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Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils.

PubMed

Walker, Jennifer K M; Egger, Keith N; Henry, Gregory H R

2008-09-01

Arctic air temperatures are expected to rise significantly over the next century. Experimental warming of arctic tundra has been shown to increase plant productivity and cause community shifts and may also alter microbial community structure. Hence, the objective of this study was to determine whether experimental warming caused shifts in soil microbial communities by measuring changes in the frequency, relative abundance and/or richness of nosZ and nifH genotypes. Five sites at a high arctic coastal lowland were subjected to a 13-year warming experiment using open-top chambers (OTCs). Sites differed by dominant plant community, soil parent material and/or moisture regimen. Six soil cores were collected from each of four replicate OTC and ambient plots at each site and subdivided into upper and lower samples. Differences in frequency and relative abundance of terminal restriction fragments were assessed graphically by two-way cluster analysis and tested statistically with permutational multivariate analysis of variance (ANOVA). Genotypic richness was compared using factorial ANOVA. The genotype frequency, relative abundance and genotype richness of both nosZ and nifH communities differed significantly by site, and by OTC treatment and/or depth at some sites. The site that showed the most pronounced treatment effect was a wet sedge meadow, where community structure and genotype richness of both nosZ and nifH were significantly affected by warming. Although warming was an important factor affecting these communities at some sites at this high arctic lowland, overall, site factors were the main determinants of community structure.

Determination of orthodontic tooth movement and tissue reaction following demineralized freeze-dried bone allograft grafting intervention

PubMed Central

Seifi, Massoud; Ghoraishian, Seyed Ahmad

2012-01-01

Background: Socket preservation after tooth extraction is one of the indications of bone grafting to enhance preorthodontic condition. The aim of this study is to determine the effects of socket preservation on the immediate tooth movement, alveolar ridge height preservation and orthodontic root resorption. Materials and Methods: In a split-mouth technique, twelve sites in three dogs were investigated as an experimental study. Crushed demineralized freeze-dried bone allograft (DFDBA) (CenoBone®) was used as the graft material. The defects were made by the extraction of 3rd premolar. On one side of each jaw, the defects were preserved by DFDBA and defects of the other side left opened as the control group. Simultaneously the teeth adjacent to the defects were pulled together by a NiTi coil spring. After eight weeks, the amount of (OTM), alveolar height, and root resorption were measured. Analysis of variance was used for purpose of comparison. Results: There was a slight increase in OTM at grafted sites as they were compared to the control sites (P<0.05). Also a significant bone resorption in control site and successful socket preservation in experimental site were observed. Reduction of root resorption at the augmented site was significant compared to the normal healing site (P<0.05). Conclusion: Using socket preservation, tooth movement can be immediately started without waiting for the healing of the recipient site. This can provide some advantages like enhanced rate of OTM, its approved effects on ridge preservation that reduces the chance of dehiscence and the reduction of root resorption. PMID:22623939

Interferon-gamma promoter hypomethylation and increased expression in chronic periodontitis

PubMed Central

Zhang, Shaoping; Crivello, Antonino; Offenbacher, Steven; Moretti, Antonio; Paquette, David W.; Barros, Silvana P.

2011-01-01

Aim The goal of this investigation was to determine whether epigenetic modifications in the IFNG promoter are associated with an increase of IFNG transcription in different stages of periodontal diseases. Materials and Methods DNA was extracted from gingival biopsy samples collected from 47 total sites from 47 different subjects: 23 periodontally healthy sites, 12 experimentally induced gingivitis sites and 12 chronic periodontitis sites. Levels of DNA methylation within the IFNG promoter containing six CpG dinucleotides were determined using pyrosequencing technology. Interferon gamma mRNA expression was analysed by quantitative polymerase chain reactions using isolated RNA from part of the biological samples mentioned above. Results The methylation level of all six analysed CpG sites within the IFNG promoter region in the periodontitis biopsies {52% [interquartile range, IQR (43.8%, 63%)]} was significantly lower than periodontally healthy samples {62% [IQR (51.3%, 74%)], p =0.007} and gingivitis biopsies {63% [IQR (55%, 74%)], p =0.02}. The transcriptional level of IFNG in periodontitis biopsies was 1.96-fold and significantly higher than tissues with periodontal health (p =0.04). Although the mRNA level from experimental gingivitis samples exhibited an 8.5-fold increase as compared with periodontally healthy samples, no significant methylation difference was observed in experimental gingivitis sample. Conclusions A hypomethylation profile within IFNG promoter region is related to an increase of IFNG transcription present in the chronic periodontitis biopsies, while such an increase of IFNG in experimentally induced gingivitis seems independent of promoter methylation alteration. PMID:20958339

Experimental Analysis of Temperature Differences During Implant Site Preparation: Continuous Drilling Technique Versus Intermittent Drilling Technique.

PubMed

Di Fiore, Adolfo; Sivolella, Stefano; Stocco, Elena; Favero, Vittorio; Stellini, Edoardo

2018-02-01

Implant site preparation through drilling procedures may cause bone thermonecrosis. The aim of this in vitro study was to evaluate, using a thermal probe, overheating at implant sites during osteotomies through 2 different drilling methods (continuous drilling technique versus intermittent drilling technique) using irrigation at different temperatures. Five implant sites 13 mm in length were performed on 16 blocks (fresh bovine ribs), for a total of 80 implant sites. The PT-100 thermal probe was positioned 5 mm from each site. Two physiological refrigerant solutions were used: one at 23.7°C and one at 6.0°C. Four experimental groups were considered: group A (continuous drilling with physiological solution at 23.7°C), group B (intermittent drilling with physiological solution at 23.7°C), group C (continuous drilling with physiological solution at 6.0°C), and group D (intermittent drilling with physiological solution at 6.0°C). The Wilcoxon rank-sum test (2-tailed) was used to compare groups. While there was no difference between group A and group B (W = 86; P = .45), statistically significant differences were observed between experimental groups A and C (W = 0; P =.0001), B and D (W = 45; P =.0005), and C and D (W = 41; P = .003). Implant site preparation did not affect the overheating of the bone. Statistically significant differences were found with the refrigerant solutions. Using both irrigating solutions, bone temperature did not exceed 47°C.

Influence of bone marrow on osseointegration in long bones: an experimental study in sheep.

PubMed

Morelli, Fabrizio; Lang, Niklaus P; Bengazi, Franco; Baffone, Davide; Vila Morales, C Dadonim; Botticelli, Daniele

2015-03-01

To evaluate the influence of yellow bone marrow on osseointegration of titanium oral implants using a long bone model. The two tibiae of eight sheep were used as experimental sites. Two osteotomies for implant installation were prepared in each tibia. At the control sites, no further treatments were performed while, at the test sites, bone marrow was removed from the osteotomy site with a curette to an extent that exceeded the implant dimensions. As a result, the apical portion of the implants at the control sites was in contact with bone marrow while, at the test sites, it was in contact with the blood clot. After 2 months, the same procedures were performed in the contralateral side. After another month, the animal was sacrificed. Ground sections were obtained for histological analysis. After 1 month of healing, no differences between test and control sites were found in the apical extension of osseointegration and the percentage of new bone-to-implant contact. However, after 3 months of healing, a higher percentage of new bone-to-implant contact was found at the test compared to the control sites in the marrow compartment. The apical extension of osseointegration, however, was similar to that found at the 1-month healing period both for test and control sites. Osseointegration appeared to be favored by the presence of a blood clot when compared to the presence of yellow fatty bone marrow. Moreover, the contact with cortical bone appeared to be a prerequisite for the osseointegration process in the long bone model. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.

PubMed

Appelt, J-U; Giordano, F A; Ecker, M; Roeder, I; Grund, N; Hotz-Wagenblatt, A; Opelz, G; Zeller, W J; Allgayer, H; Fruehauf, S; Laufs, S

2009-07-01

Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.

Multisite experimental cost study of intensive psychiatric community care.

PubMed

Rosenheck, R; Neale, M; Leaf, P; Milstein, R; Frisman, L

1995-01-01

A 2-year experimental cost study of 10 Intensive Psychiatric Community Care (IPCC) programs was conducted at Department of Veterans Affairs (VA) medical centers in the Northeast. High hospital users were randomly assigned to either IPCC (n = 454) or standard VA care (n = 419) at four neuropsychiatric (NP) and six general medical and surgical (GMS) hospitals. National computerized data were used to track all VA health care service usage and costs for 2 years following program entry. At 9 of the 10 sites, IPCC treatment resulted in reduced inpatient service usage. Overall, for IPCC patients compared with control patients, average inpatient usage was 89 days (33%) less while average cost per patient (for IPCC inpatient, and outpatient services) was $15,556 (20%) less. Additionally, costs for IPCC patients compared with control patients were $33,295 (29%) less at NP sites but were $6,273 (15%) greater at GMS sites. At both NP and GMS sites, costs were lower for IPCC patients in two subgroups: veterans over age 45 and veterans with high levels of inpatient service use before program entry. No interaction was noted between the impact of IPCC on costs and other clinical or sociodemographic characteristics. Similarly, no linear relationship was observed between the intensity of IPCC services and the impact of IPCC on VA costs, although the two sites that did not fully implement the IPCC program had the poorest results. With these sites excluded, the total cost of care for IPCC patients at GMS sites was $579 (3%) more per year than that for the control patients.

Insecticide resistance profile of Anopheles gambiae from a phase II field station in Cové, southern Benin: implications for the evaluation of novel vector control products.

PubMed

Ngufor, Corine; N'Guessan, Raphael; Fagbohoun, Josias; Subramaniam, Krishanthi; Odjo, Abibatou; Fongnikin, Augustin; Akogbeto, Martin; Weetman, David; Rowland, Mark

2015-11-18

Novel indoor residual spraying (IRS) and long-lasting insecticidal net (LLIN) products aimed at improving the control of pyrethroid-resistant malaria vectors have to be evaluated in Phase II semi-field experimental studies against highly pyrethroid-resistant mosquitoes. To better understand their performance it is necessary to fully characterize the species composition, resistance status and resistance mechanisms of the vector populations in the experimental hut sites. Bioassays were performed to assess phenotypic insecticide resistance in the malaria vector population at a newly constructed experimental hut site in Cové, a rice growing area in southern Benin, being used for WHOPES Phase II evaluation of newly developed LLIN and IRS products. The efficacy of standard WHOPES-approved pyrethroid LLIN and IRS products was also assessed in the experimental huts. Diagnostic genotyping techniques and microarray studies were performed to investigate the genetic basis of pyrethroid resistance in the Cové Anopheles gambiae population. The vector population at the Cové experimental hut site consisted of a mixture of Anopheles coluzzii and An. gambiae s.s. with the latter occurring at lower frequencies (23 %) and only in samples collected in the dry season. There was a high prevalence of resistance to pyrethroids and DDT (>90 % bioassay survival) with pyrethroid resistance intensity reaching 200-fold compared to the laboratory susceptible An. gambiae Kisumu strain. Standard WHOPES-approved pyrethroid IRS and LLIN products were ineffective in the experimental huts against this vector population (8-29 % mortality). The L1014F allele frequency was 89 %. CYP6P3, a cytochrome P450 validated as an efficient metabolizer of pyrethroids, was over-expressed. Characterizing pyrethroid resistance at Phase II field sites is crucial to the accurate interpretation of the performance of novel vector control products. The strong levels of pyrethroid resistance at the Cové experimental hut station make it a suitable site for Phase II experimental hut evaluations of novel vector control products, which aim for improved efficacy against pyrethroid-resistant malaria vectors to WHOPES standards. The resistance genes identified can be used as markers for further studies investigating the resistance management potential of novel mixture LLIN and IRS products tested at the site.

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.

microPIR2: a comprehensive database for human–mouse comparative study of microRNA–promoter interactions

PubMed Central

Piriyapongsa, Jittima; Bootchai, Chaiwat; Ngamphiw, Chumpol; Tongsima, Sissades

2014-01-01

microRNA (miRNA)–promoter interaction resource (microPIR) is a public database containing over 15 million predicted miRNA target sites located within human promoter sequences. These predicted targets are presented along with their related genomic and experimental data, making the microPIR database the most comprehensive repository of miRNA promoter target sites. Here, we describe major updates of the microPIR database including new target predictions in the mouse genome and revised human target predictions. The updated database (microPIR2) now provides ∼80 million human and 40 million mouse predicted target sites. In addition to being a reference database, microPIR2 is a tool for comparative analysis of target sites on the promoters of human–mouse orthologous genes. In particular, this new feature was designed to identify potential miRNA–promoter interactions conserved between species that could be stronger candidates for further experimental validation. We also incorporated additional supporting information to microPIR2 such as nuclear and cytoplasmic localization of miRNAs and miRNA–disease association. Extra search features were also implemented to enable various investigations of targets of interest. Database URL: http://www4a.biotec.or.th/micropir2 PMID:25425035

Immersion freezing of supermicron mineral dust particles: freezing results, testing different schemes for describing ice nucleation, and ice nucleation active site densities.

PubMed

Wheeler, M J; Mason, R H; Steunenberg, K; Wagstaff, M; Chou, C; Bertram, A K

2015-05-14

Ice nucleation on mineral dust particles is known to be an important process in the atmosphere. To accurately implement ice nucleation on mineral dust particles in atmospheric simulations, a suitable theory or scheme is desirable to describe laboratory freezing data in atmospheric models. In the following, we investigated ice nucleation by supermicron mineral dust particles [kaolinite and Arizona Test Dust (ATD)] in the immersion mode. The median freezing temperature for ATD was measured to be approximately -30 °C compared with approximately -36 °C for kaolinite. The freezing results were then used to test four different schemes previously used to describe ice nucleation in atmospheric models. In terms of ability to fit the data (quantified by calculating the reduced chi-squared values), the following order was found for ATD (from best to worst): active site, pdf-α, deterministic, single-α. For kaolinite, the following order was found (from best to worst): active site, deterministic, pdf-α, single-α. The variation in the predicted median freezing temperature per decade change in the cooling rate for each of the schemes was also compared with experimental results from other studies. The deterministic model predicts the median freezing temperature to be independent of cooling rate, while experimental results show a weak dependence on cooling rate. The single-α, pdf-α, and active site schemes all agree with the experimental results within roughly a factor of 2. On the basis of our results and previous results where different schemes were tested, the active site scheme is recommended for describing the freezing of ATD and kaolinite particles. We also used our ice nucleation results to determine the ice nucleation active site (INAS) density for the supermicron dust particles tested. Using the data, we show that the INAS densities of supermicron kaolinite and ATD particles studied here are smaller than the INAS densities of submicron kaolinite and ATD particles previously reported in the literature.

Development and application of an exchange model for anisotropic water diffusion in the microporous MOF aluminum fumarate

NASA Astrophysics Data System (ADS)

Splith, Tobias; Fröhlich, Dominik; Henninger, Stefan K.; Stallmach, Frank

2018-06-01

Diffusion of water in aluminum fumarate was studied by means of pulsed field gradient (PFG) nuclear magnetic resonance (NMR). Due to water molecules exchanging between the intracrystalline anisotropic pore space and the isotropic intercrystalline void space the model of intracrystalline anisotropic diffusion fails to describe the experimental PFG NMR data at high observation times. Therefore, the two-site exchange model developed by Kärger is extended to the case of exchange between an anisotropic and an isotropic site. This extended exchange model is solved by numerical integration. It describes the experimental data very well and yields values for the intracrystalline diffusion coefficient and the mean residence times of the respective sites. Further PFG NMR studies were performed with coatings consisting of small aluminum fumarate crystals, which are used in adsorptive heat transformation applications. The diffusion coefficients of water in the small crystal coating are compared to the values expected from the extended two-site exchange model and from the model of long-range diffusion.

Soil slippage increased by brush conversion

Treesearch

Edward S. Corbett; Raymond M. Rice

1966-01-01

After 8 fire burned the San Dimas Experimental Forest, near Glendora Calif., in 1960, about 350 acres of brushland were converted to grass. Six years later, the frequency and extent of soil slips - a form of gravitational mass movement - on this acreage was compared with those on comparable sites where brush cover was recovering naturally after the fire. Both the area...

My Student Body: A High-Risk Drinking Prevention Web Site for College Students

PubMed Central

Chiauzzi, Emil; Green, Traci Craig; Lord, Sarah; Thum, Christina; Goldstein, Marion

2007-01-01

The authors investigated the efficacy of an interactive Web site, MyStudentBody.com: Alcohol (MSB:Alcohol) that offers a brief, tailored intervention to help heavy drinking college students reduce their alcohol use. They conducted a randomized, controlled clinical trial to compare the intervention with an alcohol education Web site at baseline, postintervention, and 3-month follow-up. Students were assessed on various drinking measures and their readiness to change their drinking habits. The intervention was especially effective for women and persistent binge drinkers. Compared with women who used the control Web site, women who used the intervention significantly reduced their peak and total consumption during special occasions and also reported significantly fewer negative consequences related to drinking. In addition, persistent heavy binge drinkers in the experimental group experienced a more rapid decrease in average consumption and peak consumption compared with those in the control group. The authors judged MSB:Alcohol a useful intervention for reaching important subgroups of college binge drinkers. PMID:15900990

Kinase Identification with Supervised Laplacian Regularized Least Squares

PubMed Central

Zhang, He; Wang, Minghui

2015-01-01

Phosphorylation is catalyzed by protein kinases and is irreplaceable in regulating biological processes. Identification of phosphorylation sites with their corresponding kinases contributes to the understanding of molecular mechanisms. Mass spectrometry analysis of phosphor-proteomes generates a large number of phosphorylated sites. However, experimental methods are costly and time-consuming, and most phosphorylation sites determined by experimental methods lack kinase information. Therefore, computational methods are urgently needed to address the kinase identification problem. To this end, we propose a new kernel-based machine learning method called Supervised Laplacian Regularized Least Squares (SLapRLS), which adopts a new method to construct kernels based on the similarity matrix and minimizes both structure risk and overall inconsistency between labels and similarities. The results predicted using both Phospho.ELM and an additional independent test dataset indicate that SLapRLS can more effectively identify kinases compared to other existing algorithms. PMID:26448296

Kinase Identification with Supervised Laplacian Regularized Least Squares.

PubMed

Li, Ao; Xu, Xiaoyi; Zhang, He; Wang, Minghui

2015-01-01

Phosphorylation is catalyzed by protein kinases and is irreplaceable in regulating biological processes. Identification of phosphorylation sites with their corresponding kinases contributes to the understanding of molecular mechanisms. Mass spectrometry analysis of phosphor-proteomes generates a large number of phosphorylated sites. However, experimental methods are costly and time-consuming, and most phosphorylation sites determined by experimental methods lack kinase information. Therefore, computational methods are urgently needed to address the kinase identification problem. To this end, we propose a new kernel-based machine learning method called Supervised Laplacian Regularized Least Squares (SLapRLS), which adopts a new method to construct kernels based on the similarity matrix and minimizes both structure risk and overall inconsistency between labels and similarities. The results predicted using both Phospho.ELM and an additional independent test dataset indicate that SLapRLS can more effectively identify kinases compared to other existing algorithms.

Long distance electron-transfer mechanism in peptidylglycine alpha-hydroxylating monooxygenase: a perfect fitting for a water bridge.

PubMed

de la Lande, Aurélien; Martí, Sergio; Parisel, Olivier; Moliner, Vicent

2007-09-26

The active sites of copper enzymes have been the subject of many theoretical and experimental investigations from a number of years. Such studies have embraced topics devoted to the modeling of the first coordination sphere at the metallic cations up to the development of biomimetic, or bioinspired, catalytic systems. At least from the theoretical viewpoint, fewer efforts have been dedicated to elucidate how the two copper cations act concertedly in noncoupled dicopper enzymes such as peptidylglycine alpha-hydroxylating monooxygenase (PHM) and dopamine beta-monooxygenase (DbetaM). In these metalloenzymes, an electronic transfer is assumed between the two distant copper cations (11 A). Recent experimental results suggest that this transfer occurs through water molecules, a phenomenon which has been theoretically evidenced to be of high efficiency in the case of cytochrome b5 (Science, 2005, 310, 1311). In the present contribution dedicated to PHM, we overpass the common theoretical approaches dedicated to the electronic and geometrical structures of sites CuM or CuH restricted to their first coordination spheres and aim at directly comparing theoretical results to the experimentally measured activity of the PHM enzyme. To achieve this goal, molecular dynamics simulations were performed on wild-type and various mutants of PHM. More precisely, we provide an estimate of the electron-transfer efficiency between the CuM and CuH sites by means of such molecular dynamics simulations coupled to Marcus theory joined to the Beratan model to approximate the required coupling matrix elements. The theoretical results are compared to the kinetics measurements performed on wild and mutated PHM. The present work, the dynamic aspects of which are essential, accounts for the experimental results issued from mutagenesis. It supports the conclusion that an electronic transfer can occur between two copper(I) sites along a bridge involving a set of hydrogen and chemical bonds. Residue Gln170 is evidenced to be the keystone of this water-mediated pathway.

In silico modeling and experimental evidence of coagulant protein interaction with precursors for nanoparticle functionalization.

PubMed

Okoli, Chuka; Sengottaiyan, Selvaraj; Arul Murugan, N; Pavankumar, Asalapuram R; Agren, Hans; Kuttuva Rajarao, Gunaratna

2013-10-01

The design of novel protein-nanoparticle hybrid systems has applications in many fields of science ranging from biomedicine, catalysis, water treatment, etc. The main barrier in devising such tool is lack of adequate information or poor understanding of protein-ligand chemistry. Here, we establish a new strategy based on computational modeling for protein and precursor linkers that can decorate the nanoparticles. Moringa oleifera (MO2.1) seed protein that has coagulation and antimicrobial properties was used. Superparamagnetic nanoparticles (SPION) with precursor ligands were used for the protein-ligand interaction studies. The molecular docking studies reveal that there are two binding sites, one is located at the core binding site; tetraethoxysilane (TEOS) or 3-aminopropyl trimethoxysilane (APTES) binds to this site while the other one is located at the side chain residues where trisodium citrate (TSC) or Si60 binds to this site. The protein-ligand distance profile analysis explains the differences in functional activity of the decorated SPION. Experimentally, TSC-coated nanoparticles showed higher coagulation activity as compared to TEOS- and APTES-coated SPION. To our knowledge, this is the first report on in vitro experimental data, which endorses the computational modeling studies as a powerful tool to design novel precursors for functionalization of nanomaterials; and develop interface hybrid systems for various applications.

Zeeman perturbed nuclear quadrupole spin echo envelope modulations for spin 3/2 nuclei in polycrystalline specimens

NASA Astrophysics Data System (ADS)

Ramachandran, R.; Narasimhan, P. T.

The results of theoretical and experimental studies of Zeeman-perturbed nuclear quadrupole spin echo envelope modulations (ZSEEM) for spin 3/2 nuclei in polycrystalline specimens are presented. The response of the Zeeman-perturbed spin ensemble to resonant two pulse excitations has been calculated using the density matrix formalism. The theoretical calculation assumes a parallel orientation of the external r.f. and static Zeeman fields and an arbitrary orientation of these fields to the principal axes system of the electric field gradient. A numerical powder averaging procedure has been adopted to simulate the response of the polycrystalline specimens. Using a coherent pulsed nuclear quadrupole resonance spectrometer the ZSEEM patterns of the 35Cl nuclei have been recorded in polycrystalline specimens of potassium chlorate, barium chlorate, mercuric chloride (two sites) and antimony trichloride (two sites) using the π/2-τ-π/2 sequence. The theoretical and experimental ZSEEM patterns have been compared. In the case of mercuric chloride, the experimental 35Cl ZSEEM patterns are found to be nearly identical for the two sites and correspond to a near-zero value of the asymmetry parameter, η, of the electric field gradient tensor. The difference in the η values for the two 35Cl sites (η ˜0·06 and η˜0·16) in antimony trichloride is clearly reflected in the experimental and theoretical ZSEEM patterns. The present study indicates the feasibility of evaluating η for spin 3/2 nuclei in polycrystalline specimens from ZSEEM investigations.

First Principle and Experimental Study for Site Preferences of Formability Improved Alloying Elements in Mg Crystal

NASA Astrophysics Data System (ADS)

Zeng, Ying; Jiang, Bin; Shi, Ouling; Quan, Gaofen; Al-Ezzi, Salih; Pan, FuSheng

2018-07-01

Some alloying elements (Al, Er, Gd, Li, Mn, Sn, Y, Zn) were proved recently by calculations or experiments to improve the formability of Mg alloys, but ignoring their site preference in Mg crystals during the calculated process. A crystallographic model was built via first principle calculations to predict the site preferences of these elements. Regularities between doping elements and site preferences were summarized. Meanwhile, in the basis of the crystallographic model, a series of formulas were deduced combining the diffraction law. It predicted that a crystal plane with abnormal XRD peak intensity of the Mg-based solid solutions, compared to that of the pure Mg, prefers to possess solute atoms. Thus, three single-phase solid solution alloys were then prepared through an original In-situ Solution Treatment, and their XRD patterns were compared. Finally, the experiment further described the site preferences of these solute atoms in Mg crystal, verifying the calculation results.

First Principle and Experimental Study for Site Preferences of Formability Improved Alloying Elements in Mg Crystal

NASA Astrophysics Data System (ADS)

Zeng, Ying; Jiang, Bin; Shi, Ouling; Quan, Gaofen; Al-Ezzi, Salih; Pan, FuSheng

2018-03-01

Some alloying elements (Al, Er, Gd, Li, Mn, Sn, Y, Zn) were proved recently by calculations or experiments to improve the formability of Mg alloys, but ignoring their site preference in Mg crystals during the calculated process. A crystallographic model was built via first principle calculations to predict the site preferences of these elements. Regularities between doping elements and site preferences were summarized. Meanwhile, in the basis of the crystallographic model, a series of formulas were deduced combining the diffraction law. It predicted that a crystal plane with abnormal XRD peak intensity of the Mg-based solid solutions, compared to that of the pure Mg, prefers to possess solute atoms. Thus, three single-phase solid solution alloys were then prepared through an original In-situ Solution Treatment, and their XRD patterns were compared. Finally, the experiment further described the site preferences of these solute atoms in Mg crystal, verifying the calculation results.

A simple and efficient method for predicting protein-protein interaction sites.

PubMed

Higa, R H; Tozzi, C L

2008-09-23

Computational methods for predicting protein-protein interaction sites based on structural data are characterized by an accuracy between 70 and 80%. Some experimental studies indicate that only a fraction of the residues, forming clusters in the center of the interaction site, are energetically important for binding. In addition, the analysis of amino acid composition has shown that residues located in the center of the interaction site can be better discriminated from the residues in other parts of the protein surface. In the present study, we implement a simple method to predict interaction site residues exploiting this fact and show that it achieves a very competitive performance compared to other methods using the same dataset and criteria for performance evaluation (success rate of 82.1%).

Comparative evaluation of leachate pollution index of MSW landfill site of Kolkata with other metropolitan cities of India.

PubMed

Motling, Sanjay; Dutta, Amit; Mukherjee, S N; Kumar, Sunil

2013-07-01

The uncontrolled tipping of mixed urban solid waste in landfill site causes serious negative impacts on the environment. The major issue in this context is the generation of leachate which possesses potential of polluting freshwater ecosystem including groundwater besides associated health hazards and depletion of soil fertility. In this context, a pseudo computation quantitative tool, known as leachate pollution index (LPI), has been developed by some researchers for scaling pollution potential of landfill site owing to emergence of leachate. This paper. deals with the assessment of leachate quality of existing landfill site of Kolkata situated at Dhapa waste dumping ground through evaluation of the LPI from experimental analysis of leachate. The leachate was collected from this site in different seasons. 18 parameters were tested with real leachate samples in the Environmental Engineering Laboratory of Civil Engineering Department of Jadavpur University Kolkata. The results exhibited a very high value of organic pollutants in the leachate with COD as 21,129 mg/L and also values of TDS, Fe2+, Cr, Zn, chloride and ammonical nitrogen. The LPI value of Kolkata landfill site at Dhapa was estimated and also compared with leachate quality data of other metropolitan cities viz. Mumbai, Delhi, Chennai as available in literatures. It is found that LPI of the Kolkata landfill site is highest compared to all other landfill sites of other metropolitan cities in India.

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

PubMed Central

Hestand, Matthew S; van Galen, Michiel; Villerius, Michel P; van Ommen, Gert-Jan B; den Dunnen, Johan T; 't Hoen, Peter AC

2008-01-01

Background The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current approaches. Computational methods to reduce false positives are to look for over-representation of transcription factor binding sites in a set of similarly regulated promoters or to look for conservation in orthologous promoter alignments. Results We have developed a novel tool, "CORE_TF" (Conserved and Over-REpresented Transcription Factor binding sites) that identifies common transcription factor binding sites in promoters of co-regulated genes. To improve upon existing binding site predictions, the tool searches for position weight matrices from the TRANSFACR database that are over-represented in an experimental set compared to a random set of promoters and identifies cross-species conservation of the predicted transcription factor binding sites. The algorithm has been evaluated with expression and chromatin-immunoprecipitation on microarray data. We also implement and demonstrate the importance of matching the random set of promoters to the experimental promoters by GC content, which is a unique feature of our tool. Conclusion The program CORE_TF is accessible in a user friendly web interface at . It provides a table of over-represented transcription factor binding sites in the users input genes' promoters and a graphical view of evolutionary conserved transcription factor binding sites. In our test data sets it successfully predicts target transcription factors and their binding sites. PMID:19036135

Pain Sensitivity Risk Factors for Chronic TMD: Descriptive Data and Empirically Identified Domains from the OPPERA Case Control Study

PubMed Central

Greenspan, Joel D.; Slade, Gary D.; Bair, Eric; Dubner, Ronald; Fillingim, Roger B.; Ohrbach, Richard; Knott, Charlie; Mulkey, Flora; Rothwell, Rebecca; Maixner, William

2011-01-01

Many studies report that people with temporomandibular disorders (TMD) are more sensitive to experimental pain stimuli than TMD-free controls. Such differences in sensitivity are observed in remote body sites as well as in the orofacial region, suggesting a generalized upregulation of nociceptive processing in TMD cases. This large case-control study of 185 adults with TMD and 1,633 TMD-free controls measured sensitivity to painful pressure, mechanical cutaneous, and heat stimuli, using multiple testing protocols. Based on an unprecedented 36 experimental pain measures, 28 showed statistically significantly greater pain sensitivity in TMD cases than controls. The largest effects were seen for pressure pain thresholds at multiple body sites and cutaneous mechanical pain threshold. The other mechanical cutaneous pain measures and many of the heat pain measures showed significant differences, but with lesser effect sizes. Principal component analysis (PCA) of the pain measures derived from 1,633 controls identified five components labeled: (1) heat pain ratings, (2) heat pain aftersensations and tolerance, (3) mechanical cutaneous pain sensitivity, (4) pressure pain thresholds, and (5) heat pain temporal summation. These results demonstrate that, compared to TMD-free controls, chronic TMD cases are more sensitive to many experimental noxious stimuli at extra-cranial body sites, and provides for the first time the ability to directly compare the case-control effect sizes of a wide range of pain sensitivity measures. PMID:22074753

Site-specific electronic structure analysis by channeling EELS and first-principles calculations.

PubMed

Tatsumi, Kazuyoshi; Muto, Shunsuke; Yamamoto, Yu; Ikeno, Hirokazu; Yoshioka, Satoru; Tanaka, Isao

2006-01-01

Site-specific electronic structures were investigated by electron energy loss spectroscopy (EELS) under electron channeling conditions. The Al-K and Mn-L(2,3) electron energy loss near-edge structure (ELNES) of, respectively, NiAl2O4 and Mn3O4 were measured. Deconvolution of the raw spectra with the instrumental resolution function restored the blunt and hidden fine features, which allowed us to interpret the experimental spectral features by comparing with theoretical spectra obtained by first-principles calculations. The present method successfully revealed the electronic structures specific to the differently coordinated cationic sites.

On simulation of the atmospheric acoustic channel for some nuclear tests in former soviet test site Semipalatinsk

NASA Astrophysics Data System (ADS)

Sorokin, A. G.; Lobycheva, I. Yu.

2011-08-01

This paper presents data on the recording of infrasound from distant nuclear explosions set off in former soviet test site Semipalatinsk and recorded by infrasonic station Irkutsk-Badary of the Institute of Solar-Terrestrial Physics SB RAS in the Tunkinsky region in the Buryat Republic. We assess the state of the atmospheric acoustic channel (AAC) along the propagation path. Results of the AAC modeling are compared with experimental data.

Assessing effects of native forest restoration on soil moisture dynamics and potential aquifer recharge, Auwahi, Maui

USGS Publications Warehouse

Perkins, Kim S.; Nimmo, John R.; Medeiros, Arthur C.; Szutu, Daphne J.; von Allmen, Erica

2014-01-01

Understanding the role of soils in regulating water flow through the unsaturated zone is critical in assessing the influence of vegetation on soil moisture dynamics and aquifer recharge. Because of fire, introduced ungulates and landscape-level invasion of non-native grasses, less than 10% of original dry forest (~730 mm precipitation annually) still exists on leeward Haleakalā, Maui, Hawaiian Islands. Native dry forest restoration at Auwahi has demonstrated the potential for dramatic revegetation, allowing a unique experimental comparison of hydrologic function between tracts of restored forest and adjacent grasslands. We hypothesized that even relatively recent forest restoration can assist in the recovery of impaired hydrologic function, potentially increasing aquifer recharge. To compare restored forest and grassland sites, we experimentally irrigated and measured soil moisture and temperature with subsurface instrumentation at four locations within the reforested area and four within the grassland, each with a 2·5 × 2·5-m plot. Compared with grassland areas, water in reforested sites moved to depth faster with larger magnitude changes in water content. The median first arrival velocity of water was greater by a factor of about 13 in the reforested sites compared with the grassland sites. This rapid transport of water to depths of 1 m or greater suggests increased potential aquifer recharge. Improved characterization of how vegetation and soils influence recharge is crucial for understanding the long-term impacts of forest restoration on aquifer recharge and water resources, especially in moisture-limited regions.

Radar properties of the Huygens Landing Site on Titan

NASA Astrophysics Data System (ADS)

Lorenz, Ralph; Cassini RADAR Team

2006-09-01

The Huygens landing site on Titan was not expected to be observed with SAR imaging by the Cassini RADAR until late in the nominal tour. However, better-than-expected performance, permitting operation at higher altitudes and thus over longer times than originally anticipated, has permitted two observations of the landing site. The first was an extension to the 5-beam SAR swath on T8 (October 2005) from altitudes of 4000km to 5000km ; the second was an experimental observation at an altitude range of 10,000km-13,000km using custom pointing and SAR-processing only the central high-gain beam. The latter 'experimental' observation opens a new capability (see also the abstract by West et al) for observing targets of interest with a resolution of approximately 1-2km. Here we compare the two images, which have slightly different incidence angles and look azimuths, noting correlations and differences. These can also be compared with the optical image mosaic from the Huygens descent imager DISR. Some correlations exist (notably the two prominent dark lines - linear sand dunes) but there are many differences. Additional information on the radar properties of the landing site can be derived from the Huygens radar altimeter, and the intensity of the probe's radio signal received as Cassini set on the horizon, a fortuitous bistatic scattering experiment.

Prevention of poison ivy and poison oak allergic contact dermatitis by quaternium-18 bentonite.

PubMed

Marks, J G; Fowler, J F; Sheretz, E F; Rietschel, R L

1995-08-01

Poison ivy and poison oak are the most common causes of allergic contact dermatitis in North America. We investigated whether a new topical lotion containing 5% quaternium-18 bentonite prevents experimentally induced poison ivy and poison oak allergic contact dermatitis. A single-blind, paired comparison, randomized, multicenter investigation was used to evaluate the effectiveness and safety of quaternium-18 bentonite lotion in preventing experimentally induced poison ivy and poison oak allergic contact dermatitis in susceptible volunteers. One hour before both forearms were patch tested with urushiol, the allergenic resin from poison ivy and poison oak, 5% quaternium-18 bentonite lotion was applied on one forearm. The test patches were removed after 4 hours and the sites interpreted for reaction 2, 5, and 8 days later. The difference in reactions between treated and untreated patch test sites was statistically analyzed. Two hundred eleven subjects with a history of allergic contact dermatitis to poison ivy and poison oak were studied. One hundred forty-four subjects had positive reactions to urushiol. The test sites pretreated with quaternium-18 bentonite lotion had absent or significantly reduced reactions to the urushiol compared with untreated control sites (p < 0.0001) on all test days. When it occurred, the reaction consistently appeared later on treated than on control sites (p < 0.0001). One occurrence of mild, transient erythema at the application site was the only side effect from the quaternium-18 bentonite lotion. Quaternium-18 bentonite lotion was effective in preventing or diminishing experimentally produced poison ivy and poison oak allergic contact dermatitis.

Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

PubMed Central

Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

2016-01-01

Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

A pharmacophore model specific to active site of CYP1A2 with a novel molecular modeling explorer and CoMFA.

PubMed

Zhang, Tao; Wei, Dong-Qing; Chou, Kuo-Chen

2012-03-01

Comparative molecular field analysis (CoMFA) is a widely used 3D-QSAR method by which we can investigate the potential relation between biological activity of compounds and their structural features. In this study, a new application of this approach is presented by combining the molecular modeling with a new developed pharmacophore model specific to CYP1A2 active site. During constructing the model, we used the molecular dynamics simulation and molecular docking method to select the sensible binding conformations for 17 CYP1A2 substrates based on the experimental data. Subsequently, the results obtained via the alignment of binding conformations of substrates were projected onto the active- site residues, upon which a simple blueprint of active site was produced. It was validated by the experimental and computational results that the model did exhibit the high degree of rationality and provide useful insights into the substrate binding. It is anticipated that our approach can be extended to investigate the protein-ligand interactions for many other enzyme-catalyzed systems as well.

Photoabsorption of acridine yellow and proflavin bound to human serum albumin studied by means of quantum mechanics/molecular dynamics.

PubMed

Aidas, Kęstutis; Olsen, Jógvan Magnus H; Kongsted, Jacob; Ågren, Hans

2013-02-21

Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site 1 nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.

JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs.

PubMed

Beauclair, Guillaume; Bridier-Nahmias, Antoine; Zagury, Jean-François; Saïb, Ali; Zamborlini, Alessia

2015-11-01

Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs. JASSA is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Compared with existing web-tools, JASSA displays on par or better performances. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files. JASSA is freely accessible at http://www.jassa.fr/. Website is implemented in PHP and MySQL, with all major browsers supported. guillaume.beauclair@inserm.fr Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

An economic analysis of repositioning for the prevention of pressure ulcers.

PubMed

Moore, Zena; Cowman, Seamus; Posnett, John

2013-08-01

To compare pressure ulcer incidence and costs associated with repositioning older individuals in long-term care using two different repositioning regimes. Repositioning has not always been integrated into pressure ulcer preventative methods, with arguments that it is an expensive procedure in terms of personnel and time. Participants were randomly allocated to the experimental group (n = 99; repositioned every 3 hours, using the 30° tilt) and the control group (n = 114 standard care, repositioned every 6 hours, using the 90° lateral rotation). The analysis explored the incidence of pressure ulcer development and the cost difference between the two repositioning schedules, over a 4-week period. The mean daily nurse time for repositioning was 18·5 minutes (experimental) and 24·5 minutes (control). Nurse time cost per patient over the study period was €206·6 (experimental) and €253·1 (control), 96·6% of participants (experimental) remained free of pressure ulcers, compared with 88·1% (control). The cost per patient free of ulcer was €213·9 (experimental) and €287·3 (control). Projected annual costs were estimated for the 588 (53·5%) residents in the 12 study sites requiring repositioning. The cost would be €1·59 m (experimental) and €2·10 m (control), a cost difference of €510,000. This represents a difference of 58·8 hours of nurse time, equivalent to approximately 12 full time nurses across the 12 sites. Repositioning every 3 hours, using 30° tilt, has been shown to be more effective in less costly in terms of nurse time compared with standard care. Repositioning individuals at risk of pressure ulcer development makes both economic and clinical sense, thereby supporting the EPUAP/NPUAP 2009 guidelines. © 2013 John Wiley & Sons Ltd.

Tracer tomography: design concepts and field experiments using heat as a tracer.

PubMed

Doro, Kennedy O; Cirpka, Olaf A; Leven, Carsten

2015-04-01

Numerical and laboratory studies have provided evidence that combining hydraulic tomography with tomographic tracer tests could improve the estimation of hydraulic conductivity compared with using hydraulic data alone. Field demonstrations, however, have been lacking so far, which we attribute to experimental difficulties. In this study, we present a conceptual design and experimental applications of tracer tomography at the field scale using heat as a tracer. In our experimental design, we improve active heat tracer testing by minimizing possible effects of heat losses, buoyancy, viscosity, and changing boundary conditions. We also utilize a cost-effective approach of measuring temperature changes in situ at high resolution. We apply the presented method to the 8 m thick heterogeneous, sandy gravel, alluvial aquifer at the Lauswiesen Hydrogeological Research Site in Tübingen, Germany. Results of our tomographic heat-tracer experiments are in line with earlier work on characterizing the aquifer at the test site. We demonstrate from the experimental perspective that tracer tomography is applicable and suitable at the field scale using heat as a tracer. The experimental results also demonstrate the potential of heat-tracer tomography as a cost-effective means for characterizing aquifer heterogeneity. © 2014, National Ground Water Association.

An investigation of the sites occupied by atomic barium in solid xenon—A 2D-EE luminescence spectroscopy and molecular dynamics study

NASA Astrophysics Data System (ADS)

Davis, Barry M.; Gervais, Benoit; McCaffrey, John G.

2018-03-01

A detailed characterisation of the luminescence recorded for the 6p 1P1-6s 1S0 transition of atomic barium isolated in annealed solid xenon has been undertaken using two-dimensional excitation-emission (2D-EE) spectroscopy. In the excitation spectra extracted from the 2D-EE scans, two dominant thermally stable sites were identified, consisting of a classic, three-fold split Jahn-Teller band, labeled the blue site, and an unusual asymmetric 2 + 1 split band, the violet site. A much weaker band has also been identified, whose emission is strongly overlapped by the violet site. The temperature dependence of the luminescence for these sites was monitored revealing that the blue site has a non-radiative channel competing effectively with the fluorescence even at 9.8 K. By contrast, the fluorescence decay time of the violet site was recorded to be 4.3 ns and independent of temperature up to 24 K. The nature of the dominant thermally stable trapping sites was investigated theoretically with Diatomics-in-Molecule (DIM) molecular dynamics simulations. The DIM model was parameterized with ab initio multi-reference configuration interaction calculations for the lowest energy excited states of the BaṡXe pair. The simulated absorption spectra are compared with the experimental results obtained from site-resolved excitation spectroscopy. The simulations allow us to assign the experimental blue feature spectrum to a tetra-vacancy trapping site in the bulk xenon fcc crystal—a site often observed when trapping other metal atoms in rare gas matrices. By contrast, the violet site is assigned to a specific 5-atom vacancy trapping site located at a grain boundary.

