosphonium chloride single crystal

NASA Astrophysics Data System (ADS)

Karakaş, E.; Türkkan, E.; Dereli, Ö.; Sayιn, Ü.; Tapramaz, R.

2011-12-01

In this study, gamma-irradiated single crystals of (2-hydroxyethyl)triphenylphosphonium chloride [CH2CH2OH P(C6H5)3Cl] were investigated with electron paramagnetic resonance (EPR) spectroscopy at room temperature for different orientations in the magnetic field. The single crystals were irradiated with a 60Co-γ-ray source at 0.818 kGy/h for about 36 h. Taking the chemical structure and the experimental spectra of the irradiated single crystal of the title compound into consideration, a paramagnetic species was produced with the unpaired electron delocalized around 31P and several 1H nuclei. The anisotropic hyperfine values due to the 31P nucleus, slightly anisotropic hyperfine values due to the 1H nuclei and the g-tensor of the radical were measured from the spectra. Depending on the molecular structure and measured parameters, three possible radicals were modeled using the B3LYP/6-31+G(d) level of density-functional theory, and EPR parameters were calculated for modeled radicals using the B3LYP/TZVP method/basis set combination. The calculated hyperfine coupling constants were found to be in good agreement with the observed EPR parameters. The experimental and theoretically simulated spectra for each of the three crystallographic axes were well matched with one of the modeled radicals (discussed in the text). We thus identified the radical C˙H2CH2 P(C 6H5)3 Cl as a paramagnetic species produced in a single crystal of the title compound in two magnetically distinct sites. The experimental g-factor and hyperfine coupling constants of the radical were found to be anisotropic, with the isotropic values g iso = 2.0032, ? G, ? G, ? G and ? G for site 1 and g iso=2.0031, ? G, ? G ? G and ? G for site 2.

Analgesic duration and kinetics of liposomal bupivacaine after subcutaneous injection in mice.

PubMed

Grant, G J; Piskoun, B; Bansinath, M

2003-12-01

1. The objective of the present study was to assess the time-course profile of analgesia and bupivacaine concentrations at the site of injection after subcutaneous administration of a single dose of standard bupivacaine or a novel controlled-release liposomal bupivacaine formulation. 2. Groups of mice were injected subcutaneously with 0.2 mL of 0.5% standard bupivacaine or 0.5, 1 or 2% liposomal bupivacaine. 3. A prolonged duration of analgesia occurred in mice receiving liposomal bupivacaine. In the liposomal groups, the bupivacaine remained at the injection site for more than 96 h, compared with approximately 8 h in groups injected with standard bupivacaine. 4. These results confirm that the prolonged analgesia observed after injection of the liposomal formulation is associated with sustained higher levels of bupivacaine at the site of injection.

On Neglecting Chemical Exchange Effects When Correcting in Vivo 31P MRS Data for Partial Saturation

NASA Astrophysics Data System (ADS)

Ouwerkerk, Ronald; Bottomley, Paul A.

2001-02-01

Signal acquisition in most MRS experiments requires a correction for partial saturation that is commonly based on a single exponential model for T1 that ignores effects of chemical exchange. We evaluated the errors in 31P MRS measurements introduced by this approximation in two-, three-, and four-site chemical exchange models under a range of flip-angles and pulse sequence repetition times (TR) that provide near-optimum signal-to-noise ratio (SNR). In two-site exchange, such as the creatine-kinase reaction involving phosphocreatine (PCr) and γ-ATP in human skeletal and cardiac muscle, errors in saturation factors were determined for the progressive saturation method and the dual-angle method of measuring T1. The analysis shows that these errors are negligible for the progressive saturation method if the observed T1 is derived from a three-parameter fit of the data. When T1 is measured with the dual-angle method, errors in saturation factors are less than 5% for all conceivable values of the chemical exchange rate and flip-angles that deliver useful SNR per unit time over the range T1/5 ≤ TR ≤ 2T1. Errors are also less than 5% for three- and four-site exchange when TR ≥ T1*/2, the so-called "intrinsic" T1's of the metabolites. The effect of changing metabolite concentrations and chemical exchange rates on observed T1's and saturation corrections was also examined with a three-site chemical exchange model involving ATP, PCr, and inorganic phosphate in skeletal muscle undergoing up to 95% PCr depletion. Although the observed T1's were dependent on metabolite concentrations, errors in saturation corrections for TR = 2 s could be kept within 5% for all exchanging metabolites using a simple interpolation of two dual-angle T1 measurements performed at the start and end of the experiment. Thus, the single-exponential model appears to be reasonably accurate for correcting 31P MRS data for partial saturation in the presence of chemical exchange. Even in systems where metabolite concentrations change, accurate saturation corrections are possible without much loss in SNR.

High performance platinum single atom electrocatalyst for oxygen reduction reaction

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

Liu, Jing; Jiao, Menggai; Lu, Lanlu

For the large-scale sustainable implementation of polymer electrolyte membrane fuel cells in vehicles, high-performance electrocatalysts with low platinum consumption are desirable for use as cathode material during the oxygen reduction reaction in fuel cells. Here we report a carbon black-supported cost-effective, efficient and durable platinum single-atom electrocatalyst with carbon monoxide/methanol tolerance for the cathodic oxygen reduction reaction. The acidic single-cell with such a catalyst as cathode delivers high performance, with power density up to 680 mW cm –2 at 80 °C with a low platinum loading of 0.09 mgPt cm –2, corresponding to a platinum utilization of 0.13 gPt kWmore » –1 in the fuel cell. Good fuel cell durability is also observed. As a result, theoretical calculations reveal that the main effective sites on such platinum single-atom electrocatalysts are single-pyridinic-nitrogen-atom-anchored single-platinum-atom centres, which are tolerant to carbon monoxide/methanol, but highly active for the oxygen reduction reaction.« less

High performance platinum single atom electrocatalyst for oxygen reduction reaction

DOE PAGES

Liu, Jing; Jiao, Menggai; Lu, Lanlu; ...

2017-07-24

For the large-scale sustainable implementation of polymer electrolyte membrane fuel cells in vehicles, high-performance electrocatalysts with low platinum consumption are desirable for use as cathode material during the oxygen reduction reaction in fuel cells. Here we report a carbon black-supported cost-effective, efficient and durable platinum single-atom electrocatalyst with carbon monoxide/methanol tolerance for the cathodic oxygen reduction reaction. The acidic single-cell with such a catalyst as cathode delivers high performance, with power density up to 680 mW cm –2 at 80 °C with a low platinum loading of 0.09 mgPt cm –2, corresponding to a platinum utilization of 0.13 gPt kWmore » –1 in the fuel cell. Good fuel cell durability is also observed. As a result, theoretical calculations reveal that the main effective sites on such platinum single-atom electrocatalysts are single-pyridinic-nitrogen-atom-anchored single-platinum-atom centres, which are tolerant to carbon monoxide/methanol, but highly active for the oxygen reduction reaction.« less

Site-controlled InGaN/GaN single-photon-emitting diode

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

Zhang, Lei; Deng, Hui, E-mail: dengh@umich.edu; Teng, Chu-Hsiang

2016-04-11

We report single-photon emission from electrically driven site-controlled InGaN/GaN quantum dots. The device is fabricated from a planar light-emitting diode structure containing a single InGaN quantum well, using a top-down approach. The location, dimension, and height of each single-photon-emitting diode are controlled lithographically, providing great flexibility for chip-scale integration.

Self-energy functional theory with symmetry breaking for disordered lattice bosons

NASA Astrophysics Data System (ADS)

Hügel, Dario; Strand, Hugo U. R.; Pollet, Lode

2018-07-01

We extend the self-energy functional theory to the case of interacting lattice bosons in the presence of symmetry breaking and quenched disorder. The self-energy functional we derive depends only on the self-energies of the disorder-averaged propagators, allowing for the construction of general non-perturbative approximations. Using a simple single-site reference system with only three variational parameters, we are able to reproduce numerically exact quantum Monte Carlo (QMC) results on local observables of the Bose–Hubbard model with box disorder with high accuracy. At strong interactions, the phase boundaries are reproduced qualitatively but shifted with respect to the ones observed with QMC due to the extremely low condensate fraction in the superfluid phase. Deep in the strongly-disordered weakly-interacting regime, the simple reference system employed is insufficient and no stationary solutions can be found within its restricted variational subspace. By systematically analyzing thermodynamical observables and the spectral function, we find that the strongly interacting Bose glass is characterized by different regimes, depending on which local occupations are activated as a function of the disorder strength. We find that the particles delocalize into isolated superfluid lakes over a strongly localized background around maximally-occupied sites whenever these sites are particularly rare. Our results indicate that the transition from the Bose glass to the superfluid phase around unit filling at strong interactions is driven by the percolation of superfluid lakes which form around doubly occupied sites.

Broadband Seismic Observations at the Hawaii-2 Observatory During ODP Leg 200

NASA Astrophysics Data System (ADS)

Stephen, R. A.; Duennebier, F. K.; Harris, D.; Jolly, J.; Bolmer, S. T.; Bromirski, P. D.; Leg 200 Shipboard Scientific Party, .

2003-12-01

Ocean Drilling Project Leg 200 was the first leg in deep sea and ocean drilling history to conduct operations in the vicinity of a continuously operating broadband seafloor seismometer. In 1998 investigators from the University of Hawaii, Woods Hole Oceanographic Institution, and Incorporated Institutions for Seismology had installed a broadband, shallow buried seismometer at the site [Duennebier et al., 2002] and data has been acquired in real time in Oahu over the Hawaii-2 transoceanic cable. Hole 1224D was drilled, cased and cemented at the site so that a broadband borehole seismometer can be emplaced in the future. The noise from the JOIDES Resolution as it approached and left the site as well as during all on-site operations was observed. In addition we recorded shots with 80 cubic inch water guns during single channel seismic tests as well as whale songs and earthquake activity. The behavior of ambient noise levels near the microseism peak was also compared with local wind speed and sea state conditions as observed from the drill ship. This work was supported by a grant from JOI-USSAC. We would like to thank the Earthquake Research Institute at the University of Tokyo for a Visiting Professorship for RAS during which much of this work was carried out. [Duennebier, F.K., D.W. Harris, J. Jolly, J. Babinec, D. Copson, and K. Stiffel, The Hawaii-2 observatory seismic system, IEEE Journal of Oceanic Engineering, 27, 212-217, 2002.

Cumulants of heat transfer across nonlinear quantum systems

NASA Astrophysics Data System (ADS)

Li, Huanan; Agarwalla, Bijay Kumar; Li, Baowen; Wang, Jian-Sheng

2013-12-01

We consider thermal conduction across a general nonlinear phononic junction. Based on two-time observation protocol and the nonequilibrium Green's function method, heat transfer in steady-state regimes is studied, and practical formulas for the calculation of the cumulant generating function are obtained. As an application, the general formalism is used to study anharmonic effects on fluctuation of steady-state heat transfer across a single-site junction with a quartic nonlinear on-site pinning potential. An explicit nonlinear modification to the cumulant generating function exact up to the first order is given, in which the Gallavotti-Cohen fluctuation symmetry is found still valid. Numerically a self-consistent procedure is introduced, which works well for strong nonlinearity.

Observations at the Mars Pathfinder site: Do they provide "unequivocal" evidence of catastrophic flooding?

USGS Publications Warehouse

Chapman, M.G.; Kargel, J.S.

1999-01-01

After Mars Pathfinder landed at the mouth of Ares Vallis, a large channel that drains into the Chryse Planitia basin, the mission reports unanimously supported the interpretation that the lander site is the locus of catastrophic flooding by noting that all aspects of the scene are consistent with this interpretation. However, alternatives cannot be ruled out by any site observations, as all aspects of the scene are equally consistent with other interpretations of origin, namely, ice and mass-flow processes subsequently modified by wind erosion. The authors discuss alternative explanations for the geologic history of the channel based on a regional view of the circum-Chryse channels from Viking images (our best broad-scale information to date) and the local view from the recent Pathfinder landing site. Mega-indicators of channel origin, the regional geomorphology, geology, and planetary climatic conditions, taken together suggest some combination of flood, mass flow, glacial, and eolian processes. The macro-indicators of channel origin (sedimentologic) are also not indicative of one process of emplacement, either as single criteria or taken cumulatively. Finally, the micro-indicators of channel origin (geochemical and mineralogic composition) do not provide very tight constraints on the deposits' possible origins other than that water was in some way involved.

Incidence of Port-Site Incisional Hernia After Single-Incision Laparoscopic Surgery

PubMed Central

Rainville, Harvey; Ikedilo, Ojinika; Vemulapali, Pratibha

2014-01-01

Background and Objectives: Single-incision laparoscopic surgery is gaining popularity among minimally invasive surgeons and is now being applied to a broad number of surgical procedures. Although this technique uses only 1 port, the diameter of the incision is larger than in standard laparoscopic surgery. The long-term incidence of port-site hernias after single-incision laparoscopic surgery has yet to be determined. Methods: All patients who underwent a single-incision laparoscopic surgical procedure from May 2008 through May 2009 were included in the study. Single-incision laparoscopic surgical operations were performed either by a multiport technique or with a 3-trocar single-incision laparoscopic surgery port. The patients were seen at 30 to 36 months' follow-up, at which time they were examined for any evidence of port-site incisional hernia. Patients found to have hernias on clinical examination underwent repairs with mesh. Results: A total of 211 patients met the criteria for inclusion in the study. The types of operations included were cholecystectomy, appendectomy, sleeve gastrectomy, gastric banding, Nissen fundoplication, colectomy, and gastrojejunostomy. We found a port-site hernia rate of 2.9% at 30 to 36 months' follow-up. Conclusion: Port-site incisional hernia after single-incision laparoscopic surgical procedures remains a major setback for patients. The true incidence remains largely unknown because most patients are asymptomatic and therefore do not seek surgical aid. PMID:24960483

Structural transformations in (1 -x ) Na0.5Bi0.5TiO3-x BaTiO3 single crystals studied by Raman spectroscopy

NASA Astrophysics Data System (ADS)

de la Flor, G.; Malcherek, T.; Gorfman, S.; Mihailova, B.

2017-12-01

Hard-mode Raman spectroscopy was applied to analyze the temperature-induced transformation processes in perovskite-type (ABO3) single crystals of (1 -x ) Na0.5Bi0.5TiO3-x BaTiO3 (NBT-x BT ) in a wide temperature range between 100 and 1010 K and a composition range of x =0 -0.074 across the morphotropic phase boundary (MPB). The results show abundant uncoupled ferroic structural distortions even at 1010 K and coexistence of two types of mesoscopic-scale ferroic order at lower temperatures. Octahedral BO6 tilting is typical of pure NBT, while the incorporation of A-site Ba2 + suppresses the tilting and promotes the off centering of BO6 octahedra. The temperature evolution of the phonon modes clearly reveals the two macroscopically observed critical temperatures Tm and Td as well as, in the case of x ≠0 , two characteristic temperatures T' and T'' preceding the Tm and Td, respectively, which are attributed to mesoscopic-scale antiferroelectric and ferroelectric coupling processes within the A-site-cation subsystem. At x

Oxygen activation in flavoprotein oxidases: the importance of being positive.

PubMed

Gadda, Giovanni

2012-04-03

The oxidation of flavin hydroquinones by O(2) in solution is slow, with second-order rate constants of ~250 M(-1) s(-1). This is due to the obligatory, single-electron transfer that initiates the reaction being thermodynamically unfavored and poorly catalyzed. Notwithstanding considerations of O(2) accessibility to the reaction site, its desolvation and geometry and other factors that can also contribute to further rate acceleration, flavoprotein oxidases must activate O(2) for reaction with flavin hydroquinones to be able to achieve the 100-1000-fold rate enhancements typically observed. Protein positive charges have been identified in glucose oxidase, monomeric sarcosine oxidase, N-methyltryptophan oxidase and fructosamine oxidase that electrostatically stabilize the transition state for the initial single electron transfer that generates the O(2)(-•)/flavin semiquinone radical pair. In choline oxidase despite the presence of three histidines in the active site, the trimethylammonium group of the reaction product provides such an electrostatic stabilization. A nonpolar site proximal to the flavin C(4a) atom in choline oxidase has also been identified, which contributes to the geometry and desolvation of the O(2) reaction site. The relevance of O(2) activation by product charges to other flavoprotein oxidases, such as for example those catalyzing amine oxidations, is discussed in this review. A nonpolar site close to the flavin C(4a) atom and a positive charge is identified through structural analysis in several flavoprotein oxidases. Mutagenesis has disclosed nonpolar sites in O(2)-reducing enzymes that utilize copper/TPQ or iron. It is predicted that classes of O(2)-reducing enzymes utilizing other cofactors also contain a similar catalytic motif.

Single-Molecule Interfacial Electron Transfer

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

Lu, H. Peter

This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static andmore » dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO 2 and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO 2 nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO 2 nanoparticle surfaces by using ultrafast single-molecule spectroscopy and electrochemical AFM metal tip scanning microscopy, focusing on understanding the interfacial electron transfer dynamics at specific nanoscale electron transfer sites with high-spatially and temporally resolved topographic-and-spectroscopic characterization at individual molecule basis, characterizing single-molecule rate processes, reaction driving force, and molecule-substrate electronic coupling. One of the most significant characteristics of our new approach is that we are able to interrogate the complex interfacial electron transfer dynamics by actively pin-point energetic manipulation of the surface interaction and electronic couplings, beyond the conventional excitation and observation.« less

Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time.

PubMed

Kong, Muwen; Beckwitt, Emily C; Springall, Luke; Kad, Neil M; Van Houten, Bennett

2017-01-01

Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways. In this chapter, we demonstrate the utility of the platform by applying these techniques in the studies of proteins participating in nucleotide excision repair. © 2017 Elsevier Inc. All rights reserved.

The Connectivity Between Site-Specific Life Cycle Impact Assessment and Site-Specific Weighting

EPA Science Inventory

The goal of many LCIAs is to come to a single score with all of the impacts from a wide variety of impact assessments weighted to form this single score. My past experiences with developing site-specific impact assessment methodologies and how this can change the valuation porti...

Preferential binding of daunomycin to 5'ATCG and 5'ATGC sequences revealed by footprinting titration experiments.

PubMed

Chaires, J B; Herrera, J E; Waring, M J

1990-07-03

Results from a high-resolution deoxyribonuclease I (DNase I) footprinting titration procedure are described that identify preferred daunomycin binding sites within the 160 bp tyr T DNA fragment. We have obtained single-bond resolution at 65 of the 160 potential binding sites within the tyr T fragment and have examined the effect of 0-3.0 microM total daunomycin concentration on the susceptibility of these sites toward digestion by DNase I. Four types of behavior are observed: (i) protection from DNase I cleavage; (ii) protection, but only after reaching a critical total daunomycin concentration; (iii) enhanced cleavage; (iv) no effect of added drug. Ten sites were identified as the most strongly protected on the basis of the magnitude of the reduction of their digestion product band areas in the presence of daunomycin. These were identified as the preferred daunomycin binding sites. Seven of these 10 sites are found at the end of the triplet sequences 5'ATGC and 5'ATCG, where the notation AT indicates that either A or T may occupy the position. The remaining three strongly protected sites are found at the ends of the triplet sequence 5'ATCAT. Of the preferred daunomycin binding sites we identify in this study, the sequence 5'ATCG is consistent with the specificity predicted by the theoretical studies of Chen et al. [Chen, K.-X., Gresh, N., & Pullman, B. (1985) J. Biomol. Struct. Dyn. 3, 445-466] and is the very sequence to which daunomycin is observed to be bound in two recent X-ray crystallographic studies. Solution studies, theoretical studies, and crystallographic studies have thus converged to provide a consistent and coherent picture of the sequence preference of this important anticancer antibiotic.

The Scintillation Prediction Observations Research Task (SPORT): an International Science Mission Using a Cubesat

NASA Technical Reports Server (NTRS)

Spann, James; Swenson, Charles; Durao, Otavio; Loures, Luis; Heelis, Rod; Bishop, Rebecca; Le, Guan; Abdu, Mangalathayil; Krause, Linda; Fry, Craig;

Modification of a single tryptophan residue in human Cu,Zn-superoxide dismutase by peroxynitrite in the presence of bicarbonate.

PubMed

Yamakura, F; Matsumoto, T; Fujimura, T; Taka, H; Murayama, K; Imai, T; Uchida, K

2001-07-09

Human recombinant Cu,Zn-SOD was reacted with peroxynitrite in a reaction mixture containing 150 mM potassium phosphate buffer (pH 7.4) 25 mM sodium bicarbonate, and 0.1 mM diethylenetriamine pentaacetic acid. Disappearance of fluorescence emission at 350 nm, which could be attributed to modification of a single tryptophan residue, was observed in the modified enzyme with a pH optimum of around 8.4. A fluorescence decrease with the same pH optimum was also observed without sodium bicarbonate, but with less efficiency. Amino acid contents of the modified enzyme showed no significant difference in all amino acids except the loss of a single tryptophan residue of the enzyme. The peroxynitrite-modified enzyme showed an increase in optical absorption around 350 nm and 30% reduced enzyme activity based on the copper contents. The modified enzyme showed the same electron paramagnetic resonance spectrum as that of the control enzyme. The modified Cu,Zn-SOD showed a single protein band in sodium dodecyl sulfate--polyacrylamide gel electrophoresis (SDS--PAGE) and five protein bands in non-denaturing PAGE. From this evidence, we conclude that nitration and/or oxidation of the single tryptophan 32 and partial inactivation of the enzyme activity of Cu,Zn-SOD is caused by a peroxynitrite-carbon dioxide adduct without perturbation of the active site copper integrity.

Tuberculosis screening among homeless persons with AIDS living in single-room-occupancy hotels.

PubMed Central

Layton, M C; Cantwell, M F; Dorsinville, G J; Valway, S E; Onorato, I M; Frieden, T R

1995-01-01

Congregate facilities for homeless persons with the acquired immunodeficiency syndrome (AIDS) are often endemic for tuberculosis. We evaluated tuberculosis screening methods at single-room-occupancy hotels housing persons with AIDS. Residents were screened by cross matching the New York City Tuberculosis Registry, interviewing for tuberculosis history, skin testing, and chest radiography. Cases were classified as either previously or newly diagnosed. Among the 106 participants, 16 (15%) previously diagnosed tuberculosis cases were identified. Participants' tuberculosis histories were identified by the questionnaire (100%) or by registry match (69%). Eight participants (50%) were noncompliant with therapy. These findings prompted the establishment of a directly observed therapy program on site. PMID:7485672

Negatively Cooperative Binding of High Density Lipoprotein to the HDL Receptor SR-BI†

PubMed Central

Nieland, Thomas J.F.; Xu, Shangzhe; Penman, Marsha; Krieger, Monty

2011-01-01

Scavenger receptor class B, type I (SR-BI) is a high-density lipoprotein (HDL) receptor, which also binds low density lipoprotein (LDL), and mediates the cellular selective uptake of cholesteryl esters from lipoproteins. SR-BI also is a co-receptor for hepatitis C virus and a signaling receptor that regulates cell metabolism. Many investigators have reported that lipoproteins bind to SR-BI via a single class of independent (not interacting), high affinity binding sites (one site model). We have re-investigated the ligand concentration dependence of 125I-HDL binding to SR-BI and SR-BI-mediated specific uptake of [3H]CE from [3H]CE-HDL using an expanded range of ligand concentrations (<1 µg protein/ml, lower than previously reported). Scatchard and non-linear least squares model fitting analyses of the binding and uptake data were both inconsistent with a single class of independent binding sites binding univalent lipoprotein ligands. The data are best fit by models in which SR-BI has either two independent classes of binding sites, or one class of sites exhibiting negative cooperativity due to either classic allostery or ensemble effects (‘ lattice model’). Similar results were observed for LDL. Application of the ‘infinite dilution’ dissociation rate method established that the binding of 125I-HDL to SR-BI at 4 °C exhibits negative cooperativity. The unexpected complexity of the interactions of lipoproteins with SR-BI should be taken into account when interpreting the results of experiments that explore the mechanism(s) by which SR-BI mediates ligand binding, lipid transport and cell signaling. PMID:21254782

Robotic Single-Site Sacrocolpopexy Using Barbed Suture Anchoring and Peritoneal Tunneling Technique: Tips and Tricks.

PubMed

Guan, Xiaoming; Ma, Yingchun; Gisseman, Jordan; Kleithermes, Christopher; Liu, Juan

2017-01-01

To demonstrate the tips and tricks of a simpler technique for single-site sacrocolpopexy using barbed suture anchoring and retroperitoneal tunneling to make the procedure more efficient and reproducible. Step-by-step description of surgical tutorial using a narrated video (Canadian Task Force classification III). Academic tertiary care hospital. Patient with Stage III uterine prolapse. Sacrocolpopexy is increasing utilized since the FDA warning about complications of vaginal mesh surgery. It is the gold standard for repair of apical prolapse. However, there is great variation in the sacrocolpopexy procedure techniques and they have not been standardized. Traditional single-site laparoscopic sacrocolpopexy is very challenging as the procedure time is long and suturing is difficult. The advantages of suturing with wristed needle drivers in robotic single-site surgery simplify this complex procedure. Furthermore, using barbed suture anchoring and peritoneal tunneling technique potentially decreases the surgeon's learning curve and makes the procedure reproducible. In this video, we demonstrate a supracervial hysterectomy with a stepwise explanation of the correct technique for performing a robotic single incision sacrocolpopexy. Sacrocolpopexy is increasing used since the US Food and Drug Administration warning about complications of vaginal mesh surgery. It is the gold standard for repair of apical prolapse. However, a great variation exists in the sacrocolpopexy procedure techniques that need to be standardized. Traditional single-site laparoscopic sacrocolpopexy is very challenging because the procedure time is long and suturing is difficult. The advantages of suturing with wristed needle drivers in robotic single-site surgery simplify this complex procedure. Furthermore, using the barbed suture anchoring and peritoneal tunneling technique potentially decreases the surgeon's learning curve and makes the procedure reproducible. In this video, we demonstrate a supracervical hysterectomy with a stepwise explaation of the correct technique for performing a robotic single-incision sacrocolpopexy. The possibility of using the barbed suture and peritoneal tunneling technique with wristed needle drivers in robotic single-site sacrocolpopexy offers the possibility of an effective, safe, reproducible, and cosmetic surgical option. Copyright © 2016 AAGL. Published by Elsevier Inc. All rights reserved.

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

USGS Publications Warehouse

Prober, Suzanne M.; Leff, Jonathan W.; Bates, Scott T.; Borer, Elizabeth T.; Firn, Jennifer; Harpole, W. Stanley; Lind, Eric M.; Seabloom, Eric W.; Adler, Peter B.; Bakker, Jonathan D.; Cleland, Elsa E.; DeCrappeo, Nicole; DeLorenze, Elizabeth; Hagenah, Nicole; Hautier, Yann; Hofmockel, Kirsten S.; Kirkman, Kevin P.; Knops, Johannes M. H.; La Pierre, Kimberly J.; MacDougall, Andrew S.; McCulley, Rebecca L.; Mitchell, Charles E.; Risch, Anita C.; Schuetz, Martin; Stevens, Carly J.; Williams, Ryan J.; Fierer, Noah

2015-01-01

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

Functional cooperation between exonucleases and endonucleases—basis for the evolution of restriction enzymes

PubMed Central

Raghavendra, Nidhanapathi K.; Rao, Desirazu N.

2003-01-01

Many types of restriction enzymes cleave DNA away from their recognition site. Using the type III restriction enzyme, EcoP15I, which cleaves DNA 25–27 bp away from its recognition site, we provide evidence to show that an intact recognition site on the cleaved DNA sequesters the restriction enzyme and decreases the effective concentration of the enzyme. EcoP15I restriction enzyme is shown here to perform only a single round of DNA cleavage. Significantly, we show that an exonuclease activity is essential for EcoP15I restriction enzyme to perform multiple rounds of DNA cleavage. This observation may hold true for all restriction enzymes cleaving DNA sufficiently far away from their recognition site. Our results highlight the importance of functional cooperation in the modulation of enzyme activity. Based on results presented here and other data on well-characterised restriction enzymes, a functional evolutionary hierarchy of restriction enzymes is discussed. PMID:12655005

CD9 tetraspanin generates fusion competent sites on the egg membrane for mammalian fertilization

PubMed Central

Jégou, Antoine; Ziyyat, Ahmed; Barraud-Lange, Virginie; Perez, Eric; Wolf, Jean Philippe; Pincet, Frédéric; Gourier, Christine

2011-01-01

CD9 tetraspanin is the only egg membrane protein known to be essential for fertilization. To investigate its role, we have measured, on a unique acrosome reacted sperm brought in contact with an egg, the adhesion probability and strength with a sensitivity of a single molecule attachment. Probing the binding events at different locations of wild-type egg we described different modes of interaction. Here, we show that more gamete adhesion events occur on Cd9 null eggs but that the strongest interaction mode disappears. We propose that sperm–egg fusion is a direct consequence of CD9 controlled sperm–egg adhesion properties. CD9 generates adhesion sites responsible for the strongest of the observed gamete interaction. These strong adhesion sites impose, during the whole interaction lifetime, a tight proximity of the gamete membranes, which is a requirement for fusion to take place. The CD9-induced adhesion sites would be the actual location where fusion occurs. PMID:21690351

Revelations from a single strong-motion record retreived during the 27 June 1998 Adana (Turkey) earthquake

USGS Publications Warehouse

Celebi, M.

2000-01-01

During the 27 June 1998 Adana (Turkey) earthquake, only one strong-motion record was retrieved in the region where the most damage occurred. This single record from the station in Ceyhan, approximately 15 km from the epicenter of that earthquake, exhibits characteristics that are related to the dominant frequencies of the ground and structures. The purpose of this paper is to explain the causes of the damage as inferred from both field observations and the characteristics of a single strong-motion record retrieved from the immediate epicentral area. In the town of Ceyhan there was considerable but selective damage to a significant number of mid-rise (7-12 stories high) buildings. The strong-motion record exhibits dominant frequencies that are typically similar for the mid-rise building structures. This is further supported by spectral ratios derived using Nakamura's method [QR of RTRI, 30 (1989) 25] that facilitates computation of a spectral ratio from a single tri-axial record as the ratio of amplitude spectrum of horizontal component to that of the vertical component [R = H(f)/V(f)]. The correlation between the damage and the characteristics exhibited from the single strong-motion record is remarkable. Although deficient construction practices played a significant role in the extent of damage to the mid-rise buildings, it is clear that site resonance also contributed to the detrimental fate of most of the mid-rise buildings. Therefore, even a single record can be useful to explain the effect of site resonance on building response and performance. Such information can be very useful for developing zonation criteria in similar alluvial valleys. Published by Elsevier Science Ltd.

3-D Waveform Modeling of the 11 September 2001 World Trade Center Collapse Events in New York City

NASA Astrophysics Data System (ADS)

Yoo, S.; Rhie, J.; Kim, W.

2010-12-01

The seismic signals from collapse of the twin towers of World Trade Center (WTC), NYC were well recorded by the seismographic stations in the northeastern United States. The building collapse can be represented by a vertical single force which does not generate tangential component seismic signals during the source process. The waveforms recorded by the Basking Ridge, NJ (BRNJ) station located due west of the WTC site show that the amplitude on tangential component is negligible and indicates that a vertical single force assumption is valid and the velocity structure is more or less homogeneous along the propagation path. However, 3-component seismograms recorded at Palisades, NY (PAL), which is located 33.8 km due north of the WTC site along the Hudson River (azimuth = 15.2°), show abnormal features. The amplitude on tangential component is larger than on vertical- or on radial-component. This observation may be attributable to the complex energy conversion between Rayleigh and Love waves due to the strong low velocity anomaly associated with unconsolidated sediments under the Hudson River. To test the effects of the low velocity anomaly on the enhanced amplitude in tangential component, we developed a 3D velocity model by considering local geology such as unconsolidated sediment layer, Palisades sill, Triassic sandstone, and crystalline basement and simulated waveforms at PAL. The preliminary synthetic results show that 3D velocity structure can significantly enhance the amplitude in tangential component but it is not as large as the observation. Although a more precise 3D model is required to better explain the observations, our results confirm that the low velocity layer under the Hudson River can enhance the amplitude in tangential component at PAL. This result suggests that a good understanding of the amplitude enhancements for specific event-site pairs may be important to evaluate seismic hazard of metropolitan New York City.