The acid-base titration of montmorillonite

NASA Astrophysics Data System (ADS)

Bourg, I. C.; Sposito, G.; Bourg, A. C.

2003-12-01

Proton binding to clay minerals plays an important role in the chemical reactivity of soils (e.g., acidification, retention of nutrients or pollutants). If should also affect the performance of clay barriers for waste disposal. The surface acidity of clay minerals is commonly modelled empirically by assuming generic amphoteric surface sites (>SOH) on a flat surface, with fitted site densities and acidity constant. Current advances in experimental methods (notably spectroscopy) are rapidly improving our understanding of the structure and reactivity of the surface of clay minerals (arrangement of the particles, nature of the reactive surface sites, adsorption mechanisms). These developments are motivated by the difficulty of modelling the surface chemistry of mineral surfaces at the macro-scale (e.g., adsorption or titration) without a detailed (molecular-scale) picture of the mechanisms, and should be progressively incorporated into surface complexation models. In this view, we have combined recent estimates of montmorillonite surface properties (surface site density and structure, edge surface area, surface electrostatic potential) with surface site acidities obtained from the titration of alpha-Al2O3 and SiO2, and a novel method of accounting for the unknown initial net proton surface charge of the solid. The model predictions were compared to experimental titrations of SWy-1 montmorillonite and purified MX-80 bentonite in 0.1-0.5 mol/L NaClO4 and 0.005-0.5 mol/L NaNO3 background electrolytes, respectively. Most of the experimental data were appropriately described by the model after we adjusted a single parameter (silanol sites on the surface of montmorillonite were made to be slightly more acidic than those of silica). At low ionic strength and acidic pH the model underestimated the buffering capacity of the montmorillonite, perhaps due to clay swelling or to the interlayer adsorption of dissolved aluminum. The agreement between our model and the experimental data illustrates the complementarity of molecular and macro-scale descriptions of the clay reactivity.

Distribution of physical properties and timing of relative uplift in upper plate off Costa Rica: IODP Expedition 344

NASA Astrophysics Data System (ADS)

Saiki, A.; Hashimoto, Y.

2015-12-01

Evolution of physical properties in subduction zone is a key to understand lithification processes, location of decollement, and stress distribution. In this study, we examined the physical properties of sediments using on-board data and laboratory experimental data on sediments obtained off Costa Rica margin. Target sites are in the Integrate Ocean Drilling Program (IODP) Expedition 344 off Costa Rica, including reference sites (U1381 and U1414), mid-slope site (U1378, U1380) and upper-slope site (U1413). Seven samples from reference sites were analyzed. Laboratory experiments for velocity and porosity measurements were conducted with variation of effective pressure. Velocity-porosity relationships from on-board data and from laboratory experiments are comparable. The porosity-effective pressure curves under isotropic condition were converted to the curves under uniaxial condition (Teeuw, 1971). Using the normal consolidation curves under uniaxial stress conditions, we converted onboard porosity to effective pressure and fluid pressure. In reference sites, hydrostatic fluid pressure was estimated as expected as a reference sites, suggesting that porosity-effective pressure relationship was obtained correctly by experiments and it can be adapted to estimation of fluid pressure for the wedge sites. The porosity-effective pressure relationship under isotropic conditions were used for the estimation in wedge sites. In wedge sites, estimated pore pressures show lower than hydrostatic pressure, suggesting that onboard porosity was lower than that under normal compaction. The lower porosity can be caused by relative uplift from deeper portion. The amount of relative uplift can be estimated by differences in porosity-depth relationships between onboard data and experimental data. The amount of relative uplift for each site shows more than ~1000m up to ~5000m. The small error in porosity depth curve from experimental data makes relative uplift larger or smaller exponentially in the deeper portion. The increment of relative uplift, however, starts from about 1Ma in each site, suggesting some events were occurred at the timing. Laboratory experiments under differential stress should be conducted in the near future because smaller porosity is expected under differential stress conditions.

Deep-sea nematode assemblage has not recovered 26 years after experimental mining of polymetallic nodules (Clarion-Clipperton Fracture Zone, Tropical Eastern Pacific)

NASA Astrophysics Data System (ADS)

Miljutin, Dmitry M.; Miljutina, Maria A.; Arbizu, Pedro Martínez; Galéron, Joëlle

2011-08-01

We investigated nematode assemblages inhabiting the 26-year-old track created by experimental deep-sea mining of polymetallic nodules, and two adjacent, undisturbed sites, one with nodules and one without nodules. The aim was to compare density, assemblage structure, and diversity indices in order to assess the process of recovery of the nematode assemblage inhabiting the disturbed site. This experimental dredging was conducted in 1978 by the Ocean Minerals Company (USA) in the area of a French mining claim in the Clarion-Clipperton Fracture Zone (Tropical Eastern Pacific) at a depth of about 5000 m. The nematode assemblage had not returned its initial state 26 years after the experimental dredging: the total nematode density and biomass within the dredging track were significantly lower than outside the track; the biodiversity indices showed significantly lower nematode diversity within the track; and the structure of the nematode assemblage within the track differed significantly from those in the two undisturbed sites outside the track. However, there were no significant differences in the mean body volumes of adult nematodes and adult-juvenile ratios between the track and reference sites. Parameters such as the rate of sediment restoration (which depends on local hydrological conditions) and the degree and character of the disturbance appeared to be of considerable importance for the recovery rate of the deep-sea nematode assemblages and their ability to recolonize disturbed areas. The rates of recolonization and recovery may vary widely in different deep-sea regions.

[Variation of long-chain 3-hydroxyacyl-CoA dehydrogenase DNA methylation in placenta of different preeclampsia-like mouse models].

PubMed

Han, Yiwei; Yang, Zi; Ding, Xiaoyan; Yu, Huan; Yi, Yanhong

2015-10-01

By detecting the variation of long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) DNA methylation in preeclampsia-like mouse models generated by different ways, to explore the roles of multifactor and multiple pathways in preeclampsia pathogenesis on molecular basis. Established preeclampsia-like mouse models in different ways and divided into groups as follows: (1) Nw-nitro-L-arginine-methyl ester (L-NAME) group: wild-type pregnant mouse received subcutaneous injection of L-NAME; (2) lipopolysaccharide (LPS) group: wild-type pregnant mouse received intraperitoneal injection of LPS; (3) apolipoprotein C-III (ApoC3) group: ApoC3 transgenic pregnant mouse with dysregulated lipid metabolism received subcutaneous injection of L-NAME; (4) β2 glycoprotein I (β-2GPI) group: wild-type pregnant mouse received subcutaneous injection of β-2GPI. According to the first injection time (on day 3, 11, 16 respectively), the L-NAME, LPS and ApoC3 groups were further subdivided into: pre-implantation (PI) experimental stage, early gestation (EG) experimental stage, and late gestation (LG) experimental stage. β-2GPI group was only injected before implantation. LCHAD gene methylation levels in placental were detected in different experimental stage. Normal saline control groups were set within wild-type and ApoC3 transgenic pregnant mice simultaneously. (1) CG sites in LCHAD DNA: 45 CG sites were detected in the range of 728 bp before LCHAD gene transcription start site, the 5, 12, 13, 14, 15, 16, 19, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 43 CG sites were complex sites which contained two or more CG sequences, others were single site which contained one CG sequence. The 3, 5, 6, 11, 13, 14, 18, 28 sites in L-NAME, LPS, ApoC3 and β-2GPI groups showed different high levels of methylation; the 16, 25, 31, 42, 44 sites showed different low levels of methylation; other 32 sites were unmethylated. (2) Comparison of LCHAD gene methylation between different groups: the methylation levels of LCAHD gene at 3, 11, 13, 14, 18 sites in L-NAME, LPS, ApoC3 and β-2GPI groups were significantly higher than those in the normal saline control group (P < 0.05); and the methylation levels of 42, 44 sites in these groups were significantly lower than those in the normal saline control group (P < 0.05). (3) Methylation of LCHAD gene at the same site between different experimental stages: ① The 3, 11, 18 sites of EG experimental stage was significantly lower than PI and LG experimental stage in L-NAME group (P < 0.05); the 3, 11, 18 sites of PI experimental stage was significantly lower than EG and LG experimental stage in LPS group (P < 0.05); these sites of PI experimental stage was significantly higher than EG and LG experimental stages in ApoC3 group (P < 0.05). ② The methylation of site 5 in L-NAME and LPS groups were significantly higher than that of the normal saline control group (P < 0.05), and the LG experimental stages were significantly higher than other stages, but in ApoC3 group, only PI and EG stages were significantly higher than the normal saline control group (P < 0.05). ③ At site 6 in L-NAME group which showed high methylation level was significantly higher than the same site in other groups which showed low methylation level (P < 0.05). ④ At 13, 14 sites, earlier preeclampsia onset caused a lower methylation level in L-NAME group, but PI experimental stage was significantly higher than EG and LG experimental stages in LPS group (P < 0.05), EG experimental stage was significantly higher than PI and LG experimental stages in ApoC3 group (P < 0.05). ⑤ At site 28, earlier preeclampsia onset caused a higher methylation level in L-NAME group, but PI experimental stage was significantly lower than EG and LG experimental stages in LPS group (P < 0.05), EG experimental stage was significantly higher than PI and LG experimental stages in ApoC3 group (P < 0.05). ⑥ The 16, 25, 31 sites in ApoC3 group were significantly higher than other groups (P < 0.05). ⑦ At site 42 in β-2GPI group was unmethylated, but it in other groups showed low methylation level, the methylation level of site 42 in β-2GPI group was significantly lower than that in other groups (P < 0.05). The methylation of 6 and 42 CG sites may be related to LCHAD gene expression in placenta of L-NAME and β-2GPI induced preeclampsia-like models respectively; LCHAD gene expression and DNA methylation may not have obvious correlation in LPS and ApoC3 induced preeclampsia-like models. Differences exist in LCHAD DNA methylation in preeclampsia-like models generated by different ways, revealed a molecular basis to expand our understanding of the multi-factorial pathogenesis of preeclampsia.

76 FR 66698 - Postsecondary Educational Institutions Invited To Participate in Experiments Under the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-27

... Experiments Under the Experimental Sites Initiative AGENCY: Office of Postsecondary Education, Department of... institutions to participate in experiments under the Experimental Sites Initiative. SUMMARY: The Secretary... participate in one or more new experiments under the Experimental Sites Initiative (ESI), as authorized by...

Longitudinal analysis of student performance in a dental hygiene distance education program.

PubMed

Olmsted, Jodi L

2002-09-01

The purpose of the study was to determine if learners who receive face-to-face instruction in an educational program performed statistically better on established benchmark assessments (GPA, course averages, and NBDHE) than learners at a distance from the didactic course instructor. A comparative, quasi-experimental, ex-post facto study was conducted. The treatment variable was program type: face-to-face vs. distance. The performance of five consecutive classes was analyzed, from 1997 to 2001. These five classes consisted of 221 learners, 105 of them at the host site and 115 using distance learning. The experimental groups were divided based upon location--host or cooperating college (distance) site learners. Study results identified no significant difference between host and distance learner performance for the entire educational program. The use of interactive television (ITV) for delivery of an educational program using distance education technology provided acceptable results in learner didactic performance. Learners at both the host and cooperating college (distance) sites performed equally well. The results were used to document program outcomes.

Preferential sites for InAsP/InP quantum wire nucleation using molecular dynamics

NASA Astrophysics Data System (ADS)

Nuñez-Moraleda, Bernardo; Pizarro, Joaquin; Guerrero, Elisa; Guerrero-Lebrero, Maria P.; Yáñez, Andres; Molina, Sergio Ignacio; Galindo, Pedro Luis

2014-11-01

In this paper, stress fields at the surface of the capping layer of self-assembled InAsP quantum wires grown on an InP (001) substrate have been determined from atomistic models using molecular dynamics and Stillinger-Weber potentials. To carry out these calculations, the quantum wire compositional distribution was extracted from previous works, where the As and P distributions were determined by electron energy loss spectroscopy and high-resolution aberration-corrected Z-contrast imaging. Preferential sites for the nucleation of wires on the surface of the capping layer were studied and compared with (i) previous simulations using finite element analysis to solve anisotropic elastic theory equations and (ii) experimentally measured locations of stacked wires. Preferential nucleation sites of stacked wires were determined by the maximum stress location at the MD model surface in good agreement with experimental results and those derived from finite element analysis. This indicates that MD simulations based on empirical potentials provide a suitable and flexible tool to study strain dependent atom processes.

Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

PubMed

Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

2016-06-07

As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. Copyright © 2016 Elsevier Ltd. All rights reserved.

Vibrational spectroscopic, molecular docking and quantum chemical studies on 6-aminonicotinamide

NASA Astrophysics Data System (ADS)

Mohamed Asath, R.; Premkumar, S.; Mathavan, T.; Milton Franklin Benial, A.

2017-04-01

The most stable molecular structure of 6-aminonicotinamide (ANA) molecule was predicted by conformational analysis and vibrational spectral analysis was carried out by experimental and theoretical methods. The calculated and experimentally observed vibrational frequencies were assigned and compared. The π→π* electronic transition of the molecule was predicted by theoretically calculated ultraviolet-visible spectra in gas and liquid phase and further validated experimentally using ethanol as a solvent. Frontier molecular orbitals analysis was carried out to probe the reactive nature of the ANA molecule and further the site selectivity to specific chemical reactions were effectively analyzed by Fukui function calculation. The molecular electrostatic potential surface was simulated to confirm the reactive sites of the molecule. The natural bond orbital analysis was also performed to understand the intra molecular interactions, which confirms the bioactivity of the ANA molecule. Neuroprotective nature of the ANA molecule was analyzed by molecular docking analysis and the ANA molecule was identified as a good inhibitor against Alzheimer's disease.

Surgical site infections following colorectal cancer surgery: a randomized prospective trial comparing common and advanced antimicrobial dressing containing ionic silver.

PubMed

Biffi, Roberto; Fattori, Luca; Bertani, Emilio; Radice, Davide; Rotmensz, Nicole; Misitano, Pasquale; Cenciarelli, Sabine; Chiappa, Antonio; Tadini, Liliana; Mancini, Marina; Pesenti, Giovanni; Andreoni, Bruno; Nespoli, Angelo

2012-05-23

An antimicrobial dressing containing ionic silver was found effective in reducing surgical-site infection in a preliminary study of colorectal cancer elective surgery. We decided to test this finding in a randomized, double-blind trial. Adults undergoing elective colorectal cancer surgery at two university-affiliated hospitals were randomly assigned to have the surgical incision dressed with Aquacel Ag Hydrofiber dressing or a common dressing. To blind the patient and the nursing and medical staff to the nature of the dressing used, scrub nurses covered Aquacel Ag Hydrofiber with a common wound dressing in the experimental arm, whereas a double common dressing was applied to patients of control group. The primary end-point of the study was the occurrence of any surgical-site infection within 30 days of surgery. A total of 112 patients (58 in the experimental arm and 54 in the control group) qualified for primary end-point analysis. The characteristics of the patient population and their surgical procedures were similar. The overall rate of surgical-site infection was lower in the experimental group (11.1% center 1, 17.5% center 2; overall 15.5%) than in controls (14.3% center 1, 24.2% center 2, overall 20.4%), but the observed difference was not statistically significant (P = 0.451), even with respect to surgical-site infection grade 1 (superficial) versus grades 2 and 3, or grade 1 and 2 versus grade 3. This randomized trial did not confirm a statistically significant superiority of Aquacel Ag Hydrofiber dressing in reducing surgical-site infection after elective colorectal cancer surgery. Clinicaltrials.gov: NCT00981110.

Oxygen and sulfur adsorption on vicinal surfaces of copper and silver: Preferred adsorption sites

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

Liu, Da-Jiang; Thiel, Patricia A.

We present an extensive density functional theory (DFT) study of adsorption site energetics for oxygen and sulfur adsorbed on two vicinal surfaces of Cu and Ag, with the goal of identifying the most stable adsorption site(s), identifying trends and common themes, and comparing with experimental work in the literature where possible. We also present benchmark calculations for adsorption on the flat (111) and (100) surfaces. The first vicinal surface is the (211), and results are similar for both metals. Here, we find that the step-doubling reconstruction is favored with both adsorbates and is driven by the creation of a specialmore » stable fourfold hollow (4fh) site at the reconstructed step. Zig-zag chain structures consisting of X–M–X units (X = chalcogen, M = metal) at the step edge are considered, in which the special 4fh site is partially occupied. The zig-zag configuration is energetically competitive for oxygen but not sulfur. DFT results for oxygen agree with experiment in terms of the stability of the reconstruction, but contradict the original site assignment. The second vicinal surface is the (410), where again results are similar for both metals. For oxygen, DFT predicts that step sites are filled preferentially even at lowest coverage, followed by terrace sites, consistent with the experiment. For sulfur, in contrast, DFT predicts that terrace sites fill first. Oxygen forms O–M–O rows on the top edge of the step, where it occupies incomplete 4fh sites. This resolves an experimental ambiguity in the site assignment. Finally, for both the (211) and (410) surfaces, the interaction energy that stabilizes the X–M–X chain or row correlates with the linearity of the X–M–X unit, which may explain key differences between oxygen and sulfur.« less

Oxygen and sulfur adsorption on vicinal surfaces of copper and silver: Preferred adsorption sites

DOE PAGES

Liu, Da-Jiang; Thiel, Patricia A.

2018-03-28

We present an extensive density functional theory (DFT) study of adsorption site energetics for oxygen and sulfur adsorbed on two vicinal surfaces of Cu and Ag, with the goal of identifying the most stable adsorption site(s), identifying trends and common themes, and comparing with experimental work in the literature where possible. We also present benchmark calculations for adsorption on the flat (111) and (100) surfaces. The first vicinal surface is the (211), and results are similar for both metals. Here, we find that the step-doubling reconstruction is favored with both adsorbates and is driven by the creation of a specialmore » stable fourfold hollow (4fh) site at the reconstructed step. Zig-zag chain structures consisting of X–M–X units (X = chalcogen, M = metal) at the step edge are considered, in which the special 4fh site is partially occupied. The zig-zag configuration is energetically competitive for oxygen but not sulfur. DFT results for oxygen agree with experiment in terms of the stability of the reconstruction, but contradict the original site assignment. The second vicinal surface is the (410), where again results are similar for both metals. For oxygen, DFT predicts that step sites are filled preferentially even at lowest coverage, followed by terrace sites, consistent with the experiment. For sulfur, in contrast, DFT predicts that terrace sites fill first. Oxygen forms O–M–O rows on the top edge of the step, where it occupies incomplete 4fh sites. This resolves an experimental ambiguity in the site assignment. Finally, for both the (211) and (410) surfaces, the interaction energy that stabilizes the X–M–X chain or row correlates with the linearity of the X–M–X unit, which may explain key differences between oxygen and sulfur.« less

The Impact of Preoperative Stoma Marking on Health-Related Quality of Life: A Comparison Cohort Study.

PubMed

McKenna, Linda S; Taggart, Elizabeth; Stoelting, Joyce; Kirkbride, Geri; Forbes, Gordon B

2016-01-01

The purpose of this study was to compare health-related quality of life (HRQOL) in patients receiving preoperative stoma marking by a certified wound, ostomy and continence nurse (CWOCN) to patients who did not receive preoperative marking. Quasi-experimental, nonrandomized comparison cohort study. The sample comprised 59 patients immediately following creation of a fecal stoma during an 18-month period between 2008 and 2010. The experimental group consisted of 35 patients with a mean age of 49.7 years who received preoperative stoma site marking by a CWOCN. Six of those 35 patients (17%) received preoperative ostomy education and stoma site marking. The control group consisted of 24 patients with a mean age of 60.1 years who did not receive preoperative stoma site marking or preoperative ostomy education. The study setting was a 500-bed Midwest Magnet-designated teaching hospital. Data collection occurred at 2 points: within 72 hours before hospital discharge and 8 weeks after discharge. The Stoma Quality of Life (Stoma-QOL) instrument was used to measure HRQOL. Two CWOCNs and 3 RNs, all members of Memorial's Ostomy & Wound Services, administered the Stoma QOL within 72 hours before hospital discharge. The 2 CWOCNs followed a scripted message to collect functional lifestyle factors and administer the Stoma-QOL, for the second time at 8 weeks after discharge. Groups were compared using analysis of covariance to control for age; analysis demonstrated significantly higher HOQOL in the marked group compared to the unmarked group (F = 4.9, P = .031). Findings demonstrated that patients who underwent stoma site marking reported higher HRQOL than those who did not.

Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics

PubMed Central

Doolittle-Hall, Janet M.; Cunningham Glasspoole, Danielle L.; Seaman, William T.; Webster-Cyriaque, Jennifer

2015-01-01

Oncoviruses cause tremendous global cancer burden. For several DNA tumor viruses, human genome integration is consistently associated with cancer development. However, genomic features associated with tumor viral integration are poorly understood. We sought to define genomic determinants for 1897 loci prone to hosting human papillomavirus (HPV), hepatitis B virus (HBV) or Merkel cell polyomavirus (MCPyV). These were compared to HIV, whose enzyme-mediated integration is well understood. A comprehensive catalog of integration sites was constructed from the literature and experimentally-determined HPV integration sites. Features were scored in eight categories (genes, expression, open chromatin, histone modifications, methylation, protein binding, chromatin segmentation and repeats) and compared to random loci. Random forest models determined loci classification and feature selection. HPV and HBV integrants were not fragile site associated. MCPyV preferred integration near sensory perception genes. Unique signatures of integration-associated predictive genomic features were detected. Importantly, repeats, actively-transcribed regions and histone modifications were common tumor viral integration signatures. PMID:26569308

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

PubMed

Bretaña, Neil Arvin; Lu, Cheng-Tsung; Chiang, Chiu-Yun; Su, Min-Gang; Huang, Kai-Yao; Lee, Tzong-Yi; Weng, Shun-Long

2012-01-01

Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD) is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific phosphorylation site prediction tools. In the independent testing, the high sensitivity and specificity of the proposed method demonstrate the predictive effectiveness of the identified substrate motifs and the importance of investigating potential kinases for viral protein phosphorylation sites.

Virtual screening of cocrystal formers for CL-20

NASA Astrophysics Data System (ADS)

Zhou, Jun-Hong; Chen, Min-Bo; Chen, Wei-Ming; Shi, Liang-Wei; Zhang, Chao-Yang; Li, Hong-Zhen

2014-08-01

According to the structure characteristics of 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (CL-20) and the kinetic mechanism of the cocrystal formation, the method of virtual screening CL-20 cocrystal formers by the criterion of the strongest intermolecular site pairing energy (ISPE) was proposed. In this method the strongest ISPE was thought to determine the first step of the cocrystal formation. The prediction results for four sets of common drug molecule cocrystals by this method were compared with those by the total ISPE method from the reference (Musumeci et al., 2011), and the experimental results. This method was then applied to virtually screen the CL-20 cocrystal formers, and the prediction results were compared with the experimental results.

Experiment, monitoring, and gradient methods used to infer climate change effects on plant communities yield consistent patterns.

PubMed

Elmendorf, Sarah C; Henry, Gregory H R; Hollister, Robert D; Fosaa, Anna Maria; Gould, William A; Hermanutz, Luise; Hofgaard, Annika; Jónsdóttir, Ingibjörg S; Jónsdóttir, Ingibjörg I; Jorgenson, Janet C; Lévesque, Esther; Magnusson, Borgþór; Molau, Ulf; Myers-Smith, Isla H; Oberbauer, Steven F; Rixen, Christian; Tweedie, Craig E; Walker, Marilyn D; Walker, Marilyn

2015-01-13

Inference about future climate change impacts typically relies on one of three approaches: manipulative experiments, historical comparisons (broadly defined to include monitoring the response to ambient climate fluctuations using repeat sampling of plots, dendroecology, and paleoecology techniques), and space-for-time substitutions derived from sampling along environmental gradients. Potential limitations of all three approaches are recognized. Here we address the congruence among these three main approaches by comparing the degree to which tundra plant community composition changes (i) in response to in situ experimental warming, (ii) with interannual variability in summer temperature within sites, and (iii) over spatial gradients in summer temperature. We analyzed changes in plant community composition from repeat sampling (85 plant communities in 28 regions) and experimental warming studies (28 experiments in 14 regions) throughout arctic and alpine North America and Europe. Increases in the relative abundance of species with a warmer thermal niche were observed in response to warmer summer temperatures using all three methods; however, effect sizes were greater over broad-scale spatial gradients relative to either temporal variability in summer temperature within a site or summer temperature increases induced by experimental warming. The effect sizes for change over time within a site and with experimental warming were nearly identical. These results support the view that inferences based on space-for-time substitution overestimate the magnitude of responses to contemporary climate warming, because spatial gradients reflect long-term processes. In contrast, in situ experimental warming and monitoring approaches yield consistent estimates of the magnitude of response of plant communities to climate warming.

Core Binding Site of a Thioflavin-T-Derived Imaging Probe on Amyloid β Fibrils Predicted by Computational Methods.

PubMed

Kawai, Ryoko; Araki, Mitsugu; Yoshimura, Masashi; Kamiya, Narutoshi; Ono, Masahiro; Saji, Hideo; Okuno, Yasushi

2018-05-16

Development of new diagnostic imaging probes for Alzheimer's disease, such as positron emission tomography (PET) and single photon emission computed tomography (SPECT) probes, has been strongly desired. In this study, we investigated the most accessible amyloid β (Aβ) binding site of [ 123 I]IMPY, a Thioflavin-T-derived SPECT probe, using experimental and computational methods. First, we performed a competitive inhibition assay with Orange-G, which recognizes the KLVFFA region in Aβ fibrils, suggesting that IMPY and Orange-G bind to different sites in Aβ fibrils. Next, we precisely predicted the IMPY binding site on a multiple-protofilament Aβ fibril model using computational approaches, consisting of molecular dynamics and docking simulations. We generated possible IMPY-binding structures using docking simulations to identify candidates for probe-binding sites. The binding free energy of IMPY with the Aβ fibril was calculated by a free energy simulation method, MP-CAFEE. These computational results suggest that IMPY preferentially binds to an interfacial pocket located between two protofilaments and is stabilized mainly through hydrophobic interactions. Finally, our computational approach was validated by comparing it with the experimental results. The present study demonstrates the possibility of computational approaches to screen new PET/SPECT probes for Aβ imaging.

Monitoring of Vegetation Impact Due to Trampling on Cadillac Mountain Summit Using High Spatial Resolution Remote Sensing Data Sets

NASA Astrophysics Data System (ADS)

Kim, Min-Kook; Daigle, John J.

2012-11-01

Cadillac Mountain—the highest peak along the eastern seaboard of the United States—is a major tourist destination in Acadia National Park, Maine. Managing vegetation impact due to trampling on the Cadillac Mountain summit is extremely challenging because of the large number of visitors and the general open nature of landscape in this fragile subalpine environmental setting. Since 2000, more intensive management strategies—based on placing physical barriers and educational messages for visitors—have been employed to protect threatened vegetation, decrease vegetation impact, and enhance vegetation recovery in the vicinity of the summit loop trail. The primary purpose of this study was to evaluate the effect of the management strategies employed. For this purpose, vegetation cover changes between 2001 and 2007 were detected using multispectral high spatial resolution remote sensing data sets. A normalized difference vegetation index was employed to identify the rates of increase and decrease in the vegetation areas. Three buffering distances (30, 60, and 90 m) from the edges of the trail were used to define multiple spatial extents of the site, and the same spatial extents were employed at a nearby control site that had no visitors. No significant differences were detected between the mean rates of vegetation increase and decrease at the experimental site compared with a nearby control site in the case of a small spatial scale (≤30 m) comparison (in all cases P > 0.05). However, in the medium (≤60 m) and large (≤90 m) spatial scales, the rates of increased vegetation were significantly greater and rates of decreased vegetation significantly lower at the experimental site compared with the control site (in all cases P < 0.001). Research implications are explored that relate to the spatial extent of the radial patterns of impact of trampling on vegetation at the site level. Management implications are explored in terms of the spatial strategies used to decrease the impact of trampling on vegetation.

Monitoring of vegetation impact due to trampling on Cadillac Mountain summit using high spatial resolution remote sensing data sets.

PubMed

Kim, Min-Kook; Daigle, John J

2012-11-01

Cadillac Mountain--the highest peak along the eastern seaboard of the United States--is a major tourist destination in Acadia National Park, Maine. Managing vegetation impact due to trampling on the Cadillac Mountain summit is extremely challenging because of the large number of visitors and the general open nature of landscape in this fragile subalpine environmental setting. Since 2000, more intensive management strategies--based on placing physical barriers and educational messages for visitors--have been employed to protect threatened vegetation, decrease vegetation impact, and enhance vegetation recovery in the vicinity of the summit loop trail. The primary purpose of this study was to evaluate the effect of the management strategies employed. For this purpose, vegetation cover changes between 2001 and 2007 were detected using multispectral high spatial resolution remote sensing data sets. A normalized difference vegetation index was employed to identify the rates of increase and decrease in the vegetation areas. Three buffering distances (30, 60, and 90 m) from the edges of the trail were used to define multiple spatial extents of the site, and the same spatial extents were employed at a nearby control site that had no visitors. No significant differences were detected between the mean rates of vegetation increase and decrease at the experimental site compared with a nearby control site in the case of a small spatial scale (≤30 m) comparison (in all cases P > 0.05). However, in the medium (≤60 m) and large (≤90 m) spatial scales, the rates of increased vegetation were significantly greater and rates of decreased vegetation significantly lower at the experimental site compared with the control site (in all cases P < 0.001). Research implications are explored that relate to the spatial extent of the radial patterns of impact of trampling on vegetation at the site level. Management implications are explored in terms of the spatial strategies used to decrease the impact of trampling on vegetation.

Variations in Below Canopy Turbulent Flux From Snow in North American Mountain Environments

NASA Astrophysics Data System (ADS)

Essery, R.; Marks, D.; Pomeroy, J.; Grangere, R.; Reba, M.; Hedstrom, N.; Link, T.; Winstral, A.

2004-12-01

Sensible and latent heat and mass fluxes from the snow surface are modulated by site canopy density and structure. Forest and shrub canopies reduce wind speeds and alter the radiation and thermal environment which will alter the below canopy energetics that control the magnitude of turbulent fluxes between the snow surface and the atmosphere. In this study eddy covariance (EC) systems were located in three experimental catchments along a mountain transect through the North American Cordillera. Within each catchment, a variety of sites representing the local range of climate, weather, and canopy conditions were selected for measurement of sensible and latent heat and mass flux from the snow surface. EC measurements were made 1) below a uniform pine canopy (2745m) in the Fraser Experimental Forest in Colorado from February through June melt-out in 2003; 2) at an open, unforested site (2100m), and below an Aspen canopy (2055m) within a small headwater catchment in the Reynolds Creek Experimental Watershed, Owyhee Mts., Idaho from October, 2003, through June melt-out, 2004; and 3) at five sites, representing a range of conditions: a) below a dense spruce forest (750m); b) a north-facing shrub-tundra slope (1383m); c) a south-facing shrub-tundra slope; d) the valley bottom between b) and c) (1363m); and e) a tundra site (1402m) in the Wolf Creek Research Basin (WCRB) in the Yukon, Canada during the 2001 and 2002 snow seasons. Summary data from all sites are presented and compared including the relative significance of sublimation losses at each site, the importance of interception losses to the snowcover mass balance, and the occurrence of condensation events. Site and weather conditions that inhibit or enhance flux from the snow surface are discussed. This research will improve snow modeling by allowing better representation of turbulent fluxes from snow in forested regions, and improved simulation of the snowcover mass balance over low deposition, high latitude sites such as WCRB, and during drought conditions at mid-latitude sites such as Fraser, Colorado, and RCEW in Idaho.

[Eutrophication control in local area by physic-ecological engineering].

PubMed

Li, Qiu-Hua; Xia, Pin-Hua; Wu, Hong; Lin, Tao; Zhang, You-Chun; Li, Cun-Xiong; Chen, Li-Li; Yang, Fan

2012-07-01

An integrated physical and ecological engineering experiment for ecological remediation was performed at the Maixi River bay in Baihua Reservoir Guizhou Province, China. The results show that eutrophic parameters, such as total nitrogen, total phosphorus, chlorophyll a and chemical oxygen demand from the experimental site (enclosed water) were significantly lower than those of the reference site. The largest differences between the sites were 0.61 mg x L(-1), 0.041 mg x L(-1), 23.06 microg x L(-1), 8.4 mg x L(-1) respectively; experimental site transparency was > 1.50 m which was significantly higher than that of the reference site. The eutrophic index of the experimental site was oligo-trophic and mid-trophic, while the control site was mid-trophic state and eutrophic state. Phytoplankton abundance was 2 125.5 x 10(4) cells x L(-1) in June, 2011 at the control site,but phytoplankton abundance was lower at the experimental site with 33 x 10(4) cells x L(-1). Cyanobacteria dominated phytoplankton biomass at both sites, however the experimental site consisted of a higher proportion of diatoms and dinoflagellates. After more than one year of operation, the ecological engineering technology effectively controlled the occurrence of algae blooms, changed phytoplankton community structure, and controlled the negative impacts of eutrophication. Integrating physical and ecological engineering technology could improve water quality for reservoirs on the Guizhou plateau.

Natural Regeneration of Longleaf Pine

Treesearch

William D. Boyer

1979-01-01

Natural regeneration is now a reliable alternative for existing longleaf pine forests. The shelterwood system, or modifications of it, has been used experimentally to regenerate longleaf pine for over 20 years, and regional tests have confirmed its value for a wide range of site conditions. Natural regeneration, because of its low cost when compared to other...

Reactivity of Tic Observation Procedures to Situation and Setting

ERIC Educational Resources Information Center

Piacentini, John; Himle, Michael B.; Chang, Susanna; Baruch, David E.; Buzzella, Brian A.; Pearlman, Amanda; Woods, Douglas W.

2006-01-01

Tic frequency was assessed and compared across home and clinic as well as three experimentally-manipulated situations in order to assess the phenomenon of tic reactivity. Forty-three youngsters with chronic tic disorder recruited from two geographically-distinct sites were videotaped over three weekly laboratory visits under each of the following…

Temperature Values Variability in Piezoelectric Implant Site Preparation: Differences between Cortical and Corticocancellous Bovine Bone.

PubMed

Lamazza, Luca; Garreffa, Girolamo; Laurito, Domenica; Lollobrigida, Marco; Palmieri, Luigi; De Biase, Alberto

2016-01-01

Various parameters can influence temperature rise and detection during implant site preparation. The aim of this study is to investigate local temperature values in cortical and corticocancellous bovine bone during early stages of piezoelectric implant site preparation. 20 osteotomies were performed using a diamond tip (IM1s, Mectron Medical Technology, Carasco, Italy) on two different types of bovine bone samples, cortical and corticocancellous, respectively. A standardized protocol was designed to provide constant working conditions. Temperatures were measured in real time at a fixed position by a fiber optic thermometer. Significantly higher drilling time (154.90 sec versus 99.00 sec; p < 0.0001) and temperatures (39.26°C versus 34.73°C; p = 0.043) were observed in the cortical group compared to the corticocancellous group. A remarkable variability of results characterized the corticocancellous blocks as compared to the blocks of pure cortical bone. Bone samples can influence heat generation during in vitro implant site preparation. When compared to cortical bone, corticocancellous samples present more variability in temperature values. Even controlling most experimental factors, the impact of bone samples still remains one of the main causes of temperature variability.

Uncertainty and variability in laboratory derived sorption parameters of sediments from a uranium in situ recovery site

NASA Astrophysics Data System (ADS)

Dangelmayr, Martin A.; Reimus, Paul W.; Johnson, Raymond H.; Clay, James T.; Stone, James J.

2018-06-01

This research assesses the ability of a GC SCM to simulate uranium transport under variable geochemical conditions typically encountered at uranium in-situ recovery (ISR) sites. Sediment was taken from a monitoring well at the SRH site at depths 192 and 193 m below ground and characterized by XRD, XRF, TOC, and BET. Duplicate column studies on the different sediment depths, were flushed with synthesized restoration waters at two different alkalinities (160 mg/l CaCO3 and 360 mg/l CaCO3) to study the effect of alkalinity on uranium mobility. Uranium breakthrough occurred 25% - 30% earlier in columns with 360 mg/l CaCO3 over columns fed with 160 mg/l CaCO3 influent water. A parameter estimation program (PEST) was coupled to PHREEQC to derive site densities from experimental data. Significant parameter fittings were produced for all models, demonstrating that the GC SCM approach can model the impact of carbonate on uranium in flow systems. Derived site densities for the two sediment depths were between 141 and 178 μmol-sites/kg-soil, demonstrating similar sorption capacities despite heterogeneity in sediment mineralogy. Model sensitivity to alkalinity and pH was shown to be moderate compared to fitted site densities, when calcite saturation was allowed to equilibrate. Calcite kinetics emerged as a potential source of error when fitting parameters in flow conditions. Fitted results were compared to data from previous batch and column studies completed on sediments from the Smith-Ranch Highland (SRH) site, to assess variability in derived parameters. Parameters from batch experiments were lower by a factor of 1.1 to 3.4 compared to column studies completed on the same sediments. The difference was attributed to errors in solid-solution ratios and the impact of calcite dissolution in batch experiments. Column studies conducted at two different laboratories showed almost an order of magnitude difference in fitted site densities suggesting that experimental methodology may play a bigger role in column sorption behavior than actual sediment heterogeneity. Our results demonstrate the necessity for ISR sites to remove residual pCO2 and equilibrate restoration water with background geochemistry to reduce uranium mobility. In addition, the observed variability between fitted parameters on the same sediments highlights the need to provide standardized guidelines and methodology for regulators and industry when the GC SCM approach is used for ISR risk assessments.

Binding site and affinity prediction of general anesthetics to protein targets using docking.

PubMed

Liu, Renyu; Perez-Aguilar, Jose Manuel; Liang, David; Saven, Jeffery G

2012-05-01

The protein targets for general anesthetics remain unclear. A tool to predict anesthetic binding for potential binding targets is needed. In this study, we explored whether a computational method, AutoDock, could serve as such a tool. High-resolution crystal data of water-soluble proteins (cytochrome C, apoferritin, and human serum albumin), and a membrane protein (a pentameric ligand-gated ion channel from Gloeobacter violaceus [GLIC]) were used. Isothermal titration calorimetry (ITC) experiments were performed to determine anesthetic affinity in solution conditions for apoferritin. Docking calculations were performed using DockingServer with the Lamarckian genetic algorithm and the Solis and Wets local search method (http://www.dockingserver.com/web). Twenty general anesthetics were docked into apoferritin. The predicted binding constants were compared with those obtained from ITC experiments for potential correlations. In the case of apoferritin, details of the binding site and their interactions were compared with recent cocrystallization data. Docking calculations for 6 general anesthetics currently used in clinical settings (isoflurane, sevoflurane, desflurane, halothane, propofol, and etomidate) with known 50% effective concentration (EC(50)) values were also performed in all tested proteins. The binding constants derived from docking experiments were compared with known EC(50) values and octanol/water partition coefficients for the 6 general anesthetics. All 20 general anesthetics docked unambiguously into the anesthetic binding site identified in the crystal structure of apoferritin. The binding constants for 20 anesthetics obtained from the docking calculations correlate significantly with those obtained from ITC experiments (P = 0.04). In the case of GLIC, the identified anesthetic binding sites in the crystal structure are among the docking predicted binding sites, but not the top ranked site. Docking calculations suggest a most probable binding site located in the extracellular domain of GLIC. The predicted affinities correlated significantly with the known EC(50) values for the 6 frequently used anesthetics in GLIC for the site identified in the experimental crystal data (P = 0.006). However, predicted affinities in apoferritin, human serum albumin, and cytochrome C did not correlate with these 6 anesthetics' known experimental EC(50) values. A weak correlation between the predicted affinities and the octanol/water partition coefficients was observed for the sites in GLIC. We demonstrated that anesthetic binding sites and relative affinities can be predicted using docking calculations in an automatic docking server (AutoDock) for both water-soluble and membrane proteins. Correlation of predicted affinity and EC(50) for 6 frequently used general anesthetics was only observed in GLIC, a member of a protein family relevant to anesthetic mechanism.

Uncertainty and variability in laboratory derived sorption parameters of sediments from a uranium in situ recovery site.

PubMed

Dangelmayr, Martin A; Reimus, Paul W; Johnson, Raymond H; Clay, James T; Stone, James J

2018-06-01

This research assesses the ability of a GC SCM to simulate uranium transport under variable geochemical conditions typically encountered at uranium in-situ recovery (ISR) sites. Sediment was taken from a monitoring well at the SRH site at depths 192 and 193 m below ground and characterized by XRD, XRF, TOC, and BET. Duplicate column studies on the different sediment depths, were flushed with synthesized restoration waters at two different alkalinities (160 mg/l CaCO 3 and 360 mg/l CaCO 3 ) to study the effect of alkalinity on uranium mobility. Uranium breakthrough occurred 25% - 30% earlier in columns with 360 mg/l CaCO 3 over columns fed with 160 mg/l CaCO 3 influent water. A parameter estimation program (PEST) was coupled to PHREEQC to derive site densities from experimental data. Significant parameter fittings were produced for all models, demonstrating that the GC SCM approach can model the impact of carbonate on uranium in flow systems. Derived site densities for the two sediment depths were between 141 and 178 μmol-sites/kg-soil, demonstrating similar sorption capacities despite heterogeneity in sediment mineralogy. Model sensitivity to alkalinity and pH was shown to be moderate compared to fitted site densities, when calcite saturation was allowed to equilibrate. Calcite kinetics emerged as a potential source of error when fitting parameters in flow conditions. Fitted results were compared to data from previous batch and column studies completed on sediments from the Smith-Ranch Highland (SRH) site, to assess variability in derived parameters. Parameters from batch experiments were lower by a factor of 1.1 to 3.4 compared to column studies completed on the same sediments. The difference was attributed to errors in solid-solution ratios and the impact of calcite dissolution in batch experiments. Column studies conducted at two different laboratories showed almost an order of magnitude difference in fitted site densities suggesting that experimental methodology may play a bigger role in column sorption behavior than actual sediment heterogeneity. Our results demonstrate the necessity for ISR sites to remove residual pCO2 and equilibrate restoration water with background geochemistry to reduce uranium mobility. In addition, the observed variability between fitted parameters on the same sediments highlights the need to provide standardized guidelines and methodology for regulators and industry when the GC SCM approach is used for ISR risk assessments. Copyright © 2018 Elsevier B.V. All rights reserved.

Binding Site and Affinity Prediction of General Anesthetics to Protein Targets Using Docking

PubMed Central

Liu, Renyu; Perez-Aguilar, Jose Manuel; Liang, David; Saven, Jeffery G.

2012-01-01

Background The protein targets for general anesthetics remain unclear. A tool to predict anesthetic binding for potential binding targets is needed. In this study, we explore whether a computational method, AutoDock, could serve as such a tool. Methods High-resolution crystal data of water soluble proteins (cytochrome C, apoferritin and human serum albumin), and a membrane protein (a pentameric ligand-gated ion channel from Gloeobacter violaceus, GLIC) were used. Isothermal titration calorimetry (ITC) experiments were performed to determine anesthetic affinity in solution conditions for apoferritin. Docking calculations were performed using DockingServer with the Lamarckian genetic algorithm and the Solis and Wets local search method (https://www.dockingserver.com/web). Twenty general anesthetics were docked into apoferritin. The predicted binding constants are compared with those obtained from ITC experiments for potential correlations. In the case of apoferritin, details of the binding site and their interactions were compared with recent co-crystallization data. Docking calculations for six general anesthetics currently used in clinical settings (isoflurane, sevoflurane, desflurane, halothane, propofol, and etomidate) with known EC50 were also performed in all tested proteins. The binding constants derived from docking experiments were compared with known EC50s and octanol/water partition coefficients for the six general anesthetics. Results All 20 general anesthetics docked unambiguously into the anesthetic binding site identified in the crystal structure of apoferritin. The binding constants for 20 anesthetics obtained from the docking calculations correlate significantly with those obtained from ITC experiments (p=0.04). In the case of GLIC, the identified anesthetic binding sites in the crystal structure are among the docking predicted binding sites, but not the top ranked site. Docking calculations suggest a most probable binding site located in the extracellular domain of GLIC. The predicted affinities correlated significantly with the known EC50s for the six commonly used anesthetics in GLIC for the site identified in the experimental crystal data (p=0.006). However, predicted affinities in apoferritin, human serum albumin, and cytochrome C did not correlate with these six anesthetics’ known experimental EC50s. A weak correlation between the predicted affinities and the octanol/water partition coefficients was observed for the sites in GLIC. Conclusion We demonstrated that anesthetic binding sites and relative affinities can be predicted using docking calculations in an automatic docking server (Autodock) for both water soluble and membrane proteins. Correlation of predicted affinity and EC50 for six commonly used general anesthetics was only observed in GLIC, a member of a protein family relevant to anesthetic mechanism. PMID:22392968

The challenge of modelling nitrogen management at the field scale: simulation and sensitivity analysis of N2O fluxes across nine experimental sites using DailyDayCent

NASA Astrophysics Data System (ADS)

Fitton, N.; Datta, A.; Hastings, A.; Kuhnert, M.; Topp, C. F. E.; Cloy, J. M.; Rees, R. M.; Cardenas, L. M.; Williams, J. R.; Smith, K.; Chadwick, D.; Smith, P.

2014-09-01

The United Kingdom currently reports nitrous oxide emissions from agriculture using the IPCC default Tier 1 methodology. However Tier 1 estimates have a large degree of uncertainty as they do not account for spatial variations in emissions. Therefore biogeochemical models such as DailyDayCent (DDC) are increasingly being used to provide a spatially disaggregated assessment of annual emissions. Prior to use, an assessment of the ability of the model to predict annual emissions should be undertaken, coupled with an analysis of how model inputs influence model outputs, and whether the modelled estimates are more robust that those derived from the Tier 1 methodology. The aims of the study were (a) to evaluate if the DailyDayCent model can accurately estimate annual N2O emissions across nine different experimental sites, (b) to examine its sensitivity to different soil and climate inputs across a number of experimental sites and (c) to examine the influence of uncertainty in the measured inputs on modelled N2O emissions. DailyDayCent performed well across the range of cropland and grassland sites, particularly for fertilized fields indicating that it is robust for UK conditions. The sensitivity of the model varied across the sites and also between fertilizer/manure treatments. Overall our results showed that there was a stronger correlation between the sensitivity of N2O emissions to changes in soil pH and clay content than the remaining input parameters used in this study. The lower the initial site values for soil pH and clay content, the more sensitive DDC was to changes from their initial value. When we compared modelled estimates with Tier 1 estimates for each site, we found that DailyDayCent provided a more accurate representation of the rate of annual emissions.

A decorated raven bone from the Zaskalnaya VI (Kolosovskaya) Neanderthal site, Crimea

PubMed Central

Evans, Sarah; Stepanchuk, Vadim; Tsvelykh, Alexander; d’Errico, Francesco

2017-01-01

We analyze a radius bone fragment of a raven (Corvus corax) from Zaskalnaya VI rock shelter, Crimea. The object bears seven notches and comes from an archaeological level attributed to a Micoquian industry dated to between 38 and 43 cal kyr BP. Our study aims to examine the degree of regularity and intentionality of this set of notches through their technological and morphometric analysis, complemented by comparative experimental work. Microscopic analysis of the notches indicate that they were produced by the to-and-fro movement of a lithic cutting edge and that two notches were added to fill in the gap left between previously cut notches, probably to increase the visual consistency of the pattern. Multivariate analysis of morphometric data recorded on the archaeological notches and sets of notches cut by nine modern experimenters on radii of domestic turkeys shows that the variations recorded on the Zaskalnaya set are comparable to experimental sets made with the aim of producing similar, parallel, equidistant notches. Identification of the Weber Fraction, the constant that accounts for error in human perception, for equidistant notches cut on bone rods and its application to the Zaskalnaya set of notches and thirty-six sets of notches incised on seventeen Upper Palaeolithic bone objects from seven sites indicate that the Zaskalnaya set falls within the range of variation of regularly spaced experimental and Upper Palaeolithic sets of notches. This suggests that even if the production of the notches may have had a utilitarian reason the notches were made with the goal of producing a visually consistent pattern. This object represents the first instance of a bird bone from a Neanderthal site bearing modifications that cannot be explained as the result of butchery activities and for which a symbolic argument can be built on direct rather than circumstantial evidence. PMID:28355292

[THE FEATURES OF PHARMACOKINETICS ANTIBIOTIC CEFTRIAXONE WITH INTRAVENOUS WAY THAT ARE DEPOSITED IN AUTOLOGOUS ERYTHROCYTES AND LEUKOCYTES OF RABBIT].

PubMed

Yussifov, Z; Lokhvitskii, S; Gulyaev, A

2016-11-01

In the experiment on 18 rabbits Сeftriaxone pharmacokinetics after intravenous injection of the medication deposited in autologous erythrocytes and leukocytes were studied. The features of the pharmacokinetics when administered Сeftriaxone in erythrocytes ghost and leukocytes as compared to traditional intravenous drug administration have been determined.It is discussed the possibility of antibiotics transport in the surgical site of infection via cellular carriers in the article. We do the comparative analysis of the main pharmacokinetic parameters of Ceftriaxone in experimental conditions of leukocyte, erythrocyte transport and intravenous way. Based on these results the authors come to the conclusion about the benefits of leukocyte antibiotic transport to the site of surgical infection.

Issues and recent advances in optimal experimental design for site investigation (Invited)

NASA Astrophysics Data System (ADS)

Nowak, W.

2013-12-01

This presentation provides an overview over issues and recent advances in model-based experimental design for site exploration. The addressed issues and advances are (1) how to provide an adequate envelope to prior uncertainty, (2) how to define the information needs in a task-oriented manner, (3) how to measure the expected impact of a data set that it not yet available but only planned to be collected, and (4) how to perform best the optimization of the data collection plan. Among other shortcomings of the state-of-the-art, it is identified that there is a lack of demonstrator studies where exploration schemes based on expert judgment are compared to exploration schemes obtained by optimal experimental design. Such studies will be necessary do address the often voiced concern that experimental design is an academic exercise with little improvement potential over the well- trained gut feeling of field experts. When addressing this concern, a specific focus has to be given to uncertainty in model structure, parameterizations and parameter values, and to related surprises that data often bring about in field studies, but never in synthetic-data based studies. The background of this concern is that, initially, conceptual uncertainty may be so large that surprises are the rule rather than the exception. In such situations, field experts have a large body of experience in handling the surprises, and expert judgment may be good enough compared to meticulous optimization based on a model that is about to be falsified by the incoming data. In order to meet surprises accordingly and adapt to them, there needs to be a sufficient representation of conceptual uncertainty within the models used. Also, it is useless to optimize an entire design under this initial range of uncertainty. Thus, the goal setting of the optimization should include the objective to reduce conceptual uncertainty. A possible way out is to upgrade experimental design theory towards real-time interaction with the ongoing site investigation, such that surprises in the data are immediately accounted for to restrict the conceptual uncertainty and update the optimization of the plan.

A comparative evaluation of subepithelial connective tissue graft (SCTG) versus platelet concentrate graft (PCG) in the treatment of gingival recession using coronally advanced flap technique: A 12-month study

PubMed Central

Kumar, G. Naveen Vital; Murthy, K. Raja Venkatesh

2013-01-01

Objective: The objective of this study was to clinically evaluate and compare the efficacy of platelet concentrate graft (PCG) with that of subepithelial connective tissue graft (SCTG) using a coronally advanced flap technique in the treatment of gingival recession. Materials and Methods: Twelve patients with a total of 24 gingival recession defects were selected and randomly assigned either to experimental site-A (SCTG) or experimental site-B (PCG). The clinical parameters were recorded at baseline up to 12 months post-operatively and compared. Results: The mean vertical recession depth (VRD) statistically significantly decreased from 2.50 ± 0.48 mm to 0.54 ± 0.50 mm with PCG and from 2.75 ± 0.58 mm to 0.54 ± 0.45 mm with SCTG at 12 months. No statistically significant differences between the treatments were found for VRD and clinical attachment level (CAL), while keratinized tissue width (KTW) gain was statistically significant. Conclusion: Both the SCTG and the PCG group resulted in a significant amount of root coverage. The PCG technique was less invasive and required minimal time and clinical maneuver. It resulted in superior aesthetic outcome and lower post-surgical discomfort at the 12 months follow-up. PMID:24554889

First-principles study of uranium carbide: Accommodation of point defects and of helium, xenon, and oxygen impurities

NASA Astrophysics Data System (ADS)

Freyss, Michel

2010-01-01

Point defects and volatile impurities (helium, xenon, oxygen) in uranium monocarbide UC are studied by first-principles calculations. Preliminarily, bulk properties of UC and of two other uranium carbide phases, UC2 and U2C3 , are calculated in order to compare them to experimental data and to get confidence in the use of the generalized gradient approximation for this class of compounds. The subsequent study of different types of point defects shows that the carbon sublattice best accommodates the defects. The perturbation of the crystal structure induced by the defects is weak and the interaction between defects is found short range. Interstitial carbon dumbbells possibly play an important role in the diffusion of carbon atoms. The most favorable location of diluted helium, xenon, and oxygen impurities in the UC crystal lattice is then determined. The rare-gas atoms occupy preferably a uranium substitution site or a uranium site in a U-C bivacancy. But their incorporation in UC is, however, not energetically favorable, especially for xenon, suggesting their propensity to diffuse in the material and/or form bubbles. On the other hand, oxygen atoms are very favorably incorporated as diluted atoms in the UC lattice, confirming the easy oxidation of UC. The oxygen atoms preferably occupy a carbon substitution site or the carbon site of a U-C bivacancy. Our results are compared to available experimental data on UC and to similar studies by first-principles calculations for other carbides and nitrides with the rock-salt structure.

Site survey for optimum location of Optical Communication Experimental Facility

NASA Technical Reports Server (NTRS)

1968-01-01

Site survey was made to determine the optimum location for an Optical Communication Experimental Facility /OCEF/ and to recommend several sites, graded according to preference. A site was desired which could perform two-way laser communication with a spacecraft and laser tracking with a minimum of interruption by weather effects.

A detailed study of the magnetism of chiral {Cr₇M} rings: an investigation into parametrization and transferability of parameters.

PubMed

Garlatti, Elena; Albring, Morten A; Baker, Michael L; Docherty, Rebecca J; Mutka, Hannu; Guidi, Tatiana; Garcia Sakai, Victoria; Whitehead, George F S; Pritchard, Robin G; Timco, Grigore A; Tuna, Floriana; Amoretti, Giuseppe; Carretta, Stefano; Santini, Paolo; Lorusso, Giulia; Affronte, Marco; McInnes, Eric J L; Collison, David; Winpenny, Richard E P

2014-07-09

Compounds of general formula [Cr7MF3(Etglu)(O2C(t)Bu)15(Phpy)] [H5Etglu = N-ethyl-d-glucamine; Phpy = 4-phenylpyridine; M = Zn (1), Mn (2), Ni (3)] have been prepared. The structures contain an irregular octagon of metal sites formed around the penta-deprotonated Etglu(5-) ligand; the chirality of N-ethyl-d-glucamine is retained in the final product. The seven Cr(III) sites have a range of coordination environments, and the divalent metal site is crystallographically identified and has a Phpy ligand attached to it. By using complementary experimental techniques, including magnetization and specific heat measurements, inelastic neutron scattering, and electron paramagnetic resonance spectroscopy, we have investigated the magnetic features of this family of {Cr7M} rings. Microscopic parameters of the spin Hamiltonian have been determined as a result of best fits of the different experimental data, allowing a direct comparison with corresponding parameters found in the parent compounds. We examine whether these parameters can be transferred between compounds and compare them with those of an earlier family of heterometallic rings.

A computational model for the flow of resin in self-healing composites

NASA Astrophysics Data System (ADS)

Hall, J.; Qamar, I. P. S.; Rendall, T. C. S.; Trask, R. S.

2015-03-01

To explore the flow characteristics of healing agent leaving a vascular network and infusing a damage site within a fibre reinforced polymer composite, a numerical model of healing agent flow from an orifice has been developed using smoothed particle hydrodynamics. As an initial validation the discharge coefficient for low Reynolds number flow from a cylindrical tank is calculated numerically, using two different viscosity formulations, and compared to existing experimental data. Results of this comparison are very favourable; the model is able to reproduce experimental results for the discharge coefficient in the high Reynolds number limit, together with the power-law behaviour for low Reynolds numbers. Results are also presented for a representative delamination geometry showing healing fluid behaviour and fraction filled inside the delamination for a variety of fluid viscosities. This work provides the foundations for the vascular self-healing community in calculating not only the flow rate through the network, but also, by simulating a representative damage site, the final location of the healing fluid within the damage site in order to assess the improvement in local and global mechanical properties and thus healing efficiency.

Forest Species Compared in Ozark Plantations

Treesearch

William R. Maple

1965-01-01

Fifteen years ago a series of plantations containing native and nonnative forest tree species was established on the Henry R. Koen Experimental Forest in Newton County. The sites, which were representative of abandoned fields in the Arkansas portion of the Ozark Mountains, included loamy sand, silty clay loam, and cherty silt loam soils. All had similar histories of...

How does precipitation become runoff? Comparison of hydrologic thresholds across hillslope and catchment scales

NASA Astrophysics Data System (ADS)

Ross, C.; Ali, G.; Oswald, C. J.; McMillan, H. K.; Walter, K.

2017-12-01

A hydrologic threshold is a critical point in time when runoff behavior rapidly changes, often in response to the activation of specific storage-driven or intensity-driven processes. Hydrologic thresholds can be viewed as characteristic signatures of hydrosystems, which makes them useful for site comparison as long as their presence (or lack thereof) can be evaluated in a standard manner across a range of environments. While several previous studies have successfully identified thresholds at a variety of individual sites, only a limited number have compared dynamics prevailing at the hillslope versus catchment scale, or distinguished the role of storage versus intensity thresholds. The objective of this study was therefore to examine precipitation input thresholds as well as "precipitation minus evapotranspiration" thresholds in environments with contrasted climatic and geographic characteristics. Historical climate and hydrometric datasets were consolidated for one hillslope site located at the Panola Mountain Research Watershed (Southeastern USA) and catchments located in the HJ Andrew's Experimental Forest (Northwestern USA), the Catfish Creek Watershed (Canadian prairies), the Experimental Lakes Area (Canadian boreal ecozone), the Tarrawarra catchment (Australia) and the Mahurangi catchment (New Zealand). Individual precipitation-runoff events were delineated using the newly introduced software HydRun to derive event-specific hydrograph parameters as well surrogate measures of antecedent moisture conditions and evapotranspiration in an automated and consistent manner. Various hydrograph parameters were then plotted against those surrogate measures to detect and evaluate site-specific threshold dynamics. Preliminary results show that a range of threshold shapes (e.g., "hockey stick", heaviside and dirac) were observed across sites. The influence of antecedent precipitation on threshold magnitude and shape also appeared stronger at sites with lower topographic relief and drier climate. Future analyses will focus on the interaction between storage and intensity thresholds in order to evaluate the importance of considering both for comparative hydrological studies.

Time dependent analysis of assay comparability: a novel approach to understand intra- and inter-site variability over time

NASA Astrophysics Data System (ADS)

Winiwarter, Susanne; Middleton, Brian; Jones, Barry; Courtney, Paul; Lindmark, Bo; Page, Ken M.; Clark, Alan; Landqvist, Claire

2015-09-01

We demonstrate here a novel use of statistical tools to study intra- and inter-site assay variability of five early drug metabolism and pharmacokinetics in vitro assays over time. Firstly, a tool for process control is presented. It shows the overall assay variability but allows also the following of changes due to assay adjustments and can additionally highlight other, potentially unexpected variations. Secondly, we define the minimum discriminatory difference/ratio to support projects to understand how experimental values measured at different sites at a given time can be compared. Such discriminatory values are calculated for 3 month periods and followed over time for each assay. Again assay modifications, especially assay harmonization efforts, can be noted. Both the process control tool and the variability estimates are based on the results of control compounds tested every time an assay is run. Variability estimates for a limited set of project compounds were computed as well and found to be comparable. This analysis reinforces the need to consider assay variability in decision making, compound ranking and in silico modeling.

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

Howe, Joshua D.; Morelock, Cody R.; Jiao, Yang

We present a joint computational and experimental study of Mg–Ni-MOF-74 and Mg–Cd-MOF-74 to gain insight into the mixing of metals and understand how metal mixing affects the structure of the undercoordinated open-metal sites. Our calculations predict that metal mixing is energetically preferred in these materials. Recent experimental work has demonstrated that Mg–Ni-MOF-74 shows a much greater surface area retention in the presence of water than Mg-MOF-74. To probe this effect, we study H 2O adsorption in Mg–Ni-MOF-74, finding that the adsorption energetics and electronic structure do not change significantly at the metal sites when compared to Mg-MOF-74 and Ni-MOF-74, respectively.more » Lastly, we conclude that the increased stability of Mg–Ni-MOF-74 is a result of a M–O bond length distortion in mixed-metal MOF-74, consistent with recent work on the stability of MOF-74 under water exposure.« less

Phenotypic response of plants to simulated climate change in a long-term rain-manipulation experiment: a multi-species study.

PubMed

Hänel, Sabine; Tielbörger, Katja

2015-04-01

Many species will need to adapt to the observed climate change in order to persist. However, research about adaptation or phenotypic plasticity in response to climate change is rare. In particular, field studies are lacking that impose artificial selection for a sufficiently long time to elicit changes in phenotypic and genotypic structure of populations. Here, we present findings for an 8-year field experiment with 16 annual plant species that tested potentially adaptive phenotypic responses to precipitation change. In both a Mediterranean and a semi-arid site, annual precipitation was manipulated (±30%) and phenotypic response was recorded. We measured flowering time as a key trait related to climatic conditions and biomass and survival as fitness correlates. Differences in traits among treatments were compared to trait shifts between sites, according to space-for-time approaches. In the drier site, phenology was accelerated, but within that site, experimental drought delayed phenology, probably as a plastic response to delayed ontogenetic development. Biomass was smaller in the dry treatments of that site, but it was also reduced in irrigated plots in both sites, indicating more intense competition. The shifts from limitation by drought to limitation by competition corresponded to patterns along the gradient. This also implies a larger negative impact of climate change in the drier site. Our results suggest that experimental selection in the field caused directional responses in most species, but these were not necessarily adaptive. Furthermore, competitive release imposed by climate change may revert direct negative effects of rainfall change in determining plant performance.

Habitat selection in a rocky landscape: experimentally decoupling the influence of retreat site attributes from that of landscape features.

PubMed

Croak, Benjamin M; Pike, David A; Webb, Jonathan K; Shine, Richard

2012-01-01

Organisms selecting retreat sites may evaluate not only the quality of the specific shelter, but also the proximity of that site to resources in the surrounding area. Distinguishing between habitat selection at these two spatial scales is complicated by co-variation among microhabitat factors (i.e., the attributes of individual retreat sites often correlate with their proximity to landscape features). Disentangling this co-variation may facilitate the restoration or conservation of threatened systems. To experimentally examine the role of landscape attributes in determining retreat-site quality for saxicolous ectotherms, we deployed 198 identical artificial rocks in open (sun-exposed) sites on sandstone outcrops in southeastern Australia, and recorded faunal usage of those retreat sites over the next 29 months. Several landscape-scale attributes were associated with occupancy of experimental rocks, but different features were important for different species. For example, endangered broad-headed snakes (Hoplocephalus bungaroides) preferred retreat sites close to cliff edges, flat rock spiders (Hemicloea major) preferred small outcrops, and velvet geckos (Oedura lesueurii) preferred rocks close to the cliff edge with higher-than-average sun exposure. Standardized retreat sites can provide robust experimental data on the effects of landscape-scale attributes on retreat site selection, revealing interspecific divergences among sympatric taxa that use similar habitats.

Universal fingerprinting chip server.

PubMed

Casique-Almazán, Janet; Larios-Serrato, Violeta; Olguín-Ruíz, Gabriela Edith; Sánchez-Vallejo, Carlos Javier; Maldonado-Rodríguez, Rogelio; Méndez-Tenorio, Alfonso

2012-01-01

The Virtual Hybridization approach predicts the most probable hybridization sites across a target nucleic acid of known sequence, including both perfect and mismatched pairings. Potential hybridization sites, having a user-defined minimum number of bases that are paired with the oligonucleotide probe, are first identified. Then free energy values are evaluated for each potential hybridization site, and if it has a calculated free energy of equal or higher negative value than a user-defined free energy cut-off value, it is considered as a site of high probability of hybridization. The Universal Fingerprinting Chip Applications Server contains the software for visualizing predicted hybridization patterns, which yields a simulated hybridization fingerprint that can be compared with experimentally derived fingerprints or with a virtual fingerprint arising from a different sample. The database is available for free at http://bioinformatica.homelinux.org/UFCVH/

Assessment of vaccine testing at three laboratories using the guinea pig model of tuberculosis.

PubMed

Grover, Ajay; Troudt, Jolynn; Arnett, Kimberly; Izzo, Linda; Lucas, Megan; Strain, Katie; McFarland, Christine; Hall, Yper; McMurray, David; Williams, Ann; Dobos, Karen; Izzo, Angelo

2012-01-01

The guinea pig model of tuberculosis is used extensively in different locations to assess the efficacy of novel tuberculosis vaccines during pre-clinical development. Two key assays are used to measure protection against virulent challenge: a 30 day post-infection assessment of mycobacterial burden and long-term post-infection survival and pathology analysis. To determine the consistency and robustness of the guinea pig model for testing vaccines, a comparative assessment between three sites that are currently involved in testing tuberculosis vaccines from external providers was performed. Each site was asked to test two "subunit" type vaccines in their routine animal model as if testing vaccines from a provider. All sites performed a 30 day study, and one site also performed a long-term survival/pathology study. Despite some differences in experimental approach between the sites, such as the origin of the Mycobacterium tuberculosis strain and the type of aerosol exposure device used to infect the animals and the source of the guinea pigs, the data obtained between sites were consistent in regard to the ability of each "vaccine" tested to reduce the mycobacterial burden. The observations also showed that there was good concurrence between the results of short-term and long-term studies. This validation exercise means that efficacy data can be compared between sites. Copyright © 2011 Elsevier Ltd. All rights reserved.

Conserved nucleation sites reinforce the significance of Phi value analysis in protein-folding studies.

PubMed

Gianni, Stefano; Jemth, Per

2014-07-01

The only experimental strategy to address the structure of folding transition states, the so-called Φ value analysis, relies on the synergy between site directed mutagenesis and the measurement of reaction kinetics. Despite its importance, the Φ value analysis has been often criticized and its power to pinpoint structural information has been questioned. In this hypothesis, we demonstrate that comparing the Φ values between proteins not only allows highlighting the robustness of folding pathways but also provides per se a strong validation of the method. © 2014 International Union of Biochemistry and Molecular Biology.

Effects of Recombinant Human Bone Morphogenetic Protein-2 on Vertical Bone Augmentation in a Canine Model.

PubMed

Hsu, Yung-Ting; Al-Hezaimi, Khalid; Galindo-Moreno, Pablo; O'Valle, Francisco; Al-Rasheed, Abdulaziz; Wang, Hom-Lay

2017-09-01

Vertical bone augmentation (VBA) remains unpredictable and challenging for most clinicians. This study aims to compare hard tissue outcomes of VBA, with and without recombinant human bone morphogenetic protein (rhBMP)-2, under space-making titanium mesh in a canine model. Eleven male beagle dogs were used in the study. Experimental ridge defects were created to form atrophic ridges. VBA was performed via guided bone regeneration using titanium mesh and allografts. In experimental hemimandibles, rhBMP-2/absorbable collagen sponge was well mixed with allografts prior to procedures, whereas a control buffer was applied within controls. Dogs were euthanized after a 4-month healing period. Clinical and radiographic examinations were performed to assess ridge dimensional changes. In addition, specimens were used for microcomputed tomography (micro-CT) assessment and histologic analysis. Membrane exposure was found on five of 11 (45.5%) rhBMP-2-treated sites, whereas it was found on nine of 11 (81.8%) non-rhBMP-2-treated sites. Within 4 months of healing, rhBMP-2-treated sites showed better radiographic bone density, greater defect fill, and significantly more bone gain in ridge height (P <0.05) than controls. Experimental hemimandibles exhibited lower rates of membrane exposure and a noteworthy, ectopic bone formation above the mesh in 72% of sites. Results from micro-CT also suggested a trend of less vertical bone gain and bone mineral density in controls (P >0.05). Under light microscope, predominant lamellar patterns were found in the specimen obtained from rhBMP-2 sites. With inherent limitations of the canine model and the concern of such a demanding surgical technique, current findings suggest that the presence of rhBMP-2 in a composite graft allows an increase of vertical gain, with formation of ectopic bone over the titanium mesh in comparison with non-rhBMP-2 sites.

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

NASA Astrophysics Data System (ADS)

Rose, Francis; Hodak, Miroslav; Bernholc, Jerry

2007-03-01

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

[Study on Archaeological Lime Powders from Taosi and Yinxu Sites by FTIR].

PubMed

Wei, Guo-feng; Zhang, Chen; Chen, Guo-liang; He, Yu-ling; Gao, Jiang-tao; Zhang, Bing-jian

2015-03-01

Archaeological lime powders samples from Taosi and Yinxu sites, natural limestone and experimentally prepared lime mortar were investigated by means of Fourier transform infrared spectrometry (FTIR) to identify the raw material of lime powders from Taosi and Yinxu sites. Results show that ν2/ν4 ratio of calcite resulted from carbonation reaction of man-made lime is around 6.31, which is higher than that of calcite in natural limestone and reflects the difference in the disorder of calcite crystal structure among the natural limestone and prepared lime mortar. With additional grinding, the values of v2 and ν4 in natural limestone and prepared lime mortar decrease. Meanwhile, the trend lines of ν2 versus ν4 for calcite in experimentally prepared lime mortar have a steeper slope when compared to calcite in natural limestone. These imply that ν2/ν4 ratio and the slope of the trend lines of ν2 versus ν4 can be used to determine the archaeological man-made lime. Based on the experiment results, it is possible that the archaeological lime powder from Taosi and Yinxu sites was prepared using man-made lime and the ancient Chinese have mastered the calcining technology of man-made lime in the late Neolithic period about 4 300 years ago.

A cross-site intervention in Chinese rural migrants enhances HIV/AIDS knowledge, attitude and behavior.

PubMed

Li, Ning; Li, Xiaomei; Wang, Xueliang; Shao, Jin; Dou, Juanhua

2014-04-23

With the influx of rural migrants into urban areas, the spread of HIV has increased significantly in Shaanxi Province (China). Migrant workers are at high risk of HIV infection due to social conditions and hardships (isolation, separation, marginalization, barriers to services, etc.). We explored the efficacy of a HIV/AIDS prevention and control program for rural migrants in Shaanxi Province, administered at both rural and urban sites. Guidance concerning HIV/AIDS prevention was given to the experimental group (266 migrants) for 1 year by the center of disease control, community health agencies and family planning department. The intervention was conducted according to the HIV/AIDS Prevention Management Manual for Rural Migrants. A control group of migrants only received general population intervention. The impact of the intervention was evaluated by administering HIV/AIDS knowledge, attitudes and sexual behavior (KAB) questionnaires after 6 and 12 months. In the experimental group; 6 months of intervention achieved improvements in HIV/AIDS related knowledge. After 12 months; HIV/AIDS-related knowledge reached near maximal scores. Attitude and most behaviors scores were significantly improved. Moreover; the experimental group showed significant differences in HIV-AIDS knowledge; attitude and most behavior compared with the control group. The systematic long-term cross-site HIV/AIDS prevention in both rural and urban areas is a highly effective method to improve HIV/AIDS KAB among rural migrants.

Separating the Role of Protein Restraints and Local Metal-Site Interaction Chemistry in the Thermodynamics of a Zinc Finger Protein

PubMed Central

Dixit, Purushottam D.; Asthagiri, D.

2011-01-01

We express the effective Hamiltonian of an ion-binding site in a protein as a combination of the Hamiltonian of the ion-bound site in vacuum and the restraints of the protein on the site. The protein restraints are described by the quadratic elastic network model. The Hamiltonian of the ion-bound site in vacuum is approximated as a generalized Hessian around the minimum energy configuration. The resultant of the two quadratic Hamiltonians is cast into a pure quadratic form. In the canonical ensemble, the quadratic nature of the resultant Hamiltonian allows us to express analytically the excess free energy, enthalpy, and entropy of ion binding to the protein. The analytical expressions allow us to separate the roles of the dynamic restraints imposed by the protein on the binding site and the temperature-independent chemical effects in metal-ligand coordination. For the consensus zinc-finger peptide, relative to the aqueous phase, the calculated free energy of exchanging Zn2+ with Fe2+, Co2+, Ni2+, and Cd2+ are in agreement with experiments. The predicted excess enthalpy of ion exchange between Zn2+ and Co2+ also agrees with the available experimental estimate. The free energy of applying the protein restraints reveals that relative to Zn2+, the Co2+, and Cd2+-site clusters are more destabilized by the protein restraints. This leads to an experimentally testable hypothesis that a tetrahedral metal binding site with minimal protein restraints will be less selective for Zn2+ over Co2+ and Cd2+ compared to a zinc finger peptide. No appreciable change is expected for Fe2+ and Ni2+. The framework presented here may prove useful in protein engineering to tune metal selectivity. PMID:21943427

The electronic structure of RbTiOPO4 and the effects of the A-site cation substitution in KTiOPO4-family crystals

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Kesler, V. G.; Meng, Guangsi; Lin, Z. S.

2012-10-01

The electronic structure of RbTiOPO4 has been investigated with x-ray photoemission spectroscopy. Detailed photoemission spectra of the element core levels have been recorded under excitation by nonmonochromatic Al Kα radiation (1486.6 eV). The chemical bonding parameters are compared to those reported for complex titanates and phosphates. The band structures of KTiOPO4, RbTiOPO4, K0.535R0.465TiOPO4 and TlTiOPO4 have been calculated by ab initio methods and compared to available experimental results. It is found that the band structure of KTP-type phosphate crystals is weakly dependent on the nature of the A-site (A=K, Rb, Tl) element.

Experimental study of delivery of humidified-warm carbon dioxide during open abdominal surgery.

PubMed

Carpinteri, S; Sampurno, S; Malaterre, J; Millen, R; Dean, M; Kong, J; Chittleborough, T; Heriot, A; Lynch, A C; Ramsay, R G

2018-04-01

The aim of this study was to monitor the effect of humidified-warm carbon dioxide (HWCO 2 ) delivered into the open abdomen of mice, simulating laparotomy. Mice were anaesthetized, ventilated and subjected to an abdominal incision followed by wound retraction. In the experimental group, a diffuser device was used to deliver HWCO 2 ; the control group was exposed to passive air flow. In each group of mice, surgical damage was produced on one side of the peritoneal wall. Vital signs and core temperature were monitored throughout the 1-h procedure. The peritoneum was closed and mice were allowed to recover for 24 h or 10 days. Tumour cells were delivered into half of the mice in each cohort. Tissue was then examined using scanning electron microscopy and immunohistochemistry. Passive air flow generated ultrastructural damage including mesothelial cell bulging/retraction and loss of microvilli, as assessed at 24 h. Evidence of surgical damage was still measurable on day 10. HWCO 2 maintained normothermia, whereas open surgery alone led to hypothermia. The degree of tissue damage was significantly reduced by HWCO 2 compared with that in controls. Peritoneal expression of hypoxia inducible factor 1α and vascular endothelial growth factor A was lowered by HWCO 2 . These effects were also evident at the surgical damage sites, where protection from tissue trauma extended to 10 days. HWCO 2 did not reduce tumorigenesis in surgically damaged sites compared with passive air flow. HWCO 2 diffusion into the abdomen in the context of open surgery afforded tissue protection and accelerated tissue repair in mice, while preserving normothermia. Surgical relevance Damage to the peritoneum always occurs during open abdominal surgery, by exposure to desiccating air and by mechanical trauma/damage owing to the surgical intervention. Previous experimental studies showed that humidified-warm carbon dioxide (HWCO 2 ) reduced peritoneal damage during laparoscopic insufflation. Additionally, this intervention decreased experimental peritoneal carcinomatosis compared with the use of conventional dry-cold carbon dioxide. In the present experimental study, the simple delivery of HWCO 2 into the open abdomen reduced the amount of cellular damage and inflammation, and accelerated tissue repair. Sites of surgical intervention serve as ideal locations for cancer cell adhesion and subsequent tumour formation, but this was not changed measurably by the delivery of HWCO 2 . © 2017 The Authors. BJS published by John Wiley & Sons Ltd on behalf of BJS Society Ltd.

Highly Enhanced Gas Adsorption Properties in Vertically Aligned MoS2 Layers.

PubMed

Cho, Soo-Yeon; Kim, Seon Joon; Lee, Youhan; Kim, Jong-Seon; Jung, Woo-Bin; Yoo, Hae-Wook; Kim, Jihan; Jung, Hee-Tae

2015-09-22

In this work, we demonstrate that gas adsorption is significantly higher in edge sites of vertically aligned MoS2 compared to that of the conventional basal plane exposed MoS2 films. To compare the effect of the alignment of MoS2 on the gas adsorption properties, we synthesized three distinct MoS2 films with different alignment directions ((1) horizontally aligned MoS2 (basal plane exposed), (2) mixture of horizontally aligned MoS2 and vertically aligned layers (basal and edge exposed), and (3) vertically aligned MoS2 (edge exposed)) by using rapid sulfurization method of CVD process. Vertically aligned MoS2 film shows about 5-fold enhanced sensitivity to NO2 gas molecules compared to horizontally aligned MoS2 film. Vertically aligned MoS2 has superior resistance variation compared to horizontally aligned MoS2 even with same surface area exposed to identical concentration of gas molecules. We found that electrical response to target gas molecules correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. Density functional theory (DFT) calculations corroborate the experimental results as stronger NO2 binding energies are computed for multiple configurations near the edge sites of MoS2, which verifies that electrical response to target gas molecules (NO2) correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. We believe that this observation extends to other 2D TMD materials as well as MoS2 and can be applied to significantly enhance the gas sensor performance in these materials.

A Hierarchical Modeling Approach to Data Analysis and Study Design in a Multi-Site Experimental fMRI Study

ERIC Educational Resources Information Center

Zhou, Bo; Konstorum, Anna; Duong, Thao; Tieu, Kinh H.; Wells, William M.; Brown, Gregory G.; Stern, Hal S.; Shahbaba, Babak

2013-01-01

We propose a hierarchical Bayesian model for analyzing multi-site experimental fMRI studies. Our method takes the hierarchical structure of the data (subjects are nested within sites, and there are multiple observations per subject) into account and allows for modeling between-site variation. Using posterior predictive model checking and model…

The future of long-term USDA Forest Service research sites in the Northeast

Treesearch

Michael T. Rains

2006-01-01

The mission of the Northeastern Research Station is "Improving Lives and Protecting Our Earth Through Research." Our nine experimental sites are the keystone of this mission. Our experimental sites are located in major forest types from West Virginia to Maine, and in Baltimore, Maryland, where we have a long-term ecological research site representing urban...

Local and average structure of Mn- and La-substituted BiFeO3

NASA Astrophysics Data System (ADS)

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space group symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.

Local and average structure of Mn- and La-substituted BiFeO 3

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

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO 3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO 3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.« less

Phenology, growth, and fecundity as determinants of distribution in closely related nonnative taxa

USGS Publications Warehouse

Marushia, Robin G.; Brooks, Matthew L.; Holt, Jodie S.

2012-01-01

Invasive species researchers often ask: Why do some species invade certain habitats while others do not? Ecological theories predict that taxonomically related species may invade similar habitats, but some related species exhibit contrasting invasion patterns. Brassica nigra, Brassica tournefortii, and Hirschfeldia incana are dominant, closely related nonnative species that have overlapping, but dissimilar, distributions. Brassica tournefortii is rapidly spreading in warm deserts of the southwestern United States, whereas B. nigra and H. incana are primarily limited to semiarid and mesic regions. We compared traits of B. tournefortii that might confer invasiveness in deserts with those of related species that have not invaded desert ecosystems. Brassica tournefortii, B. nigra and H. incana were compared in controlled experiments conducted outdoors in a mesic site (Riverside, CA) and a desert site (Blue Diamond, NV), and in greenhouses, over 3 yr. Desert and mesic B. tournefortii populations were also compared to determine whether locally adapted ecotypes contribute to desert invasion. Experimental variables included common garden sites and soil water availability. Response variables included emergence, growth, phenology, and reproduction. There was no evidence for B. tournefortii ecotypes, but B. tournefortii had a more rapid phenology than B. nigra or H. incana. Brassica tournefortii was less affected by site and water availability than B. nigra and H. incana, but was smaller and less fecund regardless of experimental conditions. Rapid phenology allows B. tournefortii to reproduce consistently under variable, stressful conditions such as those found in Southwestern deserts. Although more successful in milder, mesic ecosystems, B. nigra and H. incana may be limited by their ability to reproduce under desert conditions. Rapid phenology and drought response partition invasion patterns of nonnative mustards along a gradient of aridity in the southwestern United States, and may serve as a predictive trait for other potential invaders of arid and highly variable ecosystems.

How Generalizable Is Your Experiment? An Index for Comparing Experimental Samples and Populations

ERIC Educational Resources Information Center

Tipton, Elizabeth

2014-01-01

Although a large-scale experiment can provide an estimate of the average causal impact for a program, the sample of sites included in the experiment is often not drawn randomly from the inference population of interest. In this article, we provide a generalizability index that can be used to assess the degree of similarity between the sample of…

The utility of Geographical Information Systems (GIS) in systems-oriented obesity intervention projects: The selection of comparable study sites for a quasi-experimental intervention design--TX CORD

USDA-ARS?s Scientific Manuscript database

The Texas Childhood Obesity Research Demonstration project (TX CORD) uses a systems-oriented approach to address obesity that includes individual and family interventions, community-level action, as well as environmental and policy initiatives. Given that randomization is seldom possible in communit...

Multitemporal MODIS-EVI relationships with precipitation and temperature at the Santa Rita Experimental Range

Treesearch

Jorry Z. U. Kaurivi; Alfredo R. Huete; Kamel Didan

2003-01-01

The Moderate Resolution Imaging Spectroradiometer (MODIS) provides temporal enhanced vegetation index (EVI) data at 250, 500, and 1,000 m spatial resolutions that can be compared to daily, weekly, monthly, and annual weather parameters. A study was conducted at the grassland site (less than 10 percent velvet mesquite [Prosopis juliflora, var. velutina]) and the...

Does MTV Really Do a Good Job of Evaluating Professors? An Empirical Test of the Internet Site Ratemyprofessors.com

ERIC Educational Resources Information Center

Murray, Keith B.; Zdravkovic, Srdan

2016-01-01

Considerable debate continues regarding the efficacy of the website RateMyProfessors.com (RMP). To date, however, virtually no direct, experimental research has been reported which directly bears on questions relating to sampling adequacy or item adequacy in producing what favorable correlations have been reported. The authors compare the data…

Genetic Analysis of earl field growth of loblolly pine clones and seedlings from the same full-sib families

Treesearch

Brian Baltunis; Dudley Huber; Tim Wite

2006-01-01

The Forest Biology Research Cooperative recently established a series of loblolly pine clonal trials known as CCLONES (Comparing Clonal Lines on Experimental Sites). There are three primary levels of genetic structure in this study (parental, full-sib family, clone) that strengthen the power of CCLONES for examining genetic mechanisms and interactions with cultural...

Responses to human intruders by birds nesting in colonies: Experimental results and management guidelines

USGS Publications Warehouse

Erwin, R.M.

1989-01-01

Colonies of nesting wading birds and seabirds were studied at coastal sites in Virginia and North Carolina to determine distances at which birds flushed in response to human intrusion. There were few statistically significant relationships between flushing distances and colony size. Similarly, there were few differences between responses during incubation compared to post-hatching periods.

Can Building Design Impact Physical Activity? A Natural Experiment.

PubMed

Eyler, Amy A; Hipp, Aaron; Valko, Cheryl Ann; Ramadas, Ramya; Zwald, Marissa

2018-05-01

Workplace design can impact workday physical activity (PA) and sedentary time. The purpose of this study was to evaluate PA behavior among university employees before and after moving into a new building. A pre-post, experimental versus control group study design was used. PA data were collected using surveys and accelerometers from university faculty and staff. Accelerometry was used to compare those moving into the new building (MOVERS) and those remaining in existing buildings (NONMOVERS) and from a control group (CONTROLS). Survey results showed increased self-reported PA for MOVERS and NONMOVERS. All 3 groups significantly increased in objectively collected daily energy expenditure and steps per day. The greatest steps per day increase was in CONTROLS (29.8%) compared with MOVERS (27.5%) and NONMOVERS (15.9%), but there were no significant differences between groups at pretest or posttest. Self-reported and objectively measured PA increased from pretest to posttest in all groups; thus, the increase cannot be attributed to the new building. Confounding factors may include contamination bias due to proximity of control site to experimental site and introduction of a university PA tracking contest during postdata collection. Methodology and results can inform future studies on best design practices for increasing PA.