Influence of Spatial Variation in Ground Motion Peak Acceleration on Local Site Effects Estimation at Bucovina Seismic Array (BURAR) Romania

NASA Astrophysics Data System (ADS)

Ghica, D. V.; Radulian, M.; Popa, M.; Grecu, B.

2006-05-01

Basically, array processing techniques require a high signal coherency across the seismic site; therefore the local crustal velocities below the station, signal amplitude differences between array elements and local noise conditions, resulting in local site effects will affect calculation of phase arrival times, propagation velocities and ground motion amplitudes. In general, array techniques assume a homogenous structure for all sites, and a simple relief correction is taking in account for the data analysis. To increase the results accuracy, individual element corrections must be applied, based on the biases factors systematically observed. This study aims at identifying the anomalous amplitude variations recorded at the Bucovina Seismic Array (BURAR) and at explaining their influence on site effects estimation. Maximum amplitudes for the teleseismic and regional phases in four narrow frequency bands (0.25-0.5Hz; 0.5-1Hz; 1-2Hz; 1.5-3Hz) are measured. Spatial distribution of ground motion peak acceleration in BURAR site, for each band, is plotted; a different behavior was observed at frequencies below 2Hz. The most important aspect observed is the largest amplitude exhibited by BUR07 across the whole array at high frequencies (an amplification factor of about two). This can be explained by the different geology at BUR07 site (mica schist outcrops), comparing with the rest of elements (green schist outcrops). At the lowest frequencies (0.25-0.5Hz), BUR09 peak amplitudes dominate the other sites. Considering BUR07 as reference site, peak acceleration ratios were investigated. The largest scattering of these ratios appears at the highest frequencies (1.5-3Hz), when the weight of over unit values is about 90 %. No azimuth and distance dependence was found for these effects, suggesting the absence of the dipping layer structures. Although an increase of the ratio values is noticed for epicentral distance between 8000 and 10000 km, for frequencies over 1 Hz. The results of this study are essential to further develop the calibration technique for seismic monitoring with BURAR array, in order to improve the detection and single-array location capabilities of the system.

Novel Electronically Conducting Tellurium Oxides

NASA Astrophysics Data System (ADS)

Subramanian, Mas; Siritanon, Theerunan; Sleight, Arthur

2010-03-01

Tellurium oxides seldom show measurable electronic conductivity. Tellurium oxides that appear to have Te^5+ contain Te^4+ and Te^6+ in two distinct crystallographic sites and are electronic insulators. Here we report on the synthesis and characterization of several new tellurium rich oxides of the general formula, CsMxTe2-xO6, crystallizing in modified pyrochlore structure. Most of the compounds reported here are black in color with some exhibiting good electronic conductivities (2 S/cm) and Seebeck measurements indicate all are n-type. The observation of high electronic conductivities in compounds like CsGe0.5Te1.5O6, CsAl0.33Te1.67O6 confirms that observed conductivity is arising from doping of electrons into the empty 5s orbitals of Te^6+. This reduction is apparently accompanied with some small deviation from the ideal formula: oxygen content and/or ratio of cations on octahedral sites. This is in consistent with single-crystal X-ray as well as powder neutron diffraction structure refinements and the observed sign of the Seebeck coefficient. To our knowledge, this is a first observance of high electrical conductivity in mixed valent tellurium oxides.

Site-specific incorporation of uranyl carbonate species at the calcite surface

NASA Astrophysics Data System (ADS)

Reeder, Richard J.; Elzinga, Evert J.; Tait, C. Drew; Rector, K. D.; Donohoe, Robert J.; Morris, David E.

2004-12-01

Spatially resolved luminescence spectra from U(VI) co-precipitated at the (101¯4) growth surface of synthetic calcite single crystals confirm heterogeneous incorporation corresponding to the distribution of structurally non-equivalent steps composing the vicinal surfaces of spiral growth hillocks. Spectral structure from U(VI) luminescence at the "-" vicinal regions and featureless, weak luminescence at the "+" vicinal regions are consistent with previously reported observations of enrichment at the former sites during calcite growth. Luminescence spectra differ between the non-equivalent regions of the crystal, with the spectral features from the "-" vicinal region corresponding to those observed in bulk calcite samples. Subtle spectral shifts are observed from U(VI) co-precipitated with microcrystalline calcite synthesized by a different method, and all of the U(VI)-calcite sample spectra differ significantly from that of U(VI) co-precipitated with aragonite. The step-selective incorporation of U(VI) can be explained by a proposed model in which the allowed orientation for adsorption of the dominant calcium uranyl triscarbonate species is controlled by the atomic arrangement at step edges. Differences in the tilt angles of carbonate groups between non-equivalent growth steps favor adsorption of the calcium uranyl triscarbonate species at "-" steps, as observed in experiments.

Correlation between cation conduction and ionic morphology in a PEO-based single ion conductor

NASA Astrophysics Data System (ADS)

Lin, Kan-Ju; Maranas, Janna

2011-03-01

We use molecular dynamics simulation to study ion transport and backbone mobility of a PEO-based single ion conductor. Ion mobility depends on the chemical structure and the local environment of the ions, which consequently impact ionic conductivity. We characterize the aggregation state of the ions, and assess the role of ion complexes in ionomer dynamics. In addition to solvated cations and pairs, higher order ion clusters are found. Most of the ion clusters are in string-like structure and cross-link two or more different ionomer chains through ionic binding. Ionic crosslinks decrease mobility at the ionic co-monomer; hence the mobility of the adjacent PEO segment is influenced. Na ions show slow mobility when they are inside large clusters. The hopping timescale for Na varies from 20 ns to 200. A correlation is found between Na mobility and the number of hops from one coordination site to another. Besides ether oxygens, Na ions in the ionomer also use the anion and the edge of the cluster as hopping sites. The string-like structure of clusters provide less stable sites at the two ends thus ions are more mobile in those regions. We observed Grotthus like mechanism in our ionomer, in which the positive charge migrates within the string-like cluster without the cations actually moving.

Mechanisms of Alizarin Red S and Methylene blue biosorption onto olive stone by-product: Isotherm study in single and binary systems.

PubMed

Albadarin, Ahmad B; Mangwandi, Chirangano

2015-12-01

The biosorption process of anionic dye Alizarin Red S (ARS) and cationic dye methylene blue (MB) as a function of contact time, initial concentration and solution pH onto olive stone (OS) biomass has been investigated. Equilibrium biosorption isotherms in single and binary systems and kinetics in batch mode were also examined. The kinetic data of the two dyes were better described by the pseudo second-order model. At low concentration, ARS dye appeared to follow a two-step diffusion process, while MB dye followed a three-step diffusion process. The biosorption experimental data for ARS and MB dyes were well suited to the Redlich-Peterson isotherm. The maximum biosorption of ARS dye, qmax = 16.10 mg/g, was obtained at pH 3.28 and the maximum biosorption of MB dye, qmax = 13.20 mg/g, was observed at basic pH values. In the binary system, it was indicated that the MB dye diffuses firstly inside the biosorbent particle and occupies the biosorption sites forming a monodentate complex and then the ARS dye enters and can only bind to untaken sites; forms a tridentate complex with OS active sites. Copyright © 2015 Elsevier Ltd. All rights reserved.

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

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

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

DOE PAGES

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.; ...

2017-07-07

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

Design of an allosterically modulated doxycycline and doxorubicin drug-binding protein.

PubMed

Schmidt, Karin; Gardill, Bernd R; Kern, Alina; Kirchweger, Peter; Börsch, Michael; Muller, Yves A

2018-05-14

The allosteric interplay between distant functional sites present in a single protein provides for one of the most important regulatory mechanisms in biological systems. While the design of ligand-binding sites into proteins remains challenging, this holds even truer for the coupling of a newly engineered binding site to an allosteric mechanism that regulates the ligand affinity. Here it is shown how computational design algorithms enabled the introduction of doxycycline- and doxorubicin-binding sites into the serine proteinase inhibitor (serpin) family member α1-antichymotrypsin. Further engineering allowed exploitation of the proteinase-triggered serpin-typical S-to-R transition to modulate the ligand affinities. These design variants follow strategies observed in naturally occurring plasma globulins that allow for the targeted delivery of hormones in the blood. By analogy, we propose that the variants described in the present study could be further developed to allow for the delivery of the antibiotic doxycycline and the anticancer compound doxorubicin to tissues/locations that express specific proteinases, such as bacterial infection sites or tumor cells secreting matrix metalloproteinases.

Roles of nonpolar and polar intermolecular interactions in the improvement of the drug loading capacity of PEO-b-PCL with increasing PCL content for two hydrophobic Cucurbitacin drugs.

PubMed

Patel, Sarthak K; Lavasanifar, Afsaneh; Choi, Phillip

2009-09-14

Molecular dynamics (MD) simulation was used to study the roles of nonpolar and polar intermolecular interactions in the improvement of the drug loading capacity of poly(ethylene oxide)-b-poly(epsilon-caprolactone) (PEO-b-PCL) with increasing PCL content for two water insoluble anticancer drugs: Cucurbitacin B (CuB) and Cucurbitacin I (CuI). In particular, random binary mixture models containing 10-12 wt % drug and remaining PEO-b-PCL with three different PCL/PEO (w/w) ratios (0.5, 1, and 2) were used to calculate their Flory-Huggins interaction parameters (chi). The MD simulation results show that, for both CuB and CuI, the computed chi decreases (i.e., affinity increases) with increasing PCL/PEO ratio. Such results are consistent with our experimental observation that increasing the PCL/PEO (w/w) ratio from 1 to 4.8 significantly increases the drug loading capacity of micelles formed by PEO-b-PCL for both drugs. Analysis of the energy data shows that increasing affinity (loading) at higher PCL/PEO ratio is attributed to the increase in favorable polar interactions and to the formation of additional hydrogen bonds (H-bonds) between the drugs and the PCL block rather than to the increase in the hydrophobic characteristics of the diblock copolymer as one would normally expect. In fact, the nonpolar intermolecular interactions became more unfavorable at higher PCL/PEO ratio. Analysis of the radial distribution functions of the model mixtures indicates that at high PCL/PEO ratio, multiple H-bond sites on the PCL block interacted with single H-bond sites on the drug molecules. However, at low PCL/PEO ratio, only single H-bonds formed between various H-bond sites on the drug molecules and those of the PCL and PEO blocks. It seems that formation of H-bonds between multiple H-bond sites on the PCL block and single H-bond sites on the drug molecules is responsible for inducing drug/PEO-b-PCL affinity. The finding also explains the experimental observation that release rates of both drugs decrease with increasing PCL/PEO ratio and that the decrease in the release rate of CuB is more pronounced than that of CuI. Our simulation results show that the number of H-bonds formed between CuB and the PCL block is much higher than that of CuI at high PCL/PEO ratio.

Instrumentation for single-dish observations with The Greenland Telescope

NASA Astrophysics Data System (ADS)

Grimes, Paul K.; Asada, K.; Blundell, R.; Burgos, R.; Chang, H.-H.; Chen, M. T.; Goldie, D.; Groppi, C.; Han, C. C.; Ho, P. T. P.; Huang, Y. D.; Inoue, M.; Kubo, D.; Koch, P.; Leech, J.; de Lera Acedo, E.; Martin-Cocher, P.; Nishioka, H.; Nakamura, M.; Matsushita, S.; Paine, S. N.; Patel, N.; Raffin, P.; Snow, W.; Sridharan, T. K.; Srinivasan, R.; Thomas, C. N.; Tong, E.; Wang, M.-J.; Wheeler, C.; Withington, S.; Yassin, G.; Zeng, L.-Z.

2014-07-01

The Greenland Telescope project will deploy and operate a 12m sub-millimeter telescope at the highest point of the Greenland i e sheet. The Greenland Telescope project is a joint venture between the Smithsonian As- trophysical Observatory (SAO) and the Academia Sinica Institute of Astronomy and Astrophysics (ASIAA). In this paper we discuss the concepts, specifications, and science goals of the instruments being developed for single-dish observations with the Greenland Telescope, and the coupling optics required to couple both them and the mm-VLBI receivers to antenna. The project will outfit the ALMA North America prototype antenna for Arctic operations and deploy it to Summit Station,1 a NSF operated Arctic station at 3,100m above MSL on the Greenland I e Sheet. This site is exceptionally dry, and promises to be an excellent site for sub-millimeter astronomical observations. The main science goal of the Greenland Telescope is to carry out millimeter VLBI observations alongside other telescopes in Europe and the Americas, with the aim of resolving the event horizon of the super-massive black hole at the enter of M87. The Greenland Telescope will also be outfitted for single-dish observations from the millimeter-wave to Tera-hertz bands. In this paper we will discuss the proposed instruments that are currently in development for the Greenland Telescope - 350 GHz and 650 GHz heterodyne array receivers; 1.4 THz HEB array receivers and a W-band bolometric spectrometer. SAO is leading the development of two heterodyne array instruments for the Greenland Telescope, a 48- pixel, 325-375 GHz SIS array receiver, and a 4 pixel, 1.4 THz HEB array receiver. A key science goal for these instruments is the mapping of ortho and para H2D+ in old protostellar ores, as well as general mapping of CO and other transitions in molecular louds. An 8-pixel prototype module for the 350 GHz array is currently being built for laboratory and operational testing on the Greenland Telescope. Arizona State University are developing a 650 GHz 256 pixel SIS array receiver based on the KAPPa SIS mixer array technology and ASIAA are developing 1.4 THz HEB single pixel and array receivers. The University of Cambridge and SAO are collaborating on the development of the CAMbridge Emission Line Surveyor (CAMELS), a W-band `on- hip' spectrometer instrument with a spectral resolution of R ~ 3000. CAMELS will consist of two pairs of horn antennas, feeding super conducting niobium nitride filter banks read by tantalum based Kinetic Inductance Detectors.

Nanoscale fabrication using single-ion impacts

NASA Astrophysics Data System (ADS)

Millar, Victoria; Pakes, Chris I.; Cimmino, Alberto; Brett, David; Jamieson, David N.; Prawer, Steven D.; Yang, Changyi; Rout, Bidhudutta; McKinnon, Rita P.; Dzurak, Andrew S.; Clark, Robert G.

2001-11-01

We describe a novel technique for the fabrication of nanoscale structures, based on the development of localized chemical modification caused in a PMMA resist by the implantation of single ions. The implantation of 2 MeV He ions through a thin layer of PMMA into an underlying silicon substrate causes latent damage in the resist. On development of the resist we demonstrate the formation within the PMMA layer of clearly defined etched holes, of typical diameter 30 nm, observed using an atomic force microscope employing a carbon nanotube SPM probe in intermittent-contact mode. This technique has significant potential applications. Used purely to register the passage of an ion, it may be a useful verification of the impact sites in an ion-beam modification process operating at the single-ion level. Furthermore, making use of the hole in the PMMA layer to perform subsequent fabrication steps, it may be applied to the fabrication of self-aligned structures in which surface features are fabricated directly above regions of an underlying substrate that are locally doped by the implanted ion. Our primary interest in single-ion resists relates to the development of a solid-state quantum computer based on an array of 31P atoms (which act as qubits) embedded with nanoscale precision in a silicon matrix. One proposal for the fabrication of such an array is by phosphorous-ion implantation. A single-ion resist would permit an accurate verification of 31P implantation sites. Subsequent metalisation of the latent damage may allow the fabrication of self-aligned metal gates above buried phosphorous atoms.

Intercepted signals for ionospheric science

NASA Astrophysics Data System (ADS)

Lind, F. D.; Erickson, P. J.; Coster, A. J.; Foster, J. C.; Marchese, J. R.; Berkowitz, Z.; Sahr, J. D.

2013-05-01

The ISIS array (Intercepted Signals for Ionospheric Science) is a distributed, coherent software radio array designed for the study of geospace phenomena by observing the scatter of ambient radio frequency (RF) signals. ISIS data acquisition and analysis is performed using the MIDAS-M platform (Millstone Data Acquisition System - Mobile). Observations of RF signals can be performed between HF and L-band using the Array nodes and appropriate antennas. The deployment of the Array focuses on observations of the plasmasphere boundary layer. We discuss the concept of the coherent software radio array, describe the ISIS hardware, and give examples of data from the system for selected applications. In particular, we include the first observations of E region irregularities using the Array. We also present single-site passive radar observations of both meteor trails and E region irregularities using adaptive filtering techniques.

Landscape models of brook trout abundance and distribution in lotic habitat with field validation

USGS Publications Warehouse

McKenna, James E.; Johnson, James H.

2011-01-01

Brook trout Salvelinus fontinalis are native fish in decline owing to environmental changes. Predictions of their potential distribution and a better understanding of their relationship to habitat conditions would enhance the management and conservation of this valuable species. We used over 7,800 brook trout observations throughout New York State and georeferenced, multiscale landscape condition data to develop four regionally specific artificial neural network models to predict brook trout abundance in rivers and streams. Land cover data provided a general signature of human activity, but other habitat variables were resistant to anthropogenic changes (i.e., changing on a geological time scale). The resulting models predict the potential for any stream to support brook trout. The models were validated by holding 20% of the data out as a test set and by comparison with additional field collections from a variety of habitat types. The models performed well, explaining more than 90% of data variability. Errors were often associated with small spatial displacements of predicted values. When compared with the additional field collections (39 sites), 92% of the predictions were off by only a single class from the field-observed abundances. Among “least-disturbed” field collection sites, all predictions were correct or off by a single abundance class, except for one where brown trout Salmo trutta were present. Other degrading factors were evident at most sites where brook trout were absent or less abundant than predicted. The most important habitat variables included landscape slope, stream and drainage network sizes, water temperature, and extent of forest cover. Predicted brook trout abundances were applied to all New York streams, providing a synoptic map of the distribution of brook trout habitat potential. These fish models set benchmarks of best potential for streams to support brook trout under broad-scale human influences and can assist with planning and identification of protection or rehabilitation sites.

Probing depth, attachment loss and gingival recession. Findings from a clinical examination in Ushiku, Japan.

PubMed

Yoneyama, T; Okamoto, H; Lindhe, J; Socransky, S S; Haffajee, A D

1988-10-01

The present investigation describes probing pocket depth, probing attachment level and recession data from 319 randomly selected subjects, aged 20-79 years, from Ushiku, Japan. The findings are reported as mean values, frequency distributions and percentile plots of the 3 parameters at buccal, interproximal and lingual surfaces of single rooted (incisors, canines, premolars) and molar teeth. Inter-as well as intra-examiner errors for probing pocket depth and probing attachment levels were assessed and found to be small. The data reported revealed that practically all subjects studied had one or more sites in the dentition affected by destructive periodontal disease and that the severity of disease increased with age. It was further observed that in each age group, molars had suffered more attachment loss than single rooted teeth and that the interproximal surfaces as a rule had lost more periodontal tissue support than corresponding buccal and lingual surfaces. The attachment loss difference observed between different surfaces of a given tooth or a group of teeth, however, was comparatively small. In the age groups between 20-59 years, advanced destructive periodontal disease was found in a small subgroup of the subject sample, while after the age of 60 years, widespread destructive periodontitis was common. An attempt was made to examine the progression of destructive disease with age by comparing the frequency distributions of sites with attachment loss of greater than or equal to 3 mm in subjects of different age groups. The data suggested that in younger subject groups, progression was confined to a subset of individuals, while in older age groups, more subjects and sites became involved. A major feature of destructive periodontal disease in older individuals was the accompaniment of attachment loss with recession at the gingival margin. Deep pockets were relatively infrequently detected, while advanced loss of attachment (with recession) occurred at many sites.

Lability and Basicity of Bipyridine-Carboxylate-Phosphonate Ligand Accelerate Single-Site Water Oxidation by Ruthenium-Based Molecular Catalysts

DOE PAGES

Shaffer, David W.; Xie, Yan; Szalda, David J.; ...

2017-09-24

Here, a critical step in creating an artificial photosynthesis system for energy storage is designing catalysts that can thrive in an assembled device. Single-site catalysts have an advantage over bimolecular catalysts because they remain effective when immobilized. Hybrid water oxidation catalysts described here, combining the features of single-site bis-phosphonate catalysts and fast bimolecular bis-carboxylate catalysts, have reached turnover frequencies over 100 s –1, faster than both related catalysts under identical conditions. The new [(bpHc)Ru(L) 2] (bpH 2cH = 2,2'-bipyridine-6-phosphonic acid-6'-carboxylic acid, L = 4-picoline or isoquinoline) catalysts proceed through a single-site water nucleophilic attack pathway. The pendant phosphonate base mediatesmore » O–O bond formation via intramolecular atom-proton transfer with a calculated barrier of only 9.1 kcal/mol. Additionally, the labile carboxylate group allows water to bind early in the catalytic cycle, allowing intramolecular proton-coupled electron transfer to lower the potentials for oxidation steps and catalysis. That a single-site catalyst can be this fast lends credence to the possibility that the oxygen evolving complex adopts a similar mechanism.« less

Lability and Basicity of Bipyridine-Carboxylate-Phosphonate Ligand Accelerate Single-Site Water Oxidation by Ruthenium-Based Molecular Catalysts

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

Shaffer, David W.; Xie, Yan; Szalda, David J.

Here, a critical step in creating an artificial photosynthesis system for energy storage is designing catalysts that can thrive in an assembled device. Single-site catalysts have an advantage over bimolecular catalysts because they remain effective when immobilized. Hybrid water oxidation catalysts described here, combining the features of single-site bis-phosphonate catalysts and fast bimolecular bis-carboxylate catalysts, have reached turnover frequencies over 100 s –1, faster than both related catalysts under identical conditions. The new [(bpHc)Ru(L) 2] (bpH 2cH = 2,2'-bipyridine-6-phosphonic acid-6'-carboxylic acid, L = 4-picoline or isoquinoline) catalysts proceed through a single-site water nucleophilic attack pathway. The pendant phosphonate base mediatesmore » O–O bond formation via intramolecular atom-proton transfer with a calculated barrier of only 9.1 kcal/mol. Additionally, the labile carboxylate group allows water to bind early in the catalytic cycle, allowing intramolecular proton-coupled electron transfer to lower the potentials for oxidation steps and catalysis. That a single-site catalyst can be this fast lends credence to the possibility that the oxygen evolving complex adopts a similar mechanism.« less

Long-Term Oceanographic Observations in Western Massachusetts Bay Offshore of Boston, Massachusetts: Data Report for 1989-2002

USGS Publications Warehouse

Butman, Bradford; Bothner, Michael H.; Alexander, P. Soupy; Lightsom, Frances L.; Martini, Marinna A.; Gutierrez, Benjamin T.; Strahle, William S.

2004-01-01

This data report presents long-term oceanographic observations made in western Massachusetts Bay at two locations: (1) 42 deg 22.6' N., 70 deg 47.0' W. (Site A, 33 m water depth) from December 1989 through December 2002 (figure 1), and (2) 42 deg 9.8' N., 70 deg 38.4' W. (Site B, 21 m water depth) from October 1997 through December 2002. Site A is approximately 1 km south of the new ocean outfall that began discharging treated sewage effluent from the Boston metropolitan area into Massachusetts Bay on September 6, 2000. These long-term oceanographic observations have been collected by the U.S. Geological Survey (USGS) in partnership with the Massachusetts Water Resources Authority (MWRA) and with logistical support from the U.S. Coast Guard (USCG - http://www.uscg.mil). This report presents time series data through December 2002, updating a similar report that presented data through December 2000 (Butman and others, 2002). In addition, the Statistics and Mean Flow sections include some new plots and tables and the format of the report has been streamlined by combining yearly figures into single .pdfs. Figure 1 (PDF format) The long-term measurements are planned to continue at least through 2005. The long-term oceanographic observations at Sites A and B are part of a USGS study designed to understand the transport and long-term fate of sediments and associated contaminants in the Massachusetts bays. (See http://woodshole.er.usgs.gov/project-pages/bostonharbor/ and Butman and Bothner, 1997.) The long-term observations document seasonal and inter-annual changes in currents, hydrography, and suspended-matter concentration in western Massachusetts Bay, and the importance of infrequent catastrophic events, such as major storms or hurricanes, in sediment resuspension and transport. They also provide observations for testing numerical models of circulation. This data report presents a description of the field program and instrumentation, an overview of the data through summary plots and statistics, and the data in NetCDF and ASCII format for the period December 1989 through December 2002 for Site A and October 1997 through December 2002 for Site B. The objective of this report is to make the data available in digital form and to provide summary plots and statistics to facilitate browsing of the long-term data set.

Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices

PubMed Central

Sriram, K. K.; Yeh, Jia-Wei; Lin, Yii-Lih; Chang, Yi-Ren; Chou, Chia-Fu

2014-01-01

Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites. PMID:24753422

A density functional theory for association of fluid molecules with a functionalized surface: fluid-wall single and double bonding.

PubMed

Haghmoradi, Amin; Wang, Le; Chapman, Walter G

2017-02-01

In this manuscript we extend Wertheim's two-density formalism beyond its first order to model a system of fluid molecules with a single association site close to a planar hard wall with association sites on its surface in a density functional theory framework. The association sites of the fluid molecules are small enough that they can form only one bond, while the wall association sites are large enough to bond with more than one fluid molecule. The effects of temperature and of bulk fluid and wall site densities on the fluid density profile, extent of association, and competition between single and double bonding of fluid segments at the wall sites versus distance from the wall are presented. The theory predictions are compared with new Monte Carlo simulation results and they are in good agreement. The theory captures the surface coverage over wide ranges of temperature and bulk density by introducing the effect of steric hindrance in fluid association at a wall site.

Polarization Observations with the Cosmic Background Imager

NASA Astrophysics Data System (ADS)

Cartwright, J. K.; Padin, S.; Pearson, T. J.; Readhead, A. C. S.; Shepherd, M. C.; Taylor, G. B.

2000-12-01

The linear polarization of the Cosmic Microwave Background Radiation is a fundamental prediction of the standard model. We report a limit on the polarization of the CMBR for l ~660. This limit was obtained with the Cosmic Background Imager, a 13 element interferometer which operates in the 26-36 GHz band from a site at 5000m in northern Chile. The array consists of 90-cm Cassegrain antennas mounted on a single, fully steerable platform; this platform can be rotated about the optical axis to facilitate polarization observations. The CBI employs single mode circularly polarized receivers, of which 12 are configured for LCP and one is configured for RCP. The 12 cross polarized baselines sample multipoles from l ~600 to l ~3500. The instrumental polarization of the CBI was calibrated with observations of 3C279, a bright polarized source which is unresolved by the CBI. Because the centimeter flux of 3C279 is variable, it was monitored twice per month for 8 months in '00 with the VLA at 22 and 43 GHz. These observations also established the stability of the polarization characteristics of the CBI. This work was made possible by NSF grant AST-9802989

The role of a low Earth orbiter in intercontinental time synchronization via GPS satellites

NASA Technical Reports Server (NTRS)

Wu, S. C.; Ondrasik, V. J.

1985-01-01

Time synchronization between two sites using differential GPS has been investigated by a number of researchers. When the two sites are widely separated, the common view period of any GPS satellite becomes shorter; low elevation observations are inevitable. This increase the corrupting effects of the atmospheric delay and, at the same time, narrows the window for such time synchronization. This difficulty can be alleviated by synchronization. This difficulty can be alleviated by using a transit site located midway between the two main sites. The main sites can now look at different GPS satellites which are also in view at the transit site. However, a ground transit site may not always be conveniently available, especially across the Pacific Ocean; also, the inclusion of a ground transit site introduce additional errors due to its location error and local atmospheric delay. An alternative is to use a low Earth orbiter (LEO) as the transit site. A LEO is superior to a ground transit site in three ways: (1) It covers a large part of the Earth in a short period of time and, hence, a single LEO provides worldwide transit services; (2) it is above the troposphere and thus its inclusion does not introduce additional tropospheric delay error; and (3) it provides strong dynamics needed to improve GPS satellite positions which are of importance to ultraprecise time synchronization.

A Comprehensive Study of Formic Acid Oxidation on Palladium Nanocrystals with Different Types of Facets and Twin Defects

DOE PAGES

Choi, Sang-Il; Herron, Jeffrey A.; Scaranto, Jessica; ...

2015-04-13

Palladium has been recognized as the best anodic, monometallic electrocatalyst for the formic acid oxidation (FAO) reaction in a direct formic acid fuel cell. Here we report a systematic study of FAO on a variety of Pd nanocrystals, including cubes, right bipyramids, octahedra, tetrahedra, decahedra, and icosahedra. These nanocrystals were synthesized with approximately the same size, but different types of facets and twin defects on their surfaces. Our measurements indicate that the Pd nanocrystals enclosed by {100} facets have higher specific activities than those enclosed by {111} facets, in agreement with prior observations for Pd single-crystal substrates. If comparing nanocrystalsmore » predominantly enclosed by a specific type of facet, {100} or {111}, those with twin defects displayed greatly enhanced FAO activities compared to their single-crystal counterparts. To rationalize these experimental results, we performed periodic, self-consistent DFT calculations on model single-crystal substrates of Pd, representing the active sites present in the nanocrystals used in the experiments. The calculation results suggest that the enhancement of FAO activity on defect regions, represented by Pd(211) sites, compared to the activity of both Pd(100) and Pd(111) surfaces, could be attributed to an increased flux through the HCOO-mediated pathway rather than the COOH-mediated pathway on Pd(211). Since COOH has been identified as a precursor to CO, a site-poisoning species, a lower coverage of CO at the defect regions will lead to a higher activity for the corresponding nanocrystal catalysts, containing those defect regions.« less

The exceptional recent warming signal in a long-term central-German observation site

NASA Astrophysics Data System (ADS)

Hoy, Andreas; Schönwiese, Christian-Dietrich

2017-04-01

The long-term temperature measurements of Frankfurt/Main represent a scientifically highly valuable source for investigating climatic changes in central Germany and beyond. Annual data are available since 1758 and daily observations since 1870. The 258 year long annual time series is homogenised and recalculated to the airport location outside of Frankfurt/Main city. In a first step, impacts of site changes and urbanisation effects are discussed comparing the five different inner-city monitoring points and the airport location after WWII. We show that site changes affect both extreme and average temperatures, and that they may be considerable even for small relocations. Urbanisation effects are visible all year long and stronger for minimum than maximum temperatures. Annual temperature observations show slightly decreasing temperatures until the 1840s. This development is then replaced by an increasing trend overlain by decadal-scale and yearly fluctuations. Nevertheless, until the 1980s shifting 30-year-means only fluctuate between 8.54 °C in 1829-1858 and 9.58 °C in 1948-1977. However, recent years more than doubled the 1 K spread between the coldest and warmest period, with an average of 10.82 °C in 1986-2015. In addition, this 30-year period was warmer than any single year before 1990. Record-cold calendar days almost disappeared since 1988, while record-warm calendar days appeared about three times more often than statistically expectable. Strong warming was observed year-round, only September and October showed more moderate trends.

Different enzyme kinetic models.

PubMed

Seibert, Eleanore; Tracy, Timothy S

2014-01-01

As described in Chapter 2 , a large number of enzymatic reactions can be adequately described by Michaelis-Menten kinetics. The Michaelis-Menten equation represents a rectangular hyperbola, with a y-asymptote at the V max value. In many cases, more complex kinetic models are required to explain the observed data. Atypical kinetic profiles are believed to arise from the simultaneous binding of multiple molecules within the active site of the enzyme (Tracy and Hummel, Drug Metab Rev 36:231-242, 2004). Several cytochromes P450 have large active sites that enable binding of multiple molecules (Wester et al. J Biol Chem 279:35630-35637, 2004; Yano et al. J Biol Chem 279:38091-38094, 2004). Thus, atypical kinetics are not uncommon in in vitro drug metabolism studies. This chapter covers enzyme kinetic reactions in which a single enzyme has multiple binding sites for substrates and/or inhibitors as well as reactions catalyzed by multiple enzymes.

Temporal Stability of the Human Skin Microbiome.

PubMed

Oh, Julia; Byrd, Allyson L; Park, Morgan; Kong, Heidi H; Segre, Julia A

2016-05-05

Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states. Copyright © 2016 Elsevier Inc. All rights reserved.