Musite, a tool for global prediction of general and kinase-specific phosphorylation sites.

PubMed

Gao, Jianjiong; Thelen, Jay J; Dunker, A Keith; Xu, Dong

2010-12-01

Reversible protein phosphorylation is one of the most pervasive post-translational modifications, regulating diverse cellular processes in various organisms. High throughput experimental studies using mass spectrometry have identified many phosphorylation sites, primarily from eukaryotes. However, the vast majority of phosphorylation sites remain undiscovered, even in well studied systems. Because mass spectrometry-based experimental approaches for identifying phosphorylation events are costly, time-consuming, and biased toward abundant proteins and proteotypic peptides, in silico prediction of phosphorylation sites is potentially a useful alternative strategy for whole proteome annotation. Because of various limitations, current phosphorylation site prediction tools were not well designed for comprehensive assessment of proteomes. Here, we present a novel software tool, Musite, specifically designed for large scale predictions of both general and kinase-specific phosphorylation sites. We collected phosphoproteomics data in multiple organisms from several reliable sources and used them to train prediction models by a comprehensive machine-learning approach that integrates local sequence similarities to known phosphorylation sites, protein disorder scores, and amino acid frequencies. Application of Musite on several proteomes yielded tens of thousands of phosphorylation site predictions at a high stringency level. Cross-validation tests show that Musite achieves some improvement over existing tools in predicting general phosphorylation sites, and it is at least comparable with those for predicting kinase-specific phosphorylation sites. In Musite V1.0, we have trained general prediction models for six organisms and kinase-specific prediction models for 13 kinases or kinase families. Although the current pretrained models were not correlated with any particular cellular conditions, Musite provides a unique functionality for training customized prediction models (including condition-specific models) from users' own data. In addition, with its easily extensible open source application programming interface, Musite is aimed at being an open platform for community-based development of machine learning-based phosphorylation site prediction applications. Musite is available at http://musite.sourceforge.net/.

A grammar inference approach for predicting kinase specific phosphorylation sites.

PubMed

Datta, Sutapa; Mukhopadhyay, Subhasis

2015-01-01

Kinase mediated phosphorylation site detection is the key mechanism of post translational mechanism that plays an important role in regulating various cellular processes and phenotypes. Many diseases, like cancer are related with the signaling defects which are associated with protein phosphorylation. Characterizing the protein kinases and their substrates enhances our ability to understand the mechanism of protein phosphorylation and extends our knowledge of signaling network; thereby helping us to treat such diseases. Experimental methods for predicting phosphorylation sites are labour intensive and expensive. Also, manifold increase of protein sequences in the databanks over the years necessitates the improvement of high speed and accurate computational methods for predicting phosphorylation sites in protein sequences. Till date, a number of computational methods have been proposed by various researchers in predicting phosphorylation sites, but there remains much scope of improvement. In this communication, we present a simple and novel method based on Grammatical Inference (GI) approach to automate the prediction of kinase specific phosphorylation sites. In this regard, we have used a popular GI algorithm Alergia to infer Deterministic Stochastic Finite State Automata (DSFA) which equally represents the regular grammar corresponding to the phosphorylation sites. Extensive experiments on several datasets generated by us reveal that, our inferred grammar successfully predicts phosphorylation sites in a kinase specific manner. It performs significantly better when compared with the other existing phosphorylation site prediction methods. We have also compared our inferred DSFA with two other GI inference algorithms. The DSFA generated by our method performs superior which indicates that our method is robust and has a potential for predicting the phosphorylation sites in a kinase specific manner.

Scaling Coastal Ecosystems to Oceanographic and Climatic Drivers: Making Sense of Community Variation on Rocky Shores Using the Comparative-Experimental Approach in Upwelling and Downwelling Systems

NASA Astrophysics Data System (ADS)

Menge, B. A.; Gouhier, T.; Chan, F.; Hacker, S.; Menge, D.; Nielsen, K. J.

2016-02-01

Ecology focuses increasingly on the issue of matching spatial and temporal scales responsible for ecosystem pattern and dynamics. Benthic coastal communities traditionally were studied at local scales using mostly short-term research, while environmental (oceanographic, climatic) drivers were investigated at large scales (e.g., regional to oceanic, mostly offshore) using combined snapshot and monitoring (time series) research. The comparative-experimental approach combines local-scale studies at multiple sites spanning large-scale environmental gradients in combination with monitoring of inner shelf oceanographic conditions including upwelling/downwelling wind forcing and their consequences (e.g., temperature), and inputs of subsidies (larvae, phytoplankton, detritus). Temporal scale varies depending on the questions, but can extend from years to decades. We discuss two examples of rocky intertidal ecosystem dynamics, one at a regional scale (California Current System, CCS) and one at an interhemispheric scale. In the upwelling-dominated CCS, 52% and 32% of the variance in local community structure (functional group abundances at 13 sites across 725 km) was explained by external factors (ecological subsidies, oceanographic conditions, geographic location), and species interactions, respectively. The interhemispheric study tested the intermittent upwelling hypothesis (IUH), which predicts that key ecological processes will vary unimodally along a persistent downwelling to persistent upwelling gradient. Using 14-22 sites, unimodal relationships between ecological subsidies (phytoplankton, prey recruitment), prey responses (barnacle colonization, mussel growth) and species interactions (competition rate, predation rate and effect) and the Bakun upwelling index calculated at each site accounted for 50% of the variance. Hence, external factors can account for about half of locally-expressed community structure and dynamics.

Accurate in silico prediction of species-specific methylation sites based on information gain feature optimization.

PubMed

Wen, Ping-Ping; Shi, Shao-Ping; Xu, Hao-Dong; Wang, Li-Na; Qiu, Jian-Ding

2016-10-15

As one of the most important reversible types of post-translational modification, protein methylation catalyzed by methyltransferases carries many pivotal biological functions as well as many essential biological processes. Identification of methylation sites is prerequisite for decoding methylation regulatory networks in living cells and understanding their physiological roles. Experimental methods are limitations of labor-intensive and time-consuming. While in silicon approaches are cost-effective and high-throughput manner to predict potential methylation sites, but those previous predictors only have a mixed model and their prediction performances are not fully satisfactory now. Recently, with increasing availability of quantitative methylation datasets in diverse species (especially in eukaryotes), there is a growing need to develop a species-specific predictor. Here, we designed a tool named PSSMe based on information gain (IG) feature optimization method for species-specific methylation site prediction. The IG method was adopted to analyze the importance and contribution of each feature, then select the valuable dimension feature vectors to reconstitute a new orderly feature, which was applied to build the finally prediction model. Finally, our method improves prediction performance of accuracy about 15% comparing with single features. Furthermore, our species-specific model significantly improves the predictive performance compare with other general methylation prediction tools. Hence, our prediction results serve as useful resources to elucidate the mechanism of arginine or lysine methylation and facilitate hypothesis-driven experimental design and validation. The tool online service is implemented by C# language and freely available at http://bioinfo.ncu.edu.cn/PSSMe.aspx CONTACT: jdqiu@ncu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Vasomotor response to cold stimulation in human capsaicin-induced hyperalgesic area.

PubMed

Pud, Dorit; Andersen, Ole Kaeseler; Arendt-Nielsen, Lars; Eisenberg, Elon; Yarnitsky, David

2005-07-01

Cooling the skin induces sympathetically driven vasoconstriction, with some vasoparalytic dilatation at the lowest temperatures. Neurogenic inflammation, on the other hand, entails vasodilatation. In this study we investigated the balance between vasoconstriction and vasodilatation in an area of experimentally induced secondary hyperalgesia (2 degrees HA), in response to low-temperature stimulations. Fourteen healthy volunteers were exposed to three 30-s long cold stimuli (20, 10, and 0 degrees C) applied, at three adjacent sites, before (baseline) and 8 min after intradermal injection of 50 microg capsaicin to the volar forearm. The cold stimuli were applied distally to the injection site within the 2 degrees HA. Blood flux (BF) and skin temperatures were measured at four different regions (proximally, and distally to the capsaicin injection and at the 0, 10, and 20 degrees C thermode sites) all within the 2 degrees HA. The vascular measurements were conducted five times. Results showed a marked increase in BF after baseline cold stimulation (P<0.001) at the 0 degrees C compared with the three other sites. In addition, vasodilatory effect (elevated BF) was found following the capsaicin injection compared with baseline for all regions (P<0.001): the non-cooled area was dilated by 450+/-5.1%; The vasoconstrictive effect for the 10 and 20 degrees C did not overcome the capsaicin vasodilatation, but did reduce it, with dilatation of 364+/-7.0% and 329+/-7.3%, respectively. For 0 degrees C, a dilatation of 407+/-6.5% was seen. It is concluded that in this experimental model, and potentially in the equivalent clinical syndromes, vasodilatation induced by the inflammation is only slightly reduced by cold stimulation such that it is still dominant, despite some cold-induced vasoconstriction.

Increase of crevicular interleukin 1beta under academic stress at experimental gingivitis sites and at sites of perfect oral hygiene.

PubMed

Deinzer, R; Förster, P; Fuck, L; Herforth, A; Stiller-Winkler, R; Idel, H

1999-01-01

This study analyses the effects of academic stress on crevicular interleukin-1beta(I1-1beta) both at experimental gingivitis sites and at sites of perfect oral hygiene. I1-1beta is thought to play a predominant role in periodontal tissue destruction. 13 medical students participating in a major medical exam (exam group) and 13 medical students not participating in any exam throughout the study period (control group) volunteered for the study. In a split-mouth-design, they refrained from any oral hygiene procedures in two opposite quadrants for 21 days (experimental gingivitis) while they maintained perfect hygiene levels at the remaining sites. Crevicular fluid was sampled for further I1-1beta analysis at teeth 5 and 6 of the upper jaw at days 1, 5, 8, 11, 14, 18 and 21 of the experimental gingivitis period. Exam students showed significantly higher I1-1beta levels than controls both at experimental gingivitis sites (area under the curve, exam group: 1240.64+/-140.07; control group: 697.61+/-111.30; p=0.004) and at sites of perfect oral hygiene (exam group: 290.42+/-63.19; control group: 143.98+/-42.71; p = 0.04). These results indicate that stress might affect periodontal health by increasing local I1-1beta levels especially when oral hygiene is neglected.

Position specific variation in the rate of evolution in transcription factor binding sites

PubMed Central

Moses, Alan M; Chiang, Derek Y; Kellis, Manolis; Lander, Eric S; Eisen, Michael B

2003-01-01

Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Results Here we analyse the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikatae to study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artefacts of computational motif finding algorithms. Conclusion As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative sequence data in the identification of transcription factor binding sites and is an important step toward understanding the evolution of functional non-coding DNA. PMID:12946282

Grand canonical Monte Carlo simulation of the adsorption isotherms of water molecules on model soot particles

NASA Astrophysics Data System (ADS)

Moulin, F.; Picaud, S.; Hoang, P. N. M.; Jedlovszky, P.

2007-10-01

The grand canonical Monte Carlo method is used to simulate the adsorption isotherms of water molecules on different types of model soot particles. The soot particles are modeled by graphite-type layers arranged in an onionlike structure that contains randomly distributed hydrophilic sites, such as OH and COOH groups. The calculated water adsorption isotherm at 298K exhibits different characteristic shapes depending both on the type and the location of the hydrophilic sites and also on the size of the pores inside the soot particle. The different shapes of the adsorption isotherms result from different ways of water aggregation in or/and around the soot particle. The present results show the very weak influence of the OH sites on the water adsorption process when compared to the COOH sites. The results of these simulations can help in interpreting the experimental isotherms of water adsorbed on aircraft soot.

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems.

PubMed

Wei, Yingying; Wu, George; Ji, Hongkai

2013-05-01

Mapping genome-wide binding sites of all transcription factors (TFs) in all biological contexts is a critical step toward understanding gene regulation. The state-of-the-art technologies for mapping transcription factor binding sites (TFBSs) couple chromatin immunoprecipitation (ChIP) with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip). These technologies have limitations: they are low-throughput with respect to surveying many TFs. Recent advances in genome-wide chromatin profiling, including development of technologies such as DNase-seq, FAIRE-seq and ChIP-seq for histone modifications, make it possible to predict in vivo TFBSs by analyzing chromatin features at computationally determined DNA motif sites. This promising new approach may allow researchers to monitor the genome-wide binding sites of many TFs simultaneously. In this article, we discuss various experimental design and data analysis issues that arise when applying this approach. Through a systematic analysis of the data from the Encyclopedia Of DNA Elements (ENCODE) project, we compare the predictive power of individual and combinations of chromatin marks using supervised and unsupervised learning methods, and evaluate the value of integrating information from public ChIP and gene expression data. We also highlight the challenges and opportunities for developing novel analytical methods, such as resolving the one-motif-multiple-TF ambiguity and distinguishing functional and non-functional TF binding targets from the predicted binding sites. The online version of this article (doi:10.1007/s12561-012-9066-5) contains supplementary material, which is available to authorized users.

Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study.

PubMed

Dudev, Todor; Chang, Li-Ying; Lim, Carmay

2005-03-23

Trivalent lanthanide cations are extensively being used in biochemical experiments to probe various dication-binding sites in proteins; however, the factors governing the binding specificity of lanthanide cations for these binding sites remain unclear. Hence, we have performed systematic studies to evaluate the interactions between La3+ and model Ca2+ - and Mg2+ -binding sites using density functional theory combined with continuum dielectric methods. The calculations reveal the key factors and corresponding physical bases favoring the substitution of trivalent lanthanides for divalent Ca2+ and Mg2+ in holoproteins. Replacing Ca2+ or Mg2+ with La3+ is facilitated by (1) minimizing the solvent exposure and the flexibility of the metal-binding cavity, (2) freeing both carboxylate oxygen atoms of Asp/Glu side chains in the metal-binding site so that they could bind bidentately to La3+, (3) maximizing the number of metal-bound carboxylate groups in buried sites, but minimizing the number of metal-bound carboxylate groups in solvent-exposed sites, and (4) including an Asn/Gln side chain for sites lined with four Asp/Glu side chains. In proteins bound to both Mg2+ and Ca2+, La3+ would prefer to replace Ca2+, as compared to Mg2+. A second Mg2+-binding site with a net positive charge would hamper the Mg2+ --> La3+ exchange, as compared to the respective mononuclear site, although the La3+ substitution of the first native metal is more favorable than the second one. The findings of this work are in accord with available experimental data.

Towards predicting coral calcification responses to ocean acidification: A combined modeling and experimental approach

NASA Astrophysics Data System (ADS)

Mollica, N. R.; Guo, W.; Cohen, A. L.; Foster, G. L.; Barkley, H.

2016-02-01

Experiments show that ocean acidification is detrimental to coral calcification. Nevertheless, coral sensitivities to OA vary and the mechanism(s) underlying these variable responses are not fully understood. One hypothesis is that ocean acidification affects the ability of coral's to regulate the pH of fluid at the site of calcification. We developed a numerical model of coral calcification that simulates corals' pH regulation based on physiochemical principles and predicts the rate of calcification [1]. Here we apply this model to Palauan corals, and seek to test the model's efficacy by comparing the predicted coral calcification responses with experimental measurements. Four coral cores were collected from two sites of different pH (7.84 and 8.04 respectively). Their bulk annual calcification rates, quantified from average density and extension rate measurements, vary from .83 to 1.39 g cm-2 year-1 for the low pH site and from 0.75 to 1.21 g cm-2 year-1for the high pH site. The higher bulk calcification rates observed in corals from the low pH site contrasts the expected general decrease in calcification in low pH seawater, and differs from our model prediction. We suspect this apparent discrepancy arises because fast-calcifying corals in low pH water are able to modulate the pH of fluid at the site of calcification. We test this hypothesis using boron isotope measurements from each coral. In addition, a more accurate measurement of instantaneous calcification, considering the number of corallites per measured area and the exact surface area of each polyp's 3-dimensional calcification site is applied. [1] Guo, W. (2014). AGU Fall Meeting, Abstract B41B-0033.

On the active site of mononuclear B1 metallo β-lactamases: a computational study

NASA Astrophysics Data System (ADS)

Sgrignani, Jacopo; Magistrato, Alessandra; Dal Peraro, Matteo; Vila, Alejandro J.; Carloni, Paolo; Pierattelli, Roberta

2012-04-01

Metallo-β-lactamases (MβLs) are Zn(II)-based bacterial enzymes that hydrolyze β-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from Bacillus Cereus point to either two zinc ions in two metal sites (the so-called `3H' and `DCH' sites) or a single Zn(II) ion in the 3H site, where the ion is coordinated by Asp120, Cys221 and His263 residues. However, spectroscopic studies on the B1 enzyme from B. Cereus in the mono-zinc form suggested the presence of the Zn(II) ion also in the DCH site, where it is bound to an aspartate, a cysteine, a histidine and a water molecule. A structural model of this enzyme in its DCH mononuclear form, so far lacking, is therefore required for inhibitor design and mechanistic studies. By using force field based and mixed quantum-classical (QM/MM) molecular dynamics (MD) simulations of the protein in aqueous solution we constructed such structural model. The geometry and the H-bond network at the catalytic site of this model, in the free form and in complex with two common β-lactam drugs, is compared with experimental and theoretical findings of CphA and the recently solved crystal structure of new B2 MβL from Serratia fonticola (Sfh-I). These are MβLs from the B2 subclass, which features an experimentally well established mono-zinc form, in which the Zn(II) is located in the DCH site. From our simulations the ɛɛδ and δɛδ protomers emerge as possible DCH mono-zinc reactive species, giving a novel contribution to the discussion on the MβL reactivity and to the drug design process.

Probing binding hot spots at protein-RNA recognition sites.

PubMed

Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad

2016-01-29

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Soil health research in the Goodwater Creek Experimental Watershed Long-Term Agroecosystem Research site

USDA-ARS?s Scientific Manuscript database

The Goodwater Creek Experimental Watershed (GCEW) is located in the Central Claypan Region in NE Missouri. Within GCEW, a field and plot research site has been operated by the USDA-Agricultural Research Service (ARS) Cropping Systems and Water Quality Research Unit since 1991. The GCEW site joined t...

Can selection on nest size from nest predation explain the latitudinal gradient in clutch size?

PubMed

Biancucci, Luis; Martin, Thomas E

2010-09-01

1. Latitudinal variation in clutch sizes of birds is a well described, but poorly understood pattern. Many hypotheses have been proposed, but few have been experimentally tested, and none have been universally accepted by researchers. 2. The nest size hypothesis posits that higher nest predation in the tropics favours selection for smaller nests and thereby constrains clutch size by shrinking available space for eggs and/or nestlings in the nest. We tested this hypothesis with an experiment in a tropical forest and a comparative study between temperate and tropical field sites. 3. Specifically, we tested if: (i) predation increased with nest size; (ii) tropical birds had smaller nests controlled for body size; and (iii) clutch size was explained by nest size controlled for body size. 4. Experimental swapping of nests of different sizes showed that nest predation increased with nest size in the tropical site. Moreover, nest predation rates were higher in species with larger nests in both sites. However, nest size, corrected for body mass and phylogeny, did not differ between sites and was not related to clutch size between sites. 5. Hence, nest predation can exert selection on nest size as predicted by the hypothesis. Nest size increased with adult body mass, such that adult size might indirectly influence reproductive success through effects on nest size and nest predation risk. Ultimately, however, selection from nest predation on nest size does not explain the smaller clutch sizes typical of the tropics.

Can selection on nest size from nest predation explain the latitudinal gradient in clutch size?

USGS Publications Warehouse

Biancucci, L.; Martin, T.E.

2010-01-01

1. Latitudinal variation in clutch sizes of birds is a well described, but poorly understood pattern. Many hypotheses have been proposed, but few have been experimentally tested, and none have been universally accepted by researchers. 2. The nest size hypothesis posits that higher nest predation in the tropics favours selection for smaller nests and thereby constrains clutch size by shrinking available space for eggs and/or nestlings in the nest. We tested this hypothesis with an experiment in a tropical forest and a comparative study between temperate and tropical field sites. 3. Specifically, we tested if: (i) predation increased with nest size; (ii) tropical birds had smaller nests controlled for body size; and (iii) clutch size was explained by nest size controlled for body size. 4. Experimental swapping of nests of different sizes showed that nest predation increased with nest size in the tropical site. Moreover, nest predation rates were higher in species with larger nests in both sites. However, nest size, corrected for body mass and phylogeny, did not differ between sites and was not related to clutch size between sites. 5. Hence, nest predation can exert selection on nest size as predicted by the hypothesis. Nest size increased with adult body mass, such that adult size might indirectly influence reproductive success through effects on nest size and nest predation risk. Ultimately, however, selection from nest predation on nest size does not explain the smaller clutch sizes typical of the tropics.

Sound settlement: noise surpasses land cover in explaining breeding habitat selection of secondary cavity-nesting birds.

PubMed

Kleist, Nathan J; Guralnick, Robert P; Cruz, Alexander; Francis, Clinton D

2017-01-01

Birds breeding in heterogeneous landscapes select nest sites by cueing in on a variety of factors from landscape features and social information to the presence of natural enemies. We focus on determining the relative impact of anthropogenic noise on nest site occupancy, compared to amount of forest cover, which is known to strongly influence the selection process. We examine chronic, industrial noise from natural gas wells directly measured at the nest box as well as site-averaged noise, using a well-established field experimental system in northwestern New Mexico. We hypothesized that high levels of noise, both at the nest site and in the environment, would decrease nest box occupancy. We set up nest boxes using a geospatially paired control and experimental site design and analyzed four years of occupancy data from four secondary cavity-nesting birds common to the Colorado Plateau. We found different effects of noise and landscape features depending on species, with strong effects of noise observed in breeding habitat selection of Myiarchus cinerascens, the Ash-throated Flycatcher, and Sialia currucoides, the Mountain Bluebird. In contrast, the amount of forest cover less frequently explained habitat selection for those species or had a smaller standardized effect than the acoustic environment. Although forest cover characterization and management is commonly employed by natural resource managers, our results show that characterizing and managing the acoustic environment should be an important tool in protected area management. © 2016 by the Ecological Society of America.

Carbon dioxide flux and net primary production of a boreal treed bog: responses to warming and water table manipulations

NASA Astrophysics Data System (ADS)

Munir, T. M.; Perkins, M.; Kaing, E.; Strack, M.

2014-09-01

Mid-latitude treed bogs are significant carbon (C) stocks and are highly sensitive to global climate change. In a dry continental treed bog, we compared three sites; control, recent (1-3 years; experimental) and older drained (10-13 years; drained) with water levels at 38, 74 and 120 cm below the surface, respectively. At each site we measured carbon dioxide (CO2) fluxes and tree root respiration (Rr) (across hummock-hollow microtopography of the forest floor) and net primary production (NPP) of trees during the growing seasons (May to October) of 2011-2013. The carbon (C) balance was calculated by adding net CO2 exchange of the forest floor (NEff-Rr) to the NPP of the trees. From cooler and wetter 2011 to driest and warmest 2013, The control site was a~C sink of 92, 70 and 76 g m-2, experimental site was a C source of 14, 57 and 135 g m-2, and drained site was a progressively smaller source of 26, 23 and 13 g m-2, respectively. Although all microforms at the experimental site had large net CO2 emissions, the longer-term drainage and deeper water level at the drained site resulted in the replacement of mosses with vascular plants (shrubs) at the hummocks and lichens at the hollows leading to the highest CO2 uptake at drained hummocks and significant losses at hollows. The tree NPP was highest at the drained site. We also quantified the impact of climatic warming at all water table treatments by equipping additional plots with open-top chambers (OTCs) that caused a passive warming on average of ∼1 °C and differential air warming of ∼6 °C (at mid-day full sun) across the study years. Warming significantly enhanced the shrub growth and CO2 sink function of the drained hummocks (exceeding the cumulative respiration losses at hollows induced by the lowered water level × warming). There was an interaction of water level with warming across hummocks that resulted in largest net CO2 uptake at warmed drained hummocks. Thus in 2013, the warming treatment enhanced the sink function of control by 13 g m-2, reduced the source function of experimental by 10 g m-2, and significantly enhanced the sink function of the drained site by 73 g m-2. Therefore, drying and warming in continental bogs is expected to initially accelerate C losses via respiration but persistent drought and warming is expected to restore the peatland's original C sink function as a result of transitional shift of vegetation between the microforms and increased NPP of trees over time.

Estimating Per-Pixel GPP of the Contiguous USA Directly from MODIS EVI Data

NASA Astrophysics Data System (ADS)

Rahman, A. F.; Sims, D. A.; El-Masri, B. Z.; Cordova, V. D.

2005-12-01

We estimated gross primary production (GPP) of the contiguous USA using enhanced vegetation index (EVI) data from NASA's moderate resolution imaging spectroradiometer (MODIS). Based on recently published values of correlation coefficients between EVI and GPP of North American vegetations, we derived GPP maps of the contiguous USA for 2001-2004, which included one La Nina year and three moderately El Nino years. The product was a truly per-pixel GPP estimate (named E-GPP), in contrast to the pseudo-continuous MOD17, the standard MODIS GPP product. We compared E-GPP with fine-scale experimental GPP data and MOD17 estimates from three Bigfoot experimental sites, and also with MOD17 estimates from the whole contiguous USA for the above-mentioned four years. For each of the '7 by 7' km Bigfoot experimental sites, E-GPP was able to track the primary production activity during the green-up period while MOD17 failed to do so. The E-GPP estimates during peak production season were similar to those from Bigfoot and MOD17 for most vegetation types except for the deciduous types, where it was lower. Annual E-GPP of the Bigfoot sites compared well with Bigfoot experimental GPP (r = 0.71) and MOD17 (r = 0.78). But for the contiguous USA for 2001-2004, annual E-GPP showed disagreement with MOD17 in both magnitude and seasonal trends for deciduous forests and grass lands. In this study we explored the reasons for this mismatch between E-GPP and MOD17 and also analyzed the uncertainties in E-GPP across multiple spatial scales. Our results show that the E-GPP, based on a simple regression model, can work as a robust alternative to MOD17 for large-area annual GPP estimation. The relative advantages of E-GPP are that it is truly per-pixel, solely dependent on remotely sensed data that is routinely available from NASA, easy to compute and has the potential of being used as an operational product.

Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction.

PubMed

Li, Yan; Li, Xiang; Dong, Zigang

2015-12-28

Fatty acid binding protein 4 (FABP4), reversibly binding to fatty acids and other lipids with high affinities, is a potential target for treatment of cancers. The binding site of FABP4 is buried in an interior cavity and thereby ligand binding/unbinding is coupled with opening/closing of FABP4. It is a difficult task both experimentally and computationally to illuminate the entry or exit pathway, especially with the conformational gating. In this report we combine extensive computer simulations, clustering analysis, and the Markov state model to investigate the binding mechanism of FABP4 and troglitazone. Our simulations capture spontaneous binding and unbinding events as well as the conformational transition of FABP4 between the open and closed states. An allosteric binding site on the protein surface is recognized for the development of novel FABP4 inhibitors. The binding affinity is calculated and compared with the experimental value. The kinetic analysis suggests that ligand residence on the protein surface may delay the binding process. Overall, our results provide a comprehensive picture of ligand diffusion on the protein surface, ligand migration into the buried cavity, and the conformational change of FABP4 at an atomic level.

Copper attachment to prion protein at a non-octarepeat site

NASA Astrophysics Data System (ADS)

Hodak, Miroslav; Bernholc, Jerry

2011-03-01

Prion protein (PrP) plays a causative role in a group of neurodegenerative diseases, which include ``mad cow disease'' or its human form variant Creutzfeld-Jacob disease. Normal function of PrP remains unknown, but it is now well established that PrP can efficiently bind copper ions and this ability has been linked to its function. The primary binding sites are located in the so-called octarepeat region located between residues 60-91. While these are by now well characterized, the sites located outside these region remain mostly undetermined. In this work, we investigate the properties of Cu binding site located at His 111 using recently developed hybrid Kohn-Sham/orbital-free density functional simulations. Experimental data indicate that copper is coordinated by either four nitrogens or three nitrogens and one oxygen. We investigate both possibilities, comparing their energetics and attachment geometries. Similarities and differences with other binding sites and implications for PrP function will also be discussed.

Analysis Techniques, Materials, and Methods for Treatment of Thermal Bridges in Building Envelopes

DTIC Science & Technology

2013-08-01

effects of the R-value for given increment of time ............................................. 89 64 Crystals on a post-conditioned Aspen Aerogel ... aerogel on specific sites compared to conventional polyurethane foam insulation. Figures 55 and 56 show two examples of preliminary parametric... Aerogel , and (4) Honeywell’s polyurethane. Table 14 lists the four tested insulation ma- terials, their experimental thermal properties (derived

Diffusion coefficient and shear viscosity of rigid water models.

PubMed

Tazi, Sami; Boţan, Alexandru; Salanne, Mathieu; Marry, Virginie; Turq, Pierre; Rotenberg, Benjamin

2012-07-18

We report the diffusion coefficient and viscosity of popular rigid water models: two non-polarizable ones (SPC/E with three sites, and TIP4P/2005 with four sites) and a polarizable one (Dang-Chang, four sites). We exploit the dependence of the diffusion coefficient on the system size (Yeh and Hummer 2004 J. Phys. Chem. B 108 15873) to obtain the size-independent value. This also provides an estimate of the viscosity of all water models, which we compare to the Green-Kubo result. In all cases, a good agreement is found. The TIP4P/2005 model is in better agreement with the experimental data for both diffusion and viscosity. The SPC/E and Dang-Chang models overestimate the diffusion coefficient and underestimate the viscosity.

Theory of magnetic enhancement in strontium hexaferrite through Zn-Sn pair substitution

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

Liyanage, LSI; Kim, S; Hong, YK

2013-12-01

We study the site occupancy and magnetic properties of Zn-Sn substituted M-type Sr-hexaferrite SrFe12-x(Zn0.5Sn0.5)(x)O-19 with x=1 using first-principles total-energy calculations. We find that in the lowest-energy configuration Zn2+ and Sn4+ ions preferentially occupy the 4f(1) and 4f(2) sites, respectively, in contrast to the model previously suggested by Ghasemi et al. [J. Appl. Phys, 107, 09A734 (2010)], where Zn2+ and Sn4+ ions occupy the 2b and 4f(2) sites. Density-functional theory calculations show that our model has a lower total energy by more than 0.2 eV per unit cell compared to Ghasemi's model. More importantly, the latter does not show an increasemore » in saturation magnetization (M-s) compared to the pure M-type Sr-hexaferrite, in disagreement with the experiment. On the other hand, our model correctly predicts a rapid increase in M-s as well as a decrease in magnetic anisotropy compared to the pure M-type Sr-hexaferrite, consistent with experimental measurements. (c) 2013 Elsevier B.V. All rights reserved.« less

Modelling of the acid-base properties of natural and synthetic adsorbent materials used for heavy metal removal from aqueous solutions.

PubMed

Pagnanelli, Francesca; Vegliò, Francesco; Toro, Luigi

2004-02-01

In this paper a comparison about kinetic behaviour, acid-base properties and copper removal capacities was carried out between two different adsorbent materials used for heavy metal removal from aqueous solutions: an aminodiacetic chelating resin as commercial product (Lewatit TP207) and a lyophilised bacterial biomass of Sphaerotilus natans. The acid-base properties of a S. natans cell suspension were well described by simplified mechanistic models without electrostatic corrections considering two kinds of weakly acidic active sites. In particular the introduction of two-peak distribution function for the proton affinity constants allows a better representation of the experimental data reproducing the site heterogeneity. A priori knowledge about resin functional groups (aminodiacetic groups) is the base for preliminary simulations of titration curve assuming a Donnan gel structure for the resin phase considered as a concentrated aqueous solution of aminodiacetic acid (ADA). Departures from experimental and simulated data can be interpreted by considering the heterogeneity of the functional groups and the effect of ionic concentration in the resin phase. Two-site continuous model describes adequately the experimental data. Moreover the values of apparent protonation constants (as adjustable parameters found by non-linear regression) are very near to the apparent constants evaluated by a Donnan model assuming the intrinsic constants in resin phase equal to the equilibrium constants in aqueous solution of ADA and considering the amphoteric nature of active sites for the evaluation of counter-ion concentration in the resin phase. Copper removal outlined the strong affinity of the active groups of the resin for this ion in solution compared to the S. natans biomass according to the complexation constants between aminodiacetic and mono-carboxylic groups and copper ions.

Effects of quantitative electroencephalography based neurofeedback training on autonomous regulations in patients with alcohol use disorder.

PubMed

Ko, Sangjin; Park, Wanju

2018-06-02

The study investigated whether neurofeedback training can normalize the excessive high-beta and low alpha waves indicative of hyperarousal, and subsequently improve autonomous regulation based on the self-determination theory in alcohol use disorders. A nonequivalent control group pretest-posttest design was used. Data were collected using self-report questionnaires from 36 Korean inpatients who met the Alcohol Use Disorder Identification Test in Korea criteria. Data were collected from quantitative electroencephalography to assess alpha (8-12 Hz) and high-beta (21-30 Hz) waves for hyperarousal. The questionnaires included Basic Psychological Need Satisfaction scales that assessed autonomy, competence, and relatedness, and the Alcohol Abstinence Self-Efficacy Scale and Treatment Self-Regulation Questionnaire. The experimental group underwent 10 sessions of neurofeedback training over four weeks. Data were analyzed using the chi-squared, Mann-Whitney U, and Wilcoxon signed-rank tests. In the experimental group, the alpha wave was increased in 15 of 19 sites and high-beta waves were decreased in 15 of 19 sites, but this difference was not significant. However, high-beta waves were increased in 15 of 19 sites in the control group, with seven sites (Fz, Cz, Pz, Fp2, F4, C4, and P4) showing significant increases. The experimental group showed a significant increase in basic psychological need satisfaction, alcohol abstinence self-efficacy, and self-regulation compared with the control group. Neurofeedback training is recommended for improving autonomous regulation in alcohol use disorder as a nursing intervention. However, for significantly attenuating hyperarousal through brain wave correction, it may be necessary to increase the number of neurofeedback sessions. Copyright © 2018. Published by Elsevier B.V.

Towards photonic quantum simulation of ground states of frustrated Heisenberg spin systems

PubMed Central

Ma, Xiao-song; Dakić, Borivoje; Kropatschek, Sebastian; Naylor, William; Chan, Yang-hao; Gong, Zhe-xuan; Duan, Lu-ming; Zeilinger, Anton; Walther, Philip

2014-01-01

Photonic quantum simulators are promising candidates for providing insight into other small- to medium-sized quantum systems. Recent experiments have shown that photonic quantum systems have the advantage to exploit quantum interference for the quantum simulation of the ground state of Heisenberg spin systems. Here we experimentally characterize this quantum interference at a tuneable beam splitter and further investigate the measurement-induced interactions of a simulated four-spin system by comparing the entanglement dynamics using pairwise concurrence. We also study theoretically a four-site square lattice with next-nearest neighbor interactions and a six-site checkerboard lattice, which might be in reach of current technology. PMID:24394808

Growth of nitrogen-doped graphene on copper: Multiscale simulations

NASA Astrophysics Data System (ADS)

Gaillard, P.; Schoenhalz, A. L.; Moskovkin, P.; Lucas, S.; Henrard, L.

2016-02-01

We used multiscale simulations to model the growth of nitrogen-doped graphene on a copper substrate by chemical vapour deposition (CVD). Our simulations are based on ab-initio calculations of energy barriers for surface diffusion, which are complemented by larger scale Kinetic Monte Carlo (KMC) simulations. Our results indicate that the shape of grown doped graphene flakes depends on the temperature and deposition flux they are submitted during the process, but we found no significant effect of nitrogen doping on this shape. However, we show that nitrogen atoms have a preference for pyridine-like sites compared to graphite-like sites, as observed experimentally.

Time-Dependent Material Properties of Shotcrete: Experimental and Numerical Study.

PubMed

Neuner, Matthias; Cordes, Tobias; Drexel, Martin; Hofstetter, Günter

2017-09-11

A new experimental program, focusing on the evolution of the Young's modulus, uniaxial compressive strength, shrinkage and creep of shotcrete is presented. The laboratory tests are, starting at very young ages of the material, conducted on two different types of specimens sampled at the site of the Brenner Basetunnel. The experimental results are evaluated and compared to other experiments from the literature. In addition, three advanced constitutive models for shotcrete, i.e., the model by Meschke, the model by Schädlich and Schweiger, and the model by Neuner et al., are validated on the basis of the test data, and the capabilities of the models to represent the observed shotcrete behavior are assessed. Hence, the gap between the the outdated experimental data on shotcrete available in the literature on the one hand and the nowadays available advanced shotcrete models, on the other hand, is closed.

Structural and vibrational analyses of new potential anticancer drug 2-(phenylmethyl)-2-azaspiro[5.11]heptadecane-1,3,7-trione

NASA Astrophysics Data System (ADS)

Vitnik, Željko J.; Popović-Đorđević, Jelena B.; Vitnik, Vesna D.

2017-06-01

The establishment of the most stable structures of 2-(phenylmethyl)-2-azaspiro[5.11]heptadecane-1,3,7-trione, potential anticancer and antimicrobial drug has been investigated in this work. A detailed interpretation of experimental and calculated IR, UV and NMR spectra were reported. The equilibrium geometry, harmonic vibrational frequencies and electronic properties have been investigated with Density Functional Theory using B3LYP/6-311++G(d,p) method. The scaled theoretical wavenumber showed very good agreement with the experimental values. The charge transfer in the molecule was confirmed with NBO analysis. Ultraviolet-visible spectrum was calculated using TD-DFT method and compared with experimental spectrum. The calculated energy and oscillator strength well reproduce the experimental data. The molecular electrostatic potential surface map portrays potential binding sites of the title molecule.

Soil microbes shift C-degrading activity along an ambient and experimental nitrogen gradient

NASA Astrophysics Data System (ADS)

Moore, J.; Frey, S. D.

2017-12-01

The balance between soil carbon (C) accumulation and decomposition is determined in large part by the activity and biomass of soil microbes, and yet their sensitivity to global changes remains unresolved. Atmospheric nitrogen (N) deposition has increased 22% (for NH4+) in the last two decades despite initiation of the Clean Air Act. Nitrogen deposition alters ecosystem processes by changing nutrient availability and soil pH, creating physiologically stressful environments that select for stress tolerant microbes. The functional fungal community may switch from domination by species with traits associated with decomposition via oxidative enzymes to traits associated with stress tolerance if global changes push fungal physiological limits. We examined changes in soil microbial activity across seven sites representing a gradient of ambient atmospheric N deposition, and five of these sites also had long-term N addition experiments. We measured changes in abundance of decomposition genes and C mineralization rates as indicators of microbial activity. We expected microbes to be less active with high N deposition, thus decreasing C mineralization rates. We found that C mineralization rates declined with total N deposition (ambient plus experimental additions), and this decline was more sensitive to N deposition where it occurred naturally compared to experimental treatments. Carbon mineralization declined by 3% in experimentally fertilized soils compared to 10% in control soils for every 1 kg/ha/y increase in ambient N deposition. Thus, microbes exposed to ambient levels of N deposition (2 - 12 kg/ha/y) had a stronger response than those exposed to fertilized soils (20 - 50 kg/ha/y). Long-term experimental N-addition seems to have selected for a microbial community that is tolerant of high N deposition. In sum, we provide evidence that soil microbial activity responded to N deposition, and may shift over time to a community capable of tolerating environmental change.

Carbon dioxide flux and net primary production of a boreal treed bog: Responses to warming and water-table-lowering simulations of climate change

NASA Astrophysics Data System (ADS)

Munir, T. M.; Perkins, M.; Kaing, E.; Strack, M.

2015-02-01

Midlatitude treed bogs represent significant carbon (C) stocks and are highly sensitive to global climate change. In a dry continental treed bog, we compared three sites: control, recent (1-3 years; experimental) and older drained (10-13 years), with water levels at 38, 74 and 120 cm below the surface, respectively. At each site we measured carbon dioxide (CO2) fluxes and estimated tree root respiration (Rr; across hummock-hollow microtopography of the forest floor) and net primary production (NPP) of trees during the growing seasons (May to October) of 2011-2013. The CO2-C balance was calculated by adding the net CO2 exchange of the forest floor (NEff-Rr) to the NPP of the trees. From cooler and wetter 2011 to the driest and the warmest 2013, the control site was a CO2-C sink of 92, 70 and 76 g m-2, the experimental site was a CO2-C source of 14, 57 and 135 g m-2, and the drained site was a progressively smaller source of 26, 23 and 13 g CO2-C m-2. The short-term drainage at the experimental site resulted in small changes in vegetation coverage and large net CO2 emissions at the microforms. In contrast, the longer-term drainage and deeper water level at the drained site resulted in the replacement of mosses with vascular plants (shrubs) on the hummocks and lichen in the hollows leading to the highest CO2 uptake at the drained hummocks and significant losses in the hollows. The tree NPP (including above- and below-ground growth and litter fall) in 2011 and 2012 was significantly higher at the drained site (92 and 83 g C m-2) than at the experimental (58 and 55 g C m-2) and control (52 and 46 g C m-2) sites. We also quantified the impact of climatic warming at all water table treatments by equipping additional plots with open-top chambers (OTCs) that caused a passive warming on average of ~ 1 °C and differential air warming of ~ 6 °C at midday full sun over the study years. Warming significantly enhanced shrub growth and the CO2 sink function of the drained hummocks (exceeding the cumulative respiration losses in hollows induced by the lowered water level × warming). There was an interaction of water level with warming across hummocks that resulted in the largest net CO2 uptake at the warmed drained hummocks. Thus in 2013, the warming treatment enhanced the sink function of the control site by 13 g m-2, reduced the source function of the experimental by 10 g m-2 and significantly enhanced the sink function of the drained site by 73 g m-2. Therefore, drying and warming in continental bogs is expected to initially accelerate CO2-C losses via ecosystem respiration, but persistent drought and warming is expected to restore the peatland's original CO2-C sink function as a result of the shifts in vegetation composition and productivity between the microforms and increased NPP of trees over time.

Remaining Sites Verification Package for the 100-F-54 Animal Farm Pastures, Waste Site Reclassification Form 2008-015

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

J. M. Capron

2008-04-17

The 100-F-54 waste site, part of the 100-FR-2 Operable Unit, is the soil associated with the former pastures for holding domestic farm animals used in experimental toxicology studies. Evaluation of historical information resulted in identification of the experimental animal farm pastures as having potential residual soil contamination due to excrement from experimental animals. The 100-F-54 animal farm pastures confirmatory sampling results support a reclassification of this site to No Action. The current site conditions achieve the remedial action objectives and the corresponding remedial action goals established in the Remaining Sites ROD. The results of confirmatory sampling show that residual contaminantmore » concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.« less

[Reducing stress levels and anxiety in primary-care physicians through training and practice of a mindfulness meditation technique].