Sidescan backscatter variations of cold seeps on the Hikurangi Margin (New Zealand): indications for different stages in seep development

NASA Astrophysics Data System (ADS)

Dumke, Ines; Klaucke, Ingo; Berndt, Christian; Bialas, Jörg

2014-06-01

Cold seeps on the Hikurangi Margin off New Zealand exhibit various seabed morphologies producing different intensity patterns in sidescan backscatter images. Acoustic backscatter characteristics of 25 investigated seep sites fall into four distinct types characterised by variations in backscatter intensity, distribution and inferred structural heights. The types reflect different carbonate morphologies including up to 20-m-high structures (type 1), low-relief crusts (type 2), scattered blocks (type 3) and carbonate-free sites (type 4). Each seep corresponds to a single type; intermediates were not observed. This correlates well with published data on seep fauna at each site, with the four types representing three different faunal habitats of successive stages of seep development. Backscatter signatures in sidescan sonar images of cold seeps may therefore serve as a convenient proxy for variations in faunal habitats.

Hydrocarbon Mineralization in Sediments and Plasmid Incidence in Sediment Bacteria from the Campeche Bank

PubMed Central

Leahy, Joseph G.; Somerville, Charles C.; Cunningham, Kelly A.; Adamantiades, Grammenos A.; Byrd, Jeffrey J.; Colwell, Rita R.

1990-01-01

Rates of degradation of radiolabeled hydrocarbons and incidence of bacterial plasmid DNA were investigated in sediment samples collected from the Campeche Bank, Gulf of Mexico, site of an offshore oil field containing several petroleum platforms. Overall rates of mineralization of [14C]hexadecane and [14C]phenanthrene measured for sediments were negligible; <1% of the substrate was converted to CO2 in all cases. Low mineralization rates are ascribed to nutrient limitations and to lack of adaptation by microbial communities to hydrocarbon contaminants. Plasmid frequency data for sediment bacteria similarly showed no correlation with proximity to the oil field, but, instead, showed correlation with water column depth at each sampling site. Significant differences between sites were observed for proportion of isolates carrying single or multiple plasmids and mean number of plasmids per isolate, each of which increased as a function of depth. PMID:16348204

KH2PO4 single crystals activated with the Ti4+ ions in the form of TiO2-x × nH2O nanoparticles: Structural peculiarities, point defects, and dielectric properties

NASA Astrophysics Data System (ADS)

Kuz'micheva, Galina M.; Timaeva, Olesya I.; Kaurova, Irina A.; Svetogorov, Roman D.; Mühlbauer, Martin J.

2018-03-01

Potassium dihydrogen phosphate KH2PO4 (KDP) single crystals activated with Ti4+ ions in the form of TiO2-x × nH2O nanoparticles in the η-phase, synthesized by the sulfate method using TiOSO4 × xH2SO4 × yH2O, have been first grown by the temperature lowering method and cut from pyramidal (P) and prismatic (Pr) growth sectors. The first-performed neutron powder diffraction investigation of P and Pr samples cut from the KDP:Ti4+ crystal allowed us to reveal vacancies in the K and H sites for both samples, their number being larger in the Pr structure compared to the P one. Taking into account the deficiency of the K and H sites, full occupation of the O site, presence of Ti4+ ions in the structure, and the electroneutrality condition, a partial substitution of (PO4)3- anion by the (SO4)2- one, larger for the Pr sample, was observed. The real compositions of P and Pr samples, correlated with the cation-anion internuclear distances, were refined. The dielectric permittivity of the Pr sample was significantly lower than that of the P one; it decreases with decreasing K-O, P-O, and O...H distances and increasing deficiency of the K and H sites.

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

PubMed Central

2012-01-01

Background Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. Results The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Conclusions Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family. PMID:22793672

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

PubMed

Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

Low cycle fatigue of MAR-M 200 single crystals at 760 and 870 deg C

NASA Technical Reports Server (NTRS)

Milligan, W. W.; Jayaraman, N.; Bill, R. C.

1984-01-01

Fully reversed low cycle fatigue tests were conducted on single crystals of the nickel-base superalloys Mar-M 200 at 760 C and 870 C. At 760 C, planar slip (octahedral) lead to orientation-dependent strain hardening and cyclic lives. Multiple slip crystals strain hardened the most, resulting in relatively high stress ranges and low lives. Single slip crystals strain hardened the least, resulting in relatively low stress ranges and higher lives. A preferential crack initiation site which was related to slip plane geometry was observed in single slip orientated crystals. At 870 C, the trends were quite different, and the slip character was much more homogeneous. As the tensile axis orientation deviated from 001 , the stress ranges increased and the cyclic lives decreased. Two possible mechanisms were proposed to explain the behavior: one is based on Takeuchi and Kuramoto's cube cross-slip model, and the other is based on orientation-dependent creep rates.

Multiphoton near-infrared femtosecond laser pulse-induced DNA damage with and without the photosensitizer proflavine.

PubMed

Shafirovich, V; Dourandin, A; Luneva, N P; Singh, C; Kirigin, F; Geacintov, N E

1999-03-01

The excitation of pBr322 supercoiled plasmid DNA with intense near-IR 810 nm fs laser pulses by a simultaneous multiphoton absorption mechanism results in single-strand breaks after treatment of the irradiated samples with Micrococcus luteus UV endonuclease. This enzyme cleaves DNA strands at sites of cyclobutane dimers that are formed by the simultaneous absorption of three (or more) 810 nm IR photons (pulse width approximately 140 fs, 76 MHz pulse repetition, average power output focused through 10x microscope objective is approximately 1.2 MW/cm2). Direct single-strand breaks (without treatment with M. luteus) were not observed under these conditions. However, in the presence of 6 microM of the intercalator proflavine (PF), both direct single- and double-strand breaks are observed under conditions where substantial fractions of undamaged supercoiled DNA molecules are still present. The fraction of direct double-strand breaks is 30 +/- 5% of all measurable strand cleavage events, is independent of dosage (up to 6.4 GJ/cm2) and is proportional to In, where I is the average power/area of the 810 nm fs laser pulses, and n = 3 +/- 1. The nicking of two DNA strands in the immediate vicinity of the excited PF molecules gives rise to this double-strand cleavage. In contrast, excitation of the same samples under low-power, single-photon absorption conditions (approximately 400-500 nm) gives rise predominantly to single-strand breaks, but some double-strand breaks are observed at the higher dosages. Thus, single-photon excitation with 400-500 nm light and multiphoton activation of PF by near-IR fs laser pulses produces different distributions of single- and double-strand breaks. These results suggest that DNA strand cleavage originates from unrelaxed, higher excited states when PF is excited by simultaneous IR multiphoton absorption processes.

SAW1 is required for SDSA double-strand break repair in S. cerevisiae.

PubMed

Diamante, Graciel; Phan, Claire; Celis, Angie S; Krueger, Jonas; Kelson, Eric P; Fischhaber, Paula L

2014-03-14

SAW1, coding for Saw1, is required for single-strand annealing (SSA) DNA double-strand break (DSB) repair in Saccharomycescerevisiae. Saw1 physically associates with Rad1 and Rad52 and recruits the Rad1-Rad10 endonuclease. Herein we show by fluorescence microscopy that SAW1 is similarly required for recruitment of Rad10 to sites of Synthesis-Dependent Strand Annealing (SDSA) and associates with sites of SDSA repair in a manner temporally overlapped with Rad10. The magnitude of induction of colocalized Saw1-CFP/Rad10-YFP/DSB-RFP foci in SDSA is more dramatic in S and G2 phase cells than in M phase, consistent with the known mechanism of SDSA. We observed a substantial fraction of foci in which Rad10 was localized to the repair site without Saw1, but few DSB sites that contained Saw1 without Rad10. Together these data are consistent with a model in which Saw1 recruits Rad1-Rad10 to SDSA sites, possibly even binding as a protein-protein complex, but departs the repair site in advance of Rad1-Rad10. Copyright © 2014 Elsevier Inc. All rights reserved.

Inter-seasonal maintenance of individual nest site preferences in hawksbill sea turtles.

PubMed

Kamel, Stephanie J; Mrosovsky, N

2006-11-01

Within a single population of hawksbill sea turtles (Eretmochelys imbricata), we found a behavioral polymorphism for maternal nest site choice with respect to beach microhabitat characteristics. Some females preferred to nest in littoral forest and in places with overstory vegetation cover, and others preferred to nest in more open, deforested areas. Nest site choice was consistent within and between nesting seasons two years apart. This was not a result of females simply returning to the same location along the shoreline; beach sections used by individual turtles varied between seasons. Nest site choice was not influenced by changes in beach environment (e.g., beach width and foliage cover) or by changes in females' reproductive output (e.g., clutch size), suggesting that fidelity to particular microhabitats is a major determinant of the observed nesting patterns. Because hawksbills exhibit temperature-dependent sex determination, if the behavioral polymorphism in nest site choice has a genetic basis, as is plausible, then this would have implications for sex ratio evolution and offspring survival. By taking an individual-based approach to the study of maternal behavior we reveal previously overlooked individual variation and hope to provide some impetus for more detailed studies of nest site choice.

Contaminant Residues in Demersal Fish, Invertebrates, and Deployed Mussels in Selected Areas of the Puget Sound, WA

DTIC Science & Technology

2007-03-29

meaningful decisions about cleanup of contaminated sediments and hazardous waste disposal sites, accurately assess and implement control of...invertebrate species, and dietary benchmarks were set to the No Observed Adverse Effect Level (NOAEL) for the consumption of prey by black ducks , ospreys...prey equal to NOAEL assuming 100% of diet obtained from single prey. Footnoted references cited in Sample et al. 1996. 6 Black duck (DBDuck) NOAEL

Organic and inorganic molecules as probes of mineral surfaces (Invited)

NASA Astrophysics Data System (ADS)

Sverjensky, D. A.

2010-12-01

Although the multi-site nature of mineral surfaces is to be expected based on the underlying crystal structure, definitive evidence of the need to use more than one site in modelling proton surface charge or adsorption of a single adsorbate at the mineral-water interface is lacking. Instead, a single-site approach affords a practical way of averaging over all possible crystal planes and sites in a powdered mineral sample. Extensive analysis of published proton surface charge and adsorption of metals on oxide mineral surfaces can be undertaken with a single site density for each mineral based on tritium exchange or estimation from averages of the site densities of likely exposed surfaces. Even in systems with competing metals (e.g. Cu and Pb on hematite), the same site density as used for proton surface charge can be employed depending on the reaction stoichiometry. All of this indicates that protons and metals can bind to a great variety of sites with the same overall site density. However, simple oxyanions such as carbonate, sulfate, selenate, arsenate and arsenite require a much lower site density for a given mineral. For example, on goethite these oxyanions utilize a site density that correlates with the BET surface area of the goethite. In this way, the oxyanions can be thought of as selectively probing the available sites on the mineral. The correlation probably arises because goethites with different BET surface areas have different proportions of singly and multiply-bonded oxygens, and only the singly-bonded oxygens are useful for inner-sphere surface complexation by the ligand exchange mechanism. Small organic molecules behave in a remarkably similar way. For example, adsorption of oxalate on goethite, and aspartate, glutamate, dihydroxyphenylalanine, lysine and arginine on rutile are all consistent with a much smaller site density than those required for metals such as calcium or neodymium. Overall, these results suggest that both inorganic oxyanions and organic molecules containing carboxylate functional groups serve as much more sensitive probes of the surface structures of minerals than do protons or metals.

Interaction between lysine 102 and aspartate 338 in the insect amino acid cotransporter KAAT1.

PubMed

Castagna, M; Soragna, A; Mari, S A; Santacroce, M; Betté, S; Mandela, P G; Rudnick, G; Peres, A; Sacchi, V F

2007-10-01

KAAT1 is a lepidopteran neutral amino acid transporter belonging to the NSS super family (SLC6), which has an unusual cation selectivity, being activated by K(+) and Li(+) in addition to Na(+). We have previously demonstrated that Asp338 is essential for KAAT1 activation by K(+) and for the coupling of amino acid and driver ion fluxes. By comparing sequences of NSS family members, site-directed mutagenesis, and expression in Xenopus laevis oocytes, we identified Lys102 as a residue likely to interact with Asp338. Compared with wild type, the single mutants K102V and D338E each showed altered leucine uptake and transport-associated currents in the presence of both Na(+) and K(+). However, in K102V/D338E double mutant, the K102V mutation reversed both the inhibition of Na(+)-dependent transport and the block in K(+)-dependent transport that characterize the D338E mutant. K(+)-dependent leucine currents were not observed in any mutants with D338E. In the presence of the oxidant Cu(II) (1,10-phenanthroline)(3), we observed specific and reversible inhibition of K102C/D338C mutant, but not of the corresponding single cysteine mutants, suggesting that these residues are sufficiently close to form a disulfide bond. Thus both structural and functional evidence suggests that these two residues interact. Similar results have been obtained mutating the bacterial transporter homolog TnaT. Asp338 corresponds to Asn286, a residue located in the Na(+) binding site in the recently solved crystal structure of the NSS transporter LeuT(Aa) (41). Our results suggest that Lys102, interacting with Asp338, could contribute to the spatial organization of KAAT1 cation binding site and permeation pathway.

Dynamics and associations of microbial community types across the human body.

PubMed

Ding, Tao; Schloss, Patrick D

2014-05-15

A primary goal of the Human Microbiome Project (HMP) was to provide a reference collection of 16S ribosomal RNA gene sequences collected from sites across the human body that would allow microbiologists to better associate changes in the microbiome with changes in health. The HMP Consortium has reported the structure and function of the human microbiome in 300 healthy adults at 18 body sites from a single time point. Using additional data collected over the course of 12-18 months, we used Dirichlet multinomial mixture models to partition the data into community types for each body site and made three important observations. First, there were strong associations between whether individuals had been breastfed as an infant, their gender, and their level of education with their community types at several body sites. Second, although the specific taxonomic compositions of the oral and gut microbiomes were different, the community types observed at these sites were predictive of each other. Finally, over the course of the sampling period, the community types from sites within the oral cavity were the least stable, whereas those in the vagina and gut were the most stable. Our results demonstrate that even with the considerable intra- and interpersonal variation in the human microbiome, this variation can be partitioned into community types that are predictive of each other and are probably the result of life-history characteristics. Understanding the diversity of community types and the mechanisms that result in an individual having a particular type or changing types, will allow us to use their community types to assess disease risk and to personalize therapies.

( sup 3 H)RO15-4513 binding to cerebellar diazepam-sensitive and insensitive GABAA receptors is unchanged by one week of ethanol intake

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

Martin, M.W.; Chen, J.P.; Wallis, C.

1992-02-26

({sup 3}H)RO15-4513, a partial inverse agonist at GABAA receptors, binds to two sites in cerebellar membranes, one sensitive (DZ-S) and one insensitive (DZ-IS) to inhibition by diazepam. These binding sites may represent different isoforms of the GABAA receptor and may play a role in ethanol (EtOH) dependence. The authors tested the hypothesis that chronic intake of EtOH induces changes in the binding properties of one or both of these putative GABBA receptors. Rats were fed a liquid diet of 4.5% EtOH for 7 d, gavaged with a 3g/kg dose of EtOH, and then sacrificed after 2 h, 12 h, ormore » 4.5 d. Binding of ({sup 3}H)RO15-4513 to cerebellar membranes was performed in the absence or presence of 10{mu}M diazepam (DZ-IS binding); DZ-S binding was calculated as the difference between total and DZ-IS. Nonlinear regression analysis showed that each class of binding site fit a model of mass action binding to a single, noninteractive population of sites. No significant difference was observed between any of the treatment groups in the apparent affinity (Kd) for ({sup 3}H)RO15-4513 at total, DZ-S, or DZ-IS sites following chronic EtOH intake or withdrawal. In addition, no significant difference was observed in the apparent number of DZ-S or DZ-IS binding sites or the ratio of DZ-S to DZ-IS.« less

Time-Series Spectroscopy and Photometry of the Helium Atmosphere Pulsating White Dwarf EC 20058-5234

NASA Astrophysics Data System (ADS)

Sullivan, D. J.

2017-03-01

We summarise both photometric and spectroscopic observations of the southern DBV white dwarf EC 20058-5234 (QU Tel) obtained primarily using a Magellan 6.5 m telescope. With the aim of identifying pulsation-induced spectral variations, the time-resolved 30 sMagellan spectra are phased using 54 h of contiguous time-series photometry obtained using the Mt John (NZ) 1.0 m telescope. A comparison of the DFTs obtained from a 1997 nine day multisite WET run and the two day single site Magellan observations is made. The difficulty of establishing a reliable surface temperatures for DBVs is mentioned.

Raman Spectroscopy of Rdx Single Crystals Under Static Compression

NASA Astrophysics Data System (ADS)

Dreger, Zbigniew A.; Gupta, Yogendra M.

2007-12-01

To gain insight into the high pressure response of energetic crystal of RDX, Raman measurements were performed under hydrostatic compression up to 15 GPa. Several distinct changes in the spectra were found at 4.0±0.3 GPa, confirming the α-γ phase transition previously observed in polycrystalline samples. Symmetry correlation analyses indicate that the γ-polymorph may assume a space group isomorphous with a point group D2h with eight molecules occupying the C1 symmetry sites, similar to the α-phase. It is proposed that factor group coupling can account for the observed increase in the number of modes in the γ-phase.

Earth Observing System Data Gateway

NASA Technical Reports Server (NTRS)

Pfister, Robin; McMahon, Joe; Amrhein, James; Sefert, Ed; Marsans, Lorena; Solomon, Mark; Nestler, Mark

2006-01-01

The Earth Observing System Data Gateway (EDG) software provides a "one-stop-shopping" standard interface for exploring and ordering Earth-science data stored at geographically distributed sites. EDG enables a user to do the following: 1) Search for data according to high-level criteria (e.g., geographic location, time, or satellite that acquired the data); 2) Browse the results of a search, viewing thumbnail sketches of data that satisfy the user s criteria; and 3) Order selected data for delivery to a specified address on a chosen medium (e.g., compact disk or magnetic tape). EDG consists of (1) a component that implements a high-level client/server protocol, and (2) a collection of C-language libraries that implement the passing of protocol messages between an EDG client and one or more EDG servers. EDG servers are located at sites usually called "Distributed Active Archive Centers" (DAACs). Each DAAC may allow access to many individual data items, called "granules" (e.g., single Landsat images). Related granules are grouped into collections called "data sets." EDG enables a user to send a search query to multiple DAACs simultaneously, inspect the resulting information, select browseable granules, and then order selected data from the different sites in a seamless fashion.

A new look at photometry of the Moon

USGS Publications Warehouse

Goguen, J.D.; Stone, T.C.; Kieffer, H.H.; Buratti, B.J.

2010-01-01

We use ROLO photometry (Kieffer, H.H., Stone, T.C. [2005]. Astron. J. 129, 2887-2901) to characterize the before and after full Moon radiance variation for a typical highlands site and a typical mare site. Focusing on the phase angle range 45??. ) to calculate the scattering matrix and solve the radiative transfer equation for I/. F. The mean single scattering albedo is ??=0.808, the asymmetry parameter is ???cos. ?????=0.77 and the phase function is very strongly peaked in both the forward and backward scattering directions. The fit to the observations for the highland site is excellent and multiply scattered photons contribute 80% of I/. F. We conclude that either model, roughness or multiple scattering, can match the observations, but that the strongly anisotropic phase functions of realistic particles require rigorous calculation of many orders of scattering or spurious photometric roughness estimates are guaranteed. Our multiple scattering calculation is the first to combine: (1) a regolith model matched to the measured particle size distribution and index of refraction of the lunar soil, (2) a rigorous calculation of the particle phase function and solution of the radiative transfer equation, and (3) application to lunar photometry with absolute radiance calibration. ?? 2010 Elsevier Inc.

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

PubMed Central

Pott, Sebastian

2017-01-01

Gaining insights into the regulatory mechanisms that underlie the transcriptional variation observed between individual cells necessitates the development of methods that measure chromatin organization in single cells. Here I adapted Nucleosome Occupancy and Methylome-sequencing (NOMe-seq) to measure chromatin accessibility and endogenous DNA methylation in single cells (scNOMe-seq). scNOMe-seq recovered characteristic accessibility and DNA methylation patterns at DNase hypersensitive sites (DHSs). An advantage of scNOMe-seq is that sequencing reads are sampled independently of the accessibility measurement. scNOMe-seq therefore controlled for fragment loss, which enabled direct estimation of the fraction of accessible DHSs within individual cells. In addition, scNOMe-seq provided high resolution of chromatin accessibility within individual loci which was exploited to detect footprints of CTCF binding events and to estimate the average nucleosome phasing distances in single cells. scNOMe-seq is therefore well-suited to characterize the chromatin organization of single cells in heterogeneous cellular mixtures. DOI: http://dx.doi.org/10.7554/eLife.23203.001 PMID:28653622

Examination about the Spatial Representation of PM2.5 Obtained from Limited Stations Using a Network Observation

NASA Astrophysics Data System (ADS)

Shi, X.; Zhao, C.

2017-12-01

Haze aerosol pollution has been a focus issue in China, and its characteristics is highly demanded. With limited observation sites, aerosol properties obtained from a single site is frequently used to represent the haze condition over a large domain, such as tens of kilometers. This could result in high uncertainties in the haze characteristics due to their spatial variation. Using a network observation from November 2015 to February 2016 over an urban city in North China with high spatial resolution, this study examines the spatial representation of ground site observations. A method is first developed to determine the representative area of measurements from limited stations. The key idea of this method is to determine the spatial variability of particulate matter with diameters less than 2.5 μm (PM2.5) concentration using a variance function in 2km x 2km grids. Based on the high spatial resolution (0.5km x 0.5km) measurements of PM2.5, the grids in which PM2.5 have high correlations and weak value differences are determined as the representation area of measurements at these grids. Note that the size representation area is not exactly a circle region. It shows that the size representation are for the study region and study period ranges from 0.25 km2 to 16.25 km2. The representation area varies with locations. For the 20 km x 20 km study region, 10 station observations would have a good representation of the PM2.5 observations obtained from current 169 stations at the four-month time scale.

Biogeographical distribution of Rimicaris exoculata resident gut epibiont communities along the Mid-Atlantic Ridge hydrothermal vent sites.

PubMed

Durand, Lucile; Roumagnac, Marie; Cueff-Gauchard, Valérie; Jan, Cyrielle; Guri, Mathieu; Tessier, Claire; Haond, Marine; Crassous, Philippe; Zbinden, Magali; Arnaud-Haond, Sophie; Cambon-Bonavita, Marie-Anne

2015-10-01

Rimicaris exoculata is a deep-sea hydrothermal vent shrimp whose enlarged gill chamber houses a complex trophic epibiotic community. Its gut harbours an autochthonous and distinct microbial community. This species dominates hydrothermal ecosystem megafauna along the Mid-Atlantic Ridge, regardless of contrasting geochemical conditions prevailing in them. Here, the resident gut epibiont community at four contrasted hydrothermal vent sites (Rainbow, TAG, Logatchev and Ashadze) was analysed and compiled with previous data to evaluate the possible influence of site location, using 16S rRNA surveys and microscopic observations (transmission electron microscopy, scanning electron microscopy and fluorescence in situ hybridization analyses). Filamentous epibionts inserted between the epithelial cell microvilli were observed on all examined samples. Results confirmed resident gut community affiliation to Deferribacteres, Mollicutes, Epsilonproteobacteria and to a lesser extent Gammaproteobacteria lineages. Still a single Deferribacteres phylotype was retrieved at all sites. Four Mollicutes-related operational taxonomic units were distinguished, one being only identified on Rainbow specimens. The topology of ribotype median-joining networks illustrated a community diversification possibly following demographic expansions, suggesting a more ancient evolutionary history and/or a larger effective population size at Rainbow. Finally, the gill chamber community distribution was also analysed through ribotype networks based on sequences from R. exoculata collected at the Rainbow, Snake Pit, TAG, Logatchev and Ashadze sites. Results allow the refining of hypotheses on the epibiont role and transmission pathways. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

QSAR and molecular graphics analysis of N2-phenylguanines as inhibitors of herpes simplex virus thymidine kinases.

PubMed

Gaudio, A C; Richards, W G; Takahata, Y

2000-02-01

A quantitative structure-activity relationship study of N2-(substituted)-phenylguanines (PHG) as inhibitors of herpes simplex virus thymidine kinase (HSV TK) was performed. The activity of a set of PHG derivatives were analyzed against the thymidine kinase of herpes simplex virus types 1 (HSV1 TK) and 2 (HSV2 TK). Classic and calculated physicochemical parameters were included in the analysis. The results showed that there is an important difference in the activity of the meta substituted PHG derivatives against HSV1 TK and HSV2 TK. The activity of the meta derivatives against HSV2 TK is influenced by a steric effect, which is not observed against HSV1 TK. The superposition of the three-dimensional structures of the active sites of HSV1 TK (crystal structure) and HSV2 TK (homology model) revealed that the amino acid Ile97 is located near the meta position in the HSV1 TK active site, whereas the amino acid Leu97 is located near the meta position in the HSV2 TK active site. This single difference in the active sites of both enzymes can explain the source of the steric effect and serves as an indication that our previously proposed binding mode for the PHG derivatives is plausible. However, another observed mutation in the active site region, Ala168 by Ser168, suggests that an alternative binding mode, similar to that of ganciclovir, could be possible.

Intermittent turbulence events observed with a sonic anemometer and minisodar during CASES99.

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

Coulter, R. L.; Doran, J. C.

The Cooperative Air Surface Exchange Study 1999 (CASES99), designed to investigate in detail the nocturnal boundary layer (NBL) of the atmosphere with particular emphasis on turbulence and turbulence events, took place during October 1999, within the Atmospheric Boundary Layer Experiments (ABLE) region east of Wichita KS. The principal measurement site was a heavily instrumented 2-km square located near Leon (LE), KS, but additional sites at Smileyberg (SM) and Beaumont (BE) were also used. The authors augmented the normal ABLE measurements at Beaumont (radar wind profiler, minisodar, 10-m meteorological tower, precipitation gauge) with a sonic anemometer mounted on the tower, 7more » m above the surface. For this campaign, the minisodar data were saved in single-pulse mode with no averaging. The Beaumont site is within gently rolling rangeland used primarily for grazing. The site is on a flat plain rising gradually to the east.The Flint Hills escarpment, located approximately 2 km to the east, marks the highest point in, and the eastern boundary of, the Walnut River watershed. Although most terrain features are subtle, terrain effects on atmospheric flows are still possible, particularly in stable conditions. The intent was to observe turbulence and, hopefully, turbulence events with the sonic anemometer and minisodar. The horizontal extent of these occurrences can be studied by including the Beaumont data with those obtained at the Leon site. In this report the authors are concerned with the occurrence of intermittent turbulence.« less

Reducing inpatient heritable thrombophilia testing using a clinical decision-making tool.

PubMed

Smith, Tyler W; Pi, David; Hudoba, Monika; Lee, Agnes Y Y

2014-04-01

To evaluate the impact of a clinical decision-making tool, designed to educate physicians regarding heritable thrombophilia (HT) testing, on the volume of testing in hospitalised patients in the tertiary care setting. We performed a retrospective cohort study over a 6-year period (2007-2012) at a single tertiary care centre intervention site and two regional control sites. In January 2010, the intervention site instituted a policy change whereby physicians ordering HT testing on inpatients needed to complete a pre-preprinted order (PPO) form that outlined the limitations of HT testing in the hospitalised setting. Failure to complete the PPO within 24 h resulted in test cancellation. Our main outcome measure was the volume of HT testing performed at the three study sites. Introduction of the PPO resulted in a 79.4% (95% CI 71.2% to 87.6%) reduction in factor V Leiden (FVL) testing at the intervention site. This decrease was significantly greater compared with those in the two control teaching hospitals over the same time periods (33.7% and 43.6%; both p<0.001). Reductions in FVL testing postintervention were observed among all ordering specialists. Similar postintervention reductions in testing volumes were observed for antithrombin (57.4%), protein C (61.9%) and protein S (62.2%) activity assays. In a large tertiary care hospital, the introduction of a clinical decision-making tool significantly reduced HT testing in inpatients across clinical specialties. The impact on patient outcome should be assessed in further studies.

Dynamics and associations of microbial community types across the human body

PubMed Central

Ding, Tao; Schloss, Patrick D.

2014-01-01

A primary goal of the Human Microbiome Project (HMP) was to provide a reference collection of 16S rRNA gene sequences collected from sites across the human body that would allow microbiologists to better associate changes in the microbiome with changes in health 1. The HMP Consortium has reported the structure and function of the human microbiome in 300 healthy adults at 18 body sites from a single time point 2,3. Using additional data collected over the course of 12–18 months, we used Dirichlet multinomial mixture models 4 to partition the data into community types for each body site and made three important observations. First, there were strong associations between whether they had been breastfed as an infant, their gender, and their level of education with their community types at several body sites. Second, although the specific taxonomic compositions of the oral and gut microbiomes were different, the community types observed at these sites these sites were predictive of each other. Finally, over the course of the sampling period, the community types from sites within the oral cavity were the least stable, while those in the vagina and gut were the most stable. Our results demonstrate that even with the considerable intra- and inter-personal variation in the human microbiome, this variation can be partitioned into community types that are predictive of each other and are likely the result of life history characteristics. Understanding the diversity of community types and the mechanisms that result in an individual having a particular type or changing types, will allow us to use their community types to assess disease risk and to personalize therapies. PMID:24739969

Stabilization of bacterially expressed erythropoietin by single site-specific introduction of short branched PEG chains at naturally occurring glycosylation sites.

PubMed

Hoffmann, E; Streichert, K; Nischan, N; Seitz, C; Brunner, T; Schwagerus, S; Hackenberger, C P R; Rubini, M

2016-05-24

The covalent attachment of polyethylene glycol (PEG) to therapeutic proteins can improve their physicochemical properties. In this work we utilized the non-natural amino acid p-azidophenylalanine (pAzF) in combination with the chemoselective Staudinger-phosphite reaction to install branched PEG chains to recombinant unglycosylated erythropoietin (EPO) at each single naturally occurring glycosylation site. PEGylation with two short 750 or 2000 Da PEG units at positions 24, 38, or 83 significantly decreased unspecific aggregation and proteolytic degradation while biological activity in vitro was preserved or even increased in comparison to full-glycosylated EPO. This site-specific bioconjugation approach permits to analyse the impact of PEGylation at single positions. These results represent an important step towards the engineering of site-specifically modified EPO variants from bacterial expression with increased therapeutic efficacy.

Influence of implant neck design on facial bone crest dimensions in the esthetic zone analyzed by cone beam CT: a comparative study with a 5-to-9-year follow-up.

PubMed

Chappuis, Vivianne; Bornstein, Michael M; Buser, Daniel; Belser, Urs

2016-09-01

To examine the influence of two different neck designs on facial bone crest dimensions in esthetic single implant sites after a 5-to-9-year follow-up analyzed by cone beam computed tomography (CBCT). Sixty-one patients with an implant-borne single crown following early implant placement in the esthetic zone were enrolled. The test group consisted of a bone level (BL) neck design exhibiting a hydrophilic micro-rough surface combined with a platform-switching interface (PS) (n = 20). The control group comprised a soft tissue level (STL) neck design exhibiting a hydrophobic machined surface with a matching butt-joint interface (n = 41). Standardized clinical, radiologic, and esthetic parameters were applied. The facial bone crest dimensions were assessed by CBCT. Soft tissue parameters and pink esthetic scores yielded no significant differences between the two designs. Major differences were only observed at the implant shoulder level. The height of the facial bone crest for the BL design was located 0.2 mm above the implant shoulder level, whereas for the STL design, its location was 1.6 mm below. The width of the peri-implant saucer-like bone defect was reduced by 40% for the BL implant design. No differences were observed 2 mm below the shoulder level. The results of this comparative study suggest better crestal bone stability on the facial aspect of single implant sites in the esthetic zone for a BL design with a platform-switching concept when compared with STL implants with a butt-joint interface. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments

PubMed Central

Wichgers Schreur, Paul J.; Kortekaas, Jeroen

2016-01-01

The bunyavirus genome comprises a small (S), medium (M), and large (L) RNA segment of negative polarity. Although genome segmentation confers evolutionary advantages by enabling genome reassortment events with related viruses, genome segmentation also complicates genome replication and packaging. Accumulating evidence suggests that genomes of viruses with eight or more genome segments are incorporated into virions by highly selective processes. Remarkably, little is known about the genome packaging process of the tri-segmented bunyaviruses. Here, we evaluated, by single-molecule RNA fluorescence in situ hybridization (FISH), the intracellular spatio-temporal distribution and replication kinetics of the Rift Valley fever virus (RVFV) genome and determined the segment composition of mature virions. The results reveal that the RVFV genome segments start to replicate near the site of infection before spreading and replicating throughout the cytoplasm followed by translocation to the virion assembly site at the Golgi network. Despite the average intracellular S, M and L genome segments approached a 1:1:1 ratio, major differences in genome segment ratios were observed among cells. We also observed a significant amount of cells lacking evidence of M-segment replication. Analysis of two-segmented replicons and four-segmented viruses subsequently confirmed the previous notion that Golgi recruitment is mediated by the Gn glycoprotein. The absence of colocalization of the different segments in the cytoplasm and the successful rescue of a tri-segmented variant with a codon shuffled M-segment suggested that inter-segment interactions are unlikely to drive the copackaging of the different segments into a single virion. The latter was confirmed by direct visualization of RNPs inside mature virions which showed that the majority of virions lack one or more genome segments. Altogether, this study suggests that RVFV genome packaging is a non-selective process. PMID:27548280

Designing a Dy2 Single-Molecule Magnet with Two Well-Differentiated Relaxation Processes by Using a Nonsymmetric Bis-bidentate Bipyrimidine- N-Oxide Ligand: A Comparison with Mononuclear Counterparts.

PubMed

Díaz-Ortega, Ismael F; Herrera, Juan Manuel; Aravena, Daniel; Ruiz, Eliseo; Gupta, Tulika; Rajaraman, Gopalan; Nojiri, H; Colacio, Enrique

2018-06-04

Herein we report a dinuclear [(μ-mbpymNO){(tmh) 3 Dy} 2 ] (1) single-molecule magnet (SMM) showing two nonequivalent Dy III centers, which was rationally prepared from the reaction of Dy(tmh) 3 moieties (tmh = 2,2,6,6-tetramethyl-3,5-heptanedionate) and the asymmetric bis-bidentate bridging ligand 4-methylbipyrimidine (mbpymNO). Depending on whether the Dy III ions coordinate to the N^O or N^N bidentate donor sets, the Dy III sites present a NO 7 ( D 2 d geometry) or N 2 O 6 ( D 4 d ) coordination sphere. As a consequence, two different thermally activated magnetic relaxation processes are observed with anisotropy barriers of 47.8 and 54.7 K. Ab initio calculations confirm the existence of two different relaxation phenomena and allow one to assign the 47.8 and 54.7 K energy barriers to the Dy(N 2 O 6 ) and Dy(NO 7 ) sites, respectively. Two mononuclear complexes, [Dy(tta) 3 (mbpymNO)] (2) and [Dy(tmh) 3 (phenNO)] (3), have also been prepared for comparative purposes. In both cases, the Dy III center shows a NO 7 coordination sphere and SMM behavior is observed with U eff values of 71.5 K (2) and 120.7 K (3). In all three cases, ab initio calculations indicate that relaxation of the magnetization takes place mainly via the first excited-state Kramers doublet through Orbach, Raman, and thermally assisted quantum-tunnelling mechanisms. Pulse magnetization measurements reveal that the dinuclear and mononuclear complexes exhibit hysteresis loops with double- and single-step structures, respectively, thus supporting their SMM behavior.

Urban forms, physical activity and body mass index: a cross-city examination using ISS Earth Observation photographs

NASA Technical Reports Server (NTRS)

Lin, Ge

2005-01-01

Johnson Space Center has archived thousands of astronauts acquired Earth images. Some spectacular images have been widely used in news media and in k-12 class room, but their potential utilizations in health promotion and disease prevention have relatively untapped. The project uses daytime ISS photographs to define city forms and links them to city or metropolitan level health data in a multicity context. Road connectivity, landuse mix and Shannon's information indices were used in the classification of photographs. In contrast to previous remote-sensing studies, which tend to focus on a single city or a portion of a city, this project utilized photographs of 39 U.S. cities. And in contrast to previous health-promotion studies on the built environment, which tend to rely on survey respondents' responses to evaluate road connectivity or mixed land use for a single study site, the project examined the built environments of multiple cities based on ISS photos. It was found that road connectivity and landuse mix were not statistically significant by themselves, but the composite measure of the Shannon index was significantly associated with physical activity, but not BMI. Consequently, leisure-time physical activity seems to be positively associated with the urban complexity scale. It was also concluded that unless they are planned or designed in advance, photographs taken by astronauts generally are not appropriate for a study of a single-site built environment nor are they appropriate for a study of infectious diseases at a local scale. To link urban built environment with city-wide health indicators, both the traditional nadir view and oblique views should be emphasized in future astronauts' earth observation photographs.

Interim pressure garment therapy (4-6 mmHg) and its effect on donor site healing in burn patients: study protocol for a randomised controlled trial.

PubMed

Donovan, Michelle L; Muller, Michael J; Simpson, Claire; Rudd, Michael; Paratz, Jennifer

2016-04-26

Pressure garment therapy (PGT) is well accepted and commonly used by clinicians in the treatment of burns scars and grafts. The medium to high pressures (24-40 mmHg) in these garments can support scar minimisation, and evidence is well documented for this particular application. However, PGT specifically for burn donor sites, of which a sequela is also scarring, is not well documented. This study protocol investigates the impact of a low pressure (4-6 mmHg) interim garment on donor site healing and scarring. With a primary purpose of holding donor dressings in place, the application of the interim pressure garment (IPG) appears to have been twofold. IPGs for donor sites have involved inconsistent application with a focus on securing wound dressing rather than scar management. However, anecdotal and observational evidence suggests that IPGs also make a difference to some patient's scar outcomes for donor sites. This study protocol outlines a randomised controlled trial designed to test the effectiveness of this treatment on reducing scarring to burn donor sites. This study is a single-centre, single (assessor)-blinded, randomised control trial in patients with burns donor sites to their thighs. Patients will be randomly allocated to a control group (with no compression to donor sites) or to an experimental group (with compression to donor sites) as the comparative treatment. Groups will be compared at baseline regarding the important prognostic indicators: donor site location, depth, size, age, and time since graft (5 days). The IPG treatment will be administered post-operatively (on day 5). Follow-up assessments and garment replacement will be undertaken fortnightly for a period of 2 months. This study focuses on a unique area of burns scar management using a low-pressure tubular support garment for the reduction of donor site scars. Such therapy specifically for donor scar management is poorly represented in the literature. This study was designed to test a potentially cost-effective scar prevention for patients with donor sites to the thigh. No known studies of this nature have been carried out to date, and there is a need for rigorous clinical evidence for low-pressure support garments for donor site scar minimisation. Australian New Zealand Clinical Trials Registry identifier ACTRN12610000127000 . Registered 8 Mar 2010.

76 FR 5584 - City of Salem, OR; Notice of Competing Preliminary Permit Application Accepted for Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-01

... penstock intake at the powerhouse site; (2) a new powerhouse with a single turbine/generator unit at an... powerhouse site; (2) a new powerhouse with a single turbine/generator unit at an installed capacity of 0.5 MW... Franzen reservoir to the Fairmount reservoir; (2) a new powerhouse with a single turbine/ generator unit...

Luminescence properties of Y2O3:Bi3+, Yb3+ co-doped phosphor for application in solar cells

NASA Astrophysics Data System (ADS)

Lee, E.; Kroon, R. E.; Terblans, J. J.; Swart, H. C.

2018-04-01

Bismuth (Bi3+) and ytterbium (Yb3+) co-doped yttrium oxide (Y2O3) phosphor powder was successfully synthesised using the co-precipitation technique. The X-ray diffraction (XRD) patterns confirmed that a single phase cubic structure with a Ia-3 space group was formed. The visible emission confirmed the two symmetry sites, C2 and S6, found in the Y2O3 host material and revealed that Bi3+ ions preferred the S6 site as seen the stronger emission intensity. The near-infrared (NIR) emission of Yb3+ increased significantly by the presence of the Bi3+ ions when compared to the singly doped Y2O3:Yb3+ phosphor with the same Yb3+ concentration. An increase in the NIR emission intensity was also observed by simply increasing the Yb3+ concentration in the Y2O3:Bi3+, Yb3+ phosphor material where the intensity increased up to x = 5.0 mol% of Yb3+ before decreasing due to concentration quenching.

The Tetrodotoxin Receptor of Voltage-Gated Sodium Channels—Perspectives from Interactions with μ-Conotoxins

PubMed Central

French, Robert J.; Yoshikami, Doju; Sheets, Michael F.; Olivera, Baldomero M.

2010-01-01

Neurotoxin receptor site 1, in the outer vestibule of the conducting pore of voltage-gated sodium channels (VGSCs), was first functionally defined by its ability to bind the guanidinium-containing agents, tetrodotoxin (TTX) and saxitoxin (STX). Subsequent studies showed that peptide μ-conotoxins competed for binding at site 1. All of these natural inhibitors block single sodium channels in an all-or-none manner on binding. With the discovery of an increasing variety of μ-conotoxins, and the synthesis of numerous derivatives, observed interactions between the channel and these different ligands have become more complex. Certain μ-conotoxin derivatives block single-channel currents partially, rather than completely, thus enabling the demonstration of interactions between the bound toxin and the channel’s voltage sensor. Most recently, the relatively small μ-conotoxin KIIIA (16 amino acids) and its variants have been shown to bind simultaneously with TTX and exhibit both synergistic and antagonistic interactions with TTX. These interactions raise new pharmacological possibilities and place new constraints on the possible structures of the bound complexes of VGSCs with these toxins. PMID:20714429

Classical Swine Fever Virus Glycoprotein Erns Is an Endoribonuclease with an Unusual Base Specificity

PubMed Central

Hausmann, Yvonne; Roman-Sosa, Gleyder; Thiel, Heinz-Jürgen; Rümenapf, Till

2004-01-01

The glycoprotein Erns of pestiviruses is a virion-associated and -secreted RNase that is involved in virulence. The requirements at the cleavage site in heteropolymeric RNA substrates were studied for Erns. Limited digestion of heteropolymeric RNA substrates indicated a cleavage 5′ of uridine residues irrespective of the preceding nucleotide (Np/U). To further study specificity radiolabeled RNA, molecules of 45 to 56 nucleotides in length were synthesized that contained no or a single Np/U cleavage site. Cleavage was only observed in substrates containing an ApU, CpU, GpU, or UpU dinucleotide and occurred in two steps, an initial NpU-specific and a consecutive unspecific degradation. The NpU-specific cleavage was resistant to 7 M urea while the second-order cleavage was sensitive to denaturation. Kinetic analyses revealed that Erns is a highly active endoribonuclease (kcat/Km = 2 × 106 to 10 × 106 M−1 s−1) with a strong affinity to NpU containing single-stranded RNA substrates (Km = 85 to 260 nM). PMID:15113930

Functional Dynamics within the Human Ribosome Regulate the Rate of Active Protein Synthesis.

PubMed

Ferguson, Angelica; Wang, Leyi; Altman, Roger B; Terry, Daniel S; Juette, Manuel F; Burnett, Benjamin J; Alejo, Jose L; Dass, Randall A; Parks, Matthew M; Vincent, C Theresa; Blanchard, Scott C

2015-11-05

The regulation of protein synthesis contributes to gene expression in both normal physiology and disease, yet kinetic investigations of the human translation mechanism are currently lacking. Using single-molecule fluorescence imaging methods, we have quantified the nature and timing of structural processes in human ribosomes during single-turnover and processive translation reactions. These measurements reveal that functional complexes exhibit dynamic behaviors and thermodynamic stabilities distinct from those observed for bacterial systems. Structurally defined sub-states of pre- and post-translocation complexes were sensitive to specific inhibitors of the eukaryotic ribosome, demonstrating the utility of this platform to probe drug mechanism. The application of three-color single-molecule fluorescence resonance energy transfer (smFRET) methods further revealed a long-distance allosteric coupling between distal tRNA binding sites within ribosomes bearing three tRNAs, which contributed to the rate of processive translation. Copyright © 2015 Elsevier Inc. All rights reserved.

Functional dynamics within the human ribosome regulate the rate of active protein synthesis

PubMed Central

Ferguson, Angelica; Wang, Leyi; Altman, Roger B.; Terry, Daniel S.; Juette, Manuel F.; Burnett, Benjamin J.; Alejo, Jose L.; Dass, Randall A.; Parks, Matthew M.; Vincent, Theresa C.; Blanchard, Scott C.

2015-01-01

SUMMARY The regulation of protein synthesis contributes to gene expression in both normal physiology and disease, yet kinetic investigations of the human translation mechanism are currently lacking. Using single-molecule fluorescence imaging methods, we have quantified the nature and timing of structural processes in human ribosomes during single-turnover and processive translation reactions. These measurements reveal that functional complexes exhibit dynamic behaviors and thermodynamic stabilities distinct from those observed for bacterial systems. Structurally defined sub-states of pre- and post-translocation complexes were sensitive to specific inhibitors of the eukaryotic ribosome demonstrating the utility of this platform to probe drug mechanism. The application of three-color single-molecule FRET methods further revealed a long-distance allosteric coupling between distal tRNA binding sites within ribosomes bearing three tRNAs, which contributed to the rate of processive translation. PMID:26593721

Effects of He implantation on radiation induced segregation in Cu-Au and Ni-Si alloys

NASA Astrophysics Data System (ADS)

Iwase, A.; Rehn, L. E.; Baldo, P. M.; Funk, L.

Effects of He implantation on radiation induced segregation (RIS) in Cu-Au and Ni-Si alloys were investigated using in situ Rutherford backscattering spectrometry during simultaneous irradiation with 1.5-MeV He and low-energy (100 or 400-keV) He ions at elevated temperatures. RIS during single He ion irradiation, and the effects of pre-implantation with low-energy He ions, were also studied. RIS near the specimen surface, which was pronounced during 1.5-MeV He single-ion irradiation, was strongly reduced under low-energy He single-ion irradiation, and during simultaneous irradiation with 1.5-MeV He and low-energy He ions. A similar RIS reduction was also observed in the specimens pre-implanted with low-energy He ions. The experimental results indicate that the accumulated He atoms cause the formation of small bubbles, which provide additional recombination sites for freely migrating defects.

Bird migration flight altitudes studied by a network of operational weather radars.

PubMed

Dokter, Adriaan M; Liechti, Felix; Stark, Herbert; Delobbe, Laurent; Tabary, Pierre; Holleman, Iwan

2011-01-06

A fully automated method for the detection and quantification of bird migration was developed for operational C-band weather radar, measuring bird density, speed and direction as a function of altitude. These weather radar bird observations have been validated with data from a high-accuracy dedicated bird radar, which was stationed in the measurement volume of weather radar sites in The Netherlands, Belgium and France for a full migration season during autumn 2007 and spring 2008. We show that weather radar can extract near real-time bird density altitude profiles that closely correspond to the density profiles measured by dedicated bird radar. Doppler weather radar can thus be used as a reliable sensor for quantifying bird densities aloft in an operational setting, which--when extended to multiple radars--enables the mapping and continuous monitoring of bird migration flyways. By applying the automated method to a network of weather radars, we observed how mesoscale variability in weather conditions structured the timing and altitude profile of bird migration within single nights. Bird density altitude profiles were observed that consisted of multiple layers, which could be explained from the distinct wind conditions at different take-off sites. Consistently lower bird densities are recorded in The Netherlands compared with sites in France and eastern Belgium, which reveals some of the spatial extent of the dominant Scandinavian flyway over continental Europe.

Archaeal Diversity Associated with Deep Sea Whalefalls

NASA Astrophysics Data System (ADS)

Wilpiszeski, R.; Goffredi, S.; Turk, K.; Vrijenhoek, R.; House, C. H.; Orphan, V.

2005-12-01

Deep sea whale fall sites support a diverse population of organisms in an otherwise sparsely populated environment. While the macro- and megafauna of these ecosystems have been investigated in some detail, less is known about the nature of associated microbial populations. 16S rRNA gene surveys were used to evaluate the diversity of Archaea in the sediment below one such whale fall at 2800 m water depth and at a nearby control site. A variety of Archaea were identified, including diverse uncultured marine crenarchaeota, phylotypes related to hydrogenotrophic methanogens (Methanogenium spp.), and methylotrophic methanogens associated with the Methanococcoides. No methanogens were discovered at the control site, while hydrogenotrophic methanogens accounted for approximately 20% of the samples from surface sediments below the whale and 35% of the Archaea identified from 12.5 to 15 cm below the whale; the single methylotrophic methanogen was identified within the 12.5 to 15 cm depth sample. The presence of methanogenic phylotypes associated with the whale fall corroborates geochemical observations of elevated methane concentrations observed in the shallow sediments directly beneath the whale fall. This combined geochemical and microbiological evidence suggests that near surface organic matter remineralization is occurring via a methanogenic pathway within this deep sea whale fall habitat rather than the typical sulfidogenic dominated diagenesis commonly observed at other whale fall locations and within shallow marine sediments worldwide.

Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems.

PubMed

Yao, Yining; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui

2018-01-01

Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex ® 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR ® . Identifiler ® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex ® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets. Copyright © 2017 Elsevier B.V. All rights reserved.

Bird migration flight altitudes studied by a network of operational weather radars

PubMed Central

Dokter, Adriaan M.; Liechti, Felix; Stark, Herbert; Delobbe, Laurent; Tabary, Pierre; Holleman, Iwan

2011-01-01

A fully automated method for the detection and quantification of bird migration was developed for operational C-band weather radar, measuring bird density, speed and direction as a function of altitude. These weather radar bird observations have been validated with data from a high-accuracy dedicated bird radar, which was stationed in the measurement volume of weather radar sites in The Netherlands, Belgium and France for a full migration season during autumn 2007 and spring 2008. We show that weather radar can extract near real-time bird density altitude profiles that closely correspond to the density profiles measured by dedicated bird radar. Doppler weather radar can thus be used as a reliable sensor for quantifying bird densities aloft in an operational setting, which—when extended to multiple radars—enables the mapping and continuous monitoring of bird migration flyways. By applying the automated method to a network of weather radars, we observed how mesoscale variability in weather conditions structured the timing and altitude profile of bird migration within single nights. Bird density altitude profiles were observed that consisted of multiple layers, which could be explained from the distinct wind conditions at different take-off sites. Consistently lower bird densities are recorded in The Netherlands compared with sites in France and eastern Belgium, which reveals some of the spatial extent of the dominant Scandinavian flyway over continental Europe. PMID:20519212

Variability in Bias of Gridded Sea Surface Temperature Data Products: Implications for Seasonally Resolved Marine Proxy Reconstructions

NASA Astrophysics Data System (ADS)

Ouellette, G., Jr.; DeLong, K. L.

2016-12-01

Seasonally resolved reconstructions of sea surface temperature (SST) are commonly produced using isotopic ratios and trace elemental ratios within the skeletal material of marine organisms such as corals, coralline algae, and mollusks. Using these geochemical proxies to produce paleoclimate reconstructions requires using regression methods to calibrate the proxy to observed SST, ideally with in situ SST records that span many years. Unfortunately, the few locations with in situ SST records rarely coincide with the time span of the marine proxy archive. Therefore, SST data products are often used for calibration and they are based on MOHSST or ICOADS SST observations as their main SST source but use different algorithms to produce globally gridded data products. These products include the Hadley Center's HADSST (5º) and interpolated HADISST (1º), NOAA's extended reconstructed SST (ERSST; 2º), optimum interpolation SST (OISST; 1º), and the Kaplan SST (5º). This study assessed the potential bias in these data products at marine archive sites throughout the tropical Atlantic using in situ SST where it was available, and a high-resolution (4 km) satellite-based SST data product from NOAA Pathfinder that has been shown to closely reflect in situ SST for our locations. Bias was assessed at each site, and then within each data product across the region for spatial homogeneity. Our results reveal seasonal biases in all data products, but not for all locations and not of a uniform magnitude or season among products. We found the largest differences in mean SST on the order of 1-3°C for single sites in the Gulf of Mexico, and differences for regional mean SST bias were 0.5-1°C when sites in the Gulf of Mexico were compared to sites in the Caribbean Sea within the same data product. No one SST data product outperformed the others and no systematic bias was found. This analysis illustrates regional strengths and weaknesses of these data products, and serves as a cautionary note against the wholesale use of a particular gridded data product for marine proxy calibration, whether for a single site or larger regional reconstruction, without considering the inherent heterogeneous bias present in each data product that we show varies among locations. Furthermore, this study has implications for comparing climate models and these SST data products.

Observations on the Feeding and Symptomatology of Xiphinema and Longidorus on Selected Host Roots

PubMed Central

Cohn, E.

1970-01-01

In vitro feeding of Xiphinema brevicolle, X. index and Longidorus africanus on roots of host seedlings is described. Both Xiphinema spp. fed mainly along roots rather than at tips and up to several days at a single site. Feeding of L. africanus was confined to root tips and lasted up to 15 min. No visible short term reaction of roots parasitized by the Xiphinema spp. could be discerned, but both swelling and cessation of growth of root tips were observed within 20 hr after feeding by L. africanus. Long-term (12-month) symptoms on roots of several host plants caused by cultured populations of X. brevicolle, X. index, X. italiae, L. africanus and L. brevicaudatus are described. All the Xiphinema spp. caused a thinning and distinct darkening of root systems and, at some sites, a breakdown of the cortex. Both species of Longidorus caused stubby and swollen root tips. Root symptom severity was in proportion to nematode population levels. PMID:19322291

Site-specific Installation and Study of Electroactive Units in Every Layer of Dendrons

PubMed Central

Azagarsamy, Malar A.; Krishnamoorthy, Kothandam; Sivanandan, Kulandaivelu; Thayumanavan, S.

2009-01-01

While encapsulation of functional groups at the core of dendrimers is well-understood, very little is known about their intermediate layers or even the periphery. Here we report on a systematic investigation of every layer of dendrimers by incorporating a single ferrocene unit in well-defined locations in dendrons. Site-specific incorporation of the ferrocene unit was achieved utilizing the dendrimer sequencing methodology. We show here that the redox potential values of ferrocene at intermediate layers were remarkably different from that at the core and the periphery. While redox potential values were location-dependent, no significant change in the rate of heterogeneous electron transfer (k0) was observed with respect to locations. This was attributed to the possibility that free rotation of dendrimer nullifies the distance between the electrode and ferrocene unit. Finally, we also show that no Faradaic current was observed for the amphiphilic assemblies of these dendrons, while the same dendron did exhibit significant Faradaic current in non-assembling solvent environments. PMID:19905006

The effectiveness of small changes for pressure redistribution; using the air mattress for small changes.

PubMed

Tsuchiya, Sayumi; Sato, Aya; Azuma, Eri; Urushidani, Hiroko; Osawa, Masako; Kadoya, Kanaho; Takamura, Mana; Nunomi, Makiko; Mitsuoka, Akimi; Nishizawa Yokono, Tomoe; Sugama, Junko

2016-05-01

Observing small changes (SCs) at specific sites is a new form of managing changes in position. We investigated SCs at specific sites considering interface pressure, contact area, body alignment and physical sensation in nine healthy female adults and evaluated SCs using the air mattress that was divided into six cells (A-F). Thirty-three SC combinations at one or several sites were evaluated. Pressure in the sacral region significantly decreased in 28 SC combinations compared with the supine position (p < 0.05), and the effect of pressure redistribution was greater when SCs were applied at several instead of a single site. The contact area at 17 of the 28 SC combinations significantly increased (p < 0.05). Among sites ranked based on interface pressure, body alignment and physical sensation, SCs at sites BCE, AE and BD were the most favorable. The common feature among these three combinations was that they involved tilting the buttock region and one other site. The findings suggested that SCs at the buttock region could reduce disruptions in alignment as well as the impact on physical sensation caused by the body sinking into the mattress and improve interface pressure redistribution via increased contact area with the mattress. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Tip-Enhanced Raman Voltammetry: Coverage Dependence and Quantitative Modeling.

PubMed

Mattei, Michael; Kang, Gyeongwon; Goubert, Guillaume; Chulhai, Dhabih V; Schatz, George C; Jensen, Lasse; Van Duyne, Richard P

2017-01-11

Electrochemical atomic force microscopy tip-enhanced Raman spectroscopy (EC-AFM-TERS) was employed for the first time to observe nanoscale spatial variations in the formal potential, E 0' , of a surface-bound redox couple. TERS cyclic voltammograms (TERS CVs) of single Nile Blue (NB) molecules were acquired at different locations spaced 5-10 nm apart on an indium tin oxide (ITO) electrode. Analysis of TERS CVs at different coverages was used to verify the observation of single-molecule electrochemistry. The resulting TERS CVs were fit to the Laviron model for surface-bound electroactive species to quantitatively extract the formal potential E 0' at each spatial location. Histograms of single-molecule E 0' at each coverage indicate that the electrochemical behavior of the cationic oxidized species is less sensitive to local environment than the neutral reduced species. This information is not accessible using purely electrochemical methods or ensemble spectroelectrochemical measurements. We anticipate that quantitative modeling and measurement of site-specific electrochemistry with EC-AFM-TERS will have a profound impact on our understanding of the role of nanoscale electrode heterogeneity in applications such as electrocatalysis, biological electron transfer, and energy production and storage.

Socket Preservation using Enzyme-treated Equine Bone Granules and an Equine Collagen Matrix: A Case Report with Histological and Histomorphometrical Assessment.

PubMed

Leonida, Alessandro; Todeschini, Giovanni; Lomartire, Giovanni; Cinci, Lorenzo; Pieri, Laura

2016-11-01

To histologically assess the effectiveness of a socket-preservation technique using enzyme-treated equine bone granules as a bone-graft material in combination with an equine collagen matrix as a scaffold for soft-tissue regeneration. Enzyme-treated equine bone granules and equine collagen matrix recently have been developed to help overcome alveolar bone deficiencies that develop in the wake of edentulism. The patient had one mandibular molar extracted and the socket grafted with equine bone granules. The graft was covered with the equine collagen matrix, placed in a double layer. No flap was prepared, and the gingival margins were stabilized with a single stitch, leaving the matrix partially exposed and the site to heal by secondary intention. The adjacent molar was extracted 1 month later, and that socket was left to heal by secondary intention without any further treatment. Three months after each surgery, an implant was placed and a biopsy was collected. The two biopsies underwent histological processing and qualitative evaluation. Histomorphometric analysis was also performed to calculate the percentage of newly formed bone (NFB) in the two cores. Healing at both sites was uneventful, and no inflammation or other adverse reactions were observed in the samples. Soft-tissue healing by secondary intention appeared to occur faster at the grafted site. The corresponding core showed a marked separation between soft and hard tissue that was not observed in the core from the nongrafted site, where soft-tissue hypertrophy could be observed. Newly formed bone at the grafted and nongrafted sites was not significantly different (27.2 ± 7.1 and 29.4 ± 6.2% respectively, p = 0.45). The surgical technique employed in this case appeared to facilitate postextraction soft-tissue healing by second intention and simplify soft-tissue management. Using a collagen-based matrix to cover a postextraction grafted site may facilitate second intention soft-tissue healing and proper soft-tissue growth.

Influence of Observed Diurnal Cycles of Aerosol Optical Depth on Aerosol Direct Radiative Effect

NASA Technical Reports Server (NTRS)

Arola, A.; Eck, T. F.; Huttunen, J.; Lehtinen, K. E. J.; Lindfors, A. V.; Myhre, G.; Smirinov, A.; Tripathi, S. N.; Yu, H.

2013-01-01

The diurnal variability of aerosol optical depth (AOD) can be significant, depending on location and dominant aerosol type. However, these diurnal cycles have rarely been taken into account in measurement-based estimates of aerosol direct radiative forcing (ADRF) or aerosol direct radiative effect (ADRE). The objective of our study was to estimate the influence of diurnal aerosol variability at the top of the atmosphere ADRE estimates. By including all the possible AERONET sites, we wanted to assess the influence on global ADRE estimates. While focusing also in more detail on some selected sites of strongest impact, our goal was to also see the possible impact regionally.We calculated ADRE with different assumptions about the daily AOD variability: taking the observed daily AOD cycle into account and assuming diurnally constant AOD. Moreover, we estimated the corresponding differences in ADREs, if the single AOD value for the daily mean was taken from the the Moderate Resolution Imaging Spectroradiometer (MODIS) Terra or Aqua overpass times, instead of accounting for the true observed daily variability. The mean impact of diurnal AOD variability on 24 h ADRE estimates, averaged over all AERONET sites, was rather small and it was relatively small even for the cases when AOD was chosen to correspond to the Terra or Aqua overpass time. This was true on average over all AERONET sites, while clearly there can be much stronger impact in individual sites. Examples of some selected sites demonstrated that the strongest observed AOD variability (the strongest morning afternoon contrast) does not typically result in a significant impact on 24 h ADRE. In those cases, the morning and afternoon AOD patterns are opposite and thus the impact on 24 h ADRE, when integrated over all solar zenith angles, is reduced. The most significant effect on daily ADRE was induced by AOD cycles with either maximum or minimum AOD close to local noon. In these cases, the impact on 24 h ADRE was typically around 0.1-0.2W/sq m (both positive and negative) in absolute values, 5-10% in relative ones.

Observation Data Model Core Components, its Implementation in the Table Access Protocol Version 1.1

NASA Astrophysics Data System (ADS)

Louys, Mireille; Tody, Doug; Dowler, Patrick; Durand, Daniel; Michel, Laurent; Bonnarel, Francos; Micol, Alberto; IVOA DataModel Working Group; Louys, Mireille; Tody, Doug; Dowler, Patrick; Durand, Daniel

2017-05-01

This document defines the core components of the Observation data model that are necessary to perform data discovery when querying data centers for astronomical observations of interest. It exposes use-cases to be carried out, explains the model and provides guidelines for its implementation as a data access service based on the Table Access Protocol (TAP). It aims at providing a simple model easy to understand and to implement by data providers that wish to publish their data into the Virtual Observatory. This interface integrates data modeling and data access aspects in a single service and is named ObsTAP. It will be referenced as such in the IVOA registries. In this document, the Observation Data Model Core Components (ObsCoreDM) defines the core components of queryable metadata required for global discovery of observational data. It is meant to allow a single query to be posed to TAP services at multiple sites to perform global data discovery without having to understand the details of the services present at each site. It defines a minimal set of basic metadata and thus allows for a reasonable cost of implementation by data providers. The combination of the ObsCoreDM with TAP is referred to as an ObsTAP service. As with most of the VO Data Models, ObsCoreDM makes use of STC, Utypes, Units and UCDs. The ObsCoreDM can be serialized as a VOTable. ObsCoreDM can make reference to more complete data models such as Characterisation DM, Spectrum DM or Simple Spectral Line Data Model (SSLDM). ObsCore shares a large set of common concepts with DataSet Metadata Data Model (Cresitello-Dittmar et al. 2016) which binds together most of the data model concepts from the above models in a comprehensive and more general frame work. This current specification on the contrary provides guidelines for implementing these concepts using the TAP protocol and answering ADQL queries. It is dedicated to global discovery.

Molecular Bases of cyclodextrin Adapter Interactions with Engineered Protein Nanopores

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

Banerjee, A.; Mikhailova, E; Cheley, S

2010-01-01

Engineered protein pores have several potential applications in biotechnology: as sensor elements in stochastic detection and ultrarapid DNA sequencing, as nanoreactors to observe single-molecule chemistry, and in the construction of nano- and micro-devices. One important class of pores contains molecular adapters, which provide internal binding sites for small molecules. Mutants of the {alpha}-hemolysin ({alpha}HL) pore that bind the adapter {beta}-cyclodextrin ({beta}CD) {approx}10{sup 4} times more tightly than the wild type have been obtained. We now use single-channel electrical recording, protein engineering including unnatural amino acid mutagenesis, and high-resolution x-ray crystallography to provide definitive structural information on these engineered protein nanoporesmore » in unparalleled detail.« less

Freeze frame analysis on high speed cinematography of Nd/YAG laser explosions in ocular tissues.