PubMed

Franco Justo, Clemente

2010-11-01

To check the effectiveness of a mindfulness development meditation technique on stress and anxiety in a group of primary-care physicians. Quasi-experimental with pretest/posttest/follow-up measurements in a control group and an experimental group. SITE: University of Almeria. 38 primary-care physicians enrolled in a Teaching Aptitude Course (CAP). An experimental group and a control group were formed with 19 participants in each. The experimental group took a psycho-educational meditation program for training and practice in mindfulness. The Perceived Stress Scale (PSS), the Strain Questionnaire and the State-Trait Anxiety Questionnaire were used to measure stress and anxiety levels. A comparative statistical analysis was performed using the Mann-Whitney non-parametric U test, finding a significant reduction in all the primary-care physician stress and anxiety variables in the experimental group compared to the control group in pretest-posttest and follow-up tests. The results of this study support the effectiveness of mindfulness development meditation techniques in decreasing stress and anxiety in primary-care physicians. Nevertheless, the study shows various limitations that would have to be corrected in successive studies to bring more validity to the results. Copyright © 2009 Elsevier España, S.L. All rights reserved.

The problem of site variation within red pine provenance experiments

Treesearch

Mark J. Holst

1966-01-01

In spite of care taken in the selection of site and experimental design of provenance experiments, site heterogenity within the experimental area may be more complex than was anticipated when the experiment was established. The present paper describes a problem of this nature encountered in a red pine (Pinus resinosa Ait.) provenance experiment at...

Tree-Ring Cation Response to Experimental Watershed Acidification in West Virginia and Maine

Treesearch

David R. DeWalle; Jeffrey S. Tepp; Bryan R. Swistock; William E. Sharpe; Pamela J. Edwards

1999-01-01

The impact of experimental watershed acidfication on xylem cation chemistry was evaluated in eight tree species at two sites in West Virginia (Clover Run and Fernow) and one site in Maine (Bear Brook). All sites had received regular additions of (NH4) SO4 equivalent to twice the ambient annual wet plus dry atmospheric...

A Cross-Site Intervention in Chinese Rural Migrants Enhances HIV/AIDS Knowledge, Attitude and Behavior

PubMed Central

Li, Ning; Li, Xiaomei; Wang, Xueliang; Shao, Jin; Dou, Juanhua

2014-01-01

Background: With the influx of rural migrants into urban areas, the spread of HIV has increased significantly in Shaanxi Province (China). Migrant workers are at high risk of HIV infection due to social conditions and hardships (isolation, separation, marginalization, barriers to services, etc.). Objective: We explored the efficacy of a HIV/AIDS prevention and control program for rural migrants in Shaanxi Province, administered at both rural and urban sites. Methods: Guidance concerning HIV/AIDS prevention was given to the experimental group (266 migrants) for 1 year by the center of disease control, community health agencies and family planning department. The intervention was conducted according to the HIV/AIDS Prevention Management Manual for Rural Migrants. A control group of migrants only received general population intervention. The impact of the intervention was evaluated by administering HIV/AIDS knowledge, attitudes and sexual behavior (KAB) questionnaires after 6 and 12 months. Results: In the experimental group; 6 months of intervention achieved improvements in HIV/AIDS related knowledge. After 12 months; HIV/AIDS-related knowledge reached near maximal scores. Attitude and most behaviors scores were significantly improved. Moreover; the experimental group showed significant differences in HIV-AIDS knowledge; attitude and most behavior compared with the control group. Conclusions: The systematic long-term cross-site HIV/AIDS prevention in both rural and urban areas is a highly effective method to improve HIV/AIDS KAB among rural migrants. PMID:24762671

Validation of ozone response functions for annual Mediterranean pasture species using close-to-field-conditions experiments.

PubMed

González-Fernández, Ignacio; Sanz, Javier; Calvete-Sogo, Héctor; Elvira, Susana; Alonso, Rocío; Bermejo-Bermejo, Victoria

2017-12-01

Ozone (O 3 ) critical levels have been established under the Long-Range Transboundary Air Pollution Convention to assess the risk of O 3 effects in European vegetation. A recent review study has led to the development of O 3 critical levels for annual Mediterranean pasture species using plants growing in well-watered pots at a coastal site and under low levels of competition. However, uncertainties remain in the extrapolation of the O 3 sensitivity of these species under natural conditions. The response of two O 3 -sensitive annual Mediterranean pasture Trifolium species at the coastal site was compared with the response of the same species growing at a continental site, in natural soil and subject to water-stress and inter-specific competition, representing more closely their natural habitat. The slopes of exposure- and dose-response relationships derived for the two sites showed differences in the response to O 3 between sites attributed to differences in environmental growing conditions, growing medium and the level of inter-specific competition, but the effect of the individual factors could not be assessed separately. Dose-based O 3 indices partially explained differences due to environmental growing conditions between sites. The slopes showed that plants were more sensitive to O 3 at the continental site, but homogeneity of slopes tests revealed that results from both experimental sites may be combined. Although more experimental data considering complex inter-specific competition situations and the effect of important interactive factors such as nitrogen would be needed, these results confirm the validity of applying the current flux-based O 3 critical level under close to natural growing conditions. The AOT40-based O 3 critical level derived at the coastal site was also considered a suitable risk indicator in close to natural growing conditions in the absence of soil moisture limitations on plant growth.

When linearity prevails over hierarchy in syntax

PubMed Central

Willer Gold, Jana; Arsenijević, Boban; Batinić, Mia; Becker, Michael; Čordalija, Nermina; Kresić, Marijana; Leko, Nedžad; Marušič, Franc Lanko; Milićev, Tanja; Milićević, Nataša; Mitić, Ivana; Peti-Stantić, Anita; Stanković, Branimir; Šuligoj, Tina; Tušek, Jelena; Nevins, Andrew

2018-01-01

Hierarchical structure has been cherished as a grammatical universal. We use experimental methods to show where linear order is also a relevant syntactic relation. An identical methodology and design were used across six research sites on South Slavic languages. Experimental results show that in certain configurations, grammatical production can in fact favor linear order over hierarchical structure. However, these findings are limited to coordinate structures and distinct from the kind of production errors found with comparable configurations such as “attraction” errors. The results demonstrate that agreement morphology may be computed in a series of steps, one of which is partly independent from syntactic hierarchy. PMID:29288218

Mg co-ordination with potential carcinogenic molecule acrylamide: Spectroscopic, computational and cytotoxicity studies

NASA Astrophysics Data System (ADS)

Singh, Ranjana; Mishra, Vijay K.; Singh, Hemant K.; Sharma, Gunjan; Koch, Biplob; Singh, Bachcha; Singh, Ranjan K.

2018-03-01

Acrylamide (acr) is a potential toxic molecule produced in thermally processed food stuff. Acr-Mg complex has been synthesized chemically and characterized by spectroscopic techniques. The binding sites of acr with Mg were identified by experimental and computational methods. Both experimental and theoretical results suggest that Mg coordinated with the oxygen atom of Cdbnd O group of acr. In-vitro cytotoxicity studies revealed significant decrease in the toxic level of acr-Mg complex as compared to pure acr. The decrease in toxicity on complexation with Mg may be a useful step for future research to reduce the toxicity of acr.

Atomistic simulation and XAS investigation of Mn induced defects in Bi{sub 12}TiO{sub 20}

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

Rezende, Marcos V dos S.; Santos, Denise J.; Jackson, Robert A.

2016-06-15

This work reports an investigation of the valence and site occupancy of Mn dopants in Bi{sub 12}TiO{sub 20} (BTO: Mn) host using X-ray Absorption (XAS) and atomistic simulation techniques based on energy minimisation. X-ray Absorption Near Edge Structure (XANES) at the Mn K-edges gave typical results for Mn ions with mixed valences of 3+ and 4+. Extended X-ray Absorption Fine Structure (EXAFS) results indicated that Mn ions are probably substituted at Ti sites. Atomistic simulation was performed assuming the incorporation of Mn{sup 2+}, Mn{sup 3+} and Mn{sup 4+} ions at either Bi{sup 3+} or Ti{sup 4+} sites, and the resultsmore » were compared to XANES and EXAFS measurements. Electrical conductivity for pure and doped samples was used to evaluate the consistency of the proposed model. - Graphical abstract: The structure of Bi{sub 12}TiO{sub 20} (BTO). Display Omitted - Highlights: • Pure and Mn-doped Bi{sub 12}TiO{sub 20} samples were studied by experimental techniques combined with atomistic simulation. • Good agreement between experimental and simulation results was obtained. • XANES results suggest a mixture of 3+ and 4+ valences for Mn, occupying the Ti4+ site in both cases. • Charge compensation by holes is most energetically favoured, explaining the enhancement observed in AC dark conductivity.« less

Evaluation of the source area of rooftop scalar measurements in London, UK using wind tunnel and modelling approaches.

NASA Astrophysics Data System (ADS)

Brocklehurst, Aidan; Boon, Alex; Barlow, Janet; Hayden, Paul; Robins, Alan

2014-05-01

The source area of an instrument is an estimate of the area of ground over which the measurement is generated. Quantification of the source area of a measurement site provides crucial context for analysis and interpretation of the data. A range of computational models exists to calculate the source area of an instrument, but these are usually based on assumptions which do not hold for instruments positioned very close to the surface, particularly those surrounded by heterogeneous terrain i.e. urban areas. Although positioning instrumentation at higher elevation (i.e. on masts) is ideal in urban areas, this can be costly in terms of installation and maintenance costs and logistically difficult to position instruments in the ideal geographical location. Therefore, in many studies, experimentalists turn to rooftops to position instrumentation. Experimental validations of source area models for these situations are very limited. In this study, a controlled tracer gas experiment was conducted in a wind tunnel based on a 1:200 scale model of a measurement site used in previous experimental work in central London. The detector was set at the location of the rooftop site as the tracer was released at a range of locations within the surrounding streets and rooftops. Concentration measurements are presented for a range of wind angles, with the spread of concentration measurements indicative of the source area distribution. Clear evidence of wind channeling by streets is seen with the shape of the source area strongly influenced by buildings upwind of the measurement point. The results of the wind tunnel study are compared to scalar concentration source areas generated by modelling approaches based on meteorological data from the central London experimental site and used in the interpretation of continuous carbon dioxide (CO2) concentration data. Initial conclusions will be drawn as to how to apply scalar concentration source area models to rooftop measurement sites and suggestions for their improvement to incorporate effects such as channeling.

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

Howe, Joshua D.; Morelock, Cody R.; Jiao, Yang

We present a joint computational and experimental study of Mg–Ni-MOF-74 and Mg–Cd-MOF-74 to gain insight into the mixing of metals and understand how metal mixing affects the structure of the undercoordinated open-metal sites. Our calcula tions predict that metal mixing is energetically preferred in these materials. Recent experimental work has demonstrated that Mg–Ni-MOF-74 shows a much greater surface area retention in the presence of water than Mg-MOF-74. To probe this effect, we study H2O adsorption in Mg–Ni-MOF-74, finding that the adsorption en ergetics and electronic structure do not change significantly at the metal sites when compared to Mg-MOF-74 and Ni-MOF-74,more » respectively. We conclude that the in creased stability of Mg–Ni-MOF-74 is a result of a M–O bond length distortion in mixed-metal MOF-74, consistent with recent work on the stability of MOF-74 under water exposure.« less

Understanding structure, metal distribution, and water adsorption in mixed-metal MOF-74

DOE PAGES

Howe, Joshua D.; Morelock, Cody R.; Jiao, Yang; ...

2016-11-30

We present a joint computational and experimental study of Mg–Ni-MOF-74 and Mg–Cd-MOF-74 to gain insight into the mixing of metals and understand how metal mixing affects the structure of the undercoordinated open-metal sites. Our calculations predict that metal mixing is energetically preferred in these materials. Recent experimental work has demonstrated that Mg–Ni-MOF-74 shows a much greater surface area retention in the presence of water than Mg-MOF-74. To probe this effect, we study H 2O adsorption in Mg–Ni-MOF-74, finding that the adsorption energetics and electronic structure do not change significantly at the metal sites when compared to Mg-MOF-74 and Ni-MOF-74, respectively.more » Lastly, we conclude that the increased stability of Mg–Ni-MOF-74 is a result of a M–O bond length distortion in mixed-metal MOF-74, consistent with recent work on the stability of MOF-74 under water exposure.« less

Real-time soft error rate measurements on bulk 40 nm SRAM memories: a five-year dual-site experiment

NASA Astrophysics Data System (ADS)

Autran, J. L.; Munteanu, D.; Moindjie, S.; Saad Saoud, T.; Gasiot, G.; Roche, P.

2016-11-01

This paper reports five years of real-time soft error rate experimentation conducted with the same setup at mountain altitude for three years and then at sea level for two years. More than 7 Gbit of SRAM memories manufactured in CMOS bulk 40 nm technology have been subjected to the natural radiation background. The intensity of the atmospheric neutron flux has been continuously measured on site during these experiments using dedicated neutron monitors. As the result, the neutron and alpha component of the soft error rate (SER) have been very accurately extracted from these measurements, refining the first SER estimations performed in 2012 for this SRAM technology. Data obtained at sea level evidence, for the first time, a possible correlation between the neutron flux changes induced by the daily atmospheric pressure variations and the measured SER. Finally, all of the experimental data are compared with results obtained from accelerated tests and numerical simulation.

Selective Interareal Synchronization through Gamma Frequency Differences and Slower-Rhythm Gamma Phase Reset.

PubMed

Burwick, Thomas; Bouras, Alexandros

2017-03-01

The communication-through-coherence (CTC) hypothesis states that a sending group of neurons will have a particularly strong effect on a receiving group if both groups oscillate in a phase-locked ("coherent") manner (Fries, 2005 , 2015 ). Here, we consider a situation with two visual stimuli, one in the focus of attention and the other distracting, resulting in two sites of excitation at an early cortical area that project to a common site in a next area. Taking a modeler's perspective, we confirm the workings of a mechanism that was proposed by Bosman et al. ( 2012 ) in the context of providing experimental evidence for the CTC hypothesis: a slightly higher gamma frequency of the attended sending site compared to the distracting site may cause selective interareal synchronization with the receiving site if combined with a slow-rhythm gamma phase reset. We also demonstrate the relevance of a slightly lower intrinsic frequency of the receiving site for this scenario. Moreover, we discuss conditions for a transition from bottom-up to top-down driven phase locking.

Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L.

PubMed Central

Wang, Mengxing; Liu, Hui; Ge, Lingqiao; Xing, Guangwei; Wang, Meng; Weining, Song; Nie, Xiaojun

2016-01-01

RNA editing is an important way to convert cytidine (C) to uridine (U) at specific sites within RNA molecules at a post-transcriptional level in the chloroplasts of higher plants. Although it has been systematically studied in many plants, little is known about RNA editing in the wheat D genome donor Aegilops tauschii L. Here, we investigated the chloroplast RNA editing of Ae. tauschii and compared it with other wheat relatives to trace the evolution of wheat. Through bioinformatics prediction, a total of 34 C-to-U editing sites were identified, 17 of which were validated using RT-PCR product sequencing. Furthermore, 60 sites were found by the RNA-Seq read mapping approach, 24 of which agreed with the prediction and six were validated experimentally. The editing sites were biased toward tCn or nCa trinucleotides and 5′-pyrimidines, which were consistent with the flanking bases of editing sites of other seed plants. Furthermore, the editing events could result in the alteration of the secondary structures and topologies of the corresponding proteins, suggesting that RNA editing might impact the function of target genes. Finally, comparative analysis found some evolutionarily conserved editing sites in wheat and two species-specific sites were also obtained. This study is the first to report on RNA editing in Aegilops tauschii L, which not only sheds light on the evolution of wheat from the point of view of RNA editing, but also lays a foundation for further studies to identify the mechanisms of C-to-U alterations. PMID:28042823

Monitoring tobacco brand websites to understand marketing strategies aimed at tobacco product users and potential users.

PubMed

Escobedo, Patricia; Cruz, Tess Boley; Tsai, Kai-Ya; Allem, Jon-Patrick; Soto, Daniel W; Kirkpatrick, Matthew G; Pattarroyo, Monica; Unger, Jennifer B

2017-09-11

Limited information exists about strategies and methods used on brand marketing websites to transmit pro-tobacco messages to tobacco users and potential users. This study compared age verification methods, themes, interactive activities and links to social media across tobacco brand websites. This study examined 12 tobacco brand websites representing four tobacco product categories: cigarettes, cigar/cigarillos, smokeless tobacco, and e-cigarettes. Website content was analyzed by tobacco product category and data from all website visits (n = 699) were analyzed. Adult smokers (n=32) coded websites during a one-year period, indicating whether or not they observed any of 53 marketing themes, seven interactive activities, or five external links to social media sites. Most (58%) websites required online registration before entering, however e-cigarette websites used click-through age verification. Compared to cigarette sites, cigar/cigarillo sites were more likely to feature themes related to "party" lifestyle, and e-cigarette websites were much more likely to feature themes related to harm reduction. Cigarette sites featured greater levels of interactive content compared to other tobacco products. Compared to cigarette sites, cigar/cigarillo sites were more likely to feature activities related to events and music. Compared to cigarette sites, both cigar and e-cigarette sites were more likely to direct visitors to external social media sites. Marketing methods and strategies normalize tobacco use by providing website visitors with positive themes combined with interactive content, and is an area of future research. Moreover, all tobacco products under federal regulatory authority should be required to use more stringent age verification gates. Findings indicate the Food and Drug Administration (FDA) should require brand websites of all tobacco products under its regulatory authority use more stringent age verification gates by requiring all visitors be at least 18 years of age and register online prior to entry. This is important given that marketing strategies may encourage experimentation with tobacco or deter quit attempts among website visitors. Future research should examine the use of interactive activities and social media on a wide variety of tobacco brand websites as interactive content is associated with more active information processing. © The Author 2017. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Concentration-Dependent Multiple Binding Sites on Saliva-Treated Hydroxyapatite for Streptococcus sanguis

PubMed Central

Gibbons, R. J.; Moreno, E. C.; Etherden, I.

1983-01-01

The influence of bacterial cell concentration on estimates of the number of binding sites and the affinity for the adsorption of a strain of Streptococcus sanguis to saliva-treated hydroxyapatite was determined, and the possible presence of multiple binding sites for this organism was tested. The range of concentrations of available bacteria varied from 4.7 × 106 to 5,960 × 106 cells per ml. The numbers of adsorbed bacteria increased over the entire range tested, but a suggestion of a break in an otherwise smooth adsorption isotherm was evident. Values for the number of binding sites and the affinity varied considerably depending upon the range of available bacterial concentrations used to estimate them; high correlation coefficients were obtained in all cases. The use of low bacterial cell concentrations yielded lower values for the number of sites and much higher values for the affinity constant than did the use of high bacterial cell concentrations. When data covering the entire range of bacterial concentrations were employed, values for the number of sites and the affinity were similar to those obtained by using only high bacterial cell concentrations. The simplest explanation for these results is that there are multiple binding sites for S. sanguis on saliva-treated hydroxyapatite surfaces. When present in low concentration, the streptococci evidently attach to more specific high-affinity sites which become saturated when higher bacterial concentrations are employed. The possibility of multiple binding sites was substantiated by comparing estimates of the adsorption parameters from a computer-simulated isotherm with those derived from the experimentally generated isotherm. A mathematical model describing bacterial adsorption to binary binding sites was further evidence for the existence of at least two classes of binding sites for S. sanguis. Far fewer streptococci adsorbed to experimental pellicles prepared from saliva depleted of bacterial aggregating activity when low numbers of streptococci were used, but the magnitude of this difference was considerably less when high streptococcal concentrations were employed. This suggests an association between salivary components which possess bacterial-aggregating activity and bacterial adsorption to high-affinity specific binding sites on saliva-treated hydroxyapatite surfaces. PMID:6822416

Influencing care in acute myocardial infarction: a randomized trial comparing 2 types of intervention.

PubMed

Sauaia, A; Ralston, D; Schluter, W W; Marciniak, T A; Havranek, E P; Dunn, T R

2000-01-01

The purpose of this study was to evaluate performance feedback delivered by on-site presentations compared to mailed feedback on improving acute myocardial infarction (AMI) care. We used a randomized trial including 18 hospitals nested within the Cooperative Cardiovascular Project. Patients comprised AMI Medicare patients admitted before (n = 929, 1994 and 1995) and after intervention (n = 438, 1996). Control hospitals received written feedback by mail. The experimental intervention group received a presentation led by a cardiologist and a quality improvement specialist. We assessed the proportion of patients receiving appropriate AMI care before and after the intervention. Both univariate and multivariate analyses demonstrated no effect of the intervention in increasing the proportion of patients who received reperfusion, aspirin, beta-blockers, or angiotensin-converting enzyme inhibitors. On-site feedback presentations were not associated with a larger improvement in AMI care compared to the mailed feedback. Other interventions, such as opinion leaders and patient-directed interventions, may be necessary in order to improve the care of AMI patients.

First-principles analysis of structural and opto-electronic properties of indium tin oxide

NASA Astrophysics Data System (ADS)

Tripathi, Madhvendra Nath; Shida, Kazuhito; Sahara, Ryoji; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

2012-05-01

Density functional theory (DFT) and DFT + U (DFT with on-site Coulomb repulsion corrections) calculations have been carried out to study the structural and opto-electronic properties of indium tin oxide (ITO) for both the oxidized and reduced environment conditions. Some of the results obtained by DFT calculations differ from the experimental observations, such as uncertain indication for the site preference of tin atom to replace indium atom at b-site or d-site, underestimation of local inward relaxation in the first oxygen polyhedra around tin atom, and also the improper estimation of electronic density of states and hence resulting in an inappropriate optical spectra of ITO. These discrepancies of theoretical outcomes with experimental observations in ITO arise mainly due to the underestimation of the cationic 4d levels within standard DFT calculations. Henceforth, the inclusion of on-site corrections within DFT + U framework significantly modifies the theoretical results in better agreement to the experimental observations. Within this framework, our calculations show that the indium b-site is preferential site over d-site for tin atom substitution in indium oxide under both the oxidized and reduced conditions. Moreover, the calculated average inward relaxation value of 0.16 Å around tin atom is in good agreement with the experimental value of 0.18 Å. Furthermore, DFT + U significantly modify the electronic structure and consequently induce modifications in the calculated optical spectra of ITO.

On Directional Measurement Representation in Orbit Determination

DTIC Science & Technology

2016-09-13

representations. The three techniques are then compared experimentally for a geostationary and a low Earth orbit satellite using simulated data to evaluate their...Earth Orbit (LEO) and a Geostationary Earth Orbit (GEO) satellite. Section IV discusses the results from the numerical simulations and finally Section V... Geostationary Earth Orbit (GEO) satellite with the initial orbital parameters shown in Table 1. Different ground sites are used for the LEO and ahttps

Experimental evidence of impacts of an invasive parakeet on foraging behavior of native birds

PubMed Central

2014-01-01

Resource competition is one potential behavioral mechanism by which invasive species can impact native species, but detecting this competition can be difficult due to the interactions that variable environmental conditions can have on species behavior. This is particularly the case in urban habitats where the disturbed environment can alter natural behavior from that in undisturbed habitats. The rose-ringed parakeet (Psittacula krameri), is an increasingly common invasive species, predominantly associated with large urban centers. Using an experimental approach, we tested the behavioral responses of native garden birds in response to the presence of a rose-ringed parakeet versus the presence of a similarly sized and dominant native bird, the great spotted woodpecker (Dendrocopos major). Parakeet presence significantly reduced feeding rates and increased vigilance among native birds compared with our control treatments. Of visits made by native birds in the presence of a parakeet, feeding was more likely to occur in sites within the parakeet range compared with sites outside, suggesting some habituation of native birds has occurred following prior exposure to parakeets but overall foraging behavior is still disrupted. The results of our study suggest that nonnative species can have complex and subtle impacts on native fauna and show that a nonnative competitor can impact native species simply through their presence near resources. PMID:24822022

Experimental evidence of impacts of an invasive parakeet on foraging behavior of native birds.

PubMed

Peck, Hannah L; Pringle, Henrietta E; Marshall, Harry H; Owens, Ian P F; Lord, Alexa M

2014-05-01

Resource competition is one potential behavioral mechanism by which invasive species can impact native species, but detecting this competition can be difficult due to the interactions that variable environmental conditions can have on species behavior. This is particularly the case in urban habitats where the disturbed environment can alter natural behavior from that in undisturbed habitats. The rose-ringed parakeet ( Psittacula krameri ), is an increasingly common invasive species, predominantly associated with large urban centers. Using an experimental approach, we tested the behavioral responses of native garden birds in response to the presence of a rose-ringed parakeet versus the presence of a similarly sized and dominant native bird, the great spotted woodpecker ( Dendrocopos major ). Parakeet presence significantly reduced feeding rates and increased vigilance among native birds compared with our control treatments. Of visits made by native birds in the presence of a parakeet, feeding was more likely to occur in sites within the parakeet range compared with sites outside, suggesting some habituation of native birds has occurred following prior exposure to parakeets but overall foraging behavior is still disrupted. The results of our study suggest that nonnative species can have complex and subtle impacts on native fauna and show that a nonnative competitor can impact native species simply through their presence near resources.

High contaminant loads in Lake Apopka's riparian wetland disrupt gene networks involved in reproduction and immune function in largemouth bass.

PubMed

Martyniuk, Christopher J; Doperalski, Nicholas J; Prucha, Melinda S; Zhang, Ji-Liang; Kroll, Kevin J; Conrow, Roxanne; Barber, David S; Denslow, Nancy D

2016-09-01

Lake Apopka (FL, USA) has elevated levels of some organochlorine pesticides in its sediments and a portion of its watershed has been designated a US Environmental Protection Agency Superfund site. This study assessed reproductive endpoints in Florida largemouth bass (LMB) (Micropterus salmoides floridanus) after placement into experimental ponds adjacent to Lake Apopka. LMB collected from a clean reference site (DeLeon Springs) were stocked at two periods of time into ponds constructed in former farm fields on the north shore of the lake. LMB were stocked during early and late oogenesis to determine if there were different effects of contamination on LMB that may be attributed to their reproductive stage. LMB inhabiting the ponds for ~4months had anywhere from 2 to 800 times higher contaminant load for a number of organochlorine pesticides (e.g. p, p'-DDE, methoxychlor) compared to control animals. Gonadosomatic index and plasma vitellogenin were not different between reproductively-stage matched LMB collected at reference sites compared to those inhabiting the ponds. However, plasma 17β-estradiol was lower in LMB inhabiting the Apopka ponds compared to ovary stage-matched LMB from the St. Johns River, a site used as a reference site. Sub-network enrichment analysis revealed that genes related to reproduction (granulosa function, oocyte development), endocrine function (steroid metabolism, hormone biosynthesis), and immune function (T cell suppression, leukocyte accumulation) were differentially expressed in the ovaries of LMB placed into the ponds. These data suggest that (1) LMB inhabiting the Apopka ponds showed disrupted reproduction and immune responses and that (2) gene expression profiles provided site-specific information by discriminating LMB from different macro-habitats. Copyright © 2016 Elsevier Inc. All rights reserved.

The use of Forest Service experimental forests and ranges for long-term research on invasive species

Treesearch

Ralph Holiday Crawford; Gary W. Miller

2010-01-01

The 81 experimental forests and ranges (EFRs) research sites make the U.S. Department of Agriculture (USDA), Forest Service unique among land management agencies. The EFRs were established for conducting applied research that serves as a basis for managing forests and rangelands. Most EFR research sites have long histories of experimentation and research that provide...

Environmental constraints on the invasion of Triadica sebifera in the eastern United States: an experimental field assessment.

PubMed

Pattison, Robert R; Mack, Richard N

2009-01-01

Identifying the environmental constraints that affect the distribution of an invasive species is fundamental to its effective control. Triadica sebifera (Chinese tallow tree) has invaded the southeastern United States, but its potential for further range and habitat extension has been unresolved. We explored experimentally environmental factors in macro- and microhabitats that affect its persistence at five widely separated sites along the Atlantic seaboard of the United States and at two sites inland; three sites occur well beyond the tree's current range. At each site, seeds and young vegetative plants (0.5-0.65 m tall) of T. sebifera were placed in four microhabitats (closed-canopy upland, closed-canopy lowland, open-canopy upland, and open-canopy lowland). Plant growth, leaf CO(2) assimilation rates, leaf N concentrations and delta(13)C ratios, and stem water potential were measured for two growing seasons. Percent seed germination was consistently higher in open-canopy microhabitats and lowest at northern and inland sites. T. sebifera grew in all open-canopy microhabitats, even 300-500 km beyond its current distribution. Plant growth in closed-canopy habitats was lower, attributable to lower carbon gain per unit leaf area in shaded compared with open-canopy environments, especially at northern and inland sites. Neither competition, other than canopy shade, nor grazing was a key constraint on distribution at any scale. Our results demonstrate that T. sebifera is dispersal limited at landscape scales but limited locally by dispersal and overstory shade; it has yet to occupy the full extent of its new range in North America. Quantifying environmental factors both within and well beyond a species' current range can effectively highlight the limits on its distribution.

Substantial enhancement in intrinsic coercivity on M-type strontium hexaferrite through the increase in magneto-crystalline anisotropy by co-doping of group-V and alkali elements

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

Ahn, Kyunghan, E-mail: kyunghan.ahn@samsung.com; Ryu, Byungki; Korolev, Dmitry

2013-12-09

The effect of d{sup 1} impurity doping in Sr-hexaferrite (SrM) on the magnetic anisotropy is investigated. First-principles calculations revealed that group-V elements (V, Nb) are stabilized with co-doping of alkali elements. Na{sup 1+}/K{sup 1+} doping at Sr{sup 2+}-site is found to be critical to form the d{sup 1} impurities at Fe-site. Experimentally, Na–V doped SrM shows the intrinsic coercivity of ∼5.4 kOe, which is ∼300% enhancement compared to undoped SrM and comparable value to La–Co co-doped SrM. Finally, the spin-orbit coupling from non-vanishing angular momentum of d{sup 1} impurity in SrM should be a main factor for such a substantialmore » improvement of intrinsic coercivity.« less

Second-Year Results of an Obesity Prevention Program at The Dow Chemical Company

PubMed Central

Roemer, Enid C.; Pei, Xiaofei; Short, Meghan E.; Tabrizi, Maryam J.; Wilson, Mark G.; DeJoy, David M.; Craun, Beth A.; Tully, Karen J.; White, John M.; Baase, Catherine M.

2010-01-01

Objective Evaluate innovative, evidence-based approaches to organizational/supportive environmental interventions aimed at reducing the prevalence of obesity among Dow employees after two years of implementation. Methods A quasi-experimental study design compared outcomes for two levels of intervention intensity to a control group. Propensity scores were used to weight baseline differences between intervention and control subjects. Difference-in-differences methods and multi-level modeling were used to control for individual and site-level confounders. Results Intervention participants maintained their weight and BMI while control participants gained 1.3 pounds and increased their BMI values by 0.2 over two years. Significant differences in blood pressure and cholesterol values were observed when comparing intervention employees to controls. At higher intensity sites, improvements were more pronounced. Conclusions Environmental interventions at the workplace can support weight management and risk reduction after two years. PMID:20190646

Expression of Haemophilus ducreyi Collagen Binding Outer Membrane Protein NcaA Is Required for Virulence in Swine and Human Challenge Models of Chancroid

PubMed Central

Fulcher, Robert A.; Cole, Leah E.; Janowicz, Diane M.; Toffer, Kristen L.; Fortney, Kate R.; Katz, Barry P.; Orndorff, Paul E.; Spinola, Stanley M.; Kawula, Thomas H.

2006-01-01

Haemophilus ducreyi, the etiologic agent of the sexually transmitted genital ulcer disease chancroid, has been shown to associate with dermal collagen fibers within infected skin lesions. Here we describe NcaA, a previously uncharacterized outer membrane protein that is important for H. ducreyi collagen binding and host colonization. An H. ducreyi strain lacking the ncaA gene was impaired in adherence to type I collagen but not fibronectin (plasma or cellular form) or heparin. The mutation had no effect on serum resistance or binding to HaCaT keratinocytes or human foreskin fibroblasts in vitro. Escherichia coli expressing H. ducreyi NcaA bound to type I collagen, demonstrating that NcaA is sufficient to confer collagen attachment. The importance of NcaA in H. ducreyi pathogenesis was assessed using both swine and human experimental models of chancroid. In the swine model, 20% of lesions from sites inoculated with the ncaA mutant were culture positive for H. ducreyi 7 days after inoculation, compared to 73% of wild-type-inoculated sites. The average number of CFU recovered from mutant-inoculated lesions was also significantly reduced compared to that recovered from wild-type-inoculated sites at both 2 and 7 days after inoculation. In the human challenge model, 8 of 30 sites inoculated with wild-type H. ducreyi progressed to the pustular stage, compared to 0 of 30 sites inoculated with the ncaA mutant. Together these results demonstrate that the collagen binding protein NcaA is required for H. ducreyi infection. PMID:16622201

Expression of Haemophilus ducreyi collagen binding outer membrane protein NcaA is required for virulence in swine and human challenge models of chancroid.

PubMed

Fulcher, Robert A; Cole, Leah E; Janowicz, Diane M; Toffer, Kristen L; Fortney, Kate R; Katz, Barry P; Orndorff, Paul E; Spinola, Stanley M; Kawula, Thomas H

2006-05-01

Haemophilus ducreyi, the etiologic agent of the sexually transmitted genital ulcer disease chancroid, has been shown to associate with dermal collagen fibers within infected skin lesions. Here we describe NcaA, a previously uncharacterized outer membrane protein that is important for H. ducreyi collagen binding and host colonization. An H. ducreyi strain lacking the ncaA gene was impaired in adherence to type I collagen but not fibronectin (plasma or cellular form) or heparin. The mutation had no effect on serum resistance or binding to HaCaT keratinocytes or human foreskin fibroblasts in vitro. Escherichia coli expressing H. ducreyi NcaA bound to type I collagen, demonstrating that NcaA is sufficient to confer collagen attachment. The importance of NcaA in H. ducreyi pathogenesis was assessed using both swine and human experimental models of chancroid. In the swine model, 20% of lesions from sites inoculated with the ncaA mutant were culture positive for H. ducreyi 7 days after inoculation, compared to 73% of wild-type-inoculated sites. The average number of CFU recovered from mutant-inoculated lesions was also significantly reduced compared to that recovered from wild-type-inoculated sites at both 2 and 7 days after inoculation. In the human challenge model, 8 of 30 sites inoculated with wild-type H. ducreyi progressed to the pustular stage, compared to 0 of 30 sites inoculated with the ncaA mutant. Together these results demonstrate that the collagen binding protein NcaA is required for H. ducreyi infection.

Assessing the acidity of high silica chabazite H-SSZ-13 by FTIR using CO as molecular probe: Comparison with H-SAPO-34.

PubMed

Bordiga, Silvia; Regli, Laura; Cocina, Donato; Lamberti, Carlo; Bjørgen, Morten; Lillerud, Karl Petter

2005-02-24

Zeolitic materials based on the chabazite topology, such as H-SAPO-34, possess unique shape-selectivity properties for converting methanol into light olefins. In addition to the topology, zeolite acidity is inherently linked to catalyst activity and selectivity. The acidic properties of high silica chabazite (H-SSZ-13) have attracted much attention in the past decade because the material represents an idealized model system having one acidic site per cage. Conclusions drawn so far have essentially been founded on quantum chemical methods. An experimentally based benchmark of the acidity of H-SSZ-13 has hitherto not been available. In this work, transmission FTIR spectroscopy provides a description of the different acidic sites of H-SSZ-13 by using CO as molecular probe at 70 K. The results demonstrate that H-SSZ-13 is a strongly Brønsted acidic material, essentially having two distinct families of acidic sites. In contrast to numerous preceding reports, we find it fundamental to consider proton distributions among all four possible sites, and do not delimit the interpretations to only two sites. The present data consistently suggest the most abundant family of protons to have three members being located on different crystalline positions on the eight-membered-ring window giving access to the chabazite cage. Consequently, these protons are exposed to two neighboring cages. The second, and less abundant family, is constituted by only one site that is situated on the six-membered ring defining the top/bottom of the barrel-shaped chabazite cage. This proton is therefore only exposed to one cage and requires a higher CO pressure to form adducts. Toward CO, both families of sites possess the same acidity. Parallel experiments were also carried out for the isostructural and commercially important H-SAPO-34 having an equal density of acidic sites. This is the first attempt to directly compare, on an experimental basis, the acidity of these two materials.

Fauna-associated changes in chemical and biochemical properties of soil.

PubMed

Tripathi, G; Sharma, B M

2006-12-01

To study the impacts of abundance of woodlice, termites, and mites on some functional aspects of soil in order to elucidate the specific role of soil fauna in improving soil fertility in desert. Fauna-rich sites were selected as experimental sites and adjacent areas were taken as control. Soil samples were collected from both sites. Soil respiration was measured at both sites. The soil samples were sent to laboratory, their chemical and biochemical properties were analyzed. Woodlice showed 25% decrease in organic carbon and organic matter as compared to control site. Whereas termites and mites showed 58% and 16% decrease in organic carbon and organic matter. In contrast, available nitrogen (nitrate and ammonical both) and phosphorus exhibited 2-fold and 1.2-fold increase, respectively. Soil respiration and dehydrogenase activity at the sites rich in woodlice, termites and mites produced 2.5-, 3.5- and 2-fold increases, respectively as compared to their control values. Fauna-associated increase in these biological parameters clearly reflected fauna-induced microbial activity in soil. Maximum decrease in organic carbon and increase in nitrate-nitrogen and ammonical-nitrogen, available phosphorus, soil respiration and dehydrogenase activity were produced by termites and minimum by mites reflecting termite as an efficient soil improver in desert environment. The soil fauna-associated changes in chemical (organic carbon, nitrate-nitrogen, ammonical-nitrogen, phosphorus) and biochemical (soil respiration, dehydrogenase activity) properties of soil improve soil health and help in conservation of desert pedoecosystem.

Does the Police-Monitored CCTV Scheme Really Matter on Crime Reduction? A Quasi-Experimental Test in Taiwan's Taipei City.

PubMed

Lai, Yung-Lien; Sheu, Chuen-Jim; Lu, Yi-Fen

2018-06-01

Although numerous public closed-circuit television (CCTV) initiatives have been implemented at varying levels in Taiwan's cities and counties, systematic evaluations of these crime reduction efforts have been largely overlooked. To address this void, a quasi-experimental evaluation research project was designed to assess the effect of police-monitored CCTV on crime reduction in Taipei City for a period of 54 months, including data for both before and after camera installation dates. A total of 40 viewsheds within a 100-m (328 feet) radius were selected as research sites to observe variations in four types of crime incidents that became known to police during the January 2008 to June 2012 period. While crime incidents occurring in both the target and control sites were reduced in frequency after CCTV installation, results derived from time-series analysis indicated that the monitoring had no significant effect on the reduction of property crime incidents with the sole exception of robbery. With respect to the effects of comparing target and control sites, the average Crime Reduction Quotient (CRQ) was 0.36, suggesting that CCTV has an overall marginal yet noteworthy influence. Viewed broadly, however, the police-installed CCTV system in Taipei City did not appear to be as efficient as one would expect. Conversely, cameras installed in some observation sites proved to be significantly more effective than cameras in other sites. As a recommendation, future researchers should identify how particular micro-level attributes may lead to CCTV cameras working more effectively, thereby optimizing location choices where monitoring will prove to be most productive.

Overview of topographic effects based on experimental observations: meaning, causes and possible interpretations

NASA Astrophysics Data System (ADS)

Massa, Marco; Barani, Simone; Lovati, Sara

2014-06-01

The paper presents an extensive review of topographic effects in seismology taking into account the knowledge of 40 yr of scientific literature. An overview of topographic effects based on experimental observations and numerical modelling is presented with the aim of highlighting meaning and causes of these phenomena as well as possible correlations between site response (fundamental frequency, amplification level) and geometrical (width and shape ratio of a relief) parameters. After a thorough summary of topographic effects, the paper focuses on five Italian sites whose seismic response is potentially affected by local morphology, as already evidenced by previous studies. In this study, seismic data recorded at these sites are analysed computing directional spectral ratios both in terms of horizontal to vertical spectral ratios (HVSRs) and, wherever possible, in terms of standard spectral ratios (SSRs). The analysis lead to the conclusion that wavefield tends to be polarized along a direction perpendicular to the main axis of a topographic irregularity, direction along which ground motion amplification is maximum. The final section of the article compares and contrasts different spectral ratio techniques in order to examine their effectiveness and reliability in detecting topographic effects. The examples discussed in the paper show that site responses based on HVSRs rather than SSR measurements could lead to misinterpretation of ground response results, both as concerns the definition of the site fundamental frequency and amplification level. Results and findings of this work will be used as starting point to discuss the influence of topographic effects on ground motion prediction equations and regulations for design. These topics will be discussed in the companion article.

Random Decrement Method and Modeling H/V Spectral Ratios: An Application for Soft Shallow Layers Characterization

NASA Astrophysics Data System (ADS)

Song, H.; Huerta-Lopez, C. I.; Martinez-Cruzado, J. A.; Rodriguez-Lozoya, H. E.; Espinoza-Barreras, F.

2009-05-01

Results of an ongoing study to estimate the ground response upon weak and moderate earthquake excitations are presented. A reliable site characterization in terms of its soil properties and sub-soil layer configuration are parameters required in order to do a trustworthy estimation of the ground response upon dynamic loads. This study can be described by the following four steps: (1) Ambient noise measurements were collected at the study site where a bridge was under construction between the cities of Tijuana and Ensenada in Mexico. The time series were collected using a six channels recorder with an ADC converter of 16 bits within a maximum voltage range of ± 2.5 V, the recorder has an optional settings of: Butterworth/Bessel filters, gain and sampling rate. The sensors were a three orthogonal component (X, Y, Z) accelerometers with a sensitivity of 20 V/g, flat frequency response between DC to 200 Hz, and total full range of ±0.25 of g, (2) experimental H/V Spectral Ratios were computed to estimate the fundamental vibration frequency at the site, (3) using the time domain experimental H/V spectral ratios as well as the original recorded time series, the random decrement method was applied to estimate the fundamental frequency and damping of the site (system), and (4) finally the theoretical H/V spectral ratios were obtained by means of the stiffness matrix wave propagation method.. The interpretation of the obtained results was then finally compared with a geotechnical study available at the site.