PubMed

Vernon, S A; Cheng, H

1986-05-01

High speed colour cinematography at 400 frames per second was used to photograph both single and train burst Nd/YAG laser applications in ox eyes at threshold energy levels. Measurements of the extent and speed of particle scatter and tissue distortion from the acoustic transient were made from a sequential freeze frame analysis of the films. Particles were observed to travel over 8 mm from the site of Nd/YAG application 20 milliseconds after a single pulse at initial speeds in excess of 20 km/h. The use of train bursts of pulses was seen to increase the number of particles scattered and project the wavefront of particles further from the point of laser application.

Freeze frame analysis on high speed cinematography of Nd/YAG laser explosions in ocular tissues.

PubMed Central

Vernon, S A; Cheng, H

1986-01-01

High speed colour cinematography at 400 frames per second was used to photograph both single and train burst Nd/YAG laser applications in ox eyes at threshold energy levels. Measurements of the extent and speed of particle scatter and tissue distortion from the acoustic transient were made from a sequential freeze frame analysis of the films. Particles were observed to travel over 8 mm from the site of Nd/YAG application 20 milliseconds after a single pulse at initial speeds in excess of 20 km/h. The use of train bursts of pulses was seen to increase the number of particles scattered and project the wavefront of particles further from the point of laser application. Images PMID:3754458

Possible cage motion of interstitial Fe in α-Al 2 O 3

NASA Astrophysics Data System (ADS)

Gunnlaugsson, H. P.; Johnston, K.; Masenda, H.; Mantovan, R.; Mølholt, T. E.; Bharuth-Ram, K.; Gislason, H. P.; Langouche, G.; Madsen, M. B.; Naidoo, D.; Ólafsson, S.; Weyer, G.

2013-04-01

In addition to spectral components due to Fe2 + and Fe3 + , a single line is observed in emission Mössbauer spectra following low fluence (<1015 cm - 2) implantation of 57Fe*, 57Mn and 57Co in α-Al2O3. For the 57Co and 57Mn implantations, the intensity of the single line is found to depend on the emission angle relative to the crystal symmetry axis. This angular dependence can be explained by a non-isotropic f-factor and/or motion of the Fe ion between sites in an interstitial cage. It is argued that interstitial cage motion is a more likely explanation, as this can account for the lack of quadrupole splitting of the line.

PCR-mediated site-directed mutagenesis.

PubMed

Carey, Michael F; Peterson, Craig L; Smale, Stephen T

2013-08-01

Unlike traditional site-directed mutagenesis, this protocol requires only a single PCR step using full plasmid amplification to generate point mutants. The method can introduce small mutations into promoter sites and is even better suited for introducing single or double mutations into proteins. It is elegant in its simplicity and can be applied quite easily in any laboratory using standard protein expression vectors and commercially available reagents.

New High-Resolution Marine Single-Channel Seismic Data From the Emperor Seamounts: Initial Observations From ODP Leg 197

NASA Astrophysics Data System (ADS)

Kerr, B. C.; Scholl, D. W.

2001-12-01

In July-August of 2001, ODP Leg 197 drilled Detroit, Nintoku, and Koko Seamounts of the Emperor seamount chain to obtain cores of basaltic lava flows. These basalt cores will provide radiometric age and paleomagnetic data to accurately and precisely constrain the paleolatitude of the Hawaiian hotspot. In addition, recovered cores will determine temporal changes in the geochemistry of Hawaiian hotspot volcanic products. Prior to drilling, the JOIDES Resolution, performed high-resolution single-channel seismic surveys in the vicinity of preliminary site locations to help confirm suitability for drilling, and to collect digital seismic data. Generally, at least two seismic lines (about 10 km in length) cross directly over each drill site. The acoustic source consisted of a single SSI 80 cubic-inch water gun with a peak output frequency of approximately 50 Hz. Compared to most SCS data, low ship speeds (4.5-7 knots) and higher than typical firing rates (4 or 6 seconds) helped maximize horizontal resolution, resulting in shot-point spacings between 9 and 21.5 m. A 60-phone, 100-m-long Teledyne oil-filled streamer recorded the water gun shots at near-zero offset. At the end of the leg, a calibrated hydrophone, suspended about 30 m below the water gun, recorded the gun's source signature for 11-30 consecutive shots at each of 6, 5, 4, 3, and 2 m below the sea surface. Near-ideal weather conditions during each site survey produced data with high signal-to-noise ratios. The presence of volcaniclastic and/or soil interbeds, as well as highly vesicular lava flow units, significantly affected the seismic reflection character of the volcanic basement. Strong, laterally-coherent internal reflections in the volcanic basement indicate the presence of these layers, which exhibit low velocities and low bulk densities. Generally, laterally-coherent reflections cease where the number and thickness of the low-velocity interbeds diminish. Where the seamount sediment cap is underlain by dominantly massive basalt lava flows, a strong, non-reverberatory and low-frequency reflection marks the sediment-basement contact. Truncation of dipping lava flow reflections by other basement reflections suggests distinct lava flow sequences that can be mapped with further analysis. The two site surveys conducted over Detroit Seamount produced detailed seismic sections of the Meiji sediment drift body. Observations include a shallow angular unconformity indicative of a pattern of erosion and deposition produced by a strong bottom current such as that involved in forming the Meiji sediment drift. Sigmoidal clinoforms occur deeper in the Detroit sediment cap. Preliminary observations also suggest current-controlled drift deposits are present on top of Koko Seamount.

Lessons from Astrobiological Planetary Analogue Exploration in Iceland: Biomarker Assay Performance and Downselection

NASA Technical Reports Server (NTRS)

Gentry, D. M.; Amador, E. S.; Cable, M. L.; Cantrell, T.; Chaudry, N.; Cullen, T.; Duca, Z.; Kirby, J.; Jacobsen, M.; McCaig, H.;

Stochastic simulation tools and continuum models for describing two-dimensional collective cell spreading with universal growth functions

NASA Astrophysics Data System (ADS)

Jin, Wang; Penington, Catherine J.; McCue, Scott W.; Simpson, Matthew J.

2016-10-01

Two-dimensional collective cell migration assays are used to study cancer and tissue repair. These assays involve combined cell migration and cell proliferation processes, both of which are modulated by cell-to-cell crowding. Previous discrete models of collective cell migration assays involve a nearest-neighbour proliferation mechanism where crowding effects are incorporated by aborting potential proliferation events if the randomly chosen target site is occupied. There are two limitations of this traditional approach: (i) it seems unreasonable to abort a potential proliferation event based on the occupancy of a single, randomly chosen target site; and, (ii) the continuum limit description of this mechanism leads to the standard logistic growth function, but some experimental evidence suggests that cells do not always proliferate logistically. Motivated by these observations, we introduce a generalised proliferation mechanism which allows non-nearest neighbour proliferation events to take place over a template of r≥slant 1 concentric rings of lattice sites. Further, the decision to abort potential proliferation events is made using a crowding function, f(C), which accounts for the density of agents within a group of sites rather than dealing with the occupancy of a single randomly chosen site. Analysing the continuum limit description of the stochastic model shows that the standard logistic source term, λ C(1-C), where λ is the proliferation rate, is generalised to a universal growth function, λ C f(C). Comparing the solution of the continuum description with averaged simulation data indicates that the continuum model performs well for many choices of f(C) and r. For nonlinear f(C), the quality of the continuum-discrete match increases with r.

Study of Aerosol Optical Properties Over Two Sites in the Foothills of the Central Himalayas

NASA Astrophysics Data System (ADS)

Rupakheti, D.; Kang, S.; Cong, Z.; Rupakheti, M.; Tripathee, L.; Panday, A. K.; Holben, B.

2018-04-01

Atmospheric aerosol possesses impacts on climate system and ecological environments, human health and agricultural productivity. The environment over Himalayas and Tibetan Plateau region are continuously degraded due to the transport of pollution from the foothills of the Himalayas; mostly the Indo-Gangetic Plain (IGP). Thus, analysis of aerosol optical properties over two sites; Lumbini and Kathmandu (the southern slope of central Himalayas) using AERONET's CIMEL sun photometer were conducted in this study. Aerosol optical depth (AOD at 500 nm), angstrom exponent (α or AE), volume size distribution (VSD), single scattering albedo (SSA) and asymmetry parameter (AP) were studied for 2013-2014 and the average AOD was found to be: 0.64 ± 0.41 (Lumbini) and 0.45 ± 0.30 (Kathmandu). The average AE was found to be: 1.25 ± 0.24 and 1.26 ± 0.18 respectively for two sites. The relation between AOD and AE was used to discriminate the aerosol types over these sites which indicated anthropogenic, mixed and biomass burning origin aerosol constituted the major aerosol types in Lumbini and Kathmandu. A clear bi-modal distribution of aerosol volume size was observed with highest volume concentration during the post-monsoon season in fine mode and pre-monsoon season in coarse mode (Lumbini) and highest value over both modes during pre-monsoon season in Kathmandu. The single scattering albedo (SSA) and asymmetry parameter (AP) analyses suggested aerosols over the Himalayan foothills sites are dominated by absorbing and anthropogenic aerosols from urban and industrial activities and biomass burning. Long-term studies are essential to understand and characterize the nature of aerosol over this research gap zone.

Identification of the prooxidant site of human ceruloplasmin: a model for oxidative damage by copper bound to protein surfaces

NASA Technical Reports Server (NTRS)

Mukhopadhyay, C. K.; Mazumder, B.; Lindley, P. F.; Fox, P. L.

1997-01-01

Free transition metal ions oxidize lipids and lipoproteins in vitro; however, recent evidence suggests that free metal ion-independent mechanisms are more likely in vivo. We have shown previously that human ceruloplasmin (Cp), a serum protein containing seven Cu atoms, induces low density lipoprotein oxidation in vitro and that the activity depends on the presence of a single, chelatable Cu atom. We here use biochemical and molecular approaches to determine the site responsible for Cp prooxidant activity. Experiments with the His-specific reagent diethylpyrocarbonate (DEPC) showed that one or more His residues was specifically required. Quantitative [14C]DEPC binding studies indicated the importance of a single His residue because only one was exposed upon removal of the prooxidant Cu. Plasmin digestion of [14C]DEPC-treated Cp (and N-terminal sequence analysis of the fragments) showed that the critical His was in a 17-kDa region containing four His residues in the second major sequence homology domain of Cp. A full length human Cp cDNA was modified by site-directed mutagenesis to give His-to-Ala substitutions at each of the four positions and was transfected into COS-7 cells, and low density lipoprotein oxidation was measured. The prooxidant site was localized to a region containing His426 because CpH426A almost completely lacked prooxidant activity whereas the other mutants expressed normal activity. These observations support the hypothesis that Cu bound at specific sites on protein surfaces can cause oxidative damage to macromolecules in their environment. Cp may serve as a model protein for understanding mechanisms of oxidant damage by copper-containing (or -binding) proteins such as Cu, Zn superoxide dismutase, and amyloid precursor protein.

Chemical repair of base lesions, AP-sites, and strand breaks on plasmid DNA in dilute aqueous solution by ascorbic acid

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

Hata, Kuniki; Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1195; Urushibara, Ayumi

Highlights: •We report a novel mechanism of radiation protection of DNA by chemical activity of ascorbic acid. •The “chemical repair” of DNA damage was revealed using biochemical assay and chemical kinetics analysis. •We found that ascorbic acid significantly repairs precursors of nucleobase lesions and abasic sites. •However, ascorbic acid seldom repairs precursors of DNA-strand breaks. -- Abstract: We quantified the damage yields produced in plasmid DNA by γ-irradiation in the presence of low concentrations (10–100 μM) of ascorbic acid, which is a major antioxidant in living systems, to clarify whether it chemically repairs radiation damage in DNA. The yield ofmore » DNA single strand breaks induced by irradiation was analyzed with agarose gel electrophoresis as conformational changes in closed circular plasmids. Base lesions and abasic sites were also observed as additional conformational changes by treating irradiated samples with glycosylase proteins. By comparing the suppression efficiencies to the induction of each DNA lesion, in addition to scavenging of the OH radicals derived from water radiolysis, it was found that ascorbic acid promotes the chemical repair of precursors of AP-sites and base lesions more effectively than those of single strand breaks. We estimated the efficiency of the chemical repair of each lesion using a kinetic model. Approximately 50–60% of base lesions and AP-sites were repaired by 10 μM ascorbic acid, although strand breaks were largely unrepaired by ascorbic acid at low concentrations. The methods in this study will provide a route to understanding the mechanistic aspects of antioxidant activity in living systems.« less

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.

PubMed

Bonizzoni, Paola; Rizzi, Raffaella; Pesole, Graziano

2005-10-05

Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic sequence. Apart from often being computationally expensive, this approach is vulnerable to several problems--hence the need to develop novel strategies. We propose a method, based on a novel multiple genome-EST alignment algorithm, for the detection of splice sites. To avoid limitations of splice sites prediction (mainly, over-predictions) due to independent single EST alignments to the genomic sequence our approach performs a multiple alignment of transcript data to the genomic sequence based on the combined analysis of all available data. We recast the problem of predicting constitutive and alternative splicing as an optimization problem, where the optimal multiple transcript alignment minimizes the number of exons and hence of splice site observations. We have implemented a splice site predictor based on this algorithm in the software tool ASPIC (Alternative Splicing PredICtion). It is distinguished from other methods based on BLAST-like tools by the incorporation of entirely new ad hoc procedures for accurate and computationally efficient transcript alignment and adopts dynamic programming for the refinement of intron boundaries. ASPIC also provides the minimal set of non-mergeable transcript isoforms compatible with the detected splicing events. The ASPIC web resource is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility. Extensive bench marking shows that ASPIC outperforms other existing methods in the detection of novel splicing isoforms and in the minimization of over-predictions. ASPIC also requires a lower computation time for processing a single gene and an EST cluster. The ASPIC web resource is available at http://aspic.algo.disco.unimib.it/aspic-devel/.

Stochastic simulation tools and continuum models for describing two-dimensional collective cell spreading with universal growth functions.

PubMed

Jin, Wang; Penington, Catherine J; McCue, Scott W; Simpson, Matthew J

2016-10-07

Two-dimensional collective cell migration assays are used to study cancer and tissue repair. These assays involve combined cell migration and cell proliferation processes, both of which are modulated by cell-to-cell crowding. Previous discrete models of collective cell migration assays involve a nearest-neighbour proliferation mechanism where crowding effects are incorporated by aborting potential proliferation events if the randomly chosen target site is occupied. There are two limitations of this traditional approach: (i) it seems unreasonable to abort a potential proliferation event based on the occupancy of a single, randomly chosen target site; and, (ii) the continuum limit description of this mechanism leads to the standard logistic growth function, but some experimental evidence suggests that cells do not always proliferate logistically. Motivated by these observations, we introduce a generalised proliferation mechanism which allows non-nearest neighbour proliferation events to take place over a template of [Formula: see text] concentric rings of lattice sites. Further, the decision to abort potential proliferation events is made using a crowding function, f(C), which accounts for the density of agents within a group of sites rather than dealing with the occupancy of a single randomly chosen site. Analysing the continuum limit description of the stochastic model shows that the standard logistic source term, [Formula: see text], where λ is the proliferation rate, is generalised to a universal growth function, [Formula: see text]. Comparing the solution of the continuum description with averaged simulation data indicates that the continuum model performs well for many choices of f(C) and r. For nonlinear f(C), the quality of the continuum-discrete match increases with r.

Discriminative structural approaches for enzyme active-site prediction.

PubMed

Kato, Tsuyoshi; Nagano, Nozomi

2011-02-15

Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed to date. In comparing such local sites, a simple measurement, RMSD, has been used so far. This paper introduces new machine learning algorithms that refine the similarity/deviation for comparison of local structures. The similarity/deviation is applied to two types of applications, single template analysis and multiple template analysis. In the single template analysis, a single template is used as a query to search proteins for active sites, whereas a protein structure is examined as a query to discover the possible active-sites using a set of templates in the multiple template analysis. This paper experimentally illustrates that the machine learning algorithms effectively improve the similarity/deviation measurements for both the analyses.

Synthesis of a molecularly defined single-active site heterogeneous catalyst for selective oxidation of N-heterocycles.

PubMed

Zhang, Yujing; Pang, Shaofeng; Wei, Zhihong; Jiao, Haijun; Dai, Xingchao; Wang, Hongli; Shi, Feng

2018-04-13

Generally, a homogeneous catalyst exhibits good activity and defined active sites but it is difficult to recycle. Meanwhile, a heterogeneous catalyst can easily be reused but its active site is difficult to reveal. It is interesting to bridge the gap between homogeneous and heterogeneous catalysis via controllable construction of a heterogeneous catalyst containing defined active sites. Here, we report that a molecularly defined, single-active site heterogeneous catalyst has been designed and prepared via the oxidative polymerization of maleimide derivatives. These polymaleimide derivatives can be active catalysts for the selective oxidation of heterocyclic compounds to quinoline and indole via the recycling of -C=O and -C-OH groups, which was confirmed by tracing the reaction with GC-MS using maleimide as the catalyst and by FT-IR analysis with polymaleimide as the catalyst. These results might promote the development of heterogeneous catalysts with molecularly defined single active sites exhibiting a comparable activity to homogeneous catalysts.

Geochemical investigations and interim recommendations for priority abandoned mine sites, BLM lands, upper Animas River watershed, San Juan County, Colorado

USGS Publications Warehouse

Nash, J. Thomas

1999-01-01

Field observations, sampling of mine dumps and mine drainage waters, and laboratory studies of dump materials have been made at mining areas deemed to be on public lands administered by the U. S. Bureau of Land Management (BLM) in the Upper Animas River watershed. Results of chemical analyses of dump materials, leachates of those materials, and surface waters draining mines or dumps provide indications of where acid is generated or consumed, and metal concentrations below mines or dumps. Information on sites previously identified as needing reclamation is reviewed and available geochemical information is used to rank 26 sites into four classes of priority for reclamation. Although there are more than a thousand mining sites (productive mines and prospects) on BLM lands in the Upper Animas River watershed study area, the majority are very small (less than about 70 cubic yards of dump material), are more than 2 miles from a major stream, or so inaccessible as to prohibit reclamation. In the summers of 1997 and 1998 approximately 200 sites were observed and more than 100 of these that appeared to have the potential to geochemically impact the watershed were examined more carefully and sampled. Building upon the prior work of the BLM and associated agencies, this work attempted to identify the most significant sources of mine-related contamination and to rank those sites as to priority for reclamation. These most significant mining areas have been examined within a geologic framework and were evaluated by multiple criteria, including tendency to generate acid and release toxic metals, observed damage to vegetation, potential to release metals based on leach tests, and likelihood of transport into streams of the watershed. No single measurable parameter, such as metal concentration, can be used to rank the sites. Rather, subjective estimates are required to evaluate combinations or interactions among several parameters. The most subjective estimate, while ranking feasibility of reclamation, is the relative amounts of naturally occurring metals and acidity and mine-related contamination at each mining area. Mitigation of natural contributions at mines or unmined areas is beyond the scope of my studies, but should be considered when planning reclamation. Available information for the 26 priority sites is adequate for ranking, but at some sites additional information on groundwater conditions is needed for a more complete site evaluation.

Detecting vegetation cover change on the summit of Cadillac Mountain using multi-temporal remote sensing datasets: 1979, 2001, and 2007.

PubMed

Kim, Min-Kook; Daigle, John J

2011-09-01

This study examines the efficacy of management strategies implemented in 2000 to reduce visitor-induced vegetation impact and enhance vegetation recovery at the summit loop trail on Cadillac Mountain at Acadia National Park, Maine. Using single-spectral high-resolution remote sensing datasets captured in 1979, 2001, and 2007, pre-classification change detection analysis techniques were applied to measure fractional vegetation cover changes between the time periods. This popular sub-alpine summit with low-lying vegetation and attractive granite outcroppings experiences dispersed visitor use away from the designated trail, so three pre-defined spatial scales (small, 0-30 m; medium, 0-60 m; and large, 0-90 m) were examined in the vicinity of the summit loop trail with visitor use (experimental site) and a site chosen nearby in a relatively pristine undisturbed area (control site) with similar spatial scales. Results reveal significant changes in terms of rates of vegetation impact between 1979 and 2001 extending out to 90 m from the summit loop trail with no management at the site. No significant differences were detected among three spatial zones (inner, 0-30 m; middle, 30-60 m; and outer, 60-90 m) at the experimental site, but all were significantly higher rates of impact compared to similar spatial scales at the control site (all p < 0.001). In contrast, significant changes in rates of recovery between 2001 and 2007 were observed in the medium and large spatial scales at the experimental site under management as compared to the control site (all p < 0.05). Also during this later period a higher rate of recovery was observed in the outer zone as compared to the inner zone at the experimental site (p < 0.05). The overall study results suggest a trend in the desired direction for the site and visitor management strategies designed to reduce vegetation impact and enhance vegetation recovery at the summit loop trail of Cadillac Mountain since 2000. However, the vegetation recovery has been rather minimal and did not reach the level of cover observed during the 1979 time period. In addition, the advantages and some limitations of using remote sensing technologies are discussed in detecting vegetation change in this setting and potential application to other recreation settings.

Development of Ca2+ hotspots between Lymnaea neurons during synaptogenesis

PubMed Central

Feng, Zhong-Ping; Grigoriev, Nikita; Munno, David; Lukowiak, Ken; MacVicar, Brian A; Goldberg, Jeffrey I; Syed, Naweed I

2002-01-01

Calcium (Ca2+) channel clustering at specific presynaptic sites is a hallmark of mature synapses. However, the spatial distribution patterns of Ca2+ channels at newly formed synapses have not yet been demonstrated. Similarly, it is unclear whether Ca2+ ‘hotspots’ often observed at the presynaptic sites are indeed target cell contact specific and represent a specialized mechanism by which Ca2+ channels are targeted to select synaptic sites. Utilizing both soma–soma paired (synapsed) and single neurons from the mollusk Lymnaea, we have tested the hypothesis that differential gradients of voltage-dependent Ca2+ signals develop in presynaptic neuron at its contact point with the postsynaptic neuron; and that these Ca2+ hotspots are target cell contact specific. Fura-2 imaging, or two-photon laser scanning microscopy of Calcium Green, was coupled with electrophysiological techniques to demonstrate that voltage-induced Ca2+ gradients (hotspots) develop in the presynaptic cell at its contact point with the postsynaptic neuron, but not in unpaired single cells. The incidence of Ca2+ hotspots coincided with the appearance of synaptic transmission between the paired cells, and these gradients were target cell contact specific. In contrast, the voltage-induced Ca2+ signal in unpaired neurons was uniformly distributed throughout the somata; a similar pattern of Ca2+ gradient was observed in the presynaptic neuron when it was soma–soma paired with a non-synaptic partner cell. Moreover, voltage clamp recording techniques, in conjunction with a fast, optical differential perfusion system, were used to demonstrate that the total whole-cell Ca2+ (or Ba2+) current density in single and paired cells was not significantly different. However, the amplitude of Ba2+ current was significantly higher in the presynaptic cell at its contact side with the postsynaptic neurons, compared with non-contacted regions. In summary, this study demonstrates that voltage-induced Ca2+ hotspots develop in the presynaptic cell, concomitant with the appearance of synaptic transmission between the soma–soma paired cells. The appearance of Ca2+ gradients in presynaptic neurons is target cell contact specific and is probably due to a spatial redistribution of existing channels during synaptogenesis. PMID:11850501

New insights into single-compound and binary adsorption of copper and lead ions on a treated sea mango shell: experimental and theoretical studies.

PubMed

Sellaoui, Lotfi; Edi Soetaredjo, Felycia; Ismadji, Suryadi; Cláudio Lima, Éder; Dotto, Guilherme L; Ben Lamine, Abdelmottaleb; Erto, Alessandro

2017-10-04

Herein, adsorption isotherms of Pb(ii) and Cu(ii) ions on treated sea mango fruit in both single-compound and binary systems were experimentally realized at different temperatures in the range of 30-50 °C. Experimental results show that adsorption of Pb(ii) was more as compared to that of Cu(ii) ions; however, for both ions, a significant reduction in the adsorption capacity was observed in the binary system as compared to that in the single-compound systems. Moreover, under all the investigated conditions, adsorption seems to be promoted by an increase in temperature. To understand and interpret the experimental evidences, the Hill and competitive Hill models developed on the basis of the grand canonical ensemble were applied for the analysis of adsorption equilibrium data. These models contain some physicochemical parameters that allow an exhaustive analysis of the dynamics of single-compound and binary adsorptions. Based on the fitting results, in particular, through the evaluation of the number of ions bonded per site (n and n i ), it was found that lead and copper ions interacted by inclined and horizontal positions on treated sea mango in single-compound and binary systems, respectively. In addition, based on the same parameters, a significant interaction between ions was retrieved. A study focused on the saturation adsorption capacity in single-compound and binary systems affirmed that the adsorbent was more selective for lead than for copper. The reduction of the adsorbed capacity ratio between the binary and single-compound systems (i.e. Q b /Q s ) explained and confirmed that an inhibition effect between copper and lead ions at the same receptor site occurred. Finally, based on the energetic investigations, it was deduced that the adsorption energy represented the dominant factor promoting the greater adsorption of lead than that of copper in both systems.

Nanotwin and phase transformation in tetragonal Pb(Fe1/2Nb1/2)1-xTixO3 single crystal

NASA Astrophysics Data System (ADS)

Tu, C.-S.; Tseng, C.-T.; Chien, R. R.; Schmidt, V. Hugo; Hsieh, C.-M.

2008-09-01

This work is a study of phase transformation in (001)-cut Pb(Fe1/2Nb1/2)1-xTixO3 (x =48%) single crystals by means of dielectric permittivity, domain structure, and in situ x-ray diffraction. A first-order T(TNT)-C(TNT) phase transition was observed at the Curie temperature TC≅518 K upon zero-field heating. T, TNT, and C are tetragonal, tetragonal nanotwin, and cubic phases, respectively. T(TNT) and C(TNT) indicate that minor TNT domains reside in the T and C matrices. Nanotwins, which can cause broad diffraction peak, remain above TC≅518 K and give an average microscopic cubic symmetry in the polarizing microscopy. Colossal dielectric permittivity (>104) was observed above room temperature with strong frequency dispersion. This study suggests that nanotwins can play an important role in relaxor ferroelectric crystals while phase transition takes place. The Fe ion is a potential candidate as a B-site dopant for enhancing dielectric permittivity.

Few-cycle pulse laser induced damage threshold determination of ultra-broadband optics.

PubMed

Kafka, Kyle R P; Talisa, Noah; Tempea, Gabriel; Austin, Drake R; Neacsu, Catalin; Chowdhury, Enam A

2016-12-12

A systematic study of few-cycle pulse laser induced damage threshold (LIDT) determination was performed for commercially-available ultra-broadband optics, (i.e. chirped mirrors, silver mirrors, beamsplitters, etc.) in vacuum and in air, for single and multi-pulse regime (S-on-1). Multi-pulse damage morphology at fluences below the single-pulse LIDT was studied in order to investigate the mechanisms leading to the onset of damage. Stark morphological contrast was observed between multi-pulse damage sites formed in air versus those in vacuum. One effect of vacuum testing compared to air included suppression of laser-induced periodic surface structures (LIPSS) formation, possibly influenced by a reduced presence of damage debris. Another effect of vacuum was occasional lowering of LIDT, which appears to be due to the stress-strain performance of the coating design during laser irradiation and under the external stress of vacuum ambience. A fused silica substrate is also examined, and a non-LIPSS nanostructuring is observed on the surface. Possible mechanisms are discussed.

Colorectal cancer: Metastases to a single organ

PubMed Central

Vatandoust, Sina; Price, Timothy J; Karapetis, Christos S

2015-01-01

Colorectal cancer (CRC) is a common malignancy worldwide. In CRC patients, metastases are the main cause of cancer-related mortality. In a group of metastatic CRC patients, the metastases are limited to a single site (solitary organ); the liver and lungs are the most commonly involved sites. When metastatic disease is limited to the liver and/or lungs, the resectability of the metastatic lesions will dictate the management approach and the outcome. Less commonly, the site of solitary organ CRC metastasis is the peritoneum. In these patients, cytoreduction followed by hyperthermic intraperitoneal chemotherapy may improve the outcome. Rarely, CRC involves other organs, such as the brain, bone, adrenals and spleen, as the only site of metastatic disease. There are limited data to guide clinical practice in these cases. Here, we have reviewed the disease characteristics, management approaches and prognosis based on the metastatic disease site in patients with CRC with metastases to a single organ. PMID:26557001

F429 Regulation of Tunnels in Cytochrome P450 2B4: A Top Down Study of Multiple Molecular Dynamics Simulations

PubMed Central

Mancini, Giordano; Zazza, Costantino

2015-01-01

The root causes of the outcomes of the single-site mutation in enzymes remain by and large not well understood. This is the case of the F429H mutant of the cytochrome P450 (CYP) 2B4 enzyme where the substitution, on the proximal surface of the active site, of a conserved phenylalanine 429 residue with histidine seems to hamper the formation of the active species, Compound I (porphyrin cation radical-Fe(IV) = O, Cpd I) from the ferric hydroperoxo (Fe(III)OOH-, Cpd 0) precursor. Here we report a study based on extensive molecular dynamic (MD) simulations of 4 CYP-2B4 point mutations compared to the WT enzyme, having the goal of better clarifying the importance of the proximal Phe429 residue on CYP 2B4 catalytic properties. To consolidate the huge amount of data coming from five simulations and extract the most distinct structural features of the five species studied we made an extensive use of cluster analysis. The results show that all studied single polymorphisms of F429, with different side chain properties: i) drastically alter the reservoir of conformations accessible by the protein, perturbing global dynamics ii) expose the thiolate group of residue Cys436 to the solvent, altering the electronic properties of Cpd0 and iii) affect the various ingress and egress channels connecting the distal sites with the bulk environment, altering the reversibility of these channels. In particular, it was observed that the wild type enzyme exhibits unique structural features as compared to all mutant species in terms of weak interactions (hydrogen bonds) that generate a completely different dynamical behavior of the complete system. Albeit not conclusive, the current computational investigation sheds some light on the subtle and critical effects that proximal single-site mutations can exert on the functional mechanisms of human microsomal CYPs which should go rather far beyond local structure characterization. PMID:26415031

F429 Regulation of Tunnels in Cytochrome P450 2B4: A Top Down Study of Multiple Molecular Dynamics Simulations.

PubMed

Mancini, Giordano; Zazza, Costantino

2015-01-01

The root causes of the outcomes of the single-site mutation in enzymes remain by and large not well understood. This is the case of the F429H mutant of the cytochrome P450 (CYP) 2B4 enzyme where the substitution, on the proximal surface of the active site, of a conserved phenylalanine 429 residue with histidine seems to hamper the formation of the active species, Compound I (porphyrin cation radical-Fe(IV) = O, Cpd I) from the ferric hydroperoxo (Fe(III)OOH-, Cpd 0) precursor. Here we report a study based on extensive molecular dynamic (MD) simulations of 4 CYP-2B4 point mutations compared to the WT enzyme, having the goal of better clarifying the importance of the proximal Phe429 residue on CYP 2B4 catalytic properties. To consolidate the huge amount of data coming from five simulations and extract the most distinct structural features of the five species studied we made an extensive use of cluster analysis. The results show that all studied single polymorphisms of F429, with different side chain properties: i) drastically alter the reservoir of conformations accessible by the protein, perturbing global dynamics ii) expose the thiolate group of residue Cys436 to the solvent, altering the electronic properties of Cpd0 and iii) affect the various ingress and egress channels connecting the distal sites with the bulk environment, altering the reversibility of these channels. In particular, it was observed that the wild type enzyme exhibits unique structural features as compared to all mutant species in terms of weak interactions (hydrogen bonds) that generate a completely different dynamical behavior of the complete system. Albeit not conclusive, the current computational investigation sheds some light on the subtle and critical effects that proximal single-site mutations can exert on the functional mechanisms of human microsomal CYPs which should go rather far beyond local structure characterization.

Galileo photometry of Apollo landing sites

NASA Technical Reports Server (NTRS)

Helfenstein, P.; Veverka, J.; Head, James W.; Pieters, C.; Pratt, S.; Mustard, J.; Klaasen, K.; Neukum, G.; Hoffmann, H.; Jaumann, R.

1993-01-01

As of December 1992, the Galileo spacecraft performed its second and final flyby (EM2), of the Earth-Moon system, during which it acquired Solid State Imaging (SSI) camera images of the lunar surface suitable for photometric analysis using Hapke's, photometric model. These images, together with those from the first flyby (EM1) in December 1989, provide observations of all of the Apollo landing sites over a wide range of photometric geometries and at eight broadband filter wavelengths ranging from 0.41 micron to 0.99 micron. We have completed a preliminary photometric analysis of Apollo landing sites visible in EM1 images and developed a new strategy for a more complete analysis of the combined EM1 and EM2 data sets in conjunction with telescopic observations and spectrogoniometric measurements of returned lunar samples. No existing single data set, whether from spacecraft flyby, telescopic observation, or laboratory analysis of returned samples, describes completely the light scattering behavior of a particular location on the Moon at all angles of incidence (i), emission (e), and phase angles (a). Earthbased telescopic observations of particular lunar sites provide good coverage of incidence nad phase angles, but their range in emission angle is limited to only a few degrees because of the Moon's synchronous rotation. Spacecraft flyby observations from Galileo are now available for specific lunar features at many photometric geometries unobtainable from Earth; however, this data set lacks coverage at very small phase angles (a less than 13 deg) important for distinguishing the well-known 'opposition effect'. Spectrogoniometric measurements from returned lunar samples can provide photometric coverage at almost any geometry; however, mechanical properties of prepared particulate laboratory samples, such as particle compaction and macroscopic roughness, likely differ from those on the lunar surface. In this study, we have developed methods for the simultaneous analysis of all three types of data: we combine Galileo and telescopic observations to obtain the most complete coverage with photometric geometry, and use spectrogoniometric observations of lunar soils to help distinguish the photometric effects of macroscopic roughness from those caused by particle phase function behavior (i.e., the directional scattering properties of regolith particles).

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

DOE PAGES

Taddei, Keith M.; Sturza, M.; Chung, Duck -Yung; ...

2015-09-14

By simultaneously displaying magnetism and superconductivity in a single phase, the iron-based superconductors provide a model system for the study of magnetism's role in superconductivity. The class of intercalated iron selenide superconductors is unique among these in having the additional property of phase separation and coexistence of two distinct phases—one majority phase with iron vacancy ordering and strong antiferromagnetism, and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfully synthesized separate frommore » the majority phase. In order to better understand this minority phase, a series of high-quality Cs xFe 2–ySe 2 single crystals with (0.8 ≤ x ≤ 1;0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show that the average I4/mmm structure of the minority phase is distinctly different from the high-temperature I4/mmm parent structure. Moreover, single-crystal diffraction reveals the presence of discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from three-dimensional Cs vacancy ordering. This model predicts a 25% vacancy of the Cs site in the minority phase which is consistent with the site's refined occupancy. Magnetization measurements performed in tandem with neutron single-crystal diffraction provide evidence that the minority phase is the host of superconductivity. Lastly, our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the nominal valence of iron.« less

One- and two-photon states for quantum information

NASA Astrophysics Data System (ADS)

Peters, Nicholas A.

To find expression stability among transgenic lines, the Recombinase Mediated Transgene Integration (RMTI) technology using the Cre/ lox-mediated site-specific gene integration system was used. The objectives were to develop an efficient method of site-specific transgene integration and to test the effectiveness of this method by assaying transgene expression in the RMTI lines. The RMTI technology allows the precise integration of a transgene in a previously placed target genomic location containing a lox site. The efficiency of CRE-mediated site-specific integration in rice by particle bombardment was found to vary from 3 to 28% in nine different experiments. Some hemizygous site-specific integration plants that were derived from homozygous target locus were found to undergo CRE-mediated reversion of the integration locus. No reversion was observed in callus; however, reverting cells may have been excluded due to selection pressure. The expression of the transgene gus was studied in all 40 callus lines, 12 regenerated T0 plants and the T1 and T2 progenies of 5 lines. The isogenic SC lines had an average expression level based on the activity of beta-glucuronidase of 158 +/- 9 units/mg protein (mean +/- SEM; n=3; variance within SC lines are expressed as standard error of the mean SEM) indicating a significantly higher level of expression, as compared to MC lines that had a much lower expression level 44 +/- 8 units/mg protein (mean +/- SEM; n=3) and the imprecise lines that had 22 +/- 8 units/mg protein (mean +/- SEM; n=3). Transgene expression in the callus cells of precise single copy lines varied by ˜3 fold, whereas that in multi-copy lines varied by ˜30 fold. Furthermore, precise single copy lines, on an average, contained ˜3.5 fold higher expression than multi-copy lines. Transgene expression in the plants of precise single-copy lines was highly variable, which was found to be due to the loss of the integration because of CRE-mediated reversion in the locus. (Abstract shortened by UMI.)

Laparoendoscopic single-site extraperitoneal inguinal hernia repair: initial experience in 10 patients.

PubMed

Do, Minh; Liatsikos, Evangelos; Beatty, John; Haefner, Tim; Dunn, Ian; Kallidonis, Panagiotis; Stolzenburg, Jens-Uwe

2011-06-01

Recent technical advances and a trend toward laparoscopic single incision surgery have led us to explore the feasibility of laparoendoscopic single-site (LESS) hernia repair. We present our technique and initial experience with LESS extraperitoneal inguinal hernia repair in 10 consecutive men with unilateral inguinal hernias. Age range was 43.7 (28-64) years. Mean body mass index was 28 (range 24-30). Six were left inguinal hernias. There were six indirect and four direct hernias. Three patients had undergone previous open appendectomy. Incarcerated or bilateral hernias were excluded from our initial series. All cases were performed by three surgeons who were experienced in conventional totally extraperitoneal laparoscopic hernia repair as well as experienced in LESS. A literature review of current single-port inguinal hernia repair data is also presented. The mean operative time was 53 minutes (range 45-65  min). The average length of skin incision was 2.8  cm (range 2.3-3.2  cm). No drain was necessary in any of the patients, while no recordable bleeding was observed. There were no intraoperative or immediate postoperative complications. Hospitalization period was 2 days for all patients. After a limited follow-up of 1 month, there have been no recurrences and no complaints of testicular pain. The results of the current series compare favorably with those found in a literature review. LESS extraperitoneal inguinal hernia repair is both feasible and safe, although more technically demanding than its conventional laparoscopic counterpart. Although the cosmetic result with the former approach may prove superior, there are standing questions regarding the complications and long-term outcome. Randomized and if possible blinded trials that compare conventional and single-incision laparoscopic hernia repair may help to distinguish the most advantageous technique.

Site directed recombination

DOEpatents

Jurka, Jerzy W.

1997-01-01

Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

Site-specific ligation of anthracene-1,8-dicarboxylates to an Mn12 core: a route to the controlled functionalisation of single-molecule magnets.

PubMed

Pacchioni, Mirko; Cornia, Andrea; Fabretti, Antonio C; Zobbi, Laura; Bonacchi, Daniele; Caneschi, Andrea; Chastanet, Guillaume; Gatteschi, Dante; Sessoli, Roberta

2004-11-21

A novel single-molecule magnet of the Mn12 family, [Mn12O12(O2CC6H5)8(L)4(H2O)4].8CH2Cl2, has been synthesised by site-specific ligand exchange using a tailor-made dicarboxylate (L2-), which leads to selective occupation of axial binding sites.

New insights into Cu/SSZ-13 SCR catalyst acidity. Part I: Nature of acidic sites probed by NH 3 titration

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

Luo, Jinyong; Gao, Feng; Kamasamudram, Krishna

In this work we investigated an unusual acidity feature of a Cu/SSZ-13 catalyst used in selective catalytic reduction of NOx with NH3 (NH3-SCR). In particular, this catalyst showed two distinct NH3 desorption peaks in NH3-TPD measurements, in contrast to single, unresolved desorption peaks observed for other Cu-exchanged zeolites conventionally used in the SCR studies, including its isostructural but chemically different analogue Cu/SAPO-34. We further observed that the intensities of the two TPD peaks, which represented the amount of stored NH3, changed in opposite directions in response to progressive mild hydrothermal aging, while the total storage capacity was preserved. We proposedmore » an explanation for this remarkable behavior, by using model reference samples and additional characterization techniques. At least three NH3 storage sites were identified: two distinct populations of Cu sites responsible for low-temperature NH3 storage, and Brønsted acid sites responsible for high-temperature NH3 storage. Contrary to the commonly accepted mechanism that Brønsted acid site loss during hydrothermal aging is driven by dealumination, we concluded that the decline in the number of Brønsted acid sites upon mild hydrothermal aging for Cu/SSZ-13 was not due to dealumination, but rather transformation of Cu sites, i.e., gradual conversion of ZCuOH (Cu2+ singly coordinated with Zeolite) to Z2Cu (Cu2+ doubly coordinated with Zeolite). This transformation was responsible for the increased low-temperature desorption peak in NH3-TPD since each ZCuOH adsorbed ~1 NH3 molecule while each Z2Cu adsorbed ~2 NH3 molecules under the conditions used here. These findings were used in Part II of this series of studies to develop a method for quantifying hydrothermal ageing of industrial Cu/SSZ-13 SCR catalysts. Authors would like to thank Randall Jines for his help with collecting the reactor data, Nancy W. Washton for measuring the NMR data and Tamas Varga for in-situ XRD measurements. FG and CHFP gratefully acknowledge supports from the United States Department of Energy (DOE), Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Part of the research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle.« less

Integrating seasonal information on nutrients and benthic algal biomass into stream water quality monitoring

USGS Publications Warehouse

Konrad, Christopher P.; Munn, Mark D.

2016-01-01

Benthic chlorophyll a (BChl a) and environmental factors that influence algal biomass were measured monthly from February through October in 22 streams from three agricultural regions of the United States. At-site maximum BChl a ranged from 14 to 406 mg/m2 and generally varied with dissolved inorganic nitrogen (DIN): 8 out of 9 sites with at-site median DIN >0.5 mg/L had maximum BChl a >100 mg/m2. BChl aaccrued and persisted at levels within 50% of at-site maximum for only one to three months. No dominant seasonal pattern for algal biomass accrual was observed in any region. A linear model with DIN, water surface gradient, and velocity accounted for most of the cross-site variation in maximum chlorophyll a(adjusted R2 = 0.7), but was no better than a single value of DIN = 0.5 mg/L for distinguishing between low and high-biomass sites. Studies of nutrient enrichment require multiple samples to estimate algal biomass with sufficient precision given the magnitude of temporal variability of algal biomass. An effective strategy for regional stream assessment of nutrient enrichment could be based on a relation between maximum BChl a and DIN based on repeat sampling at sites selected to represent a gradient in nutrients and application of the relation to a larger number of sites with synoptic nutrient information.

Investigation of hydrogen interaction with defects in zirconia

NASA Astrophysics Data System (ADS)

Melikhova, O.; Kuriplach, J.; Čížek, J.; Procházka, I.; Brauer, G.; Anwand, W.

2010-04-01

Defect studies of a ZrO2 + 9 mol. % Y2O3 single crystal were performed in this work using a high resolution positron lifetime spectroscopy combined with slow positron implantation spectroscopy. In order to elucidate the nature of positron trapping sites observed experimentally, the structural relaxations of several types of vacancy-like defects in zirconia were performed and positron characteristics for them were calculated. Relaxed atomic configurations of studied defects were obtained by means of ab initio pseudopotential method within the supercell approach. Theoretical calculations indicated that neither oxygen vacancies nor their neutral complexes with substitute yttrium atoms are capable of positron trapping. On the other hand, zirconium vacancies are deep positron traps and are most probably responsible for the saturated positron trapping observed in yttria stabilized zirconia single crystals. However, the calculated positron lifetime for zirconium vacancy is apparently longer than the experimental value corresponding to a single-component spectrum measured for the cubic ZrO2 + 9 mol. % Y2O3 single crystal. It was demonstrated that this effect can be explained by hydrogen trapped in zirconium vacancies. On the basis of structure relaxations, we found that zirconium vacancy - hydrogen complexes represent deep positron traps with the calculated lifetime close to the experimental one. In zirconium vacancy - hydrogen complexes the hydrogen atom forms an O-H bond with one of the nearest neighbour oxygen atoms. The calculated bond length is close to 1 Å.

Superposition model analysis of zero field splitting for Mn2+ in some host single crystals

NASA Astrophysics Data System (ADS)

Bansal, R. S.; Ahlawat, P.; Bharti, M.; Hooda, S. S.

2013-07-01

The Newman superposition model has been used to investigate the substitution of Mn2+ for Zn2+ site in ammonium tetra flurozincate dihydrate and for Co2+ site in cobalt ammonium phosphate hexahydrate and cobalt potassium phosphate hexahydrate single crystals. The calculated values of zero field splitting parameter b 2 0 at room temperature fit the experimental data with average intrinsic parameters overline{b}2 (F) = -0.0531 cm-1 for fluorine and overline{b}2 (O) = -0.0280 cm-1 for oxygen, taken t 2 = 7 for Mn2+ doped in ammonium tetra fluorozincate dihydrate single crystals. The values of overline{b}2 determined for Mn2+ doped in cobalt ammonium phosphate hexahydrate are -0.049 cm-1 for site I and -0.045 cm-1 for site II and in cobalt pottasium phosphate hexahydrate single crystals it is found to be overline{b}2 = -0.086 cm-1. We find close agreement between theoretical and experimental values of b 2 0.

Single site laparoscopic right hemicolectomy: an oncological feasible option

PubMed Central

2010-01-01

Introduction We present the first 7 cases of single site right hemicolectomy in Asia using the new Single Site Laparoscopy (SSL) access system from Ethicon Endo-surgery. Methods Right hemicolectomy was performed using the new Single Site Laparoscopy (SSL) access system. Patient demographics, operative time, histology and post operative recovery and complications were collected and analysed. Results The median operative time was 90 mins (range 60 - 150 mins) and a median wound size of 2.5 cm (range 2 to 4.5 cm). The median number of lymph nodes harvested was 24 (range 20 to 34 lymph nodes). The median length of proximal margin was 70 mm (range 30 to 145 mm) and that of distal margin was 50 mm (35 to 120 mm). All patients had a median hospital stay of 7 days (range 5 to 11) and there were no significant perioperative complications except for 1 patient who had a minor myocardial event. Conclusion Right hemicolectomy using SSL access system is feasible and safe for oncologic surgery. PMID:20825658

Adjustment of regional regression equations for urban storm-runoff quality using at-site data

USGS Publications Warehouse

Barks, C.S.

1996-01-01

Regional regression equations have been developed to estimate urban storm-runoff loads and mean concentrations using a national data base. Four statistical methods using at-site data to adjust the regional equation predictions were developed to provide better local estimates. The four adjustment procedures are a single-factor adjustment, a regression of the observed data against the predicted values, a regression of the observed values against the predicted values and additional local independent variables, and a weighted combination of a local regression with the regional prediction. Data collected at five representative storm-runoff sites during 22 storms in Little Rock, Arkansas, were used to verify, and, when appropriate, adjust the regional regression equation predictions. Comparison of observed values of stormrunoff loads and mean concentrations to the predicted values from the regional regression equations for nine constituents (chemical oxygen demand, suspended solids, total nitrogen as N, total ammonia plus organic nitrogen as N, total phosphorus as P, dissolved phosphorus as P, total recoverable copper, total recoverable lead, and total recoverable zinc) showed large prediction errors ranging from 63 percent to more than several thousand percent. Prediction errors for 6 of the 18 regional regression equations were less than 100 percent and could be considered reasonable for water-quality prediction equations. The regression adjustment procedure was used to adjust five of the regional equation predictions to improve the predictive accuracy. For seven of the regional equations the observed and the predicted values are not significantly correlated. Thus neither the unadjusted regional equations nor any of the adjustments were appropriate. The mean of the observed values was used as a simple estimator when the regional equation predictions and adjusted predictions were not appropriate.

Runoff-generated debris flows: observations and modeling of surge initiation, magnitude, and frequency

USGS Publications Warehouse

Kean, Jason W.; McCoy, Scott W.; Tucker, Gregory E.; Staley, Dennis M.; Coe, Jeffrey A.

2013-01-01

Runoff during intense rainstorms plays a major role in generating debris flows in many alpine areas and burned steeplands. Yet compared to debris flow initiation from shallow landslides, the mechanics by which runoff generates a debris flow are less understood. To better understand debris flow initiation by surface water runoff, we monitored flow stage and rainfall associated with debris flows in the headwaters of two small catchments: a bedrock-dominated alpine basin in central Colorado (0.06 km2) and a recently burned area in southern California (0.01 km2). We also obtained video footage of debris flow initiation and flow dynamics from three cameras at the Colorado site. Stage observations at both sites display distinct patterns in debris flow surge characteristics relative to rainfall intensity (I). We observe small, quasiperiodic surges at low I; large, quasiperiodic surges at intermediate I; and a single large surge followed by small-amplitude fluctuations about a more steady high flow at high I. Video observations of surge formation lead us to the hypothesis that these flow patterns are controlled by upstream variations in channel slope, in which low-gradient sections act as “sediment capacitors,” temporarily storing incoming bed load transported by water flow and periodically releasing the accumulated sediment as a debris flow surge. To explore this hypothesis, we develop a simple one-dimensional morphodynamic model of a sediment capacitor that consists of a system of coupled equations for water flow, bed load transport, slope stability, and mass flow. This model reproduces the essential patterns in surge magnitude and frequency with rainfall intensity observed at the two field sites and provides a new framework for predicting the runoff threshold for debris flow initiation in a burned or alpine setting.

Evaluation and Optimization of China's Anthropogenic CO2 Emissions using Observations from Northern China (2005-2009).

NASA Astrophysics Data System (ADS)

Dayalu, A.; Munger, J. W.; Wang, Y.; Wofsy, S.; Zhao, Y.; Nielsen, C. P.; Nehrkorn, T.; McElroy, M. B.; Chang, R.

2017-12-01

China has pledged to peak carbon emissions by 2030, but there continues to be significant uncertainty in estimates of its anthropogenic carbon dioxide (CO2) emissions. In this study, we evaluate the performance of three anthropogenic CO2 inventories, two global and one regional, using five years of continuous hourly observations from a site in Northern China. We model five years of continuous hourly observations (2005 to 2009) using the Stochastic Time-Inverted Lagrangian Transport Model (STILT) run in backward time mode driven by high resolution meteorology from the Weather Research and Forecasting Model version 3.6.1 (WRF) with vegetation fluxes prescribed by a simple biosphere model. We calculate regional enhancements to advected background CO2 derived from NOAA CarbonTracker on seasonal and annual bases and use observations to optimize emissions inventories within the site's influence region at these timescales. Finally, we use annual enhancements to examine carbon intensity of provinces in and adjacent to Northern China as CO2 per unit of the region's GDP to evaluate the effects of local and global economic events on CO2 emissions. With the exception of peak growing season where discrepancies are confounded by errors in the vegetation model, we find the regional inventory agrees significantly better with observations than the global inventories at all timescales. Here we use a single measurement site; significant improvements in inventory optimizations can be achieved with a network of measurements stations. This study highlights the importance of China-specific data over global averages in emissions evaluation and demonstrates the value of top-down studies in independently evaluating inventory performance. We demonstrate the framework's ability to resolve differences of at least 20% among inventories, establishing a benchmark for ongoing efforts to decrease uncertainty in China's reported CO2 emissions estimates.

Coastal sea level measurements using a single geodetic GPS receiver

NASA Astrophysics Data System (ADS)

Larson, Kristine M.; Löfgren, Johan S.; Haas, Rüdiger

2013-04-01

This paper presents a method to derive local sea level variations using data from a single geodetic-quality Global Navigation Satellite System (GNSS) receiver using GPS (Global Positioning System) signals. This method is based on multipath theory for specular reflections and the use of Signal-to-Noise Ratio (SNR) data. The technique could be valuable for altimeter calibration and validation. Data from two test sites, a dedicated GPS tide gauge at the Onsala Space Observatory (OSO) in Sweden and the Friday Harbor GPS site of the EarthScope Plate Boundary Observatory (PBO) in USA, are analyzed. The sea level results are compared to independently observed sea level data from nearby and in situ tide gauges. For OSO, the Root-Mean-Square (RMS) agreement is better than 5 cm, while it is in the order of 10 cm for Friday Harbor. The correlation coefficients are better than 0.97 for both sites. For OSO, the SNR-based results are also compared with results from a geodetic analysis of GPS data of a two receivers/antennae tide gauge installation. The SNR-based analysis results in a slightly worse RMS agreement with respect to the independent tide gauge data than the geodetic analysis (4.8 cm and 4.0 cm, respectively). However, it provides results even for rough sea surface conditions when the two receivers/antennae installation no longer records the necessary data for a geodetic analysis.

Identification of a common single nucleotide polymorphism at the primer binding site of D2S1360 that causes heterozygote peak imbalance when using the Investigator HDplex Kit.

PubMed

Inokuchi, Shota; Yamashita, Yasuhiro; Nishimura, Kazuma; Nakanishi, Hiroaki; Saito, Kazuyuki

2017-11-01

Phenomena known as null alleles and peak imbalance can occur because of mutations in the primer binding sites used for DNA typing. In these cases, an accurate statistical evaluation of DNA typing is difficult. The estimated likelihood ratio is incorrectly calculated because of the null allele and allele dropout caused by mutation-induced peak imbalance. Although a number of studies have attempted to uncover examples of these phenomena, few reports are available on the human identification kit manufactured by Qiagen. In this study, 196 Japanese individuals who were heterozygous at D2S1360 were genotyped using an Investigator HDplex Kit with optimal amounts of DNA. A peak imbalance was frequently observed at the D2S1360 locus. We performed a sequencing analysis of the area surrounding the D2S1360 repeat motif to identify the cause for peak imbalance. A point mutation (G>A transition) 136 nucleotides upstream from the D2S1360 repeat motif was discovered in a number of samples. The allele frequency of the mutation was 0.0566 in the Japanese population. Therefore, human identification or kinship testing using the Investigator HDplex Kit requires caution because of the higher frequency of single nucleotide polymorphisms at the primer binding site of D2S1360 locus in the Japanese population.

Double Pass 595 nm Pulsed Dye Laser Does Not Enhance the Efficacy of Port Wine Stains Compared with Single Pass: A Randomized Comparison with Histological Examination.

PubMed

Yu, Wenxin; Zhu, Jiafang; Wang, Lizhen; Qiu, Yajing; Chen, Yijie; Yang, Xi; Chang, Lei; Ma, Gang; Lin, Xiaoxi

2018-03-27

To compare the efficacy and safety of double-pass pulsed dye laser (DWL) and single-pass PDL (SWL) in treating virgin port wine stain (PWS). The increase in the extent of vascular damage attributed to the use of double-pass techniques for PWS remains inconclusive. A prospective, side-by-side comparison with a histological study for virgin PWS is still lacking. Twenty-one patients (11 flat PWS, 10 hypertrophic PWS) with untreated PWS underwent 3 treatments at 2-month intervals. Each PWS was divided into three treatment sites: SWL, DWL, and untreated control. Chromametric and visual evaluation of the efficacy and evaluation of side effects were conducted 3 months after final treatment. Biopsies were taken at the treated sites immediately posttreatment. Chromametric and visual evaluation suggested that DWL sites showed no significant improvement compared with SWL (p > 0.05) in treating PWS. The mean depth of photothermal damage to the vessels was limited to a maximum of 0.36-0.41 mm in both SWL and DWL sides. Permanent side effects were not observed in any patients. Double-pass PDL does not enhance PWS clearance. To improve the clearance of PWS lesions, either the depth of laser penetration should be increased or greater photothermal damage to vessels should be generated.

The action of blocking agents applied to the inner face of Ca(2+)-activated K+ channels from human erythrocytes.

PubMed

Dunn, P M

1998-09-15

The actions of clotrimazole and cetiedil, two drugs known to inhibit the Gardos channel, have been studied on single intermediate conductance calcium-activated potassium (IKCa) channels in inside out patches from human red blood cells, and compared with those of TEA and Ba2+ applied to the cytoplasmic face of the membrane. TEA produced a fast block which was observed as a reduction in the amplitude of the single channel current. This effect was weakly voltage dependent with the fraction of the membrane potential sensed by TEA at its binding site (delta) of 0.18 and a Kd at 0 mV of 20.5 mM. Ba2+ was a very potent blocker of the channel, breaking the single channel activity up into bursts, inter-spersed with silent periods lasting several seconds. The effect of Ba2+ was very voltage sensitive, delta = 0.44, and a Kd at 0 mV of 0.15 microM. Clotrimazole applied to the inner face of the membrane at a concentration < or = 1 microM produced a slow block resulting in bursts of channel activity separated by quiescent periods lasting many seconds. The effect of clotrimazole was mimicked by a quaternary derivative UCL 1559, in keeping with an action at the cytoplasmic face of the channel. A high concentration of cetiedil (100 microM) produced only a weak block of the channel. The kinetics of this action were very slow, with burst and inter-burst intervals lasting several minutes. While inhibition of the Gardos channel by cetiedil is unlikely to involve an intracellular site of action, if clotrimazole is able to penetrate the membrane, part of its effect may result from binding to an intracellular site on the channel.

Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations.

PubMed

Capoferri, Luigi; Leth, Rasmus; ter Haar, Ernst; Mohanty, Arun K; Grootenhuis, Peter D J; Vottero, Eduardo; Commandeur, Jan N M; Vermeulen, Nico P E; Jørgensen, Flemming Steen; Olsen, Lars; Geerke, Daan P

2016-03-01

Cytochrome P450 BM3 (CYP102A1) mutant M11 is able to metabolize a wide range of drugs and drug-like compounds. Among these, M11 was recently found to be able to catalyze formation of human metabolites of mefenamic acid and other nonsteroidal anti-inflammatory drugs (NSAIDs). Interestingly, single active-site mutations such as V87I were reported to invert regioselectivity in NSAID hydroxylation. In this work, we combine crystallography and molecular simulation to study the effect of single mutations on binding and regioselective metabolism of mefenamic acid by M11 mutants. The heme domain of the protein mutant M11 was expressed, purified, and crystallized, and its X-ray structure was used as template for modeling. A multistep approach was used that combines molecular docking, molecular dynamics (MD) simulation, and binding free-energy calculations to address protein flexibility. In this way, preferred binding modes that are consistent with oxidation at the experimentally observed sites of metabolism (SOMs) were identified. Whereas docking could not be used to retrospectively predict experimental trends in regioselectivity, we were able to rank binding modes in line with the preferred SOMs of mefenamic acid by M11 and its mutants by including protein flexibility and dynamics in free-energy computation. In addition, we could obtain structural insights into the change in regioselectivity of mefenamic acid hydroxylation due to single active-site mutations. Our findings confirm that use of MD and binding free-energy calculation is useful for studying biocatalysis in those cases in which enzyme binding is a critical event in determining the selective metabolism of a substrate. © 2016 Wiley Periodicals, Inc.

Site-specific treatment outcome in smokers following 12 months of supportive periodontal therapy.

PubMed

Bunaes, Dagmar F; Lie, Stein Atle; Åstrøm, Anne Nordrehaug; Mustafa, Kamal; Leknes, Knut N

2016-12-01

To evaluate the effect of cigarette smoking on periodontal health at patient, tooth, and site levels following supportive therapy. Eighty chronic periodontitis patients, 40 smokers and 40 non-smokers, were recruited to a single-arm clinical trial. Periodontal examinations were performed at baseline (T0), 3 months following active periodontal therapy (T1), and 12 months following supportive periodontal therapy (T2). Smoking status was validated measuring serum cotinine levels. Probing depth (PD) ≥ 5 mm with bleeding on probing (BoP) was defined as the primary outcome. Logistic regression analyses adjusted for clustered observations of patients, teeth, and sites and mixed effects models were employed to analyse the data. All clinical parameters improved from T0 to T2 (p < 0.001), whereas PD, bleeding index (BI), and plaque index (PI) increased from T1 to T2 in smokers and non-smokers (p < 0.001). An overall negative effect of smoking was revealed at T2 (OR = 2.78, CI: 1.49, 5.18, p < 0.001), with the most pronounced effect at maxillary single-rooted teeth (OR = 5.08, CI: 2.01, 12.78, p < 0.001). At the patient level, less variation in treatment outcome was detected within smokers (ICC = 0.137) compared with non-smokers (ICC = 0.051). Smoking has a negative effect on periodontal health following 12 months of supportive therapy, in particular at maxillary single-rooted teeth. © 2016 The Authors. Journal of Clinical Periodontology Published by John Wiley & Sons Ltd.

A Comprehensive Study of Formic Acid Oxidation on Palladium Nanocrystals with Different Types of Facets and Twin Defects

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

Choi, Sang; Herron, Jeffrey A.; Scaranto, Jessica

2015-07-13

Palladium has been recognized as the best anodic, monometallic electrocatalyst for the formic acid oxidation (FAO) reaction in a direct formic acid fuel cell. Here we report a systematic study of FAO on a variety of Pd nanocrystals, including cubes, right bipyramids, octahedra, tetrahedra, decahedra, and icosahedra. These nanocrystals were synthesized with approximately the same size, but different types of facets and twin defects on their surfaces. Our measurements indicate that the Pd nanocrystals enclosed by {1 0 0} facets have higher specific activities than those enclosed by {1 1 1} facets, in agreement with prior observations for Pd single-crystalmore » substrates. If comparing nanocrystals predominantly enclosed by a specific type of facet, {1 0 0} or {1 1 1}, those with twin defects displayed greatly enhanced FAO activities compared to their single-crystal counterparts. To rationalize these experimental results, we performed periodic, self-consistent DFT calculations on model single-crystal substrates of Pd, representing the active sites present in the nanocrystals used in the experiments. The calculation results suggest that the enhancement of FAO activity on defect regions, represented by Pd(2 1 1) sites, compared to the activity of both Pd(1 0 0) and Pd(1 1 1) surfaces, could be attributed to an increased flux through the HCOO-mediated pathway rather than the COOH-mediated pathway on Pd(2 1 1). Since COOH has been identified as a precursor to CO, a site-poisoning species, a lower coverage of CO at the defect regions will lead to a higher activity for the corresponding nanocrystal catalysts, containing those defect regions.« less

Simple Models of SL-9 Impact Plumes

NASA Astrophysics Data System (ADS)

Harrington, J.; Deming, L. D.

1996-09-01

The impacts of the larger fragments of Comet Shomaker-Levy 9 on Jupiter left debris patterns of consistent appearance, likely caused by the landing of the observed impact plumes. Realistic fluid simulations of impact plume evolution may take months to years for even single computer runs. To provide guidance for these models and to elucidate the most basic aspects of the plumes, debris patterns, and their ultimate effect on the atmosphere, we have developed simple models that reproduce many of the key features. These Monte-Carlo models divide the plume into discrete mass elements, assign to them a velocity distribution based on numerical impact models, and follow their ballistic trajectories until they hit the planet. If particles go no higher than the observed ~ 3,000 km plume heights, they cannot reach the observed crescent pattern located ~ 10,000 km from the impact sites unless they slide horizontally after ballistic flight. By introducing parameterized sliding or higher trajectories, we can reproduce most of the observed impact features, including the central streak, the crescent, and the ephemeral ring located ~ 30,000 km from the impact sites. We also keep track of the amounts of energy and momentum delivered to the atmosphere as a function of time and location, for use in atmospheric models (D. Deming and J. Harrington, this meeting).

Inland Sea Spray Aerosol Transport and Incomplete Chloride Depletion: Varying Degrees of Reactive Processing Observed during SOAS

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

Bondy, Amy L.; Wang, Bingbing; Laskin, Alexander

Multiphase reactions involving sea spray aerosol (SSA) impact trace gases budgets in coastal regions by acting as a reservoir for oxidized nitrogen and sulfur species, as well as a source of halogen gases (HCl, ClNO2, etc.). While most studies of multiphase reactions on SSA have focused on marine environments, far less is known about SSA transported inland. Herein, single particle measurements of SSA are reported at a site > 320 km from the Gulf of Mexico, with transport times of 7-68 h. Samples were collected during the Southern Oxidant and Aerosol Study (SOAS) in June-July 2013 near Centreville, Alabama. SSAmore » was observed in 93% of 42 time periods analyzed. During two marine air mass periods, SSA represented significant number fractions of particles in the accumulation (0.2-1.0 μm, 11%) and coarse (1.0-10.0 μm, 35%) modes. Chloride content of SSA particles ranged from full to partial depletion, with 24% of SSA particles containing chloride (mole fraction of Cl/Na > 0.1, 90% chloride depletion). Both the frequent observation of SSA at an inland site and the range of chloride depletion observed, suggest that SSA may represent an underappreciated inland sink for NOx/SO2 and source of halogen gases.« less

Overproduced esterases in Culex pipiens quinquefasciatus (Diptera: Culicidae) from Vietnam.