Educational Web-Based Intervention for High School Students to Increase Knowledge and Promote Positive Attitudes toward Organ Donation

ERIC Educational Resources Information Center

Vinokur, Amiram D.; Merion, Robert M.; Couper, Mick P.; Jones, Eleanor G.; Dong, Yihui

2006-01-01

A sample of 490 high school students from 81 schools in Michigan participated in an experiment in which they were randomly assigned to either a control or an experimental Web site. The experimental Web site provided exposure to educational material about the process of organ donation and organ transplantation. The control Web site provided…

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.

PubMed

Wang, Yanan; Song, Jiangning; Marquez-Lago, Tatiana T; Leier, André; Li, Chen; Lithgow, Trevor; Webb, Geoffrey I; Shen, Hong-Bin

2017-07-18

Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies have identified type-specific target substrates; however, the complete repertoire of MMP substrates remains uncharacterized. Indeed, computational prediction of substrate-cleavage sites associated with MMPs is a challenging problem. This holds especially true when considering MMPs with few experimentally verified cleavage sites, such as for MMP-2, -3, -7, and -8. To fill this gap, we propose a new knowledge-transfer computational framework which effectively utilizes the hidden shared knowledge from some MMP types to enhance predictions of other, distinct target substrate-cleavage sites. Our computational framework uses support vector machines combined with transfer machine learning and feature selection. To demonstrate the value of the model, we extracted a variety of substrate sequence-derived features and compared the performance of our method using both 5-fold cross-validation and independent tests. The results show that our transfer-learning-based method provides a robust performance, which is at least comparable to traditional feature-selection methods for prediction of MMP-2, -3, -7, -8, -9 and -12 substrate-cleavage sites on independent tests. The results also demonstrate that our proposed computational framework provides a useful alternative for the characterization of sequence-level determinants of MMP-substrate specificity.

The EUROSEISTEST Experimental Test Site in Greece

NASA Astrophysics Data System (ADS)

Pitilakis, K.; Manos, G.; Raptakis, D.; Anastasiadis, A.; Makra, K.; Manakou, M.

2009-04-01

The European experimental site EUROSEISTEST has been established since 1993 in the epicentral area of the June 20th 1978 earthquake (40.8˚ N, 23.2˚ E, Ms 6.5, Imax VIII+ MSK, Papazachos et al., 1979), located in the active tectonic Mygdonian basin, 30km NNE from Thessaloniki, Greece. Euroseistest has been funded by the European Commission - Directorate General for Research and Development under the framework of consecutive EC research projects (EuroseisTest, EuroseisMod and Eurroseisrisk). It is specially designed and dedicated to conduct experimental and theoretical studies on site effects, soil and site characterization and soil-foundation-structure interaction phenomena. The geological, geophysical and geotechnical conditions of the Euroseistest valley (Mygdonian graben) is very well constrained through numerous in situ campaigns and laboratory tests. The permanent accelerometric network comprises 21 digital 3D stations, including vertical arrays down to 200m (schist bedrock), covering a surface of about 100 sq Km. The site is also covered by a permanent seismological network. A number of high quality recordings, from temporary and permanent arrays, gave the possibility to perform advanced experimental and theoretical studies on site effects (e.g. Raptakis et al., 1998; Pitilakis et al., 1999; Raptakis et al., 2000; Chávez-García et al., 2000; Makra, 2000; Makra et al., 2001 & 2005). The main advantage of Euroseistest is the detailed knowledge of the 3D geological-geotechnical structure of the basin (Manakou, 2007) and its dense permanent accelerometric network. For this reason the site has been recently selected by CEA to validate and check the advanced numerical codes to be used in Cadarache ITER project. Besides the study of site effects, Euroseistest offers interesting possibilities to study SSI problems through two model structures (scaled 1:3). A 6-storey building and a bridge pier, which have been constructed and instrumented in the centre of the valley, close to the main vertical array. Euroseistest experimental site provides a rigorous high quality database comprising geological, geotechnical, geophysical and seismological data, as well as a valuable set of experimental facilities to study both experimentally and theoretically complex site effects and soil-foundation structure problems. Numerous publications have been already released (see in the web page). It is foreseen to strengthen in the near future the possibility to provide wide access to European and international scientific community to perform joint studies, to validate their models and to improve or develop new ones.

The influence of surface roughness and solution concentration on pool boiling process in Diethanolamine aqueous solution

NASA Astrophysics Data System (ADS)

Khoshechin, Mohsen; Salimi, Farhad; Jahangiri, Alireza

2018-04-01

In this research, the effect of surface roughness and concentration of solution on bubble departing frequency and nucleation site density for pool boiling of water/diethanolamine (DEA) binary solution were investigated experimentally. In this investigation, boiling heat transfer coefficient, bubble departing frequency and nucleation site density have been experimentally investigated in various concentrations and heat fluxes. Microstructured surfaces with a wide range of well-defined surface roughness were fabricated, and a heat flux between 1.5-86 kW/m2 was achieved under atmospheric conditions. The Results indicated that surface roughness and concentration of solution increase the bubble departing frequency and nucleation site density with increasing heat flux. The boiling heat transfer coefficient in mixtures of water/DEA increases with increasing concentration of DEA in water. The experimental results were compared with predictions of several used correlations in the literatures. Results showed that the boiling heat transfer coefficients of this case study are much higher than the predicted values by major existing correlations and models. The excellent agreement for bubble departing frequency found between the models of Jackob and Fritz (1966) and experimental data and also the nucleation site density were in close agreement with the model of Paul (1983) data. f bubble departure frequency, 1/s or Hz N Number of nucleation sites per area per time R c Minimum cavity size, m D c critical diameter, m g gravitational acceleration, m/s2 ρ density, kg/m3 T temperature, °c ΔT temperature difference, °c d d vapor bubble diameter, m h fg enthalpy of vaporization, J/kg R Roughness, μm Ja Jakob number cp specific heat, J/kg °c Pr Prandtl number Ar Archimedes number h Heat transfer coefficient, J/(m2 °c) tg time it takes to grow a bubble, s q/A heat flux (kW/m2) tw time required to heat the layer, s gc Correction coefficient of incompatible units R a Surface roughness A heated surface area d departure ONB onset of nucleate boiling w surface wall s saturation v vapor l liquid θ groove angle (o) γ influence parameter of heating surface material σ surface tension, N/m.

Mineralogical effects of an experimental forest fire on a goethite/ferrihydrite soil - an attempt to solve the presence of hematite and maghemite in topsoils in a temperate region

NASA Astrophysics Data System (ADS)

Nørnberg, Per; Vendelboe, Anders L.; Gunnlaugsson, Haraldur P.; Merrison, Jonathan P.; Finster, Kai; Jensen, Svend K.

2010-05-01

Isolated soil spots, a few square metres in size, as red as Munsell colour 10R ¾ are found in Denmark. These spots are well known as places that have been exposed to fire. However, a long-standing unresolved puzzle is the presence of extended areas with high iron content (8-40 %) where goethite and ferrihydrite are present in the topsoil along with hematite and maghemite. Hematite and particularly maghemite would normally not be expected to occur under the temperate humid Danish climate, but be interpreted as the result of high temperature as found in tropical areas or after forest fires. However, a body of evidence argues against these sites having been exposed to fire. In an attempt to get closer to an explanation of this iron mineralogy, an experimental forest fire was produced. The results showed a clear mineralogical zonation down to 10 cm depth. This was not observed at the natural sites, which contained a uniform mixture of goethite/ferrihydrite, hematite and maghemite down to 20 cm depth. The experimental forest fire furthermore left charcoal and ashes at the topsoil, produced high pH and decreased organic matter content, all of which is in contrast to the natural sites. Physical and chemical date as well as XRD, Mössbauer spectroscopic data and TEM micrographs from the sites will be presented. The conclusion from this work is that the mineralogy of these sites is not consistent with exposure to fire, but may rather result from long term transformation within a reducing environment, possibly involving microorganisms. References: Nørnberg, P., Vendelboe, A.L., Gunnlaugsson, H.P., Merrison, J.P., Finster, K., Jensen, S.K. 2009 Mineralogy after an experimental forest fire on Quaternary soil goethite, compared with a hematite, maghemite, goethite containing topsoil. Clay Minerals, 44, 239-247. Nørnberg, P., Gunnlaugsson, H.P., Merrison, J.P., Vendelboe, A.L. 2009: Salten Skov I: A Martian dust analogue. Planetary and Space Science, 57, 628-631. Nørnberg, P., Schwertmann, U., Stanjek, C.B., An¬dersen, T., Gunnlaugsson, H.P. 2004: Mineralogy of Quaternary iron oxide rich formations in Denmark.Clay Minerals, 39, 85-98.

Patient-centered evaluation of microsurgical management of gingival recession using coronally advanced flap with platelet-rich fibrin or amnion membrane: A comparative analysis

PubMed Central

Agarwal, Sumit Kumar; Jhingran, Rajesh; Bains, Vivek Kumar; Srivastava, Ruchi; Madan, Rohit; Rizvi, Iram

2016-01-01

Objective: To evaluate the efficacy of coronally advanced flap (CAF) procedure under microsurgical approach for the management of Miller's Class I and II gingival recession defects with the use of either platelet-rich fibrin (PRF) or amnion membrane (AM) in comparison to CAF alone. Materials and Methods: A total of 45 sites with Miller's Class I or II gingival recession defect were randomly distributed for: Experimental Group I (CAF with PRF) sites (n = 15) which were treated with the microsurgical approach using CAF along with PRF; experimental Group II (CAF with AM) sites (n = 15) were treated with the microsurgical approach using CAF along with AM; control Group III (CAF alone) sites (n = 15) were treated with the microsurgical approach using CAF alone. Vertical gingival recession (VGR), horizontal gingival recession (HGR), gingival thickness (GT) (using transgingival probing [TGP] and ultrasonography [USG]) and patients’ response and acceptance were documented at baseline, 3 months and 6 months after surgical interventions. Results: CAF alone and in combination with PRF or AM, were effective techniques for root coverage with average VGR values of 1.47 ± 0.92 mm (56%), 0.67 ± 1.23 mm (36%) and 0.60 ± 1.06 mm (33%) in Group I (CAF with PRF), Group II (CAF with AM), and Group III (CAF alone), respectively. Complete coverage (100%) was obtained in 33.3% sites of Group I (CAF with PRF), 26.6% sites of Group II (CAF with AM) and 13.3% in Group III (CAF alone). Patients’ response and acceptance for surgical treatment modality in terms of patient esthetic score and decrease in hypersensitivity score was highest for Group I (CAF with PRF), whereas patient comfort score was highest for Group II (CAF with AM). At 6 months follow-up, significant increase in GT measurements (using TGP and USG) in Group I (CAF with PRF), whereas, nonsignificant increase for Group II (CAF with AM) and no change or decrease for Group III (CAF alone) as compared to baseline was observed. Conclusion: The present study observed enhancement in root coverage when PRF or AM are used in conjunction with CAF as compared to CAF alone. These results are based on 6-month follow-up. Therefore, the long-term evaluation may be necessary to appreciate the clinical effect of autologous PRF and AM. PMID:27011751

Chloroperoxidase-catalyzed oxidation of 4,6-dimethyldibenzothiophene as dimer complexes: evidence for kinetic cooperativity.

PubMed

Torres, Eduardo; Aburto, Jorge

2005-05-15

A sigmoidal kinetic behavior of chloroperoxidase for the oxidation of 4,6-dimethyldibenzothiophene (4,6-DMDBT) in water-miscible organic solvent is for the first time reported. Kinetics of 4,6-DMDBT oxidation showed a cooperative profile probably due to the capacity of chloroperoxidase to recognize a substrate dimer (pi-pi dimer) in its active site. Experimental evidence is given for dimer formation and its presence in the active site of chloroperoxidase. The kinetic data were adjusted for a binding site able to interact with either monomer or dimer substrates, producing a cooperative model describing a one-site binding of two related species. Determination of kinetics constants by iterative calculations of possible oxidation paths of 4,6-DMDBT suggests that kinetics oxidation of dimer substrate is preferred when compared to monomer oxidation. Steady-state fluorometry of substrate in the absence and presence of chloroperoxidase, described by the spectral center of mass, supports this last conclusion.

Application of remote sensing for prediction and detection of thermal pollution, phase 2

NASA Technical Reports Server (NTRS)

Veziroglu, T. N.; Lee, S. S.

1975-01-01

The development of a predictive mathematical model for thermal pollution in connection with remote sensing measurements was continued. A rigid-lid model has been developed and its application to far-field study has been completed. The velocity and temperature fields have been computed for different atmospheric conditions and for different boundary currents produced by tidal effects. In connection with the theoretical work, six experimental studies of the two sites in question (Biscayne Bay site and Hutchinson Island site) have been carried out. The temperature fields obtained during the tests at the Biscayne Bay site have been compared with the predictions of the rigid-lid model and these results are encouraging. The rigid-lid model is also being applied to near-field study. Preliminary results for a simple case have been obtained and execution of more realistic cases has been initiated. The development of a free-surface model also been initiated. The governing equations have been formulated and the computer programs have been written.

Comparative safety, immunogenicity, and efficacy of several anti‐H5N1 influenza experimental vaccines in a mouse and chicken models (Testing of killed and live H5 vaccine)

PubMed Central

Gambaryan, Alexandra S.; Lomakina, Natalia F.; Boravleva, Elizaveta Y.; Kropotkina, Ekaterina A.; Mashin, Vadim V.; Krasilnikov, Igor V.; Klimov, Alexander I.; Rudenko, Larisa G.

2011-01-01

Please cite this paper as: Gambaryan et al. (2011) Comparative safety, immunogenicity, and efficacy of several anti‐H5N1 influenza experimental vaccines in a mouse and chicken models. Parallel testing of killed and live H5 vaccine. Influenza and Other Respiratory Viruses 6(3), 188–195. Objective  Parallel testing of inactivated (split and whole virion) and live vaccine was conducted to compare the immunogenicity and protective efficacy against homologous and heterosubtypic challenge by H5N1 highly pathogenic avian influenza virus. Method  Four experimental live vaccines based on two H5N1 influenza virus strains were tested; two of them had hemagglutinin (HA) of A/Vietnam/1203/04 strain lacking the polybasic HA cleavage site, and two others had hemagglutinins from attenuated H5N1 virus A/Chicken/Kurgan/3/05, with amino acid substitutions of Asp54/Asn and Lys222/Thr in HA1 and Val48/Ile and Lys131/Thr in HA2 while maintaining the polybasic HA cleavage site. The neuraminidase and non‐glycoprotein genes of the experimental live vaccines were from H2N2 cold‐adapted master strain A/Leningrad/134/17/57 (VN‐Len and Ku‐Len) or from the apathogenic H6N2 virus A/Gull/Moscow/3100/2006 (VN‐Gull and Ku‐Gull). Inactivated H5N1 and H1N1 and live H1N1 vaccine were used for comparison. All vaccines were applied in a single dose. Safety, immunogenicity, and protectivity against the challenge with HPAI H5N1 virus A/Chicken/Kurgan/3/05 were estimated. Results  All experimental live H5 vaccines tested were apathogenic as determined by weight loss and conferred more than 90% protection against lethal challenge with A/Chicken/Kurgan/3/05 infection. Inactivated H1N1 vaccine in mice offered no protection against challenge with H5N1 virus, while live cold‐adapted H1N1 vaccine reduced the mortality near to zero level. Conclusions  The high yield, safety, and protectivity of VN‐Len and Ku‐Len made them promising strains for the production of inactivated and live vaccines against H5N1 viruses. PMID:21951678

AmeriFlux US-Wkg Walnut Gulch Kendall Grasslands

DOE Data Explorer

Scott, Russell [United States Department of Agriculture

2016-01-01

This is the AmeriFlux version of the carbon flux data for the site US-Wkg Walnut Gulch Kendall Grasslands. Site Description - This site is located in a small, intensively-studied, experimental watershed within USDA-ARS's Walnut Gulch Experimental Watershed. Eddy covariance measurements of energy, water and CO2 fluxes began in the spring of 2004, though meteorological (including Bowen ratio) and hydrological measurements are available much further back.

Long-term monitoring sites and trends at the Marcell Experimental Forest. Chapter 2.

Treesearch

Stephen D. Sebestyen; Carrie Dorrance; Donna M. Olson; Elon S. Verry; Randall K. Kolka; Art E. Elling; Richard Kyllander

2011-01-01

The MEF is one of few long-term research programs on the hydrology and ecology of undrained peatlands in boreal forests. No other site in the Experimental Forest and Range Network of the Forest Service and few sites around the globe have studied the hydrology and biogeochemistry of peatland watersheds with the intensity or longevity as on the MEF. In this chapter, we...

On the molecular structure, vibrational spectra, HOMO-LUMO, molecular electrostatic potential, UV-Vis, first order hyperpolarizability, and thermodynamic investigations of 3-(4-chlorophenyl)-1-(1yridine-3-yl) prop-2-en-1-one by quantum chemistry calculations

NASA Astrophysics Data System (ADS)

Rahmani, Rachida; Boukabcha, Nourdine; Chouaih, Abdelkader; Hamzaoui, Fodil; Goumri-Said, Souraya

2018-03-01

A recent experimental study has allowed synthesis of a new organic nonlinear optical material 3-(4-chlorophenyl)-1-(pyridin-3-yl)prop-2-en-1-one(CPP) with a high second harmonic generation efficiency. We apply density functional theory (DFT, GGA and B3LYP) and Hartree-Fock (HF) methods to calculate the vibrational wavenumbers. They are assigned with by using the potential energy distribution method. The calculated first hyperpolarizability of the title compound is comparable with the reported values of similar derivatives and 25 times that of the standard NLO material urea. The HOMO-LUMO calculations lead to consider GGA-PBE as the best functional to determine the electronic band gap of CPP molecule. We complete this study with assignment of the vibrational modes and perform a comparison with the experimental results. The analysis of MEP map shows that the most reactive site of the CPP molecule is the site containing the oxygen atom. Furthermore, because of the enhancement of molecular vibration within the CPP molecule, the thermodynamic parameters are increasing with the increase of temperature. The FTIR, Raman and NMR spectra are calculated using DFT approach and corroborate the experimental available data.

NEVADA TEST SITE EXPERIMENTAL FARM: SUMMARY REPORT 1963-1981

EPA Science Inventory

This report summarizes the findings from experiments conducted at the Experimental Dairy Farm located on the Nevada Test Site. These experiments included the air-forage-cow-milk transport of the radioiodines, and the metabolism and milk transfer of other fission products and seve...

Comparison of two cannulation methods for assessment of intracavernosal pressure in a rat model

PubMed Central

Luo, Lianmin; Wang, Jiamin; Li, Ermao; Luo, Jintai; Liu, Luhao; Wan, ShawPong

2018-01-01

Intracavernous pressure (ICP) measurement is a well-established technique for assessing the erectile function, which was performed by cannulating either crus or shaft of the penis. However, there are no studies concerning the experimental performance of the two cannulation sites yet. The aim of this study was to compare the measuring outcomes using two different cannulation sites. To validate the capacity of our study, both normal and the castration-induced erectile dysfunction rat models were conducted. Fifty adult male Sprague-Dawley rats were randomized equally into two groups: an intact group and a castration group. Five rats from each group firstly underwent different stimulation parameters to detect the optimal erectile responses. The residual rats in each group were further assigned into two subgroups (n = 10 per subgroup) according to two different cannulation sites (crus or shaft of the corpus cavernosum). The ICP values were compared between groups after different interventions. The optimal parameters for mean maximum ICP were recorded at 2.5V and a frequency of 15 Hz. The rats under the two different cannulation sites tended to show similar ICP values in both the intact and the castration groups. However, the success rate in monitoring ICP was significantly higher in the groups cannulating into the shaft of the penis compared to the crus (100% vs. 70%; P = 0.02). Our data suggested that the method of cannulation into the penile shaft could serve as a better alternative for the ICP measurement in rats. PMID:29486011

Effects of an increase in population of sika deer on beetle communities in deciduous forests.

PubMed

Iida, Taichi; Soga, Masashi; Koike, Shinsuke

2016-01-01

The overabundance of large herbivores is now recognized as a serious ecological problem. However, the resulting ecological consequences remain poorly understood. The ecological effects of an increase in sika deer, Cervus nippon Temminck (Cervidae), on three insect groups of beetles was investigated: ground beetles (Carabidae), carrion beetles (Silphidae), and dung beetles (Scarabaeidae and Geotrupidae) on Nakanoshima Island, Hokkaido, northern Japan. We collected beetles on Nakanoshima Island (experimental site) and lakeshore areas (control site) and compared the species richness, abundance, diversity index, and community composition of beetles between the sites. Results showed that although both species diversity and abundance of carabid beetles were significantly higher at the lakeshore site, those of dung and carrion beetles were higher at the island site. It was additionally observed that abundance of larger carabid beetles was higher at the lakeshore site, whereas that of small-sized carabid beetles did not differ between the lakeshore and island sites. For dung beetles, abundance of smaller species was higher at the island site, whereas that of large species did not differ between the lakeshore and island sites. Abundance of two body sizes (small and large) of carrion beetles were both higher at the island site. Overall, the findings of this study demonstrated that an increase in deer population altered the insect assemblages at an island scale, suggesting further changes in ecosystem functions and services in this region.

Trout density and health in a stream with variable water temperatures and trace element concentrations: does a cold-water source attract trout to increased metal exposure?

USGS Publications Warehouse

Harper, D.D.; Farag, A.M.; Hogstr, C.; MacConnell, Elizabeth

2009-01-01

A history of hard-rock mining has resulted in elevated concentrations of heavy metals in Prickly Pear Creek (MT. USA). Remediation has improved water quality; however, dissolved zinc and cadmium concentrations still exceed U.S. Environmental Protection Agency water-quality criteria. Physical habitat, salmonid density, fish health, and water quality were assessed, and metal concentrations in fish tissues, biofilm, and macroinvertebrates were determined to evaluate the existing condition in the watershed. Cadmium, zinc, and lead concentrations in fish tissues, biofilm, and invertebrates were significantly greater than those at the upstream reference site and an experimental site farther downstream of the confluence. Fish densities were greatest, and habitat quality for trout was better, downstream of the confluence, where water temperatures were relatively cool (16??C). Measures of fish health (tissue metal residues, histology, metallothionein concentrations, and necropsies), however, indicate that the health of trout at this site was negatively affected. Trout were in colder but more contaminated water and were subjected to increased trace element exposures and associated health effects. Maximum water temperatures in Prickly Pear Creek were significantly lower directly below Spring Creek (16??C) compared to those at an experimental site 10 km downstream (26??C). Trout will avoid dissolved metals at concentrations below those measured in Prickly Pear Creek; however, our results suggest that the preference of trout to use cool water temperatures may supersede behaviors to avoid heavy metals. ?? 2009 SETAC.

One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections

PubMed Central

Mingo, Janire; Erramuzpe, Asier; Luna, Sandra; Aurtenetxe, Olaia; Amo, Laura; Diez, Ibai; Schepens, Jan T. G.; Hendriks, Wiljan J. A. J.; Cortés, Jesús M.; Pulido, Rafael

2016-01-01

Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis. PMID:27548698

Experimental evidence for route integration and strategic planning in wild capuchin monkeys.

PubMed

Janson, Charles H

2007-07-01

Both in captivity and the wild, primates are found to travel mostly to the nearest available resource, but they may skip over the closest resource and travel to more distant resources, which are often found to be more productive. This study examines the tradeoff between distance and reward in the foraging choices of one group of wild capuchin monkeys (Cebus apella nigritus) using feeding platforms in large-scale foraging experiments conducted over four years. Three feeding sites were arrayed in an oblique triangle, such that once the monkey group had chosen one site to feed, they had a choice between two remaining sites, a close one with less food and the other up to 2.3 times as far away but with more food. Sites were provisioned once per day. The capuchins generally chose the closer feeding site, even when the more distant site offered up to 12 times as much food. The distances to, rewards of, or various profitability measures applied to each alternative site individually did not explain the group's choices in ways consistent with foraging theory or principles of operant psychology. The group's site choices were predicted only by comparing efficiency measures of entire foraging pathways: (1) direct travel to the more rewarding distant site, versus (2) the longer 'detour' through the closer site on the way to the more distant one. The group chose the detour more often when the reward was larger and the added detour distance shorter. They appeared to be more sensitive to the absolute increase in detour distance than to the relative increase compared to the straight route. The qualitative and quantitative results agree with a simple rule: do not use the detour unless the energy gain from extra food outweighs the energy cost of extra travel. These results suggest that members of this group integrate information on spatial location, reward, and perhaps potential food competition in their choice of multi-site foraging routes, with important implications for social foraging.

Effect of diet-induced vitamin D deficiency on rotator cuff healing in a rat model.

PubMed

Angeline, Michael E; Ma, Richard; Pascual-Garrido, Cecilia; Voigt, Clifford; Deng, Xiang Hua; Warren, Russell F; Rodeo, Scott A

2014-01-01

Few studies have considered hormonal influences, particularly vitamin D, on healing. Vitamin D deficiency would have a negative effect on the structure of the healing tendon-bone interface in a rat model and would result in decreased tendon attachment strength. Controlled laboratory study. Vitamin D deficiency was induced in 28 male Sprague-Dawley rats using a specialized vitamin D-deficient diet and ultraviolet light restriction. Serum levels of vitamin D were measured after 6 weeks. These vitamin D-deficient animals (experimental group) plus 32 rats with normal vitamin D levels (controls) underwent unilateral detachment of the right supraspinatus tendon from the greater tuberosity of the humerus, followed by immediate repair using bone tunnel suture fixation. The animals were sacrificed at 2- and 4-week intervals after surgery for biomechanical analysis. A paired t test was used to compare serum vitamin D levels at day 0 and at 6 weeks. A nonparametric Mann-Whitney U test was used to compare load-to-failure and stiffness values between the experimental group and controls. Bone density and new bone formation at the tendon insertion site on the greater tuberosity were assessed with micro-computed tomography (CT). The organization of collagen tissue, new bone formation, vascularity at the tendon-bone interface, fibrocartilage at the tendon-bone interface, and collagen fiber continuity between the tendon and bone tissue were evaluated with safranin O and picrosirius red staining. Blood draws confirmed vitamin D deficiency at 6 weeks compared with time zero/baseline for rats in the experimental group (10.9 ng/mL vs 6.5 ng/mL, respectively; P < .001). Biomechanical testing demonstrated a significant decrease in load to failure in the experimental group compared with controls at 2 weeks (5.8 ± 2.0 N vs 10.5 ± 4.4 N, respectively; P < .006). There was no difference in stiffness at 2 weeks between the control and experimental groups. At 4 weeks, there was no significant difference in load to failure or stiffness between the control and experimental groups. Histological analysis showed less bone formation and less collagen fiber organization in the vitamin D-deficient specimens at 4 weeks as compared with controls. Micro-CT analysis showed no significant difference between groups for total mineral density and bone volume fraction of cortical, whole, or trabecular bone at 4 weeks. The biomechanical and histological data from this study suggest that low vitamin D levels may negatively affect early healing at the rotator cuff repair site. It is estimated that 1 billion people worldwide are vitamin D deficient. In the deficient state, acutely injured rotator cuffs may have a reduced ability for tendon healing. Further studies are needed to determine the exact mechanism by which vitamin D affects tendon healing and whether vitamin D supplementation can improve rotator cuff tendon healing and reduce the incidence of retears.

Experimental and theoretical study of Co sorption in clay montmorillonites

NASA Astrophysics Data System (ADS)

Gil Rebaza, A. V.; Montes, M. L.; Taylor, M. A.; Errico, L. A.; Alonso, R. E.

2018-03-01

Montmorillonite (MMT) clays are 2:1 layered structures which in natural state may allocate different hydrated cations such as M-nH2O (M = Na, Ca, Fe, etc) in its interlayer space. Depending on the capability for ion sorption, these materials are interesting for environmental remediation. In this work we experimentally study the Co sorption in a natural Na-MMT using UV-visible spectrometry and XRD on semi-oriented samples, and then analyze the sorption ability of this clay by means of ab initio calculation performed on pristine MMT. The structural properties of Na-MMT and Co-adsorbed MMT, and the hyperfine parameters at different atomic sites were analyzed and compared with the experimental ones for the first, and for the case of the hyperfine parameters, presented for the first time for the last. The theoretical predictions based on total energy considerations confirm that Co incorporation replacing Na is energetically favorable. Also, the basal spacing d001 experimentally obtained is well reproduced.

Comparison of hydrogen and deuterium adsorption on Pd(100).

PubMed

Gladys, M J; Kambali, I; Karolewski, M A; Soon, A; Stampfl, C; O'Connor, D J

2010-01-14

Low energy ion recoil spectroscopy is a powerful technique for the determination of adsorbate position on metal surfaces. In this study, this technique is employed to compare the adsorption sites of hydrogen and deuterium on Pd(100) by detection of either H or D recoil ions produced by Ne(+) bombardment. Comparisons of experimental and Kalypso simulated azimuthal yield distributions show that, at room temperature, both hydrogen isotopes are adsorbed in the fourfold hollow site of Pd(100), however, at different heights above the surface (H-0.20 A and D-0.25 A). The adsorbates remain in the hollow site at all temperatures up to 383 K even though they move up to 0.40-0.45 A above the surface. Density functional theory calculations show a similar coverage dependent adsorption height for both H and D and confirm a real difference between the H and D adsorption heights based on zero point energies.

4d Electronic structure analysis of ruthenium in the perovskite oxides by Ru K- and L-edge XAS.

PubMed

Kim, J Y; Hwang, S H; Kim, S J; Demazeau, G; Choy, J H; Shimada, H

2001-03-01

The 4d electronic structure of ruthenium in the perovskite oxides, La2MRuIVO6 (M = Zn, Mg, and Li) and Ba2YRuVO6, has been investigated by the Ru K-and L-edge XANES and EXAFS analyses. Such X-ray absorption spectroscopic results clarify that the RuIV (d4) and RuV (d3) ions are stabilized in nearly regular Oh site. Comparing the Ru L-edge XANES spectra of perovskites containing isovalent ruthenium, it has been found that the t2g state is mainly influenced by A site cation, whereas the eg is mainly affected by neighboring B site cation. The experimental EXAFS spectra in the range of R < or = approximately 4.5 A are well reproduced by ab-initio calculation based on crystallographic data, which supports the long-range structure presented by Rietveld refinement.

Controllable quantum dynamics of inhomogeneous nitrogen-vacancy center ensembles coupled to superconducting resonators

PubMed Central

Song, Wan-lu; Yang, Wan-li; Yin, Zhang-qi; Chen, Chang-yong; Feng, Mang

2016-01-01

We explore controllable quantum dynamics of a hybrid system, which consists of an array of mutually coupled superconducting resonators (SRs) with each containing a nitrogen-vacancy center spin ensemble (NVE) in the presence of inhomogeneous broadening. We focus on a three-site model, which compared with the two-site case, shows more complicated and richer dynamical behavior, and displays a series of damped oscillations under various experimental situations, reflecting the intricate balance and competition between the NVE-SR collective coupling and the adjacent-site photon hopping. Particularly, we find that the inhomogeneous broadening of the spin ensemble can suppress the population transfer between the SR and the local NVE. In this context, although the inhomogeneous broadening of the spin ensemble diminishes entanglement among the NVEs, optimal entanglement, characterized by averaging the lower bound of concurrence, could be achieved through accurately adjusting the tunable parameters. PMID:27627994

Scaffold-Based Delivery of Autologous Mesenchymal Stem Cells for Mandibular Distraction Osteogenesis: Preliminary Studies in a Porcine Model

PubMed Central

Sun, Zongyang; Tee, Boon Ching; Kennedy, Kelly S.; Kennedy, Patrick M.; Kim, Do-Gyoon; Mallery, Susan R.; Fields, Henry W.

2013-01-01

Purpose Bone regeneration through distraction osteogenesis (DO) is promising but remarkably slow. To accelerate it, autologous mesenchymal stem cells have been directly injected to the distraction site in a few recent studies. Compared to direct injection, a scaffold-based method can provide earlier cell delivery with potentially better controlled cell distribution and retention. This pilot project investigated a scaffold-based cell-delivery approach in a porcine mandibular DO model. Materials and Methods Eleven adolescent domestic pigs were used for two major sets of studies. The in-vitro set established methodologies to: aspirate bone marrow from the tibia; isolate, characterize and expand bone marrow-derived mesenchymal stem cells (BM-MSCs); enhance BM-MSC osteogenic differentiation using FGF-2; and confirm cell integration with a gelatin-based Gelfoam scaffold. The in-vivo set transplanted autologous stem cells into the mandibular distraction sites using Gelfoam scaffolds; completed a standard DO-course and assessed bone regeneration by macroscopic, radiographic and histological methods. Repeated-measure ANOVAs and t-tests were used for statistical analyses. Results From aspirated bone marrow, multi-potent, heterogeneous BM-MSCs purified from hematopoietic stem cell contamination were obtained. FGF-2 significantly enhanced pig BM-MSC osteogenic differentiation and proliferation, with 5 ng/ml determined as the optimal dosage. Pig BM-MSCs integrated readily with Gelfoam and maintained viability and proliferative ability. After integration with Gelfoam scaffolds, 2.4–5.8×107 autologous BM-MSCs (undifferentiated or differentiated) were transplanted to each experimental DO site. Among 8 evaluable DO sites included in the final analyses, the experimental DO sites demonstrated less interfragmentary mobility, more advanced gap obliteration, higher mineral content and faster mineral apposition than the control sites, and all transplanted scaffolds were completely degraded. Conclusion It is technically feasible and biologically sound to deliver autologous BM-MSCs to the distraction site immediately after osteotomy using a Gelfoam scaffold to enhance mandibular DO. PMID:24040314

A validation study of the Automated Self-Administered 24-Hour Dietary Recall for Children (ASA24-Kids) among 9 to 11-year-old youth

PubMed Central

Diep, Cassandra S.; Hingle, Melanie; Chen, Tzu-An; Dadabhoy, Hafza R.; Beltran, Alicia; Baranowski, Janice; Subar, Amy F.; Baranowski, Tom

2015-01-01

Background Valid methods of diet assessment are important for nutrition research and practice but can be difficult with children. Objective To validate ASA24-Kids-2012, a self-administered web-based 24-hour dietary recall (24hDR) among 9-11-year-old children, in two sites. Design Quasi-experimental Participants/setting In one site, trained staff observed and recorded foods and drinks consumed by children (n=38) during school lunch. The next day, the observed children completed both ASA24-Kids-2012 and an interviewer-administered 24hDR in a randomized order. Procedures in a second site (n=31) were similar, except observations occurred during dinner in a community location. Statistical analyses Foods were classified as matches (reported and consumed), intrusions (reported, but not consumed), or omissions (not reported, but consumed) for each participant. Rates of matches, intrusions, and omissions were calculated. Rates were compared between each recall method using repeated measures analysis of covariance. For matched foods, the authors determined correlation coefficients between observed and reported serving sizes. Results Match, intrusion, and omission rates between ASA24-Kids-2012 and observed intakes in site 1 were 37%, 27%, and 35%, respectively. Comparable rates for interviewer-administered 24hDRs were 57%, 20%, and 23%, respectively. In site 2, match, intrusion, and omission rates between ASA24-Kids-2012 and observed intakes were 53%, 12%, and 36%, respectively, vs. 76% matches, 9% intrusions, and 15% omissions for interviewer-administered 24hDRs. The relationship strength between reported and observed serving sizes for matched foods was 0.18 in site 1 and 0.09 in site 2 for ASA24-Kids-2012, and 0.46 in site 1 and 0.11 in site 2 for interviewer-administered 24hDRs. Conclusions ASA24-Kids-2012 was less accurate than interviewer-administered 24hDRs when compared to observed intakes, but both performed poorly. Additional research should assess the age at which children can complete recalls without the help of a parent or guardian, as well as to elucidate under which circumstances recalls can reasonably be used among children. PMID:25887784

Large-scale Proteomics Analysis of the Human Kinome

PubMed Central

Oppermann, Felix S.; Gnad, Florian; Olsen, Jesper V.; Hornberger, Renate; Greff, Zoltán; Kéri, György; Mann, Matthias; Daub, Henrik

2009-01-01

Members of the human protein kinase superfamily are the major regulatory enzymes involved in the activity control of eukaryotic signal transduction pathways. As protein kinases reside at the nodes of phosphorylation-based signal transmission, comprehensive analysis of their cellular expression and site-specific phosphorylation can provide important insights into the architecture and functionality of signaling networks. However, in global proteome studies, low cellular abundance of protein kinases often results in rather minor peptide species that are occluded by a vast excess of peptides from other cellular proteins. These analytical limitations create a rationale for kinome-wide enrichment of protein kinases prior to mass spectrometry analysis. Here, we employed stable isotope labeling by amino acids in cell culture (SILAC) to compare the binding characteristics of three kinase-selective affinity resins by quantitative mass spectrometry. The evaluated pre-fractionation tools possessed pyrido[2,3-d]pyrimidine-based kinase inhibitors as immobilized capture ligands and retained considerable subsets of the human kinome. Based on these results, an affinity resin displaying the broadly selective kinase ligand VI16832 was employed to quantify the relative expression of more than 170 protein kinases across three different, SILAC-encoded cancer cell lines. These experiments demonstrated the feasibility of comparative kinome profiling in a compact experimental format. Interestingly, we found high levels of cytoplasmic and low levels of receptor tyrosine kinases in MV4–11 leukemia cells compared with the adherent cancer lines HCT116 and MDA-MB-435S. The VI16832 resin was further exploited to pre-fractionate kinases for targeted phosphoproteomics analysis, which revealed about 1200 distinct phosphorylation sites on more than 200 protein kinases. This hitherto largest survey of site-specific phosphorylation across the kinome significantly expands the basis for functional follow-up studies on protein kinase regulation. In conclusion, the straightforward experimental procedures described here enable different implementations of kinase-selective proteomics with considerable potential for future signal transduction and kinase drug target analysis. PMID:19369195

International co-operative program on assessment and monitoring of air pollution effects on forests: The Sierra Ancha Experimental Forest, Arizona

Treesearch

Boris Poff; Daniel G. Neary

2008-01-01

At the end of the 2007 Fiscal Year, the Experimental Forests and Ranges (EFR) Synthesis Network Committee awarded funds to 18 sites to establish a strategic ICP Level II (described below) synthesis network in the United States. Eleven Experimental Forest were selected to be included in the network, as well as seven Long Term Ecological Research (LTER) sites. This will...

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.

Changes in crash risk following re-timing of traffic signal change intervals.

PubMed

Retting, Richard A; Chapline, Janella F; Williams, Allan F

2002-03-01

More than I million motor vehicle crashes occur annually at signalized intersections in the USA. The principal method used to prevent crashes associated with routine changes in signal indications is employment of a traffic signal change interval--a brief yellow and all-red period that follows the green indication. No universal practice exists for selecting the duration of change intervals, and little is known about the influence of the duration of the change interval on crash risk. The purpose of this study was to estimate potential crash effects of modifying the duration of traffic signal change intervals to conform with values associated with a proposed recommended practice published by the Institute of Transportation Engineers. A sample of 122 intersections was identified and randomly assigned to experimental and control groups. Of 51 eligible experimental sites, 40 (78%) needed signal timing changes. For the 3-year period following implementation of signal timing changes, there was an 8% reduction in reportable crashes at experimental sites relative to those occurring at control sites (P = 0.08). For injury crashes, a 12% reduction at experimental sites relative to those occurring at control sites was found (P = 0.03). Pedestrian and bicycle crashes at experimental sites decreased 37% (P = 0.03) relative to controls. Given these results and the relatively low cost of re-timing traffic signals, modifying the duration of traffic signal change intervals to conform with values associated with the Institute of Transportation Engineers' proposed recommended practice should be strongly considered by transportation agencies to reduce the frequency of urban motor vehicle crashes.

A green infrastructure experimental site for developing and evaluating models

EPA Science Inventory

The Ecosystems Research Division (ERD) of the U.S. EPA’s National Exposure Research Laboratory (NERL) in Athens, GA has a 14-acre urban watershed which has become an experimental research site for green infrastructure studies. About half of the watershed is covered by pervious la...

Estimation of radioactive contamination of soils from the "Balapan" and the "Experimental field" technical areas of the Semipalatinsk nuclear test site.

PubMed

Evseeva, T; Belykh, E; Geras'kin, S; Majstrenko, T

2012-07-01

In spite of the long history of the research, radioactive contamination of the Semipalatinsk nuclear test site (SNTS) in the Republic of Kazakhstan has not been adequately characterized. Our cartographic investigation has demonstrated highly variable radioactive contamination of the SNTS. The Cs-137, Sr-90, Eu-152, Eu-154, Co-60, and Am-241 activity concentrations in soil samples from the "Balapan" site were 42.6-17646, 96-18250, 1.05-11222, 0.6-4865, 0.23-4893, and 1.2-1037 Bq kg(-1), correspondingly. Cs-137 and Sr-90 activity concentrations in soil samples from the "Experimental field" site were varied from 87 up to 400 and from 94 up to 1000 Bq kg(-1), respectively. Activity concentrations of Co-60, Eu-152, and Eu-154 were lower than the minimum detectable activity of the method used. Concentrations of naturally occurring radionuclides (K-40, Ra-226, U-238, and Th-232) in the majority of soil samples from the "Balapan" and the "Experimental field" sites did not exceed typical for surrounding of the SNTS areas levels. Estimation of risks associated with radioactive contamination based on the IAEA clearance levels for a number of key radionuclides in solid materials shows that soils sampled from the "Balapan" and the "Experimental field" sites might be considered as radioactive wastes. Decrease in specific activity of soil from the sites studied up to safety levels due to Co-60, Cs-137, Sr-90, Eu-152, Eu-154 radioactive decay and Am-241 accumulation-decay will occur not earlier than 100 years. In contrast, soils from the "Experimental field" and the "Balapan" sites (except 0.5-2.5 km distance from the "Chagan" explosion point) cannot be regarded as the radioactive wastes according safety norms valid in Russia and Kazakhstan. Copyright © 2012 Elsevier Ltd. All rights reserved.

Prediction of distal residue participation in enzyme catalysis

PubMed Central

Brodkin, Heather R; DeLateur, Nicholas A; Somarowthu, Srinivas; Mills, Caitlyn L; Novak, Walter R; Beuning, Penny J; Ringe, Dagmar; Ondrechen, Mary Jo

2015-01-01

A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues. PMID:25627867

Theoretical Investigations into Defected Graphene for Electrochemical Reduction of CO 2

DOE PAGES

Siahrostami, Samira; Jiang, Kun; Karamad, Mohammadreza; ...