PubMed

Pasteur, N; Marquine, M; Hoang, T H; Nam, V S; Failloux, A B

2001-09-01

The electrophoretic polymorphism of loci encoding for 10 enzymes was studied in Culex p. quinquefasciatus Say from six localities of Vietnam. The analysis of 11 "neutral genes" showed that differentiation among samples was low, but significant (Fst = 0.06), and significantly related to geographic distance between sample sites. These results are similar to those observed in other countries (Europe and west Africa). A single type of overproduced esterases (A2-B2) was observed, and its frequency was high (60-100%) in all samples. This situation is in sharp contrast with that observed in other countries of South East Asia (China, South Korea and Japan), where two or more types of overproduced esterases have been reported. A map summarizing the geographic distribution of Asian Cr. p. quinquefasciatus with overproduced esterases is provided.

Evaluating the use of the Cleo 90 infusion set for patients on a palliative care unit.

PubMed

Schneider, Michael; Hoffmann, Martin; Lorenzl, Stefan

2009-08-01

Although the use of subcutaneous infusion is common in palliative care, problems can occur. Normally, butterfly needles are used; however, there are occasional issues with patients being able to walk around or with restless patients who suffer from delirium. In these cases, needles often dislocate; therefore, a small observational study was undertaken to evaluate the use of the Cleo 90 infusion set. The use of this needle system has been well established in diabetic patients who require continuous subcutaneous infusion of insulin, but has never been tested in a wider range of patients with other medications. In this 6-month study, 45 patients were identified for subcutaneous infusion and a total of 112 needles were used for this study, since we initially changed each site after 2 days to control the local site for adverse reactions. We have not observed any complications with drug combinations delivered via the attached tube and the needle, and have used up to five different drugs mixed together in a single syringe. Needles could be used for a mean time of 5 +/- 2 days (range 2-12 days). Local site reactions have been observed only with sodium chloride infusions, which were not delivered via a pump system. Reddening and induration of the skin occurred, but they were reversible after removing the needle. As this was a small study in only one unit, without standardization the results can only be observational. However, it has shown, for the first time, that the Cleo 90 needle can be safe and comfortable.

Effects of Transition-Metal Mixing on Na Ordering and Kinetics in Layered P 2 Oxides

NASA Astrophysics Data System (ADS)

Zheng, Chen; Radhakrishnan, Balachandran; Chu, Iek-Heng; Wang, Zhenbin; Ong, Shyue Ping

2017-06-01

Layered P 2 oxides are promising cathode materials for rechargeable sodium-ion batteries. In this work, we systematically investigate the effects of transition-metal (TM) mixing on Na ordering and kinetics in the NaxCo1 -yMnyO2 model system using density-functional-theory (DFT) calculations. The DFT-predicted 0-K stability diagrams indicate that Co-Mn mixing reduces the energetic differences between Na orderings, which may account for the reduction of the number of phase transformations observed during the cycling of mixed-TM P 2 layered oxides compared to a single TM. Using ab initio molecular-dynamics simulations and nudged elastic-band calculations, we show that the TM composition at the Na(1) (face-sharing) site has a strong influence on the Na site energies, which in turn impacts the kinetics of Na diffusion towards the end of the charge. By employing a site-percolation model, we establish theoretical upper and lower bounds for TM concentrations based on their effect on Na(1) site energies, providing a framework to rationally tune mixed-TM compositions for optimal Na diffusion.

Multiple core-hole formation by free-electron laser radiation in molecular nitrogen

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Surface Landing Site Weather Analysis for Constellation Program

NASA Technical Reports Server (NTRS)

Altino, Karen M.; Burns, K. Lee

2008-01-01

Weather information is an important asset for NASA's Constellation Program in developing the next generation space transportation system to fly to the International Space Station, the Moon and, eventually, to Mars. Weather conditions can affect vehicle safety and performance during multiple mission phases ranging from pre-launch ground processing to landing and recovery operations, including all potential abort scenarios. Meteorological analysis is an important contributor, not only to the development and verification of system design requirements but also to mission planning and active ground operations. Of particular interest are the surface atmospheric conditions at both nominal and abort landing sites for the manned Orion capsule. Weather parameters such as wind, rain, and fog all play critical roles in the safe landing of the vehicle and subsequent crew and vehicle recovery. The Marshall Space Flight Center Natural Environments Branch has been tasked by the Constellation Program with defining the natural environments at potential landing zones. Climatological time series of operational surface weather observations are used to calculate probabilities of occurrence of various sets of hypothetical vehicle constraint thresholds, Data are available for numerous geographical locations such that statistical analysis can be performed for single sites as well as multiple-site network configurations. Results provide statistical descriptions of how often certain weather conditions are observed at the site(s) and the percentage that specified criteria thresholds are matched or exceeded. Outputs are tabulated by month and hour of day to show both seasonal and diurnal variation. This paper will describe the methodology used for data collection and quality control, detail the types of analyses performed, and provide a sample of the results that can be obtained,

Modelling the range expansion of the Tiger mosquito in a Mediterranean Island accounting for imperfect detection.

PubMed

Tavecchia, Giacomo; Miranda, Miguel-Angel; Borrás, David; Bengoa, Mikel; Barceló, Carlos; Paredes-Esquivel, Claudia; Schwarz, Carl

2017-01-01

Aedes albopictus (Diptera; Culicidae) is a highly invasive mosquito species and a competent vector of several arboviral diseases that have spread rapidly throughout the world. Prevalence and patterns of dispersal of the mosquito are of central importance for an effective control of the species. We used site-occupancy models accounting for false negative detections to estimate the prevalence, the turnover, the movement pattern and the growth rate in the number of sites occupied by the mosquito in 17 localities throughout Mallorca Island. Site-occupancy probability increased from 0.35 in the 2012, year of first reported observation of the species, to 0.89 in 2015. Despite a steady increase in mosquito presence, the extinction probability was generally high indicating a high turnover in the occupied sites. We considered two site-dependent covariates, namely the distance from the point of first observation and the estimated yearly occupancy rate in the neighborhood, as predicted by diffusion models. Results suggested that mosquito distribution during the first year was consistent with what predicted by simple diffusion models, but was not consistent with the diffusion model in subsequent years when it was similar to those expected from leapfrog dispersal events. Assuming a single initial colonization event, the spread of Ae. albopictus in Mallorca followed two distinct phases, an early one consistent with diffusion movements and a second consistent with long distance, 'leapfrog', movements. The colonization of the island was fast, with ~90% of the sites estimated to be occupied 3 years after the colonization. The fast spread was likely to have occurred through vectors related to human mobility such as cars or other vehicles. Surveillance and management actions near the introduction point would only be effective during the early steps of the colonization.

FINAL REPORT (DE-FG02-97ER62338): Single-column modeling, GCM parameterizations, and ARM data

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

Richard C. J. Somerville

2009-02-27

Our overall goal is the development of new and improved parameterizations of cloud-radiation effects and related processes, using ARM data at all three ARM sites, and the implementation and testing of these parameterizations in global models. To test recently developed prognostic parameterizations based on detailed cloud microphysics, we have compared SCM (single-column model) output with ARM observations at the SGP, NSA and TWP sites. We focus on the predicted cloud amounts and on a suite of radiative quantities strongly dependent on clouds, such as downwelling surface shortwave radiation. Our results demonstrate the superiority of parameterizations based on comprehensive treatments ofmore » cloud microphysics and cloud-radiative interactions. At the SGP and NSA sites, the SCM results simulate the ARM measurements well and are demonstrably more realistic than typical parameterizations found in conventional operational forecasting models. At the TWP site, the model performance depends strongly on details of the scheme, and the results of our diagnostic tests suggest ways to develop improved parameterizations better suited to simulating cloud-radiation interactions in the tropics generally. These advances have made it possible to take the next step and build on this progress, by incorporating our parameterization schemes in state-of-the-art three-dimensional atmospheric models, and diagnosing and evaluating the results using independent data. Because the improved cloud-radiation results have been obtained largely via implementing detailed and physically comprehensive cloud microphysics, we anticipate that improved predictions of hydrologic cycle components, and hence of precipitation, may also be achievable.« less

Does physical or psychosocial workload modify the effect of musculoskeletal pain on sickness absence? A prospective study among the Finnish population.

PubMed

Neupane, Subas; Pensola, Tiina; Haukka, Eija; Ojajärvi, Anneli; Leino-Arjas, Päivi

2016-07-01

Previously, among food industry workers, multisite pain predicted sickness absence (SA) only in those with low biomechanical workload. Here we studied among a wide range of occupations whether the relationship of pain with SA was modified by the level of physical or psychosocial workload. A nationally representative sample (Health 2000 Survey) comprised 3420 occupationally active Finns aged 30-55 years. Baseline data on musculoskeletal pain during the preceding month, strenuous work history, current physical workload, job demands, job control, support at work, lifestyle, and chronic diseases were obtained in 2000/2001 by questionnaire, interview, and clinical examination. Musculoskeletal pain in 18 body locations was combined into four sites (neck, upper limbs, low back, and lower limbs) and classified as no pain, single-site pain, and multisite pain (2-4 sites). The data were linked with information from national registers on annual SA periods lasting ≥10 workdays for 2002-2008. Negative binomial regression analysis was used. At baseline, one-third of the study sample reported single-site and one-third multisite pain. Allowing for gender and age, the employees with multisite pain in strata with high physical workload and high job demands tended to have the highest risk of SA, but no statistically significant interactive effects between work factors and pain were observed. Further adjustment for health-related lifestyle and chronic diseases decreased the risk estimates in all strata. We did not find evidence for significant modification by physical or psychosocial workload of the relationship between musculoskeletal pain and SA periods lasting ≥10 workdays.

Characterizing Solution Surface Loop Conformational Flexibility of the GM2 Activator Protein

PubMed Central

2015-01-01

GM2AP has a β-cup topology with numerous X-ray structures showing multiple conformations for some of the surface loops, revealing conformational flexibility that may be related to function, where function is defined as either membrane binding associated with ligand binding and extraction or interaction with other proteins. Here, site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and molecular dynamic (MD) simulations are used to characterize the mobility and conformational flexibility of various structural regions of GM2AP. A series of 10 single cysteine amino acid substitutions were generated, and the constructs were chemically modified with the methanethiosulfonate spin label. Continuous wave (CW) EPR line shapes were obtained and subsequently simulated using the microscopic order macroscopic disorder (MOMD) program. Line shapes for sites that have multiple conformations in the X-ray structures required two spectral components, whereas spectra of the remaining sites were adequately fit with single-component parameters. For spin labeled sites L126C and I66C, spectra were acquired as a function of temperature, and simulations provided for the determination of thermodynamic parameters associated with conformational change. Binding to GM2 ligand did not alter the conformational flexibility of the loops, as evaluated by EPR and NMR spectroscopies. These results confirm that the conformational flexibility observed in the surface loops of GM2AP crystals is present in solution and that the exchange is slow on the EPR time scale (>ns). Furthermore, MD simulation results are presented and agree well with the conformational heterogeneity revealed by SDSL. PMID:25127419

An active-site phenylalanine directs substrate binding and C-H cleavage in the alpha-ketoglutarate-dependent dioxygenase TauD.

PubMed

McCusker, Kevin P; Klinman, Judith P

2010-04-14

Enzymes that cleave C-H bonds are often found to depend on well-packed hydrophobic cores that influence the distance between the hydrogen donor and acceptor. Residue F159 in taurine alpha-ketoglutarate dioxygenase (TauD) is demonstrated to play an important role in the binding and orientation of its substrate, which undergoes a hydrogen atom transfer to the active site Fe(IV)=O. Mutation of F159 to smaller hydrophobic side chains (L, V, A) leads to substantially reduced rates for substrate binding and for C-H bond cleavage, as well as increased contribution of the chemical step to k(cat) under steady-state turnover conditions. The greater sensitivity of these substrate-dependent processes to mutation at position 159 than observed for the oxygen activation process supports a previous conclusion of modularity of function within the active site of TauD (McCusker, K. P.; Klinman, J. P. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 19791-19795). Extraction of intrinsic deuterium kinetic isotope effects (KIEs) using single turnover transients shows 2- to 4-fold increase in the size of the KIE for F159V in relation to wild-type and F159L. It appears that there is a break in behavior following removal of a single methylene from the side chain of F159L to generate F159V, whereby the protein active site loses its ability to restore the internuclear distance between substrate and Fe(IV)=O that supports optimal hydrogenic wave function overlap.

Ultrasound-guided steroid tendon sheath injections in juvenile idiopathic arthritis: a 10-year single-center retrospective study.

PubMed

Peters, Shannon E; Laxer, Ronald M; Connolly, Bairbre L; Parra, Dimitri A

2017-04-11

The aims of this study were to: (a) Identify tendon sheaths most commonly treated with steroid injections in a pediatric patient population with Juvenile Idiopathic Arthritis (JIA); (b) Describe technical aspects of the procedure; (c) Characterize sonographic appearance of tenosynovitis in JIA; (d) Assess agreement between clinical request and sites injected. This was a 10 year single-center retrospective study (May 2006-April 2016) of patients with JIA referred by Rheumatology for ultrasound-guided tendon sheath injections. Patient demographics, clinical referral information, sonographic appearance of the tendon sheaths and technical aspects of the procedure were analyzed. There were 308 procedures of 244 patients (75% female, mean age 9.6 years) who underwent a total of 926 tendon sheath injections. Ankle tendons were most commonly injected (84.9%), specifically the tendon sheaths of tibialis posterior (22.3%), peroneus longus (20%) and brevis (19.7%). The majority of treated sites (91.9%) showed peritendinous fluid and sheath thickening on ultrasound. There were 2 minor intra-procedure complications without sequelae. A good agreement between clinical request and sites injected was observed. Ultrasound-guided tendon sheath injections with steroids are used frequently to treat patients with JIA. It is a safe intervention with a high technical success rate. The ankle region, specifically the medial compartment, is the site most commonly injected in this group of patients. The most common sonographic finding is peritendinous fluid and sheath thickening. These findings might assist clinicians and radiologists to characterize and more effectively manage tenosynovitis in patients with JIA.

Stability of detectability over 17 years at a single site and other lizard detection comparisons from Guam

USGS Publications Warehouse

Rodda, Gordon H.; Dean-Bradley, Kathryn; Campbell, Earl W.; Fritts, Thomas H.; Lardner, Bjorn; Yackel Adams, Amy A.; Reed, Robert N.

2015-01-01

To obtain quantitative information about population dynamics from counts of animals, the per capita detectabilities of each species must remain constant over the course of monitoring. We characterized lizard detection constancy for four species over 17 yr from a single site in northern Guam, a relatively benign situation because detection was relatively easy and we were able to hold constant the site, habitat type, species, season, and sampling method. We monitored two species of diurnal terrestrial skinks (Carlia ailanpalai [Curious Skink], Emoia caeruleocauda [Pacific Bluetailed Skink]) using glueboards placed on the ground in the shade for 3 h on rainless mornings, yielding 10,286 skink captures. We additionally monitored two species of nocturnal arboreal geckos (Hemidactylus frenatus [Common House Gecko]; Lepidodactylus lugubris [Mourning Gecko]) on the basis of 15,212 sightings. We compared these count samples to a series of complete censuses we conducted from four or more total removal plots (everything removed to mineral soil) totaling 400 m2(about 1% of study site) in each of the years 1995, 1999, and 2012, providing time-stamped quantification of detectability for each species. Unfortunately, the actual population trajectories taken by the four species were masked by unexplained variation in detectability. This observation of debilitating latent variability in lizard detectability under nearly ideal conditions undercuts our trust in population estimation techniques that fail to quantify venue-specific detectability, rely on pooled detection probability estimates, or assume that modulation in predefined environmental covariates suffices for estimating detectability.

Characterization of the rat RALDH1 promoter. A functional CCAAT and octamer motif are critical for basal promoter activity.

PubMed

Guimond, Julie; Devost, Dominic; Brodeur, Helene; Mader, Sylvie; Bhat, Pangala V

2002-12-12

Retinal dehydrogenase type 1 (RALDH1) catalyzes the oxidation of retinal to retinoic acid (RA), a metabolite of vitamin A important for embryogenesis and tissue differentiation. Rat RALDH1 is expressed to high levels in developing kidney, and in stomach, intestine epithelia. To understand the mechanisms of the transcriptional regulation of rat RALDH1, we cloned a 1360-base pair (bp) 5'-flanking region of RALDH1 gene. Using luciferase reporter constructs transfected into HEK 293 and LLCPK (kidney-derived) cells, basal promoter activity was associated with sequences between -80 and +43. In this minimal promoter region, TATA and CCAAT cis-acting elements as well as SP1, AP1 and octamer (Oct)-binding sites were present. The CCAAT box and Oct-binding site, located between positions -72 and -68 and -56 and -49, respectively, were shown by deletion analysis and site-directed mutation to be critical for promoter activity. Nuclear extracts from kidney cells contain proteins specifically binding the Oct and CCAAT sequences, resulting in the formation of six complexes, while different patterns of complexes were observed with non-kidney cell extracts. Gel shift assays using either single or double mutations of the Oct and CCAAT sequences as well as super shift assays demonstrated single and double occupancy of these two sites by Oct-1 and CBF-A. In addition, unidentified proteins also bound the Oct motif specifically in the absence of CBF-A binding. These results demonstrate specific involvement of Oct and CCAAT-binding proteins in the regulation of RALDH1 gene.

Time-Dependent Mechanical Response of APbX 3 (A = Cs, CH 3NH 3; X = I, Br) Single Crystals [The Dynamic Mechanical Properties of Lead-Halide Perovskite Single Crystals are Independent of A-site Cation Chemistry

DOE PAGES

Reyes-Martinez, Marcos A.; Abdelhady, Ahmed L.; Saidaminov, Makhsud I.; ...

2017-05-02

The ease of processing hybrid organic–inorganic perovskite (HOIPs) films, belonging to a material class with composition ABX 3, from solution and at mild temperatures promises their use in deformable technologies, including flexible photovoltaic devices, sensors, and displays. To successfully apply these materials in deformable devices, knowledge of their mechanical response to dynamic strain is necessary. The authors elucidate the time- and rate-dependent mechanical properties of HOIPs and an inorganic perovskite (IP) single crystal by measuring nanoindentation creep and stress relaxation. The observation of pop-in events and slip bands on the surface of the indented crystals demonstrate dislocation-mediated plastic deformation. Themore » magnitudes of creep and relaxation of both HOIPs and IPs are similar, negating prior hypothesis that the presence of organic A-site cations alters the mechanical response of these materials. Moreover, these samples exhibit a pronounced increase in creep, and stress relaxation as a function of indentation rate whose magnitudes reflect differences in the rates of nucleation and propagation of dislocations within the crystal structures of HOIPs and IP. In conclusion, this contribution provides understanding that is critical for designing perovskite devices capable of withstanding mechanical deformations.« less

The learning curve of laparoendoscopic single-site (LESS) cholecystectomy: definable, short, and safe.

PubMed

Hernandez, Jonathan; Ross, Sharona; Morton, Connor; McFarlin, Kellie; Dahal, Sujat; Golkar, Farhaad; Albrink, Michael; Rosemurgy, Alexander

2010-11-01

The applications of laparoendoscopic single-site (LESS) surgery, including cholecystectomy, are occurring quickly, although little is generally known about issues associated with the learning curve of this new technique including operative time, conversion rates, and safety. We prospectively followed all patients undergoing LESS cholecystectomy, and compared operations undertaken at our institutions in cohorts of 25 patients with respect to operative times, conversion rates, and complications. One-hundred fifty patients of mean age 46 years underwent LESS cholecystectomy. No significant differences in operative times were demonstrable between any of the 25-patient cohorts operated on at our institution. A significant reduction in operative times (p < 0.001) after completion of 75 LESS procedures was, however, identified with the experience of a single surgeon. No significant reduction in the number of procedures requiring an additional trocar(s) or conversion to open operations was observed after completion of 25 LESS cholecystectomies. Complication rates were low, and not significantly different between any 25-patient cohorts. For surgeons proficient with multi-incision laparoscopic cholecystectomy, the learning curve for LESS cholecystectomy begins near proficiency. Operative complications and conversions were infrequent and unchanged across successive 25-patient cohorts, and were similar to those reported for multi-incision laparoscopic cholecystectomy after the learning curve. Copyright © 2010 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Differences in the dynamics of serotonin reuptake transporter occupancy may explain superior clinical efficacy of escitalopram versus citalopram.

PubMed

Kasper, Siegfried; Sacher, Julia; Klein, Nikolas; Mossaheb, Nilufar; Attarbaschi-Steiner, Trawat; Lanzenberger, Rupert; Spindelegger, Christoph; Asenbaum, Susanne; Holik, Alexander; Dudczak, Robert

2009-05-01

Escitalopram the S-enantiomer of the racemate citalopram, is clinically more effective than citalopram in the treatment of major depressive disorder. However, the precise mechanism by which escitalopram achieves superiority over citalopram is yet to be determined. It has been hypothesized that the therapeutically inactive R-enantiomer competes with the serotonin-enhancing S-enantiomer at a low-affinity allosteric site on serotonin reuptake transporters (SERTs), and reduces the effectiveness of the S-enantiomer at the primary, high-affinity serotonin-binding site. This study summarizes the results of two recent single-photon emission computerized tomography studies measuring SERT occupancy in citalopram-treated and escitalopram-treated healthy volunteers, after a single dose and multiple doses (i.e. under steady-state conditions). The single-dose study showed no attenuating effect of R-citalopram. After multiple dosing, however, SERT occupancy was significantly reduced in the presence of R-citalopram. Under steady-state conditions, R-enantiomer concentrations were greater than for the S-enantiomer because of slower clearance of R-citalopram. A pooled analysis suggests that build-up of the R-enantiomer after repeated citalopram dosing may lead to increased inhibition of S-enantiomer occupancy of SERT. This review adds to the growing body of evidence regarding differences in the dynamics of SERT occupancy, that is, molecular mechanisms underlying the often-observed superior clinical efficacy of escitalopram compared with citalopram in major depressive disorder.

A giant X-ray flare on Lambda Eridani (B2e)

NASA Technical Reports Server (NTRS)

Smith, Myron A.; Grady, Carol A.; Peters, Geraldine J.; Feigelson, Eric D.

1993-01-01

A 30 ks observation with the ROSAT PSPC distributed over 39 hr shows that the putatively single, mild B2e star Lambda Eri emits at most times a soft X-ray flux at a rate and temperature consistent with other B stars. However, during the middle of our observations, this star's X-ray flux increased by a factor of 6 before returning to the basal level. This brightening, due entirely to photon energies of 0.7 keV or greater, can be fitted well to a Raymond-Smith temperature parameter of 14 MK and luminosity 4 x 10 exp 31 ergs/s; these are characteristics of giant stellar flares. With an estimated duration of about 50,000 s, this event is arguably the strongest X-ray flare yet observed. We consider several possible scenarios for the site of the flare, including several with an active cool secondary or degenerate companion. We find that IUE and optical spectra do not support a binary picture and that it is most probable that the flare site is on or related to Lambda Eri itself. This supports other evidence for violent magnetic activity on some B-type stars.

In-situ high-resolution visualization of laser-induced periodic nanostructures driven by optical feedback.

PubMed

Aguilar, Alberto; Mauclair, Cyril; Faure, Nicolas; Colombier, Jean-Philippe; Stoian, Razvan

2017-11-28

Optical feedback is often evoked in laser-induced periodic nanostructures. Visualizing the coupling between surfaces and light requires highly-resolved imaging methods. We propose in-situ structured-illumination-microscopy to observe ultrafast-laser-induced nanostructures during fabrication on metallic glass surfaces. This resolves the pulse-to-pulse development of periodic structures on a single irradiation site and indicates the optical feedback on surface topographies. Firstly, the quasi-constancy of the ripples pattern and the reinforcement of the surface relief with the same spatial positioning indicates a phase-locking mechanism that stabilizes and amplifies the ordered corrugation. Secondly, on sites with uncorrelated initial corrugation, we observe ripple patterns spatially in-phase. These feedback aspects rely on the electromagnetic interplay between the laser pulse and the surface relief, stabilizing the pattern in period and position. They are critically dependent on the space-time coherence of the exciting pulse. This suggests a modulation of energy according to the topography of the surface with a pattern phase imposed by the driving pulse. A scattering and interference model for ripple formation on surfaces supports the experimental observations. This relies on self-phase-stabilized far-field interaction between surface scattered wavelets and the incoming pulse front.

Hard versus soft dynamics for adsorption-desorption kinetics: Exact results in one-dimension.

PubMed

Manzi, S J; Huespe, V J; Belardinelli, R E; Pereyra, V D

2009-11-01

The adsorption-desorption kinetics is discussed in the framework of the kinetic lattice-gas model. The master equation formalism has been introduced to describe the evolution of the system, where the transition probabilities are written as an expansion of the occupation configurations of all neighboring sites. Since the detailed balance principle determines half of the coefficients that arise from the expansion, it is necessary to introduce ad hoc, a dynamic scheme to get the rest of them. Three schemes of the so-called hard dynamics, in which the probability of transition from single site cannot be factored into a part which depends only on the interaction energy and one that only depends on the field energy, and five schemes of the so-called soft dynamics, in which this factorization is possible, were introduced for this purpose. It is observed that for the hard dynamic schemes, the equilibrium and nonequilibrium observables, such as adsorption isotherms, sticking coefficients, and thermal desorption spectra, have a normal or physical sustainable behavior. While for the soft dynamics schemes, with the exception of the transition state theory, the equilibrium and nonequilibrium observables have several problems. Some of them can be regarded as abnormal behavior.

Institutional prescreening for detection and eradication of methicillin-resistant Staphylococcus aureus in patients undergoing elective orthopaedic surgery.

PubMed

Kim, David H; Spencer, Maureen; Davidson, Susan M; Li, Ling; Shaw, Jeremy D; Gulczynski, Diane; Hunter, David J; Martha, Juli F; Miley, Gerald B; Parazin, Stephen J; Dejoie, Pamela; Richmond, John C

2010-08-04

Surgical site infection has been identified as one of the most important preventable sources of morbidity and mortality associated with medical treatment. The purpose of the present study was to evaluate the feasibility and efficacy of an institutional prescreening program for the preoperative detection and eradication of both methicillin-resistant and methicillin-sensitive Staphylococcus aureus in patients undergoing elective orthopaedic surgery. Data were collected prospectively during a single-center study. A universal prescreening program, employing rapid polymerase chain reaction analysis of nasal swabs followed by an eradication protocol of intranasal mupirocin and chlorhexidine showers for identified carriers, was implemented. Surgical site infection rates were calculated and compared with a historical control period immediately preceding the start of the screening program. During the study period, 7019 of 7338 patients underwent preoperative screening before elective surgery, for a successful screening rate of 95.7%. One thousand five hundred and eighty-eight (22.6%) of the patients were identified as Staphylococcus aureus carriers, and 309 (4.4%) were identified as methicillin-resistant Staphylococcus aureus carriers. A significantly higher rate of surgical site infection was observed among methicillin-resistant Staphylococcus aureus carriers (0.97%; three of 309) compared with noncarriers (0.14%; seven of 5122) (p = 0.0162). Although a higher rate of surgical site infection was also observed among methicillin-sensitive Staphylococcus aureus carriers (0.19%; three of 1588) compared with noncarriers, this difference did not achieve significance (p = 0.709). Overall, thirteen cases of surgical site infection were identified during the study period, for an institutional infection rate of 0.19%. This rate was significantly lower than that observed during the control period (0.45%; twenty-four cases of surgical site infection among 5293 patients) (p = 0.0093). Implementation of an institution-wide prescreening program for the identification and eradication of methicillin-resistant and methicillin-sensitive Staphylococcus aureus carrier status among patients undergoing elective orthopaedic surgery is feasible and can lead to significant reductions in postoperative rates of surgical site infection. Therapeutic Level III. See Instructions to Authors for a complete description of levels of evidence.

Observations of Aerosol Optical Properties over 15 AERONET Sites in Southeast Asia

NASA Astrophysics Data System (ADS)

Chan, J. D.; Lagrosas, N.; Uy, S. N.; Holben, B. N.; Dorado, S.; Tobias, V., Jr.; Anh, N. X.; Po-Hsiung, L.; Janjai, S.; Salinas Cortijo, S. V.; Liew, S. C.; Lim, H. S.; Lestari, P.

2014-12-01

Mean column-integrated optical properties from ground sun photometers of the Aerosol Robotic Network (AERONET) are studied to provide an overview of the characteristics of aerosols over the region as part of the 7 Southeast Asian Studies (7-SEAS) mission. The 15 AERONET sites with the most available level 2 data products are selected from Thailand (Chiang Mai, Mukdahan, Songkhla and Silpakorn University), Malaysia (University Sains Malaysia), Laos (Vientiane), Vietnam (Bac Giang, Bac Lieu and Nha Trang), Taiwan (National Cheng Kung University and Central Weather Bureau Taipei), Singapore, Indonesia (Bandung) and the Philippines (Manila Observatory and Notre Dame of Marbel University). For all 15 sites, high angstrom exponent values (α>1) have been observed. Chiang Mai and USM have the highest mean Angstrom exponent indicating the dominance of fine particles that can be ascribed to biomass burning and urbanization. Sites with the lowest Angstrom exponent values include Bac Lieu (α=1.047) and Manila Observatory (α=1.021). From the average lognormal size distribution curves, Songkhla and NDMU show the smallest annual variation in the fine mode region, indicating the observed fine aerosols are local to the sites. The rest of the sites show high variation which could be due to large scale forcings (e.g., monsoons and biomass burnings) that affect aerosol properties in these sites. Both high and low single scattering albedo at 440 nm (ω0440) values are found in sites located in major urban areas. Silpakorn University, Manila Observatory and Vientiane have all mean ω0440 < 0.90. Singapore and CWB Taipei have ω0440 > 0.94. The discrepancy in ω0 suggests different types of major emission sources present in urban areas. The absorptivity of urban aerosols can vary depending on the strength of traffic emissions, types of fuel combusted and automobile engines used, and the effect of biomass burning aerosols during the dry season. High aerosol optical depth values (τa550 > 0.4) are mainly found over inland sites north of Songkhla and south of China on mainland Asia. Major pollution types in the region include biomass burning smoke and urban aerosols. The highest average τa550 is measured in Bac Giang, which has been studied to be greatly affected by aerosol sources from Eastern China during the later parts of the year.

EPR and optical absorption studies of paramagnetic molecular ion (VO2+) in Lithium Sodium Acid Phthalate single crystal

NASA Astrophysics Data System (ADS)

Subbulakshmi, N.; Kumar, M. Saravana; Sheela, K. Juliet; Krishnan, S. Radha; Shanmugam, V. M.; Subramanian, P.

2017-12-01

Electron Paramagnetic Resonance (EPR) spectroscopic studies of VO2+ ions as paramagnetic impurity in Lithium Sodium Acid Phthalate (LiNaP) single crystal have been done at room temperature on X-Band microwave frequency. The lattice parameter values are obtained for the chosen system from Single crystal X-ray diffraction study. Among the number of hyperfine lines in the EPR spectra only two sets are reported from EPR data. The principal values of g and A tensors are evaluated for the two different VO2+ sites I and II. They possess the crystalline field around the VO2+ as orthorhombic. Site II VO2+ ion is identified as substitutional in place of Na1 location and the other site I is identified as interstitial location. For both sites in LiNaP, VO2+ are identified in octahedral coordination with tetragonal distortion as seen from the spin Hamiltonian parameter values. The ground state of vanadyl ion in the LiNaP single crystal is dxy. Using optical absorption data the octahedral and tetragonal parameters are calculated. By correlating EPR and optical data, the molecular orbital bonding parameters have been discussed for both sites.