2017-10-10

Here, despite numerous experimental efforts that have been dedicated to studying carbon-based materials for electrochemical reduction of CO 2, a rationalization of the associated trends in the intrinsic activity of different active motifs has so far been elusive. In the present work, we employ density functional theory calculations to examine a variety of different active sites in N-doped graphene to give a comprehensive outline of the trends in activity. We find that adsorption energies of COOH* and CO* do not follow the linear scaling relationships observed for the pure transition metals, and this unique scaling is rationalized through differences inmore » electronic structure between transition metals and defected graphene. This finding rationalizes most of the experimental observations on the carbon-based materials which present promising catalysts for the two-electron reduction of CO 2 to CO. With this simple thermodynamic analysis, we identify several active sites that are expected to exhibit a comparable or even better activity to the state-of-the-art gold catalyst, and several configurations are suggested to be selective for CO 2RR over HER.« less

Identification of adsorption sites in Cu-BTC by experimentation and molecular simulation.

PubMed

García-Pérez, Elena; Gascón, Jorge; Morales-Flórez, Víctor; Castillo, Juan Manuel; Kapteijn, Freek; Calero, Sofía

2009-02-03

The adsorption of several quadrupolar and nonpolar gases on the Metal Organic Framework Cu-BTC has been studied by combining experimental measurements and Monte Carlo simulations. Four main adsorption sites for this structure have been identified: site I close to the copper atoms, site I' in the bigger cavities, site II located in the small octahedral cages, and site III at the windows of the four open faces of the octahedral cage. Our simulations identify the octahedral cages (sites II and III) and the big cages (site I') as the preferred positions for adsorption, while site I, near the copper atoms, remains empty over the entire range of pressures analyzed due to its reduced accessibility. The occupation of the different sites for ethane and propane in Cu-BTC proceeds similarly as for methane, and shows small differences for O2 and N2 that can be attributed to the quadrupole moment of these molecules. Site II is filled predominantly for methane (the nonpolar molecule), whereas for N2, the occupation of II and I' can be considered almost equivalent. The molecular sitting for O2 shows an intermediate behavior between those observed for methane and for N2. The differences between simulated and experimental data at elevated temperatures for propane are tentatively attributed to a reversible change in the lattice parameters of Cu-BTC by dehydration and by temperature, blocking the accessibility to site III and reducing that to site I'. Adsorption parameters of the investigated molecules have been determined from the simulations.

Comprehensive Study On The Metastable Negative Ion Fragmentation Of Individual Dna Components And Larger Oligonucleotides

NASA Astrophysics Data System (ADS)

Ingolfsson, O.; Flosadottir, H. D.; Omarsson, B.; Ilko, B.

2010-07-01

Here we present a systematic study on the unimolecular decay pathways of the deprotonated building blocks of DNA and RNA to address the following questions: 1. Are the negative ion fragmentation patterns observed in the metastable decay of individual DNA components still evident when these are combined to larger oligonucleotides? 2. What is the significance of the charge location in determining the fragmentation pathways in the metastable decay process? 3. Are those metastable decay channels relevant in dissociative electron attachment to DNA components? To address these questions we have studied the fragmentation patterns of the deprotonated ribose and ribose 5'-monophosphate, the fragmentation patterns of the individual bases, all nucleosides and all 2'-deoxynucleosides as well as the individual nucleotides and several combinations of hexameric oligonucleotides. Furthermore, to understand the significance of the charge location in determining the fragmentation path in the metastable decay process of these deprotonated ions we have also studied modified uridine and guanosine. These have been modified to block different deprotonation sites and thus to control the initial step in the in the fragmentation process i.e. the site of deprotonation. In addition to our experimental approach we have also simulated the metastable fragmentation of the deprotonated uridine and 2'-deoxyguanosine to clarify the mechanisms and fragmentation patterns observed. Where data is available, the results are compared to dissociative electron attachment to DNA components and discussed in context to the underlying mechanism. Experiments on modified nucleosides where selected deprotonation sites have been blocked are used to verify the predicted reaction paths and imulations on uridine and 2'-deoxyguanosine are compared to the experimental results and used to shed light on the mechanisms involved.

Role of water molecules in structure and energetics of Pseudomonas aeruginosa lectin I interacting with disaccharides.

PubMed

Nurisso, Alessandra; Blanchard, Bertrand; Audfray, Aymeric; Rydner, Lina; Oscarson, Stefan; Varrot, Annabelle; Imberty, Anne

2010-06-25

Calcium-dependent lectin I from Pseudomonas aeruginosa (PA-IL) binds specifically to oligosaccharides presenting an alpha-galactose residue at their nonreducing end, such as the disaccharides alphaGal1-2betaGalOMe, alphaGal1-3betaGalOMe, and alphaGal1-4betaGalOMe. This provides a unique model for studying the effect of the glycosidic linkage of the ligands on structure and thermodynamics of the complexes by means of experimental and theoretical tools. The structural features of PA-IL in complex with the three disaccharides were established by docking and molecular dynamics simulations and compared with those observed in available crystal structures, including PA-IL.alphaGal1-2betaGalOMe complex, which was solved at 2.4 A resolution and reported herein. The role of a structural bridge water molecule in the binding site of PA-IL was also elucidated through molecular dynamics simulations and free energy calculations. This water molecule establishes three very stable hydrogen bonds with O6 of nonreducing galactose, oxygen from Pro-51 main chain, and nitrogen from Gln-53 main chain of the lectin binding site. Binding free energies for PA-IL in complex with the three disaccharides were investigated, and the results were compared with the experimental data determined by titration microcalorimetry. When the bridge water molecule was included in the free energy calculations, the simulations predicted the correct binding affinity trends with the 1-2-linked disaccharide presenting three times stronger affinity ligand than the other two. These results highlight the role of the water molecule in the binding site of PA-IL and indicate that it should be taken into account when designing glycoderivatives active against P. aeruginosa adhesion.

Theoretical study of hydrogen absorption-desorption on LaNi3.8Al1.2-xMnx using statistical physics treatment

NASA Astrophysics Data System (ADS)

Bouaziz, Nadia; Ben Manaa, Marwa; Ben Lamine, Abdelmottaleb

2017-11-01

The hydrogen absorption-desorption isotherms on LaNi3.8Al1.2-xMnx alloy at temperature T = 433 K is studied through various theoretical models. The analytical expressions of these models were deduced exploiting the grand canonical ensemble in statistical physics by taking some simplifying hypotheses. Among these models an adequate model which presents a good correlation with the experimental curves has been selected. The physicochemical parameters intervening in the absorption-desorption processes and involved in the model expressions could be directly deduced from the experimental isotherms by numerical simulation. Six parameters of the model are adjusted, namely the numbers of hydrogen atoms per site n1 and n2, the receptor site densities N1m and N2m, and the energetic parameters P1 and P2. The behaviors of these parameters are discussed in relation with absorption and desorption processes to better understand and compare these phenomena. Thanks to the energetic parameters, we calculated the sorption energies which are typically ranged between 266 and 269.4 KJ/mol for absorption process and between 267 and 269.5 KJ/mol for desorption process comparable to usual chemical bond energies. Using the adopted model expression, the thermodynamic potential functions which govern the absorption/desorption process such as internal energy Eint, free enthalpy of Gibbs G and entropy Sa are derived.

The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators

NASA Astrophysics Data System (ADS)

Taha, Mutasem O.; Habash, Maha; Khanfar, Mohammad A.

2014-05-01

Glucokinase (GK) is involved in normal glucose homeostasis and therefore it is a valid target for drug design and discovery efforts. GK activators (GKAs) have excellent potential as treatments of hyperglycemia and diabetes. The combined recent interest in GKAs, together with docking limitations and shortages of docking validation methods prompted us to use our new 3D-QSAR analysis, namely, docking-based comparative intermolecular contacts analysis (dbCICA), to validate docking configurations performed on a group of GKAs within GK binding site. dbCICA assesses the consistency of docking by assessing the correlation between ligands' affinities and their contacts with binding site spots. Optimal dbCICA models were validated by receiver operating characteristic curve analysis and comparative molecular field analysis. dbCICA models were also converted into valid pharmacophores that were used as search queries to mine 3D structural databases for new GKAs. The search yielded several potent bioactivators that experimentally increased GK bioactivity up to 7.5-folds at 10 μM.

Delayed repair of radiation induced clustered DNA damage: Friend or foe?

PubMed Central

Eccles, Laura J.; O’Neill, Peter; Lomax, Martine E.

2011-01-01

A signature of ionizing radiation exposure is the induction of DNA clustered damaged sites, defined as two or more lesions within one to two helical turns of DNA by passage of a single radiation track. Clustered damage is made up of double strand breaks (DSB) with associated base lesions or abasic (AP) sites, and non-DSB clusters comprised of base lesions, AP sites and single strand breaks. This review will concentrate on the experimental findings of the processing of non-DSB clustered damaged sites. It has been shown that non-DSB clustered damaged sites compromise the base excision repair pathway leading to the lifetime extension of the lesions within the cluster, compared to isolated lesions, thus the likelihood that the lesions persist to replication and induce mutation is increased. In addition certain non-DSB clustered damaged sites are processed within the cell to form additional DSB. The use of E. coli to demonstrate that clustering of DNA lesions is the major cause of the detrimental consequences of ionizing radiation is also discussed. The delayed repair of non-DSB clustered damaged sites in humans can be seen as a “friend”, leading to cell killing in tumour cells or as a “foe”, resulting in the formation of mutations and genetic instability in normal tissue. PMID:21130102

QM/MM structural and spectroscopic analysis of the di-iron(II) and di-iron(III) ferroxidase site in M ferritin.

PubMed

Harris, Travis V; Morokuma, Keiji

2013-08-05

Ferritins are cage-like proteins composed of 24 subunits that take up iron(II) and store it as an iron(III) oxide mineral core. A critical step is the ferroxidase reaction, in which oxygen reacts with a di-iron(II) site, proceeding through a peroxo intermediate, to form μ-oxo/hydroxo-bridged di-iron(III) products. The recent crystal structures of copper(II)- and iron(III)-bound frog M ferritin at 2.8 Å resolution [Bertini; et al. J. Am. Chem. Soc. 2012, 134, 6169-6176] provided an opportunity to theoretically investigate the detailed structures of the reactant state and products. In this study, the quantum mechanical/molecular mechanical ONIOM method is used to structurally optimize a series of single-subunit models with various hydration, protonation, and coordination states of the ferroxidase site. Calculated exchange coupling constants (J), Mössbauer parameters, and time-dependent density functional theoretical (TD-DFT) circular dichroism spectra with electronic embedding are compared with the available experimental data. The di-iron(II) model with the most experimentally consistent structural and spectroscopic parameters has 5-coordinate iron centers with Glu23, Glu58, His61, and two waters completing one coordination sphere, and His54, Glu58, Glu103, and Asp140 completing the other. In contrast to a previously proposed structure, Gln137 is not directly coordinated, but it is involved in hydrogen bonding with several iron ligands. For the di-iron(III) products, we find that a μ-oxo-bridged and two doubly bridged (μ-hydroxo and μ-oxo/hydroxo) species are likely coproduced. Although four quadrupole doublets were observed experimentally, we find that two doublets may arise from a single asymmetrically coordinated ferroxidase site. These proposed key structures will help to explore the pathway connecting the di-Fe(II) state to the peroxo intermediate and the branching mechanisms leading to the multiple products.

The comparative evaluation of xanthan gel with chlorhexidine (Chlosite) in smokers and non-smokers: A clinical and microbiological assessment

PubMed Central

Chandra, Chetan; Valavalkar, Narayan; Vandana, K. L.

2011-01-01

Background and Objectives: Prevention of the periodontal disease progression is the primary goal of periodontal therapy. When conventional therapy is found inadequate to attain periodontal health in chronic periodontitis, local antimicrobial agents have been used as an adjunct with scaling and root planning (SRP) which has reproduced encouraging results. Hence, this study was undertaken to evaluate the new sustained released local drug Chlosite clinically and microbiologically in smokers and non-smokers. Materials and Methods: The patients were grouped into experimental group A treated with SRP plus Chlosite (SRP + CHL), experimental group B treated with Chlosite alone (CHL), and control group C treated only with SRP alone. A total number of 141 sites from six patients (67 sites from three non-smoker patients and 74 sites from three smoker patients) participated in this study. The clinical parameters, Plaque index (PI), Gingival index (GI), Bleeding index (BI), and Relative attachment level (RAL), were recorded and subgingival plaque samples were collected and subjected to microbiological analysis. Results: On comparison of smokers and non-smokers, in SRP group, non-smokers showed a higher reduction in BI and GI and smokers showed a higher reduction in PI. There was no significant gain in RAL of both smokers and non-smokers. In SRP + CHL group, non-smokers showed a higher reduction in relation to BI and GI and smokers showed a higher reduction in relation to PI. There was no significant gain in RAL of both smokers and non-smokers. In CHL group, both smokers and non-smokers showed a nonsignificant reduction in BI, GI, and RAL, but smokers showed a significant reduction in PI as compared with non-smokers. All the groups showed reduction in the microbial count of Fusobacterium nucleatum, Porphyromonas gingivalis, and Tannerella forsythia which were found to be statistically not significant when it was compared between non-smokers and smokers. Interpretation and Conclusion: In this study, all treatment groups were found to be efficacious in the treatment of periodontal disease as demonstrated by improvement in PI, GI, BI, and RAL. Combination of SRP and Chlosite resulted in added benefits compared with the two treatment groups. PMID:22028508

From clusters to bulk: A relativistic density functional investigation on a series of gold clusters Aun, n=6,…,147

NASA Astrophysics Data System (ADS)

Häberlen, Oliver D.; Chung, Sai-Cheong; Stener, Mauro; Rösch, Notker

1997-03-01

A series of gold clusters spanning the size range from Au6 through Au147 (with diameters from 0.7 to 1.7 nm) in icosahedral, octahedral, and cuboctahedral structure has been theoretically investigated by means of a scalar relativistic all-electron density functional method. One of the main objectives of this work was to analyze the convergence of cluster properties toward the corresponding bulk metal values and to compare the results obtained for the local density approximation (LDA) to those for a generalized gradient approximation (GGA) to the exchange-correlation functional. The average gold-gold distance in the clusters increases with their nuclearity and correlates essentially linearly with the average coordination number in the clusters. An extrapolation to the bulk coordination of 12 yields a gold-gold distance of 289 pm in LDA, very close to the experimental bulk value of 288 pm, while the extrapolated GGA gold-gold distance is 297 pm. The cluster cohesive energy varies linearly with the inverse of the calculated cluster radius, indicating that the surface-to-volume ratio is the primary determinant of the convergence of this quantity toward bulk. The extrapolated LDA binding energy per atom, 4.7 eV, overestimates the experimental bulk value of 3.8 eV, while the GGA value, 3.2 eV, underestimates the experiment by almost the same amount. The calculated ionization potentials and electron affinities of the clusters may be related to the metallic droplet model, although deviations due to the electronic shell structure are noticeable. The GGA extrapolation to bulk values yields 4.8 and 4.9 eV for the ionization potential and the electron affinity, respectively, remarkably close to the experimental polycrystalline work function of bulk gold, 5.1 eV. Gold 4f core level binding energies were calculated for sites with bulk coordination and for different surface sites. The core level shifts for the surface sites are all positive and distinguish among the corner, edge, and face-centered sites; sites in the first subsurface layer show still small positive shifts.

Where's water? The many binding sites of hydantoin.

PubMed

Gruet, Sébastien; Pérez, Cristóbal; Steber, Amanda L; Schnell, Melanie

2018-02-21

Prebiotic hydantoin and its complexes with one and two water molecules are investigated using high-resolution broadband rotational spectroscopy in the 2-8 GHz frequency range. The hyperfine structure due to the nuclear quadrupole coupling of the two 14 N atoms is analysed for the monomer and the complexes. This characteristic hyperfine structure will support a definitive assignment from low frequency radioastronomy data. Experiments with H 2 18 O provide accurate experimental information on the preferred binding sites of water, which are compared with quantum-chemically calculated coordinates. In the 2-water complexes, the water molecules bind to hydantoin as a dimer instead of individually, indicating the strong water-water interactions. This information provides first insight on how hydantoin interacts with water on the molecular level.

Optical absorption and disorder in delafossites

DOE PAGES

Senty, Tess R.; Haycock, Barry; Lekse, Jonathan; ...

2017-07-06

Here, we present compelling experimental results of the optical characteristics of transparent oxide CuGaO 2 and related CuGa 1-xFe xO 2 (with 0.00 ≤ x ≤ 0.05) alloys, whereby the forbidden electronic transitions for CuGaO 2 become permissible in the presence of B-site (Ga sites) alloying with Fe. Our computational structural results imply a correlation between the global strain on the system and a decreased optical absorption edge. However, herein, we show that the relatively ordered CuGa 1-xFe xO 2 (for 0.00 ≤ x ≤ 0.04) structures exhibit much weaker vis-absorption compared to the relatively disordered CuGa 0.95Fe 0.05O 2.

The active site structure of tetanus neurotoxin resolved by multiple scattering analysis in X-Ray absorption spectroscopy.

PubMed Central

Meneghini, C; Morante, S

1998-01-01

A detailed study of the x-ray absorption spectrum of tetanus neurotoxin in the K-edge EXAFS region of the zinc absorber is presented that allows the complete identification of the amino acid residues coordinated to the zinc active site. A very satisfactory interpretation of the experimental data can be given if multiple scattering contributions are included in the analysis. Comparing the absorption spectrum of tetanus neurotoxin to that of two other structurally similar zinc-endopeptidases, thermolysin and astacin, in which the zinc coordination mode is known from crystallographic data, we conclude that in tetanus neurotoxin, besides a water molecule, zinc is coordinated to two histidines and a tyrosine. PMID:9746536

Comparative analysis of amino acid composition in the active site of nirk gene encoding copper-containing nitrite reductase (CuNiR) in bacterial spp.

PubMed

Adhikari, Utpal Kumar; Rahman, M Mizanur

2017-04-01

The nirk gene encoding the copper-containing nitrite reductase (CuNiR), a key catalytic enzyme in the environmental denitrification process that helps to produce nitric oxide from nitrite. The molecular mechanism of denitrification process is definitely complex and in this case a theoretical investigation has been conducted to know the sequence information and amino acid composition of the active site of CuNiR enzyme using various Bioinformatics tools. 10 Fasta formatted sequences were retrieved from the NCBI database and the domain and disordered regions identification and phylogenetic analyses were done on these sequences. The comparative modeling of protein was performed through Modeller 9v14 program and visualized by PyMOL tools. Validated protein models were deposited in the Protein Model Database (PMDB) (PMDB id: PM0080150 to PM0080159). Active sites of nirk encoding CuNiR enzyme were identified by Castp server. The PROCHECK showed significant scores for four protein models in the most favored regions of the Ramachandran plot. Active sites and cavities prediction exhibited that the amino acid, namely Glycine, Alanine, Histidine, Aspartic acid, Glutamic acid, Threonine, and Glutamine were common in four predicted protein models. The present in silico study anticipates that active site analyses result will pave the way for further research on the complex denitrification mechanism of the selected species in the experimental laboratory. Copyright © 2016. Published by Elsevier Ltd.

Molecular models of site-isolated cobalt, rhodium, and iridium catalysts supported on zeolites: Ligand bond dissociation energies

DOE PAGES

Chen, Mingyang; Serna, Pedro; Lu, Jing; ...

2015-09-28

The chemistry of zeolite-supported site-isolated cobalt, rhodium, and iridium complexes that are essentially molecular was investigated with density functional theory (DFT) and the results compared with experimentally determined spectra characterizing rhodium and iridium species formed by the reactions of Rh(C 2H 4) 2(acac) and Ir(C 2H 4) 2(acac) (acac = acetylacetonate) with acidic zeolites such as dealuminated HY zeolite. The experimental results characterize ligand exchange reactions and catalytic reactions of adsorbed ligands, including olefin hydrogenation and dimerization. Two molecular models were used to characterize various binding sites of the metal complexes in the zeolites, and the agreement between experimental andmore » calculated infrared frequencies and metal-ligand distances determined by extended X-ray absorption fine structure spectroscopy was generally very good. The calculated structures and energies indicate a metal-support-oxygen (M(I)-O) coordination number of two for most of the supported complexes and a value of three when the ligands include the radicals C 2H 5 or H. The results characterizing various isomers of the supported metal complexes incorporating hydrocarbon ligands indicate that some carbene and carbyne ligands could form. Ligand bond dissociation energies (LDEs) are reported to explain the observed reactivity trends. The experimental observations of a stronger M-CO bond than M-(C 2H 4) bond for both Ir and Rh match the calculated LDEs, which show that the single-ligand LDEs of the mono and dual-ligand complexes for CO are similar to 12 and similar to 15 kcal/mol higher in energy (when the metal is Rh) and similar to 17 and similar to 20 kcal/mol higher (when the metal is Ir) than the single-ligand LDEs of the mono and dual ligand complexes for C 2H 4, respectively. The results provide a foundation for the prediction of the catalytic properties of numerous supported metal complexes, as summarized in detail here.« less

Evaluation of water displacement energetics in protein binding sites with grid cell theory.

PubMed

Gerogiokas, G; Southey, M W Y; Mazanetz, M P; Heifetz, A; Hefeitz, A; Bodkin, M; Law, R J; Michel, J

2015-04-07

Excess free energies, enthalpies and entropies of water in protein binding sites were computed via classical simulations and Grid Cell Theory (GCT) analyses for three pairs of congeneric ligands in complex with the proteins scytalone dehydratase, p38α MAP kinase and EGFR kinase respectively. Comparative analysis is of interest since the binding modes for each ligand pair differ in the displacement of one binding site water molecule, but significant variations in relative binding affinities are observed. Protocols that vary in their use of restraints on protein and ligand atoms were compared to determine the influence of protein-ligand flexibility on computed water structure and energetics, and to assess protocols for routine analyses of protein-ligand complexes. The GCT-derived binding affinities correctly reproduce experimental trends, but the magnitude of the predicted changes in binding affinities is exaggerated with respect to results from a previous Monte Carlo Free Energy Perturbation study. Breakdown of the GCT water free energies into enthalpic and entropic components indicates that enthalpy changes dominate the observed variations in energetics. In EGFR kinase GCT analyses revealed that replacement of a pyrimidine by a cyanopyridine perturbs water energetics up three hydration shells away from the ligand.

Evaluation of free to grow: head start partnerships to promote substance-free communities.

PubMed

Wolfson, Mark; Champion, Heather; Rogers, Todd; Neiberg, Rebecca H; Barker, Dianne C; Talton, Jennifer W; Ip, Edward H; D'Agostino, Ralph B; Parries, Maria T; Easterling, Doug

2011-04-01

Free to Grow: Head Start Partnerships to Promote Substance-free Communities (FTG) was a national initiative in which local Head Start (HS) agencies, in partnership with other community organizations, implemented a mix of evidence-based family-strengthening and community-strengthening strategies. The evaluation of FTG used a quasi-experimental design to compare 14 communities that participated in the FTG intervention with 14 matched comparison communities. Telephone surveys were conducted with two cohorts of the primary caregivers of children in HS at baseline and then annually for 2 years. The survey was also administered to repeated cross-sectional samples of primary caregivers of young children who were not enrolled in HS. No consistent evidence was found in changes in family functioning or neighborhood conditions when the 14 FTG sites were compared to 14 matched sites. However, caregivers of young children who were not in HS in three high-implementing FTG sites showed evidence of improvements in neighborhood organization, neighborhood norms against substance abuse, and child disciplinary practices. Results provide highly limited support for the concept that family and neighborhood conditions that are likely to affect child development and well-being can be changed through organized efforts implemented by local HS programs.

Evaluation of a social marketing campaign targeting preschool children.

PubMed

Johnson, Susan L; Bellows, Laura; Beckstrom, Leslie; Anderson, Jennifer

2007-01-01

To determine the effectiveness of a pilot social marketing program to increase preschoolers' willingness to try new foods. Four Head Start centers participated (2 experimental, 2 control) in a study using a quasi-experimental design. Experimental sites received a 12-week intervention developed using social marketing techniques. The program was evaluated via preference assessments, classroom observations, and teacher surveys. Increased preference for and willingness to try new foods were observed in children from the experimental sites (P<0.05). The program was positively received by Head Start staff. A social marketing campaign is an effective method to reduce children's neophobia.

Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes

PubMed Central

Oezguen, Numan; Zhou, Bin; Negi, Surendra S.; Ivanciuc, Ovidiu; Schein, Catherine H.; Labesse, Gilles; Braun, Werner

2008-01-01

Similarities in sequences and 3D structures of allergenic proteins provide vital clues to identify clinically relevant IgE cross-reactivities. However, experimental 3D structures are available in the Protein Data Bank for only 5% (45/829) of all allergens catalogued in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP). Here, an automated procedure was used to prepare 3D-models of all allergens where there was no experimentally determined 3D structure or high identity (95%) to another protein of known 3D structure. After a final selection by quality criteria, 433 reliable 3D models were retained and are available from our SDAP Website. The new 3D models extensively enhance our knowledge of allergen structures. As an example of their use, experimentally derived “continuous IgE epitopes” were mapped on 3 experimentally determined structures and 13 of our 3D-models of allergenic proteins. Large portions of these continuous sequences are not entirely on the surface and therefore cannot interact with IgE or other proteins. Only the surface exposed residues are constituents of “conformational IgE epitopes” which are not in all cases continuous in sequence. The surface exposed parts of the experimental determined continuous IgE epitopes showed a distinct statistical distribution as compared to their presence in typical protein-protein interfaces. The amino acids Ala, Ser, Asn, Gly and particularly Lys have a high propensity to occur in IgE binding sites. The 3D-models will facilitate further analysis of the common properties of IgE binding sites of allergenic proteins. PMID:18621419

Local and average structure of Mn- and La-substituted BiFeO{sub 3}

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

Jiang, Bo; Selbach, Sverre M., E-mail: selbach@ntnu.no

2017-06-15

The local and average structure of solid solutions of the multiferroic perovskite BiFeO{sub 3} is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO{sub 3}. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions. - Graphical abstract: The experimental and simulated partial pair distribution functions (PDF) for BiFeO{sub 3}, BiFe{sub 0.875}Mn{sub 0.125}O{sub 3}, BiFe{sub 0.75}Mn{sub 0.25}O{sub 3} and Bi{sub 0.9}La{sub 0.1}FeO{sub 3}.« less

The Russian Academy of Education's Centers for Innovative Development

ERIC Educational Resources Information Center

Martirosian, B. P.; Rubtsova, N. E.; Shapovalova, I. A.

2014-01-01

The article presents a review of the experience of practical testing (based in 385 experimental sites of the Russian Academy of Education) of current achievements of scientific academic schools that are developing the traditions of education. The organization of the innovative scientific and practical activity of the experimental sites of the…

Early Results in Capella's Prior Learning Assessment Experimental Site Initiative

ERIC Educational Resources Information Center

Klein, Jillian

2017-01-01

In July 2014, the U.S. Department of Education announced a new round of experimental sites focusing on competency-based education. Capella University was selected to participate in three of the Department of Education's competency-based education (CBE) experiments and began by implementing the prior learning assessment experiment, which allows…

Investigating the Lewis acidity of aluminium fluoride surfaces

NASA Astrophysics Data System (ADS)

Bailey, C. L.; Mukhopadhyay, S.; Wander, A.; Harrison, N. M.

2008-03-01

The current study employs state of the art hybrid-exchange density functional theory (DFT) to investigate the Lewis acidic sites on the β-AlF3 (100) surface. It is shown that the strong Lewis base, NH3, binds to the surface with a binding energy of up to 1.9 eV. This demonstrates that the material is strongly Lewis acidic. We also consider the binding of the weak Lewis base CO to the surface. We calculate the shift in its stretch frequency compared to the gas phase molecule. Shifts are compared to experimental data and are shown to be typical of strong Lewis acidity.

Incorporating evolution of transcription factor binding sites into annotated alignments.

PubMed

Bais, Abha S; Grossmann, Stefen; Vingron, Martin

2007-08-01

Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield "conserved TFBSs". Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits)are generated. Moreover,the pair- profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions,as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs,we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification methods do not explicitly consider this.Additionally, prediction of conserved binding sites is carried out in a multi-step approach that segregates alignment from TFBS annotation. In this paper, we demonstrate how the simultaneous alignment and annotation approach of SimAnn can be further extended to incorporate TFBS evolutionary relationships. We study how alignments and binding site predictions interplay at varying evolutionary distances and for various profile qualities.

Integrated experimental and modeling assessment of potential effects of gas leakages on groundwater composition

NASA Astrophysics Data System (ADS)

Berta, Marton; Dethlefsen, Frank; Ebert, Markus; Schäfer, Dirk

2017-04-01

Storing renewably produced energy is one of the major challenges for the energy systems of the upcoming decades. Power-to-gas technologies coupled to geological storage of compressed air, methane, and hydrogen offer a comparatively safe and cost-efficient way for large-scale energy storage. However, the stored gases can potentially escape from their geological reservoir and may thus affect protected natural goods such as groundwater. The geochemical reactions responsible for these composition changes are usually investigated separately in experiments and numerical models. Here we present the outcomes of an integrated experimental and modeling approach through the example of a compressed air leakage scenario. A main consequence of the presence of oxygen to be assessed in an aquifer is pyrite oxidation, well known from acid mine drainage sites. However, in contrast to acid mine drainage sites exhibiting unsaturated sediments and fed by meteoric low-carbonate water, aquifers such as in Northern Germany contain a considerable amount of solid and dissolved inorganic carbon species potentially buffering pH changes. High pressure flow-through column experiments representing an intrusion of compressed air into an aquifer were carried out to quantify pyrite oxidation kinetics and to incorporate the observations into a descriptive reaction model. Surface passivation was found to decrease the reactivity of pyrite by more than 90% after a few months of experimental run time. We propose that the carbonate buffer system enables the precipitation of a passivating mineral layer on the pyrite surface reducing the overall reaction rate significantly. Consequently, an established rate law from the literature was extended by a reactive surface passivation term[1]. This improved reaction rate equation was incorporated into a 3D numerical model using OpenGeoSys with parameters representing similarly typical aquifer conditions the experiments had characterized. These boundaries include pyrite content, oxygen dissolution kinetics, groundwater composition including the carbonate buffer, and diffusive and advective transport parameters. The results of site-scale multiphase reactive transport modeling revealed the expected spatial distribution of redox-sensitive species such as oxygen, pyrite, and sulfate in an aquifer following a leakage. The changes in concentration of sulfate, dissolved oxygen, and H+ observed in the lab-scale experiments were qualitatively reproduced by the models applying the same boundary conditions on a site-scale. This integrated study acknowledged that the combination of experiments and models is a powerful tool to prognose the geochemical consequences of gas leakage on site scale. However, it is yet unknown how the passivation would be effected if the carbonate buffer depleted on the long term and under what circumstances a transition from the passivating pyrite oxidation process to the non-passivating process observed for instance in acid mine drainage setups occurs. These restrictions mark the limits of validity of our experimental and modeling concept. This conclusion suggests the feasibility of the presented integrated approach also when evaluating comparable scenarios on methane and hydrogen storage based on experimental results gathered similarly[2]. [1]Berta et al. Environ Earth Sci (2016) 75:1175, DOI 10.1007/s12665-016-5985-7. [2]Berta et al. First Break (2015) 33,93-95, ISSN 1365-2397. This work is part of the ANGUS+ project funded by the BMBF-FK03EK3022.

Defects in doped LaGaO3 anionic conductors: linking NMR spectral features, local environments, and defect thermodynamics.

PubMed

Blanc, Frédéric; Middlemiss, Derek S; Gan, Zhehong; Grey, Clare P

2011-11-09

Doped lanthanum gallate perovskites (LaGaO(3)) constitute some of the most promising electrolyte materials for solid oxide fuel cells operating in the intermediate temperature regime. Here, an approach combining experimental multinuclear NMR spectroscopy with density functional theory total energy and GIPAW NMR calculations yields a comprehensive understanding of the structural and defect chemistries of Sr- and Mg-doped LaGaO(3) anionic conductors. The DFT energetics demonstrate that Ga-V(O)-Ga (V(O) = oxygen vacancy) environments are favored (vs Ga-V(O)-Mg, Mg-V(O)-Mg and Mg-O-Mg-V(O)-Ga) across a range y = 0.0625, 0.125, and 0.25 of fractional Mg contents in LaGa(1-y)Mg(y)O(3-y/2). The results are interpreted in terms of doping and mean phase formation energies (relative to binary oxides) and are compared with previous calculations and experimental calorimetry data. Experimental multinuclear NMR data reveal that while Mg sites remain six-fold coordinated across the range of phase stoichiometries, albeit with significant structural disorder, a stoichiometry-dependent minority of the Ga sites resonate at a shift consistent with Ga(V) coordination, demonstrating that O vacancies preferentially locate in the first anion coordination shell of Ga. The strong Mg-V(O) binding inferred by previous studies is not observed here. The (17)O NMR spectra reveal distinct resonances that can be assigned by using the GIPAW NMR calculations to anions occupying equatorial and axial positions with respect to the Ga(V)-V(O) axis. The disparate shifts displayed by these sites are due to the nature and extent of the structural distortions caused by the O vacancies.

Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

PubMed

Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

2017-09-05

Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

Anatexis at the roof of an oceanic magma chamber at IODP Site 1256 (equatorial Pacific): an experimental study

NASA Astrophysics Data System (ADS)

Erdmann, Martin; Fischer, Lennart A.; France, Lydéric; Zhang, Chao; Godard, Marguerite; Koepke, Jürgen

2015-04-01

Replenished axial melt lenses at fast-spreading mid-oceanic ridges may move upward and intrude into the overlying hydrothermally altered sheeted dikes, resulting in high-grade contact metamorphism with the potential to trigger anatexis in the roof rocks. Assumed products of this process are anatectic melts of felsic composition and granoblastic, two-pyroxene hornfels, representing the residue after partial melting. Integrated Ocean Drilling Program Expeditions 309, 312, and 335 at Site 1256 (eastern equatorial Pacific) sampled such a fossilized oceanic magma chamber. In this study, we simulated magma chamber roof rock anatectic processes by performing partial melting experiments using six different protoliths from the Site 1256 sheeted dike complex, spanning a lithological range from poorly to strongly altered basalts to partially or fully recrystallized granoblastic hornfels. Results show that extensively altered starting material lacking primary magmatic minerals cannot reproduce the chemistry of natural felsic rocks recovered in ridge environments, especially elements sensitive to hydrothermal alteration (e.g., K, Cl). Natural geochemical trends are reproduced through partial melting of moderately altered basalts from the lower sheeted dikes. Two-pyroxene hornfels, the assumed residue, were reproduced only at low melting degrees (<20 vol%). The overall amphibole absence in the experiments confirms the natural observation that amphibole is not produced during peak metamorphism. Comparing experimental products with the natural equivalents reveals that water activity ( aH2O) was significantly reduced during anatectic processes, mainly based on lower melt aluminum oxide and lower plagioclase anorthite content at lower aH2O. High silica melt at the expected temperature (1000-1050 °C; peak thermal overprint of two-pyroxene hornfels) could only be reproduced in the experimental series performed at aH2O = 0.1.

Treatment of periodontal intrabony defects using β-TCP alone or in combination with rhPDGF-BB: a randomized controlled clinical and radiographic study.

PubMed

Maroo, Sneha; Murthy, K Raja V

2014-01-01

The need to increase the predictability of periodontal regeneration has encouraged clinicians and researchers to employ cell-stimulating proteins in combination with osteoconductive scaffolds, based on the principles of tissue engineering. The purpose of this clinical and radiographic study was to compare the regenerative potential of the combination of β-tricalcium phosphate (β-TCP) and recombinant human platelet-derived growth factor BB (rhPDGF-BB) in the grafting of intraosseous defects with the established technique of bone grafting with (β-TCP alone. A total of 30 sites from 15 patients with infrabony defects in two different quadrants were selected, and the sites were randomly divided into test sites (rhPDGF + β-TCP) and control sites (β-TCP alone) using a split-mouth design. Clinical parameters, including probing pocket depth, clinical attachment level, and gingival recession, were recorded at baseline, 6 months, and 9 months. Radiographic evaluation was carried out to evaluate defect fill, change in alveolar crest height, and percentage of defect fill at baseline, 6 months, and 9 months. Both the experimental groups showed statistically significant reduction in probing pocket depth and gain in clinical attachment level. On intergroup comparison, sites treated with rhPDGF + β-TCP demonstrated a significantly greater pocket depth reduction (P < .05) and greater gain in clinical attachment level (P < .01). Mean percentage defect fill was significantly greater in test sites as compared with control sites at 6 and 9 months (P < .01). rhPDGF + β-TCP-treated sites demonstrated a significant gain in mean alveolar crest height at 6 and 9 months (P < .05), while β-TCP-treated sites demonstrated crestal resorption. Both groups demonstrated potential in enhancing periodontal regeneration; however, on comparison between the two groups, the results obtained by rhPDGF + β-TCP were significantly better with respect to both clinical and radiographic parameters.

Sorption of uranium (VI) on homoionic sodium smectite experimental study and surface complexation modeling.

PubMed

Korichi, Smain; Bensmaili, Aicha

2009-09-30

This paper is an extension of a previous paper where the natural and purified clay in the homoionic Na form were physico-chemically characterized (doi:10.1016/j.clay.2008.04.014). In this study, the adsorption behavior of U (VI) on a purified Na-smectite suspension is studied using batch adsorption experiments and surface complexation modeling (double layer model). The sorption of uranium was investigated as a function of pH, uranium concentration, solid to liquid ratio, effect of natural organic matter (NOM) and NaNO(3) background electrolyte concentration. Using the MINTEQA2 program, the speciation of uranium was calculated as a function of pH and uranium concentration. Model predicted U (VI) aqueous speciation suggests that important aqueous species in the [U (VI)]=1mg/L and pH range 3-7 including UO(2)(2+), UO(2)OH(+), and (UO(2))(3)(OH)(5)(+). The concentration of UO(2)(2+) decreased and that of (UO(2))(3)(OH)(5)(+) increased with increasing pH. The potentiometric titration values and uptake of uranium in the sodium smectite suspension were simulated by FITEQL 4.0 program using a two sites model, which is composed of silicate and aluminum reaction sites. We compare the acidity constants values obtained by potentiometric titration from the purified sodium smectite with those obtained from single oxides (quartz and alpha-alumina), taking into account the surface heterogeneity and the complex nature of natural colloids. We investigate the uranium sorption onto purified Na-smectite assuming low, intermediate and high edge site surfaces which are estimated from specific surface area percentage. The sorption data is interpreted and modeled as a function of edge site surfaces. A relationship between uranium sorption and total site concentration was confirmed and explained through variation in estimated edge site surface value. The modeling study shows that, the convergence during DLM modeling is related to the best estimation of the edge site surface from the N(2)-BET specific surface area, SSA(BET) (thus, total edge site concentrations). The specific surface area should be at least 80-100m(2)/g for smectite clays in order to reach convergence during the modeling. The range of 10-20% SSA(BET) was used to estimate the values of edge site surfaces that led to the convergence during modeling. An agreement between the experimental data and model predictions is found reasonable when 15% SSA(BET) was used as edge site surface. However, the predicted U (VI) adsorption underestimated and overestimated the experimental observations at the 10 and 20% of the measured SSA(BET), respectively. The dependence of uranium sorption modeling results on specific surface area and edge site surface is useful to describe and predict U (VI) retardation as a function of chemical conditions in the field-scale reactive transport simulations. Therefore this approach can be used in the environmental quality assessment.

Identification of Conserved Water Sites in Protein Structures for Drug Design.

PubMed

Jukič, Marko; Konc, Janez; Gobec, Stanislav; Janežič, Dušanka

2017-12-26

Identification of conserved waters in protein structures is a challenging task with applications in molecular docking and protein stability prediction. As an alternative to computationally demanding simulations of proteins in water, experimental cocrystallized waters in the Protein Data Bank (PDB) in combination with a local structure alignment algorithm can be used for reliable prediction of conserved water sites. We developed the ProBiS H2O approach based on the previously developed ProBiS algorithm, which enables identification of conserved water sites in proteins using experimental protein structures from the PDB or a set of custom protein structures available to the user. With a protein structure, a binding site, or an individual water molecule as a query, ProBiS H2O collects similar proteins from the PDB and performs local or binding site-specific superimpositions of the query structure with similar proteins using the ProBiS algorithm. It collects the experimental water molecules from the similar proteins and transposes them to the query protein. Transposed waters are clustered by their mutual proximity, which enables identification of discrete sites in the query protein with high water conservation. ProBiS H2O is a robust and fast new approach that uses existing experimental structural data to identify conserved water sites on the interfaces of protein complexes, for example protein-small molecule interfaces, and elsewhere on the protein structures. It has been successfully validated in several reported proteins in which conserved water molecules were found to play an important role in ligand binding with applications in drug design.

Organic-Silica Interactions in Saline: Elucidating the Structural Influence of Calcium in Low-Salinity Enhanced Oil Recovery.

PubMed

Desmond, J L; Juhl, K; Hassenkam, T; Stipp, S L S; Walsh, T R; Rodger, P M

2017-09-08

Enhanced oil recovery using low-salinity solutions to sweep sandstone reservoirs is a widely-practiced strategy. The mechanisms governing this remain unresolved. Here, we elucidate the role of Ca 2+ by combining chemical force microscopy (CFM) and molecular dynamics (MD) simulations. We probe the influence of electrolyte composition and concentration on the adsorption of a representative molecule, positively-charged alkylammonium, at the aqueous electrolyte/silica interface, for four electrolytes: NaCl, KCl, MgCl 2 , and CaCl 2 . CFM reveals stronger adhesion on silica in CaCl 2 compared with the other electrolytes, and shows a concentration-dependent adhesion not observed for the other electrolytes. Using MD simulations, we model the electrolytes at a negatively-charged amorphous silica substrate and predict the adsorption of methylammonium. Our simulations reveal four classes of surface adsorption site, where the prevalence of these sites depends only on CaCl 2 concentration. The sites relevant to strong adhesion feature the O - silica site and Ca 2+ in the presence of associated Cl - , which gain prevalence at higher CaCl 2 concentration. Our simulations also predict the adhesion force profile to be distinct for CaCl 2 compared with the other electrolytes. Together, these analyses explain our experimental data. Our findings indicate in general how silica wettability may be manipulated by electrolyte concentration.

Ebolavirus comparative genomics

DOE PAGES

Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; ...

2015-07-14

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. We examine the dynamics of this genome, comparing more than one hundred currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus, and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of themore » same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP), and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. In conclusion, this information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies.« less

Important Aspects of Post-Prandial Antidiabetic Drug, Acarbose.