Site specific passive acoustic detection and densities of humpback whale calls off the coast of California

NASA Astrophysics Data System (ADS)

Helble, Tyler Adam

Passive acoustic monitoring of marine mammal calls is an increasingly important method for assessing population numbers, distribution, and behavior. Automated methods are needed to aid in the analyses of the recorded data. When a mammal vocalizes in the marine environment, the received signal is a filtered version of the original waveform emitted by the marine mammal. The waveform is reduced in amplitude and distorted due to propagation effects that are influenced by the bathymetry and environment. It is important to account for these effects to determine a site-specific probability of detection for marine mammal calls in a given study area. A knowledge of that probability function over a range of environmental and ocean noise conditions allows vocalization statistics from recordings of single, fixed, omnidirectional sensors to be compared across sensors and at the same sensor over time with less bias and uncertainty in the results than direct comparison of the raw statistics. This dissertation focuses on both the development of new tools needed to automatically detect humpback whale vocalizations from single-fixed omnidirectional sensors as well as the determination of the site-specific probability of detection for monitoring sites off the coast of California. Using these tools, detected humpback calls are "calibrated" for environmental properties using the site-specific probability of detection values, and presented as call densities (calls per square kilometer per time). A two-year monitoring effort using these calibrated call densities reveals important biological and ecological information on migrating humpback whales off the coast of California. Call density trends are compared between the monitoring sites and at the same monitoring site over time. Call densities also are compared to several natural and human-influenced variables including season, time of day, lunar illumination, and ocean noise. The results reveal substantial differences in call densities between the two sites which were not noticeable using uncorrected (raw) call counts. Additionally, a Lombard effect was observed for humpback whale vocalizations in response to increasing ocean noise. The results presented in this thesis develop techniques to accurately measure marine mammal abundances from passive acoustic sensors.

The P gene of bovine parainfluenza virus 3 expresses all three reading frames from a single mRNA editing site.

PubMed Central

Pelet, T; Curran, J; Kolakofsky, D

1991-01-01

The P gene of bovine parainfluenza virus 3 (bPIV3) contains two downstream overlapping ORFs, called V and D. By comparison with the mRNA editing sites of other paramyxoviruses, two editing sites were predicted for bPIV3; site a to express the D protein, and site b to express the V protein. Examination of the bPIV3 mRNAs, however, indicates that site b is non-functional whereas site a operates frequently. Insertions at site a give rise to both V and D protein mRNAs, because a very broad distribution of Gs is added when insertions occur. This broad distribution is very different from the editing sites of Sendai virus or SV5, where predominantly one form of edited mRNA containing either a one or two G insertion respectively is created, to access the single overlapping ORF of these viruses. A model is proposed to explain how paramyxoviruses control the range of G insertions on that fraction of the mRNAs where insertions occur. The bPIV3 P gene is unique as far as we know, in that a sizeable portion of the gene expresses all 3 reading frames as protein. bPIV3 apparently does this from a single editing site by removing the constraints which control the number of slippage rounds which take place. Images PMID:1846805

Habitat impacts of offshore drilling, eastern Gulf of Mexico

USGS Publications Warehouse

Shinn, Eugene A.; Lidz, Barbara H.; Reich, Christopher D.

1994-01-01

In this survey six offshore exploratory drill sites in a variety of environments and water depths were examined using a small research submersible. Sites varied from locations off northwest Florida to as far west as offshore Alabama. Water depths ranged from 21 m (70 ft) to 149 m (489 ft), and bottom sediments ranged from carbonate mud to Shelly quartz sand and silt to hard limestone. The age of the sites (the time between cessation of drilling activities and our observations) ranged from 15 months to 17 years . In a previous MMS-funded study, Shinn et al. (1989) and Dustan et al . (1991) examined eight sites off South Florida, where the age of the sites ranged from 2 to 29 years. The study documented repeatedly variability of impact from site to site . In the present study, we note a similar wide divergence of impacts . Using the concentration of barium (the major component of drill mud), cuttings, and trace metals as a basis, we found that time is the single most important factor determining the nature of habitat recovery. Older sites, particularly the 17-year-old site, were relatively pristine. At a 7-year-old site, two hurricanes did far more damage than drilling . At other sites, we documented a significant amount of discarded debris, and at two 5-year-old sites, large concentrations of barium and cuttings. Impacts, such as the extent of debris and cuttings, affected the bottom ranging in area from almost negligible (17-year-old site) to as much as 3 acres (4-year-old site) . As suspected, those sites with the most debris and/or open boreholes attracted the most abundant and diverse fish fauna.

Measurements of aerosol absorption and scattering in the Mexico City Metropolitan Area during the MILAGRO field campaign: a comparison of results from the T0 and T1 sites

NASA Astrophysics Data System (ADS)

Marley, N. A.; Gaffney, J. S.; Castro, T.; Salcido, A.; Frederick, J.

2008-07-01

Measurements of aerosol absorption and scattering were obtained in Mexico City during the MILAGRO (Megacity Initiative: Local and Global Research Observations) field campaign in March 2006. A comparison of aerosol absorption and scattering was obtained in Mexico City at site T0 located in the northern part of Mexico City at the Instituto Mexicano del Petróleo Laboratories and at site T1 located at the Universidad Tecnológica de Tecamac, 18 miles northwest of T0. Hourly averages of aerosol absorption were similar at both sites, ranging from 6 93 Mm-1 with an average of 31 Mm-1 at T0; and from 2 104 Mm-1 with an average of 19 Mm-1 at T1. Aerosol scattering at T0 ranged from 16 344 Mm-1 with an average of 105 Mm-1; while the scattering values at T1 were lower than T0 ranging from 2 136 with an average of 53 Mm-1. Aerosol single scattering albedos (SSAs) were determined at both sites using these data. SSAs at T1 ranged from 0.44 0.90 with an average 0.75 as compared to hose at T0, range 0.51 0.93 with an average of 0.77. Broadband UV-B intensity was found to be higher at site T0, with an average of 64 μW/cm2 at solar noon, than at site T1, which had an average of 54 μW/cm2 at solar noon. Comparisons of clear-sky modeled UV-B intensities with the simultaneous UV-B measurements obtained at site T0 and at site T1 for cloudless days indicate a larger diffuse radiation field at site T0 than at site T1. The determination of aerosol scattering Ångstrom coefficient at T0 suggests the larger diffuse radiation is due to the predominance of submicron aerosols at T0 with aerosol scattering of UV-B radiation peaked in the forward direction, leading to the enhancement observed at ground level.

Identification of Clostridium difficile Reservoirs in The Patient Environment and Efficacy of Aerial Hydrogen Peroxide Decontamination.

PubMed

Yui, Samuel; Ali, Shanom; Muzslay, Monika; Jeanes, Annette; Wilson, A Peter R

2017-12-01

OBJECTIVE To identify, using a novel enhanced method of recovery, environmental sites where spores of Clostridium difficile persist despite cleaning and hydrogen peroxide aerial decontamination. DESIGN Cohort study. SETTING Tertiary referral center teaching hospital. METHODS In total, 16 sites representing high-frequency contact or difficult-to-clean surfaces in a single-isolation room or bed area in patient bed bays were sampled before and after terminal or hydrogen peroxide disinfection using a sponge swab. In some rooms, individual sites were not present (eg, there were no en-suite rooms in the ICU). Swab contents were homogenized, concentrated by membrane-filtration, and plated onto selective media. Results of C. difficile sampling were used to focus cleaning. RESULTS Over 1 year, 2,529 sites from 146 rooms and 44 bays were sampled. Clostridium difficile was found on 131 of 572 surfaces (22.9%) before terminal cleaning, on 105 of 959 surfaces (10.6%) after terminal cleaning, and on 43 of 967 surfaces (4.4%) after hydrogen peroxide disinfection. Clostridium difficile persisted most frequently on floor corners (97 of 334; 29.0%) after disinfection. Between the first and third quarters, we observed a significant decrease in the number of positive sites (25 of 390 vs 6 of 256). However, no similar change in the number of isolates before terminal cleaning was observed. CONCLUSION Persistence of C. difficile in the clinical environment was widespread. Although feedback of results did not improve the efficacy of manual disinfection, numbers of C. difficile following hydrogen peroxide gradually declined. Infect Control Hosp Epidemiol 2017;38:1487-1492.

Pharmacokinetics and Disposition of Rilpivirine (TMC278) Nanosuspension as a Long-Acting Injectable Antiretroviral Formulation▿

PubMed Central

van ′t Klooster, Gerben; Hoeben, Eva; Borghys, Herman; Looszova, Adriana; Bouche, Marie-Paule; van Velsen, Frans; Baert, Lieven

2010-01-01

The next-generation human immunodeficiency virus type 1 (HIV-1) nonnucleoside reverse transcriptase inhibitor rilpivirine (TMC278) was administered in rats and dogs as single intramuscular (IM) or subcutaneous (SC) injections, formulated as a 200-nm nanosuspension. The plasma pharmacokinetics, injection site concentrations, disposition to lymphoid tissues, and tolerability were evaluated in support of its potential use as a once-monthly antiretroviral agent in humans. Rilpivirine plasma concentration-time profiles showed sustained and dose-proportional release over 2 months in rats and over 6 months in dogs. The absolute bioavailability approached 100%, indicating a complete release from the depot, in spite of rilpivirine concentrations still being high at the injection site(s) 3 months after administration in dogs. For both species, IM administration was associated with higher initial peak plasma concentrations and a more rapid washout than SC administration, which resulted in a stable plasma-concentration profile over at least 6 weeks in dogs. The rilpivirine concentrations in the lymph nodes draining the IM injection site exceeded the plasma concentrations by over 100-fold 1 month after administration, while the concentrations in the lymphoid tissues decreased to 3- to 6-fold the plasma concentrations beyond 3 months. These observations suggest uptake of nanoparticles by macrophages, which generates secondary depots in these lymph nodes. Both SC and IM injections were generally well tolerated and safe, with observations of a transient inflammatory response at the injection site. The findings support clinical investigations of rilpivirine nanosuspension as a long-acting formulation to improve adherence during antiretroviral therapy and for preexposure prophylaxis. PMID:20160045

THE PENETRATION OF REOVIRUS RNA AND INITIATION OF ITS GENETIC FUNCTION IN L-STRAIN FIBROBLASTS

PubMed Central

Silverstein, Samuel C.; Dales, Samuel

1968-01-01

Reovirus type 3 is phagocytized by L cells and rapidly sequestered inside lysosomes. Hydrolases within these organelles are capable of stripping the viral coat proteins, but they fail to degrade the double-stranded RNA genome. These observations support the view that sojourn of reovirus in lysosomes, when the lytic enzymes uncoat its genome, is an obligatory step in the sequence of infection. Although the mechanism for transferring the uncoated RNA out of lysosomes remains to be elucidated, evidence is presented suggesting that progeny genomes are bound to site(s) possessing the fine structure of viral inclusions or factories. It appears that both the synthesis of single- and double-stranded viral RNA and the morphogenesis of progeny virus particles occur in such factories. PMID:19806702

An Experimental and Theoretical Evaluation of Multi-site Cadmium(II) Exchange in Designed Three-Stranded Coiled Coil Peptides

PubMed Central

Chakraborty, Saumen; Iranzo, Olga; Zuiderweg, Erik R.P.; Pecoraro, Vincent L.

2012-01-01

An important factor that defines the toxicity of elements such as cadmium(II), mercury(II), and lead(II) with biological macromolecules is metal ion exchange dynamics. Intriguingly, little is known about the fundamental rates and mechanisms of metal ion exchange into proteins, especially helical bundles. Herein, we investigate the exchange kinetics of cadmium(II) using de novo designed three-stranded coiled coil peptides that contain metal complexing cysteine thiolates as a model for the incorporation of this ion into trimeric, parallel helical bundles. Peptides were designed containing both single cadmium(II) binding site, GrandL12AL16C [Grand=AcG-(LKALEEK)5-GNH2], GrandL26AL30C, and GrandL26AE28QL30C, as well as GrandL12AL16CL26AL30C with two cadmium(II) binding sites. The binding of cadmium(II) to any of these sites is of high affinity (KA > 3×107 M−1). Using 113Cd NMR spectroscopy, cadmium(II) binding to these designed peptides was monitored. While the cadmium(II) binding is in extreme slow exchange without showing any chemical shift changes, incremental line broadening for the bound 113cadmium(II) signal is observed when excess 113cadmium(II) is titrated into the peptides. Most dramatically, for one site, L26AL30C, all 113cadmium(II) NMR signals disappear once a 1.7:1 ratio of cadmium(II)/(peptide)3 is reached. The observed processes are not compatible with simple “free-bound” two-site exchange kinetics at any time regime. The experimental results can, however, be simulated in detail with a multi-site binding model, which features additional cadmium(II) binding site(s) which, once occupied, perturb the primary binding site. This model is expanded into differential equations for five-site NMR chemical exchange. The numerical integration of these equations exhibits progressive loss of the primary site NMR signal without a chemical shift change and with limited line broadening, in good agreement with the observed experimental data. The mathematical model is interpreted in molecular terms as representing binding of excess cadmium(II) to surface Glu residues located at the helical interfaces. In the absence of cadmium(II), the Glu residues stabilize the three-helical structure though salt bridge interactions with surface Lys residues. We hypothesize that cadmium(II) interferes with these surface ion pairs, destabilizing the helical structure, and perturbing the primary cadmium(II) binding site. This hypothesis is supported by the observation that the cadmium(II)-excess line broadening is attenuated in GrandL26AE28QL30C where a surface Glu(28), close to the metal binding site, was changed to Gln. The external binding site may function as an entry pathway for cadmium(II) to find its internal binding site following a molecular rearrangement which may serve as a basis for our understanding of metal complexation, transport and exchange in complex native systems containing α-helical bundles. PMID:22394049

Comparison of the Local Tolerability to 5 Long-acting Drug Nanosuspensions with Different Stabilizing Excipients, Following a Single Intramuscular Administration in the Rat.

PubMed

Chamanza, Ronnie; Darville, Nicolas; van Heerden, Marjolein; De Jonghe, Sandra

2018-01-01

To investigate the effects of common nanosuspension-stabilizing excipients on the nature and temporal evolution of histopathological changes at intramuscular (i.m.) administration sites, 5 groups of 39 male rats per group received a single injection of 1 of the 5 analogous crystalline drug nanosuspensions containing 200 mg/ml of an antiviral compound with particle sizes of ±200 nm and identical vehicle compositions, except for the type of nanosuspension stabilizer. The investigated stabilizers were poloxamer 338, poloxamer 407, d-α-tocopherol polyethylene glycol 1,000-succinate (TPGS), polysorbate 80, and polysorbate 80 combined with egg phosphatidylglycerol. Histopathology and immunohistochemistry revealed progressive inflammatory changes at the i.m. administration sites and the draining lymph nodes that differed according to the time point of sacrifice and the type of stabilizer. Although the overall time course of inflammatory changes was similar across the groups, differences in the nature, severity, and timing of the inflammatory response were observed between animals injected with poloxamer- or TPGS-containing nanosuspensions and those injected with formulations containing polysorbate 80. A more severe and prolonged active inflammatory phase, the presence of multinucleate giant cells, prolonged macrophage infiltration of the formulation depot, and more persistent histiocytic infiltrates in the lymph nodes were observed in the polysorbate 80-containing nanosuspension groups. Such vehicle-mediated effects could influence the overall tolerability profile of long-acting nanosuspensions.

New 50-m-class single-dish telescope: Large Submillimeter Telescope (LST)

NASA Astrophysics Data System (ADS)

Kawabe, Ryohei; Kohno, Kotaro; Tamura, Yoichi; Takekoshi, Tatsuya; Oshima, Tai; Ishii, Shun

2016-08-01

We report on a plan to construct a 50-m-class single-dish telescope, the Large Submillimeter Telescope (LST). The conceptual design and key science behind the LST are presented, together with its tentative specifications. This telescope is optimized for wide-area imaging and spectroscopic surveys in the 70-420 GHz frequency range, which spans the main atmospheric windows at millimeter and submillimeter wavelengths for good observation sites such as the Atacama Large Millimeter/submillimeter Array (ALMA) site in Chile. We also target observations at higher frequencies of up to 1 THz, using an inner high-precision surface. Active surface control is required in order to correct gravitational and thermal deformations of the surface, and will be useful for correction of the wind-load deformation. The LST will facilitate new discovery spaces such as wide-field imaging with both continuum and spectral lines, along with new developments for time-domain science. Through exploitation of its synergy with ALMA and other telescopes, the LST will contribute to research on a wide range of topics in the fields of astronomy and astrophysics, e.g., astrochemistry, star formation in our Galaxy and galaxies, the evolution of galaxy clusters via the Sunyaev-Zel'dovich (SZ) effect, the search for transients such as γ-ray burst reverse shocks produced during the epoch of re-ionization, electromagnetic follow up of detected gravitational wave sources, and examination of general relativity in the vicinity of super massive black holes via submillimeter very-long-baseline interferometry (VLBI).

Current status and future directions of robotic single-site surgery: a systematic review.

PubMed

Autorino, Riccardo; Kaouk, Jihad H; Stolzenburg, Jens-Uwe; Gill, Inderbir S; Mottrie, Alex; Tewari, Ash; Cadeddu, Jeffrey A

2013-02-01

Despite the increasing interest in laparoendoscopic single-site surgery (LESS) worldwide, the actual role of this novel approach in the field of minimally invasive urologic surgery remains to be determined. It has been postulated that robotic technology could be applied to LESS to overcome the current constraints. To summarize and critically analyze the available evidence on the current status and future of robotic applications in single-site surgery. A systematic literature review was performed in April 2011 using PubMed and the Thomson-Reuters Web of Science. In the free-text protocol, the following terms were applied: robotic single site surgery, robotic single port surgery, robotic single incision surgery, and robotic laparoendoscopic single site surgery. Review articles, editorials, commentaries, and letters to the editor were included only if deemed to contain relevant information. In addition, cited references from the selected articles and from review articles retrieved in the search were assessed for significant manuscripts not previously included. The authors selected 55 articles according to the search strategy based on Preferred Reporting Items for Systematic Reviews and Meta-analysis criteria. The volume of available clinical outcomes of robotic LESS (R-LESS) has considerably grown since the pioneering description of the first successful clinical series of single-port robotic procedures. So far, a cumulative number of roughly 150 robotic urologic LESS cases have been reported by different institutions across the globe with a variety of techniques and port configurations. The feasibility of robot-assisted single-incision colorectal procedures, as well as of many gynecologic procedures, has also been demonstrated. A novel set of single-site instruments specifically dedicated to LESS is now commercially available for use with the da Vinci Si surgical system, and both experimental and clinical use have been reported. However, the current robotic systems were specifically designed for LESS. The ideal robotic platform should have a low external profile, the possibility of being deployed through a single access site, and the possibility of restoring intra-abdominal triangulation while maintaining the maximum degree of freedom for precise maneuvers and strength for reliable traction. Several purpose-built robotic prototypes for single-port surgery are being tested. Significant advances have been achieved in the field of R-LESS since the first reported clinical series in 2009. Given the several advantages offered by current the da Vinci system, it is likely that its adoption in this field will increase. The recent introduction of purpose-built instrumentation is likely to further foster the application of robotics to LESS. However, we are still far from the ideal robotic platform. Significant improvements are needed before this technique might reach widespread adoption beyond selected centers. Further advances in the field of robotic technology are expected to provide the optimal interface to facilitate LESS. Copyright © 2012 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Reliability of quadriceps surface electromyography measurements is improved by two vs. single site recordings.

PubMed

Balshaw, T G; Fry, A; Maden-Wilkinson, T M; Kong, P W; Folland, J P

2017-06-01

The reliability of surface electromyography (sEMG) is typically modest even with rigorous methods, and therefore further improvements in sEMG reliability are desirable. This study compared the between-session reliability (both within participant absolute reliability and between-participant relative reliability) of sEMG amplitude from single vs. average of two distinct recording sites, for individual muscle (IM) and whole quadriceps (WQ) measures during voluntary and evoked contractions. Healthy males (n = 20) performed unilateral isometric knee extension contractions: voluntary maximum and submaximum (60%), as well as evoked twitch contractions on two separate days. sEMG was recorded from two distinct sites on each superficial quadriceps muscle. Averaging two recording sites vs. using single site measures improved reliability for IM and WQ measurements during voluntary (16-26% reduction in within-participant coefficient of variation, CV W ) and evoked contractions (40-56% reduction in CV W ). For sEMG measurements from large muscles, averaging the recording of two distinct sites is recommended as it improves within-participant reliability. This improved sensitivity has application to clinical and research measurement of sEMG amplitude.

Non-invasive quantification of melanin in the stratum corneum: a novel indicator of skin lesions in pigmentation diseases.

PubMed

Matsunaka, H; Yamamoto, Y; Furukawa, F

2017-02-01

Skin melanin content is an important indicator for ascertaining the pathology of skin pigmentation diseases, but its analysis necessitates a biopsy or other means of collecting tissue, posing a considerable burden to the patient, and making it difficult to observe how a given skin site changes over time. Here, we aimed to establish a non-invasive method for quantifying the eumelanin and pheomelanin content of the stratum corneum. Sun-exposed and non-exposed samples from 10 healthy Japanese subjects were compared. We harvested the outermost layer of the stratum corneum by tape-stripping, considering the outer side of the forearm as a sun-exposed area, and medial side of the upper arm as a non-exposed area. Four additional subjects were included in the analysis of change in melanin content over time at the same skin site. The anterior lower leg received a single exposure to two minimal erythema dose sunlight, and the stratum corneum was harvested from the same site over a period of 20 weeks; we subsequently quantified the levels of eumelanin and pheomelanin using high-performance liquid chromatography. We were able to accurately quantify the eumelanin and pheomelanin contents of the stratum corneum, and to observe the evolution of the same skin site over time. Eumelanin levels were significantly higher in the sun-exposed area, with a peak in melanin observed after 11-15 weeks of sun exposure. This non-invasive method can serve as a marker for pathology of skin pigmentation diseases such as malignant tumors. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Properties of Coronal Shocks at the Origin of SEP events Observed by Only One Single Spacecraft

NASA Astrophysics Data System (ADS)

Lario, D.; Kwon, R.

2017-12-01

The simultaneous observation of solar energetic particle (SEP) events by multiple spacecraft distributed in the interplanetary medium depends not only on the spatial separation among the different spacecraft, but also on the properties of the particle sources and the characteristics of the SEP transport in interplanetary space. Among the SEP events observed by STEREO-A, STEREO-B and/or near-Earth spacecraft during solar cycle 24, we select SEP events observed by a single spacecraft (specifically, the SEP events observed only by near-Earth spacecraft on 2012 April 5, 2011 September 4, and 2013 August 17). We analyze whether the properties of the coronal shock associated with the origin of the events (as seen in extreme-ultraviolet and white-light coronal images) differ from those associated with SEP events observed by two or three spacecraft. For the selected events we find that the associated CMEs are, in general, narrower than those associated with SEP events observed by two or three spacecraft. The confined extension of the parent coronal shock and the absence of magnetic connection between distant spacecraft and the regions of the expanding coronal shock able to efficiently accelerate SEPs seem to be the conditions leading to intense SEP events observed only over narrow regions of interplanetary space by spacecraft magnetically connected to regions close to the parent eruption site. Weak and gradual intensity increases observed in extended regions of space might involve transport processes and/or later connections established with interplanetary shocks. Systematic analyses of a larger number of events are required before drawing firm conclusions.

Remote observing capability with Subaru Telescope

NASA Astrophysics Data System (ADS)

Kosugi, George; Sasaki, Toshiyuki; Yagi, Masafumi; Ogasawara, Ryusuke; Mizumoto, Yoshihiko; Noumaru, Junichi; Kawai, Jun A.; Koura, Norikazu; Kusumoto, Toyoaki; Yamamoto, Tadahiro; Watanabe, Noboru; Ukawa, Kentaro

2004-09-01

We've implemented remote observing function to Subaru telescope Observation Software system (SOSs). Subaru telescope has three observing-sites, i.e., a telescope local-site and two remote observing-sites, Hilo base facility in Hawaii and Mitaka NAOJ headquarter in Japan. Our remote observing system is designed to allow operations not only from one of three observing-sites, but also from more than two sites concurrently or simultaneously. Considering allowance for delay in observing operations and a bandwidth of the network between the telescope-site and the remote observing-sites, three types of interfaces (protocols) have been implemented. In the remote observing mode, we use socket interface for the command and the status communication, vnc for ready-made applications and pop-up windows, and ftp for the actual data transfer. All images taken at the telescope-site are transferred to both of two remote observing-sites immediately after the acquisition to enable the observers' evaluation of the data. We present the current status of remote observations with Subaru telescope.

Association analysis of a polymorphism of the monoamine oxidase B gene with Parkinson`s disease in a Japanese population

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

Morimoto, Yuji; Murayama, Nobuhiro; Kuwano, Akira

1995-12-18

The polymorphic allele of the monoamine oxidase B (MAO-B) gene detected by polymerase chain reaction (PCR) and single-stranded conformation polymorphism (SSCP) was associated with Parkinson`s disease (PD) in Caucasians. We characterized this polymorphic allele, allele 1, of the MAO-B gene using direct sequencing of PCR products. A single DNA substitution (G-A), resulting gain of Mae III restriction site was detected in intron 13 of the MAO-B gene. The allele associated with PD in Caucasians was twice as frequent as in healthy Japanese, but the association of the allele of the MAO-B gene was not observed in Japanese patients with PD.more » 7 refs., 2 figs., 1 tab.« less

ARM - Midlatitude Continental Convective Clouds - Single Column Model Forcing (xie-scm_forcing)

DOE Data Explorer

Xie, Shaocheng; McCoy, Renata; Zhang, Yunyan

2012-10-25

The constrained variational objective analysis approach described in Zhang and Lin [1997] and Zhang et al. [2001]was used to derive the large-scale single-column/cloud resolving model forcing and evaluation data set from the observational data collected during Midlatitude Continental Convective Clouds Experiment (MC3E), which was conducted during April to June 2011 near the ARM Southern Great Plains (SGP) site. The analysis data cover the period from 00Z 22 April - 21Z 6 June 2011. The forcing data represent an average over the 3 different analysis domains centered at central facility with a diameter of 300 km (standard SGP forcing domain size), 150 km and 75 km, as shown in Figure 1. This is to support modeling studies on various-scale convective systems.

133Cs-NMR Study on the Ground State of the Equilateral Triangular Spin Tube CsCrF4

NASA Astrophysics Data System (ADS)

Matsui, K.; Goto, T.; Manaka, H.; Miura, Y.

2018-03-01

We have investigated the hyperfine coupling between Cs and Cr on the S = 3/2 equilateral triangular spin tube CsCrF4, utilizing 133Cs-NMR. At paramagnetic state above 80 K, we have obtained spectra containing a single peak, which reflects the single crystallographic Cs site. From the temperature dependence of the peak shift and peak width, we evaluated effective values of the isotropic and the anisotropic part of hyperfine coupling. The latter was compared with the calculated dipole contribution. Using obtained parameters with assumed spin structure, we tried to reproduce the broadened spectrum in the ordered state at 2.0 K. The preliminary analysis shows the 120-degree structure does not accord with the observed spectra at the ordered state.

Single crystal growth, magnetic and thermal properties of perovskite YFe0.6Mn0.4O3 single crystal

NASA Astrophysics Data System (ADS)

Xie, Tao; Shen, Hui; Zhao, Xiangyang; Man, Peiwen; Wu, Anhua; Su, Liangbi; Xu, Jiayue

2016-11-01

High quality YFe0.6Mn0.4O3 single crystal was grown by floating zone technique using a four-mirror-image-furnace under flowing air. Powder X-ray diffraction gives well evidence that the specimen has an orthorhombic structure, with space group Pbnm. Temperature dependence of the magnetizations of YFe0.6Mn0.4O3 single crystal were studied under ZFC and FC modes in the temperature range from 5 K to 400 K. A clear spin reorientation transition behavior (Γ4→Γ1) is observed in the temperature range of 322-316 K, due to the substitution of Mn at the Fe site of YFeO3. Its Néel temperature is around 385 K. Moreover, the spin reorientation is verified by the change of magnetic hysteresis loops of the sample along [001] axis in the temperature range of 50-385 K. The thermal properties of the sample were measured by the differential scanning calorimeter (DSC) from 300 K to 500 K, which also clearly appear anomaly in the spin reorientation region.

Energy transfer in PPV-based conjugated polymers: a defocused widefield fluorescence microscopy study.

PubMed

Hooley, E N; Tilley, A J; White, J M; Ghiggino, K P; Bell, T D M

2014-04-21

Both pendant and main chain conjugated MEH-PPV based polymers have been studied at the level of single chains using confocal and widefield fluorescence microscopy techniques. In particular, defocused widefield fluorescence is applied to reveal the extent of energy transfer in these polymers by identifying whether they act as single emitters. For main chain conjugated MEH-PPV, molecular weight and the surrounding matrix play a primary role in determining energy transport processes and whether single emitter behaviour is observed. Surprisingly in polymers with a saturated backbone but containing the same pendant MEH-PPV oligomer on each repeating unit, intra-chain energy transfer to a single emitter is also apparent. The results imply there is chromophore heterogeneity that can facilitate energy funneling to the emitting site. Both main chain conjugated and pendant MEH-PPV polymers exhibit changes in orientation of the emission dipole during a fluorescence trajectory of many seconds, whereas a model MEH-PPV oligomer does not. The results suggest that, in the polymers, the nature of the emitting chromophores can change during the time trajectory.

A New Approach to Pathogen Containment in the Operating Room: Sheathing the Laryngoscope After Intubation.

PubMed

Birnbach, David J; Rosen, Lisa F; Fitzpatrick, Maureen; Carling, Philip; Arheart, Kristopher L; Munoz-Price, L Silvia

2015-11-01

Anesthesiologists may contribute to postoperative infections by means of the transmission of blood and pathogens to the patient and the environment in the operating room (OR). Our primary aims were to determine whether contamination of the IV hub, the anesthesia work area, and the patient could be reduced after induction of anesthesia by removing the risk associated with contaminants on the laryngoscope handle and blade. Therefore, we conducted a study in a simulated OR where some of the participants sheathed the laryngoscope handle and blade in a glove immediately after it was used to perform an endotracheal intubation. Forty-five anesthesiology residents (postgraduate year 2-4) were enrolled in a study consisting of identical simulation sessions. On entry to the simulated OR, the residents were asked to perform an anesthetic, including induction and endotracheal intubation timed to approximately 6 minutes. Of the 45 simulation sessions, 15 were with a control group conducted with the intubating resident wearing single gloves, 15 with the intubating resident using double gloves with the outer pair removed and discarded after verified intubation, and 15 wearing double gloves and sheathing the laryngoscope in one of the outer gloves after intubation. Before the start of the scenario, the lips and inside of the mouth of the mannequin were coated with a fluorescent marking gel. After each of the 45 simulations, an observer examined the OR using an ultraviolet light to determine the presence of fluorescence on 25 sites: 7 on the patient and 18 in the anesthesia environment. Of the 7 sites on the patient, ultraviolet light detected contamination on an average of 5.7 (95% confidence interval, 4.4-7.2) sites under the single-glove condition, 2.1 (1.5-3.1) sites with double gloves, and 0.4 (0.2-1.0) sites with double gloves with sheathing. All 3 conditions were significantly different from one another at P < 0.001. Of the 18 environmental sites, ultraviolet light detected fluorescence on an average of 13.2 (95% confidence interval, 11.3-15.6) sites under the single-glove condition, 3.5 (2.6-4.7) with double gloves, and 0.5 (0.2-1.0) with double gloves with sheathing. Again, all 3 conditions were significantly different from one another at P < 0.001. The results of this study suggest that when an anesthesiologist in a simulated OR sheaths the laryngoscope immediately after endotracheal intubation, contamination of the IV hub, patient, and intraoperative environment is significantly reduced.

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site

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

Strauch, Eva-Maria; Bernard, Steffen M.; La, David

Many viral surface glycoproteins and cell surface receptors are homo-oligomers1, 2, 3, 4, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites5, 6, 7, 8. In the first step, a small protein ismore » designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.« less