PubMed

Singla, Rajeev Kumar; Singh, Radha; Dubey, Ashok Kumar

2016-01-01

Acarbose, a well known and efficacious α-amylase and α-glucosidase inhibitor, is a postprandial acting antidiabetic drug. DNS-based α-amylase inhibitory assays showed that use of acarbose at concentrations above 125 µg/ml resulted in release of reducing sugar in the reaction, an unexpected observation. Objective of the present study was to design experimental strategies to address this unusual finding. Acarbose was found to be susceptible to thermo-lysis. Further, besides being an inhibitor, it could also be hydrolyzed by porcine pancreatic α-amylase, but had weaker affinity for α - amylase compared to starch. GRIP docking was done for the mechanistic analysis of the active site in the enzyme for substrate, inhibitor and, inhibitor's metabolite (K2). Interaction between acarbose and α-amylase involved significant hydrogen binding compared to that of starch, producing a stronger enzyme-inhibitor complex. Further, docking analysis led us to predict the site on α-amylase where the inhibitor (acarbose) bound more tightly, which possibly affected the binding and hydrolysis of starch exerting its effective anti-diabetic function.

Ecotoxicity of quinoline and hydroxylated derivatives and their occurrence in groundwater of a tar-contaminated field site.

PubMed

Neuwoehner, Judith; Reineke, Anne-Kirsten; Hollender, Juliane; Eisentraeger, Adolf

2009-03-01

In the groundwater of a timber impregnation site higher concentrations of hydroxylated quinolines compared to their parent compounds quinoline and isoquinoline were found. Studying the toxicity of parent compounds and metabolites, genotoxicity was found with metabolic activation in the SOS-Chromotest and Ames fluctuation test only for quinoline. An adverse effect on algae was observed only for the parent compounds quinoline and isoquinoline, while in the Daphnia magna immobilization assay most hydroxylated quinoline derivatives showed toxicity. The highest ecotoxic potential was observed in the Vibrio fischeri luminescence-inhibition assay. Comparing experimental EC50-values with QSAR predicted ones, for all compounds apart from isoquinoline and 2(1H)-quinolinone in the V. fischeri test baseline toxicity or polar nacrosis is indicated. In conclusion, the hydroxylation of quinoline leads to a detoxification of the genotoxic potential, while taken additive mixture toxicity and a safety factor into account parent compounds and metabolites are found of ecotoxicological relevance in the groundwater.

Biodiversity mediates top-down control in eelgrass ecosystems: a global comparative-experimental approach.

PubMed

Duffy, J Emmett; Reynolds, Pamela L; Boström, Christoffer; Coyer, James A; Cusson, Mathieu; Donadi, Serena; Douglass, James G; Eklöf, Johan S; Engelen, Aschwin H; Eriksson, Britas Klemens; Fredriksen, Stein; Gamfeldt, Lars; Gustafsson, Camilla; Hoarau, Galice; Hori, Masakazu; Hovel, Kevin; Iken, Katrin; Lefcheck, Jonathan S; Moksnes, Per-Olav; Nakaoka, Masahiro; O'Connor, Mary I; Olsen, Jeanine L; Richardson, J Paul; Ruesink, Jennifer L; Sotka, Erik E; Thormar, Jonas; Whalen, Matthew A; Stachowicz, John J

2015-07-01

Nutrient pollution and reduced grazing each can stimulate algal blooms as shown by numerous experiments. But because experiments rarely incorporate natural variation in environmental factors and biodiversity, conditions determining the relative strength of bottom-up and top-down forcing remain unresolved. We factorially added nutrients and reduced grazing at 15 sites across the range of the marine foundation species eelgrass (Zostera marina) to quantify how top-down and bottom-up control interact with natural gradients in biodiversity and environmental forcing. Experiments confirmed modest top-down control of algae, whereas fertilisation had no general effect. Unexpectedly, grazer and algal biomass were better predicted by cross-site variation in grazer and eelgrass diversity than by global environmental gradients. Moreover, these large-scale patterns corresponded strikingly with prior small-scale experiments. Our results link global and local evidence that biodiversity and top-down control strongly influence functioning of threatened seagrass ecosystems, and suggest that biodiversity is comparably important to global change stressors. © 2015 John Wiley & Sons Ltd/CNRS.

Trampling impacts on thermotolerant vegetation of geothermal areas in New Zealand.

PubMed

Burns, Bruce R; Ward, Jonet; Downs, Theresa M

2013-12-01

Geothermal features such as geysers, mud pools, sinter terraces, fumaroles, hot springs, and steaming ground are natural attractions often visited by tourists. Visitation rates for such areas in the Taupo Volcanic Zone of New Zealand are in the order of hundreds of thousands annually. These areas are also habitat for rare and specialized plant and microbial communities that live in the steam-heated soils of unusual chemical composition. We evaluated historical and current trampling impacts of tourists on the thermotolerant vegetation of the Waimangu and Waiotapu geothermal areas near Rotorua, and compared the results to experimental trampling at a third site (Taheke) not used by tourists. Historical tourism has removed vegetation and soil from around key features, and remaining subsoil is compacted into an impervious pavement on which vegetation recolonization is unlikely in the short term. Social tracks made by tourists were present at both tourist sites often leading them onto hotter soils than constructed tracks. Vegetation height and cover were lower on and adjacent to social tracks than further from them. Thermotolerant vegetation showed extremely low resistance to experimental trampling. This confirms and extends previous research that also shows that thallophytes and woody shrubs, life forms that dominate in thermotolerant vegetation, are vulnerable to trampling damage. Preservation of these vulnerable ecosystems must ensure that tourist traffic is confined to existing tracks or boardwalks, and active restoration of impacted sites may be warranted.

Investigating plausible mechanisms for the photo-induced partial unfolding of a globular protein

NASA Astrophysics Data System (ADS)

Parker, James E.

Two hypotheses are proposed to explain the photo-induced unfolding of β-lactoglobulin (BLG) that occurs when non-covalently bound to a dye molecule, meso-tetrakis (p-sulfonatophenyl) porphyrin (TSPP), and illuminated by a laser in the post-Tanford transition configuration. The first involves a photo-induced electron transfer from the porphyrin to the protein. The second involves the production of kynurenine by singlet oxygen that is generated during photo-excitation of the porphyrin. To evaluate these hypotheses, a series of computational and experimental results have been combined to establish the physical state of the BLG-TSPP complex and to estimate the likelihood of a post-irradiation event to initiate the partial unfolding. Determining the binding site location is crucial to establish the position of the photo-induced events and the likely end-product. A study of the vibronic state of the BLG-TSPP complex using resonant Raman and absorption spectroscopy coupled with density functional theory (DFT) and docking simulations is used to estimate the location of the binding site. Once the binding site is found, molecular dynamics simulations of the post-irradiation event relaxations in the protein are used to estimate the resulting secondary structure. This structure is compared to experimental estimates of the secondary structure of the unfolded protein to determine which hypothesis is the most likely mechanism to explain the unfolding.

Theoretical evidence of the observed kinetic order dependence on temperature during the N(2)O decomposition over Fe-ZSM-5.

PubMed

Guesmi, Hazar; Berthomieu, Dorothee; Bromley, Bryan; Coq, Bernard; Kiwi-Minsker, Lioubov

2010-03-28

The characterization of Fe/ZSM5 zeolite materials, the nature of Fe-sites active in N(2)O direct decomposition, as well as the rate limiting step are still a matter of debate. The mechanism of N(2)O decomposition on the binuclear oxo-hydroxo bridged extraframework iron core site [Fe(II)(mu-O)(mu-OH)Fe(II)](+) inside the ZSM-5 zeolite has been studied by combining theoretical and experimental approaches. The overall calculated path of N(2)O decomposition involves the oxidation of binuclear Fe(II) core sites by N(2)O (atomic alpha-oxygen formation) and the recombination of two surface alpha-oxygen atoms leading to the formation of molecular oxygen. Rate parameters computed using standard statistical mechanics and transition state theory reveal that elementary catalytic steps involved into N(2)O decomposition are strongly dependent on the temperature. This theoretical result was compared to the experimentally observed steady state kinetics of the N(2)O decomposition and temperature-programmed desorption (TPD) experiments. A switch of the reaction order with respect to N(2)O pressure from zero to one occurs at around 800 K suggesting a change of the rate determining step from the alpha-oxygen recombination to alpha-oxygen formation. The TPD results on the molecular oxygen desorption confirmed the mechanism proposed.

Distribution of amoxicillin and clavulanic acid in infected animals and efficacy against experimental infections.

PubMed Central

Boon, R J; Beale, A S; Comber, K R; Pierce, C V; Sutherland, R

1982-01-01

The therapeutic effects produced by formulations of amoxicillin plus clavulanic acid (BRL 25 000A and BRL 25 000G) were compared with those of amoxicillin and clavulanic acid separately against a variety of infections produced by amoxicillin-susceptible and beta-lactamase-producing (amoxicillin-resistant) bacteria. The infection models studied included intraperitoneal infections, a mouse pneumonia, experimental pyelonephritis, and local lesions caused by Staphylococcus aureus and Bacteroides fragilis. The distribution of amoxicillin and clavulanic acid in infected animals after the administration of amoxicillin-clavulanic acid was evaluated by measurement of the concentrations of the substances present in specimens collected at the sites of infection. The results showed that both amoxicillin and clavulanic acid were well distributed in the animal body after the administration of amoxicillin-clavulanic acid formulations, being present in significant concentrations at various sites of infection, e.g., peritoneal washings, pleural fluid, pus, and infected tissue homogenates. In a number of cases, the amoxicillin concentrations measured after the administration of BRL 25000 were higher than those found after treatment with amoxicillin alone, presumably as a result of inhibition of bacterial beta-lactamases by clavulanic acid at the site of infection. The ability of clavulanic acid to protect amoxicillin in vivo was confirmed by the efficacy of amoxicillin-clavulanic acid formulations in the treatment of the infections studied, most of which were refractory to therapy with amoxicillin. PMID:7137980

Trampling Impacts on Thermotolerant Vegetation of Geothermal Areas in New Zealand

NASA Astrophysics Data System (ADS)

Burns, Bruce R.; Ward, Jonet; Downs, Theresa M.

2013-12-01

Geothermal features such as geysers, mud pools, sinter terraces, fumaroles, hot springs, and steaming ground are natural attractions often visited by tourists. Visitation rates for such areas in the Taupo Volcanic Zone of New Zealand are in the order of hundreds of thousands annually. These areas are also habitat for rare and specialized plant and microbial communities that live in the steam-heated soils of unusual chemical composition. We evaluated historical and current trampling impacts of tourists on the thermotolerant vegetation of the Waimangu and Waiotapu geothermal areas near Rotorua, and compared the results to experimental trampling at a third site (Taheke) not used by tourists. Historical tourism has removed vegetation and soil from around key features, and remaining subsoil is compacted into an impervious pavement on which vegetation recolonization is unlikely in the short term. Social tracks made by tourists were present at both tourist sites often leading them onto hotter soils than constructed tracks. Vegetation height and cover were lower on and adjacent to social tracks than further from them. Thermotolerant vegetation showed extremely low resistance to experimental trampling. This confirms and extends previous research that also shows that thallophytes and woody shrubs, life forms that dominate in thermotolerant vegetation, are vulnerable to trampling damage. Preservation of these vulnerable ecosystems must ensure that tourist traffic is confined to existing tracks or boardwalks, and active restoration of impacted sites may be warranted.

Probing numerical Laplace inversion methods for two and three-site molecular exchange between interconnected pore structures.

PubMed

Silletta, Emilia V; Franzoni, María B; Monti, Gustavo A; Acosta, Rodolfo H

2018-01-01

Two-dimension (2D) Nuclear Magnetic Resonance relaxometry experiments are a powerful tool extensively used to probe the interaction among different pore structures, mostly in inorganic systems. The analysis of the collected experimental data generally consists of a 2D numerical inversion of time-domain data where T 2 -T 2 maps are generated. Through the years, different algorithms for the numerical inversion have been proposed. In this paper, two different algorithms for numerical inversion are tested and compared under different conditions of exchange dynamics; the method based on Butler-Reeds-Dawson (BRD) algorithm and the fast-iterative shrinkage-thresholding algorithm (FISTA) method. By constructing a theoretical model, the algorithms were tested for a two- and three-site porous media, varying the exchange rates parameters, the pore sizes and the signal to noise ratio. In order to test the methods under realistic experimental conditions, a challenging organic system was chosen. The molecular exchange rates of water confined in hierarchical porous polymeric networks were obtained, for a two- and three-site porous media. Data processed with the BRD method was found to be accurate only under certain conditions of the exchange parameters, while data processed with the FISTA method is precise for all the studied parameters, except when SNR conditions are extreme. Copyright © 2017 Elsevier Inc. All rights reserved.

Irrigation of Abdomen With Imipenem Solution Decreases Surgical Site Infections in Patients With Perforated Appendicitis: A Randomized Clinical Trial

PubMed Central

Hesami, Mohammad Ali; Alipour, Hamid; Nikoupour Daylami, Hamed; Alipour, Bijan; Bazargan-Hejazi, Shahrzad; Ahmadi, Alireza

2014-01-01

Background: Perforated appendicitis is one of the most common causes of acute abdomen requiring emergent surgery for immediate appendectomy and peritoneal cavity irrigation; however, the efficacy of irrigation with antibiotic solutions is controversial. Objectives: The aim of this study was to assess the efficacy of imipenem solution irrigation on post-operative surgical site infections (SSIs), hospital length of stay, and hospital costs. We hypothesized that there would be lower rate of SSIs, a shorter hospital stay, and lower hospital cost in patients with perforated appendicitis who received peritoneal cavity irrigation with imipenem solution in comparison to their counterparts who received irrigation with normal saline. Patients and Methods: In this randomized single-blind parallel-group clinical trial, we enrolled 90 patients with perforated appendicitis with 12-50 years of age and randomly allocated them into experimental group (n = 45) and control group (n = 45). The control group received peritoneal irrigation with normal saline (0.9%) and experimental group underwent peritoneal irrigation with imipenem solution (1 mg/mL). All surgical procedures were performed in Imam Reza Hospital of Kermanshah University of Medical Sciences. The study primary outcome was surgical site infections (including wound infection and abdominal abscess) and the secondary outcomes were length of hospital stay and hospital cost. Chi-squared and t-tests were used to analyze the study data. Results: Imipenem solution irrigation was associated with significant clinical improvement at one-month follow-up. The experimental group presented with significantly lower rate of SSIs and shorter length of hospital stay. The experimental group had lower rate of SSIs compared to the control group (4.4% vs. 22.2%, respectively) (p= 0.013). The duration of hospital stay was nearly one day longer in control group (5.84 ± 2.58 days) vs. experimental group (4.91 ± 1.29 days) (P = 0.034), and hospital costs were $50 lower in experimental group ($500 ± $292) vs. control group ($450 ± $170) (P = 0.281). Conclusions: The study findings revealed that peritoneal lavage with imipenem solution (1 mg/mL) decreases the rate of post-operative SSIs in patients with perforated appendicitis in comparison to patients irrigated with normal saline alone. These patients also had shorter hospital stay, and lower hospital costs. PMID:24910794

Atomistic Modeling of Cation Diffusion in Transition Metal Perovskites La1-xSrxMnO3+/-δfor Solid Oxide Fuel Cell Cathodes Applications

NASA Astrophysics Data System (ADS)

Lee, Yueh-Lin; Duan, Yuhua; Morgan, Dane; Sorescu, Dan; Abernathy, Harry

Cation diffusion in La1-xSrxMnO3+/-δ (LSM) and in related perovskite materials play an important role in controlling long term performance and stability of solid oxide fuel cell (SOFCs) cathodes. Due to sluggish rates of cation diffusion and complex coupling between defect chemistry and cation diffusion pathways, currently there is still lack of quantitative theoretical model predictions on cation diffusivity vs. T and P(O2) to describe experimental cation tracer diffusivities. In this work, based on ab initio modeling of LSM defect chemistry and migration barriers of the possible cation diffusion pathways, we assess the rates of A-site and B-site cation diffusion in a wide range of T and P(O2) at x =0.0 and 0.2 for SOFC applications. We demonstrate the active cation diffusion pathways in LSM involve cation defect clusters as cation transport carriers, where reduction in the cation migration barriers, which are governed by the steric effect associated with the metal-oxygen cage in the perovskite lattice, is much greater than the penalty of repulsive interaction in the A-site and B-site cation vacancy clusters, leading to higher cation diffusion rates as compared to those of single cation vacancy hopping mechanisms. The predicted Mn and La/Sr cation self-diffusion coefficients of LSM at at x =0.0 and 0.2 along with their 1/T and P(O2) dependences, are in good agreement with the experimental tracer diffusion coefficients.

Adsorption and Gas Separation of Molecules by Carbon Nanohorns.

PubMed

Gatica, Silvina M; Nekhai, Anton; Scrivener, Adam

2016-05-19

In this paper, we report the results of Monte Carlo simulations of the adsorption of neon, argon, methane and carbon dioxide in carbon nanohorns. We model the nanohorns as an array of carbon cones and obtained adsorption isotherms and isosteric heats. The main sites of adsorption are inside the cones and in the interstices between three cones. We also calculated the selectivity of carbon dioxide/methane, finding that nanohorns are a suitable substrate for gas separation. Our simulations are compared to available experimental data.

XAS Characterization of the Zn Site of Non-structural Protein 3 (NS3) from Hepatitis C Virus

NASA Astrophysics Data System (ADS)

Ascone, I.; Nobili, G.; Benfatto, M.; Congiu-Castellano, A.

2007-02-01

XANES spectra of non structural protein 3 (NS3) have been calculated using 4 Zn coordination models from three crystallographic structures in the Protein Data Base (PDB): 1DY9, subunit B, 1CU1 subunit A and B, and 1JXP subunit B. Results indicate that XANES is an appropriate tool to distinguish among them. Experimental XANES spectra have been simulated refining crystallographic data. The model obtained by XAS is compared with the PDB models.

Evaluation of the predictive capability of coupled thermo-hydro-mechanical models for a heated bentonite/clay system (HE-E) in the Mont Terri Rock Laboratory

DOE PAGES

Garitte, B.; Shao, H.; Wang, X. R.; ...

2017-01-09

Process understanding and parameter identification using numerical methods based on experimental findings are a key aspect of the international cooperative project DECOVALEX. Comparing the predictions from numerical models against experimental results increases confidence in the site selection and site evaluation process for a radioactive waste repository in deep geological formations. In the present phase of the project, DECOVALEX-2015, eight research teams have developed and applied models for simulating an in-situ heater experiment HE-E in the Opalinus Clay in the Mont Terri Rock Laboratory in Switzerland. The modelling task was divided into two study stages, related to prediction and interpretation ofmore » the experiment. A blind prediction of the HE-E experiment was performed based on calibrated parameter values for both the Opalinus Clay, that were based on the modelling of another in-situ experiment (HE-D), and modelling of laboratory column experiments on MX80 granular bentonite and a sand/bentonite mixture .. After publication of the experimental data, additional coupling functions were analysed and considered in the different models. Moreover, parameter values were varied to interpret the measured temperature, relative humidity and pore pressure evolution. The analysis of the predictive and interpretative results reveals the current state of understanding and predictability of coupled THM behaviours associated with geologic nuclear waste disposal in clay formations.« less

Evaluation of the predictive capability of coupled thermo-hydro-mechanical models for a heated bentonite/clay system (HE-E) in the Mont Terri Rock Laboratory

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

Garitte, B.; Shao, H.; Wang, X. R.

Process understanding and parameter identification using numerical methods based on experimental findings are a key aspect of the international cooperative project DECOVALEX. Comparing the predictions from numerical models against experimental results increases confidence in the site selection and site evaluation process for a radioactive waste repository in deep geological formations. In the present phase of the project, DECOVALEX-2015, eight research teams have developed and applied models for simulating an in-situ heater experiment HE-E in the Opalinus Clay in the Mont Terri Rock Laboratory in Switzerland. The modelling task was divided into two study stages, related to prediction and interpretation ofmore » the experiment. A blind prediction of the HE-E experiment was performed based on calibrated parameter values for both the Opalinus Clay, that were based on the modelling of another in-situ experiment (HE-D), and modelling of laboratory column experiments on MX80 granular bentonite and a sand/bentonite mixture .. After publication of the experimental data, additional coupling functions were analysed and considered in the different models. Moreover, parameter values were varied to interpret the measured temperature, relative humidity and pore pressure evolution. The analysis of the predictive and interpretative results reveals the current state of understanding and predictability of coupled THM behaviours associated with geologic nuclear waste disposal in clay formations.« less

Cholesterol-Binding Sites in GIRK Channels: The Devil is in the Details.

PubMed

Rosenhouse-Dantsker, Avia

2018-01-01

In recent years, it has become evident that cholesterol plays a direct role in the modulation of a variety of ion channels. In most cases, cholesterol downregulates channel activity. In contrast, our earlier studies have demonstrated that atrial G protein inwardly rectifying potassium (GIRK) channels are upregulated by cholesterol. Recently, we have shown that hippocampal GIRK currents are also upregulated by cholesterol. A combined computational-experimental approach pointed to putative cholesterol-binding sites in the transmembrane domain of the GIRK2 channel, the primary subunit in hippocampal GIRK channels. In particular, the principal cholesterol-binding site was located in the center of the transmembrane domain in between the inner and outer α-helices of 2 adjacent subunits. Further studies pointed to a similar cholesterol-binding site in GIRK4, a major subunit in atrial GIRK channels. However, a close look at a sequence alignment of the transmembrane helices of the 2 channels reveals surprising differences among the residues that interact with the cholesterol molecule in these 2 channels. Here, we compare the residues that form putative cholesterol-binding sites in GIRK2 and GIRK4 and discuss the similarities and differences among them.

Clusterization Effects in III-V Nitrides: Nitrogen Vacancies, and Si and Mg Impurities in Aluminum Nitride and Gallium Nitride

NASA Astrophysics Data System (ADS)

Gubanov, V. A.; Pentaleri, E. A.; Boekema, C.; Fong, C. Y.; Klein, B. M.

1997-03-01

We have investigated clusterization of nitrogen vacancies and Si and Mg doping impurities in zinc-blende aluminum nitride (c-AlN) and gallium nitride (c-GaN) by the tight-binding LMTO technique. The calculations used 128-site supercells. Si and Mg atoms replacing ions in both the cation and anion sublattices of the host lattices of the host crystals have been considered. The Mg impurity at cation sites is found to form partially occupied states at the valence-band edge, and may result in p-type conductivity. When Si substitutes for Ga, the impurity band is formed at the conduction-band edge, resulting in n-type conductivity. Si impurities at cation sites, and Mg impurity at anion sites are able to form resonance states in the gap. The influence of impurity clusterization in the host lattice and interstitial sites on electronic properties of c-AlN and c-GaN crystals are modeled. The changes in vacancy- and impurity-state energies, bonding type, localization, density of states at the Fermi level in different host lattices, their dependence on impurity/vacancy concentration are analyzed and compared with the experimental data.

SPEER-SERVER: a web server for prediction of protein specificity determining sites

PubMed Central

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J.; Panchenko, Anna R.; Chakrabarti, Saikat

2012-01-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/. PMID:22689646

Coarse-Grained Model for Water Involving a Virtual Site.

PubMed

Deng, Mingsen; Shen, Hujun

2016-02-04

In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones.

Impacts of off-road vehicles on nitrogen cycles in biological soil crusts: Resistance in different U.S. deserts

USGS Publications Warehouse

Belnap, Jayne

2002-01-01

Biological soil crusts are an important component of desert ecosystems, as they influence soil stability and fertility. This study examined and compared the short-term vehicular impacts on lichen cover and nitrogenase activity (NA) of biological soil crusts. Experimental disturbance was applied to different types of soil in regions throughout the western U.S. (Great Basin, Colorado Plateau, Sonoran, Chihuahuan, and Mojave deserts). Results show that pre-disturbance cover of soil lichens is significantly correlated with the silt content of soils, and negatively correlated with sand and clay. While disturbance appeared to reduce NA at all sites, differences were statistically significant at only 12 of the 26 sites. Cool desert sites showed a greater decline than hot desert sites, which may indicate non-heterocystic cyanobacterial species are more susceptible to disturbance than non-heterocystic species. Sandy soils showed greater reduction of NA as sand content increased, while fine-textured soils showed a greater decline as sand content increased. At all sites, higher NA before the disturbance resulted in less impact to NA post-disturbance. These results may be useful in predicting the impacts of off-road vehicles in different regions and different soils.

MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction.

PubMed

Wang, Duolin; Zeng, Shuai; Xu, Chunhui; Qiu, Wangren; Liang, Yanchun; Joshi, Trupti; Xu, Dong

2017-12-15

Computational methods for phosphorylation site prediction play important roles in protein function studies and experimental design. Most existing methods are based on feature extraction, which may result in incomplete or biased features. Deep learning as the cutting-edge machine learning method has the ability to automatically discover complex representations of phosphorylation patterns from the raw sequences, and hence it provides a powerful tool for improvement of phosphorylation site prediction. We present MusiteDeep, the first deep-learning framework for predicting general and kinase-specific phosphorylation sites. MusiteDeep takes raw sequence data as input and uses convolutional neural networks with a novel two-dimensional attention mechanism. It achieves over a 50% relative improvement in the area under the precision-recall curve in general phosphorylation site prediction and obtains competitive results in kinase-specific prediction compared to other well-known tools on the benchmark data. MusiteDeep is provided as an open-source tool available at https://github.com/duolinwang/MusiteDeep. xudong@missouri.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

SPEER-SERVER: a web server for prediction of protein specificity determining sites.

PubMed

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J; Panchenko, Anna R; Chakrabarti, Saikat

2012-07-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids' Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/.

Post-operative shampoo effects in neurosurgical patients: a pilot experimental study.

PubMed

Palese, Alvisa; Moreale, Renzo; Noacco, Massimo; Pistrino, Flavia; Mastrolia, Irene; Sartor, Assunta; Scarparo, Claudio; Skrap, Miran

2015-04-01

Neurosurgical site infections are an important issue. Among the acknowledged preventive tactics, the non-shaving technique is well established in the neurosurgical setting. However, given that patient's hair around the surgical site may retain biologic material that emerges during the surgical procedure or that may simply become dirty, which may increase the risk of surgical site infections, if and when shampooing should be offered remains under debate. A pilot experimental study was undertaken from 2011 to 2012. A series of neurosurgical patients not affected by conditions that would increase the risk of post-operative infection were assigned randomly to the exposed group (receiving shampoo 72 h after surgical procedure) or control group (receiving standard dressing surveillance without shampooing). Comfort, surgical site contamination (measured as the number of colony-forming units [CFU]), and SSIs at 30 d after surgery were the main study outcomes. A total of 53 patients were included: 25 (47.2%) received a shampoo after 72 h whereas 28 (52.8%) received standard care. Patients who received a shampoo reported a similar level of comfort (average=8.04; standard deviation [SD] 1.05) compared with those receiving standard care (average 7.3; SD 3.2) although this was not statistically significant (p=0.345). No statistically significant difference emerged in the occurrence of surgical site contamination between the groups, and no SSIs were detected within 30 d. In our pilot study, the results of which are not generalizable because of the limited sample of patients involved, a gentle shampoo offered 72 h after the surgical procedure did not increase the SSIs occurrence or the contamination of the surgical site, although it may increase the perception of comfort by patients. Further studies are strongly recommended involving a larger sample size and designed to include more diversified neurosurgical patients undergoing surgical procedures in different centers.

GPS-CCD: A Novel Computational Program for the Prediction of Calpain Cleavage Sites

PubMed Central

Gao, Xinjiao; Ma, Qian; Ren, Jian; Xue, Yu

2011-01-01

As one of the most essential post-translational modifications (PTMs) of proteins, proteolysis, especially calpain-mediated cleavage, plays an important role in many biological processes, including cell death/apoptosis, cytoskeletal remodeling, and the cell cycle. Experimental identification of calpain targets with bona fide cleavage sites is fundamental for dissecting the molecular mechanisms and biological roles of calpain cleavage. In contrast to time-consuming and labor-intensive experimental approaches, computational prediction of calpain cleavage sites might more cheaply and readily provide useful information for further experimental investigation. In this work, we constructed a novel software package of GPS-CCD (Calpain Cleavage Detector) for the prediction of calpain cleavage sites, with an accuracy of 89.98%, sensitivity of 60.87% and specificity of 90.07%. With this software, we annotated potential calpain cleavage sites for hundreds of calpain substrates, for which the exact cleavage sites had not been previously determined. In this regard, GPS-CCD 1.0 is considered to be a useful tool for experimentalists. The online service and local packages of GPS-CCD 1.0 were implemented in JAVA and are freely available at: http://ccd.biocuckoo.org/. PMID:21533053

In-Situ Tuff Water Migration/Heater Experiment: posttest thermal analysis

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

Eaton, R.R.; Johnstone, J.K.; Nunziato, J.W.

This report describes posttest laboratory experiments and thermal computations for the In-Situ Tuff Water Migration/Heater Experiment that was conducted in Grouse Canyon Welded Tuff in G-Tunnel, Nevada Test Site. Posttest laboratory experiments were designed to determine the accuracy of the temperatures measured by the rockwall thermocouples during the in-situ test. The posttest laboratory experiments showed that the measured in-situ rockwall temperatures were 10 to 20{sup 0}C higher than the true rockwall temperatures. The posttest computational results, obtained with the thermal conduction code COYOTE, were compared with the experimentally obtained data and with calculated pretest results. Daily heater output power fluctuationsmore » (+-4%) caused by input power line variations and the sensitivity of temperature to heater output power required care in selecting the average heater output power values used in the code. The posttest calculated results compare reasonably well with the experimental data. 10 references, 14 figures, 5 tables.« less

Staged invasions across disparate grasslands: effects of seed provenance, consumers and disturbance on productivity and species richness.

PubMed

Maron, John L; Auge, Harald; Pearson, Dean E; Korell, Lotte; Hensen, Isabell; Suding, Katharine N; Stein, Claudia

2014-04-01

Exotic plant invasions are thought to alter productivity and species richness, yet these patterns are typically correlative. Few studies have experimentally invaded sites and asked how addition of novel species influences ecosystem function and community structure and examined the role of competitors and/or consumers in mediating these patterns. We invaded disturbed and undisturbed subplots in and out of rodent exclosures with seeds of native or exotic species in grasslands in Montana, California and Germany. Seed addition enhanced aboveground biomass and species richness compared with no-seeds-added controls, with exotics having disproportionate effects on productivity compared with natives. Disturbance enhanced the effects of seed addition on productivity and species richness, whereas rodents reduced productivity, but only in Germany and California. Our results demonstrate that experimental introduction of novel species can alter ecosystem function and community structure, but that local filters such as competition and herbivory influence the magnitude of these impacts. © 2014 John Wiley & Sons Ltd/CNRS.

Altitudinal variation of secondary metabolite profiles in flowering heads of Arnica montana cv. ARBO.

PubMed

Spitaler, Renate; Schlorhaufer, P Daniel; Ellmerer, Ernst P; Merfort, Irmgard; Bortenschlager, Sigmar; Stuppner, Hermann; Zidorn, Christian

2006-02-01

The altitudinal variation on the contents of secondary metabolites in flowering heads of Arnica montana was assessed. Plants of A. montana cultivar ARBO were grown in nine experimental plots at altitudes between 590 and 2230m at Mount Patscherkofel near Innsbruck/Austria. The total contents of sesquiterpene lactones and flavonoids were not positively correlated with the altitude of the growing site. However, the proportion of flavonoids with vicinal free hydroxy groups in ring B to flavonoids lacking this feature significantly increased with elevation. Additionally, the level of caffeic acid derivatives also positively correlated with the altitude of the growing site. In particular amounts of 1-methoxyoxaloyl-3,5-dicaffeoylquinic acid significantly increased in higher sites and samples from the summit region contained 85% more of this compound than samples from valley sites. These results are discussed with regards to chemosystematic studies comparing samples collected in different altitudes as well as in the light of a UV-B protective and radical scavenging function of phenolics and their significance for plant life in environments with elevated UV-B radiation.

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

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

Jayasinghe, Reyka G.; Cao, Song; Gao, Qingsong

For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared tomore » missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Finally, our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.« less

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

PubMed

Jayasinghe, Reyka G; Cao, Song; Gao, Qingsong; Wendl, Michael C; Vo, Nam Sy; Reynolds, Sheila M; Zhao, Yanyan; Climente-González, Héctor; Chai, Shengjie; Wang, Fang; Varghese, Rajees; Huang, Mo; Liang, Wen-Wei; Wyczalkowski, Matthew A; Sengupta, Sohini; Li, Zhi; Payne, Samuel H; Fenyö, David; Miner, Jeffrey H; Walter, Matthew J; Vincent, Benjamin; Eyras, Eduardo; Chen, Ken; Shmulevich, Ilya; Chen, Feng; Ding, Li

2018-04-03

For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Adsorption of O2, SO2, and SO3 on nickel oxide. Mechanism for sulfate formation

NASA Technical Reports Server (NTRS)

Mehandru, S. P.; Anderson, A. B.

1985-01-01

Calculations based on the atom superposition and electron delocalization molecular orbital (ASED-MO) technique suggest that O2 will adsorb perferentially end-on at an angle 45 deg from normal on a nickel cation site on the (100) surface of NiO. SO2 adsorption is also stronger on the nickel site; SO2 bonds through the sulfur atom is a plane perpendicular to the surface. Adsorption energies for SO3 on the nickel and oxygen sites are comparable in the perferred orientation in which the SO3 plane is parallel to the surface. On activation, SO3 adsorbed to an O2(-) site forms a trigonal pyramidal SO4 species which yields, with a low barrier, a tetrahedral sulfate anion. Subsequently the anion reorients on the surface. Possibilities for alternative mechanisms which require the formation of Ni3(+) or O2(-) are discussed. NiSO4 thus formed leads to the corrosion of Ni at high temperatures in the SO2+O2/SO3 The SO2+O2/SO3 atmosphere, as discussed in the experimental literature.

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

DOE PAGES

Jayasinghe, Reyka G.; Cao, Song; Gao, Qingsong; ...

2018-04-05

For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared tomore » missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Finally, our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.« less

Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

PubMed Central

Picón, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; Doumy, G.; Erk, B.; Ferguson, K. R.; Gorkhover, T.; Ho, P. J.; Kanter, E. P.; Krässig, B.; Krzywinski, J.; Lutman, A. A.; March, A. M.; Moonshiram, D.; Ray, D.; Young, L.; Pratt, S. T.; Southworth, S. H.

2016-01-01

New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Particularly, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. Here we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site. PMID:27212390

Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics.

PubMed

Picón, A; Lehmann, C S; Bostedt, C; Rudenko, A; Marinelli, A; Osipov, T; Rolles, D; Berrah, N; Bomme, C; Bucher, M; Doumy, G; Erk, B; Ferguson, K R; Gorkhover, T; Ho, P J; Kanter, E P; Krässig, B; Krzywinski, J; Lutman, A A; March, A M; Moonshiram, D; Ray, D; Young, L; Pratt, S T; Southworth, S H

2016-05-23

New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Particularly, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. Here we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF2 molecules following X-ray absorption at the Xe site.

Bone modelling at fresh extraction sockets: immediate implant placement versus spontaneous healing: an experimental study in the beagle dog.

PubMed

Vignoletti, Fabio; Discepoli, Nicola; Müller, Anna; de Sanctis, Massimo; Muñoz, Fernando; Sanz, Mariano

2012-01-01

The purpose of this investigation is to describe histologically the undisturbed healing of fresh extraction sockets when compared to immediate implant placement. In eight beagle dogs, after extraction of the 3P3 and 4P4, implants were inserted into the distal sockets of the premolars, while the mesial sockets were left to heal spontaneously. Each animal provided four socket sites (control) and four implant sites (test). After 6 weeks, animals were sacrificed and tissue blocks were dissected, prepared for ground sectioning. The relative vertical buccal bone resorption in relation to the lingual bone was similar in both test and control groups. At immediate implant sites, however, the absolute buccal bone loss observed was 2.32 (SD 0.36) mm, what may indicate that while an apical shift of both the buccal and lingual bone crest occurred at the implant sites, this may not happen in naturally healing sockets. The results from this investigation showed that after tooth extraction the buccal socket wall underwent bone resorption at both test and control sites. This resorption appeared to be more pronounced at the implant sites, although the limitations of the histological evaluation method utilized preclude a definite conclusion. © 2011 John Wiley & Sons A/S.

The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin.

PubMed

Collins, Richard A; Stajich, Jason E; Field, Deborah J; Olive, Joan E; DeAbreu, Diane M

2015-05-01

When we expressed a small (0.9 kb) nonprotein-coding transcript derived from the mitochondrial VS plasmid in the nucleus of Neurospora we found that it was efficiently spliced at one or more of eight 5' splice sites and ten 3' splice sites, which are present apparently by chance in the sequence. Further experimental and bioinformatic analyses of other mitochondrial plasmids, random sequences, and natural nuclear genes in Neurospora and other fungi indicate that fungal spliceosomes recognize a wide range of 5' splice site and branchpoint sequences and predict introns to be present at high frequency in random sequence. In contrast, analysis of intronless fungal nuclear genes indicates that branchpoint, 5' splice site and 3' splice site consensus sequences are underrepresented compared with random sequences. This underrepresentation of splicing signals is sufficient to deplete the nuclear genome of splice sites at locations that do not comprise biologically relevant introns. Thus, the splicing machinery can recognize a wide range of splicing signal sequences, but splicing still occurs with great accuracy, not because the splicing machinery distinguishes correct from incorrect introns, but because incorrect introns are substantially depleted from the genome. © 2015 Collins et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Site-preference and valency for rare-earth sites in (R-Ce)2Fe14B magnets

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

Alam, Aftab; Khan, Mahmud; McCallum, R. W.

2013-01-28

Rare-earth (R) permanent magnets of R2Fe14B have technological importance due to their high energy products, and they have two R-sites (Wyckoff 4f and 4g, with four-fold multiplicity) that affect chemistry and valence. Designing magnetic behavior and stability via alloying is technologically relevant to reduce critical (expensive) R-content while retaining key properties; cerium, an abundant (cheap) R-element, offers this potential. We calculate magnetic properties and Ce site preference in (R1-xCex)2Fe14B [R=La,Nd] using density functional theory (DFT) methods—including a DFT+U scheme to treat localized 4f-electrons. Fe moments compare well with neutron data—almost unaffected by Hubbard U, and weakly affected by spin-orbit coupling.more » In La2Fe14B, Ce alloys for 0 ≤ x ≤ 1 and prefers smaller R(4f) sites, as observed, a trend we find unaffected by valence. Whereas, in Nd2Fe14B, Ce is predicted to have limited alloying (x ≤ 0.3) with a preference for larger R(4g) sites, resulting in weak partial ordering and segregation. The Curie temperatures versus x for (Nd,Ce) were predicted for a typical sample processing and verified experimentally.« less

OH-PRED: prediction of protein hydroxylation sites by incorporating adapted normal distribution bi-profile Bayes feature extraction and physicochemical properties of amino acids.

PubMed

Jia, Cang-Zhi; He, Wen-Ying; Yao, Yu-Hua

2017-03-01

Hydroxylation of proline or lysine residues in proteins is a common post-translational modification event, and such modifications are found in many physiological and pathological processes. Nonetheless, the exact molecular mechanism of hydroxylation remains under investigation. Because experimental identification of hydroxylation is time-consuming and expensive, bioinformatics tools with high accuracy represent desirable alternatives for large-scale rapid identification of protein hydroxylation sites. In view of this, we developed a supporter vector machine-based tool, OH-PRED, for the prediction of protein hydroxylation sites using the adapted normal distribution bi-profile Bayes feature extraction in combination with the physicochemical property indexes of the amino acids. In a jackknife cross validation, OH-PRED yields an accuracy of 91.88% and a Matthew's correlation coefficient (MCC) of 0.838 for the prediction of hydroxyproline sites, and yields an accuracy of 97.42% and a MCC of 0.949 for the prediction of hydroxylysine sites. These results demonstrate that OH-PRED increased significantly the prediction accuracy of hydroxyproline and hydroxylysine sites by 7.37 and 14.09%, respectively, when compared with the latest predictor PredHydroxy. In independent tests, OH-PRED also outperforms previously published methods.

Comparative analysis of effluent water quality from a municipal treatment plant and two on-site wastewater treatment systems.

PubMed

Garcia, Santos N; Clubbs, Rebekah L; Stanley, Jacob K; Scheffe, Brian; Yelderman, Joe C; Brooks, Bryan W

2013-06-01

Though decentralized on-site technologies are extensively employed for wastewater treatment around the globe, an understanding of effluent water quality impairments associated with these systems remain less understood than effluent discharges from centralized municipal wastewater treatment facilities. Using a unique experimental facility, a novel comparative analysis of effluent water quality was performed from model decentralized aerobic (ATS) and septic (STS) on-site wastewater treatment systems and a centralized municipal wastewater treatment plant (MTP). The ATS and STS units did not benefit from further soil treatment. Each system received common influent wastewater from the Waco, Texas, USA Metropolitan Area Regional Sewerage System. We tested the hypothesis that MTP effluent would exhibit higher water quality than on-site effluents, based on parameters selected for study. A tiered testing approach was employed to assess the three effluent discharges: select routine water quality parameters (Tier I), whole effluent toxicity (Tier II), and select endocrine-active compounds (Tier III). Contrary to our hypothesis, ATS effluent was not statistically different from MTP effluents, based on Tier I and III parameters, but reproductive responses of Daphnia magna were slightly more sensitive to ATS than MTP effluents. STS effluent water quality was identified as most degraded of the three wastewater treatment systems. Parameters used to assess centralized wastewater treatment plant effluent water quality such as whole effluent toxicity and endocrine active substances appear useful for water quality assessments of decentralized discharges. Aerobic on-site wastewater treatment systems may represent more robust options than traditional septic systems for on-site wastewater treatment in watersheds with appreciable groundwater - surface water exchange. Copyright © 2013 Elsevier Ltd. All rights reserved.

Wind erodibility of soils at Fort Irwin, California (Mojave Desert), USA, before and after trampling disturbance: Implications for land management

USGS Publications Warehouse

Belnap, J.; Phillips, S.L.; Herrick, J.E.; Johansen, J.R.

2007-01-01

Recently disturbed and 'control' (i.e. less recently disturbed) soils in the Mojave Desert were compared for their vulnerability to wind erosion, using a wind tunnel, before and after being experimentally trampled. Before trampling, control sites had greater cyanobacterial biomass, soil surface stability, threshold friction velocities (TFV, i.e. the wind speed required to move soil particles), and sediment yield than sites that had been more recently disturbed by military manoeuvres. After trampling, all sites showed a large drop in TFVs and a concomitant increase in sediment yield. Simple correlation analyses showed that the decline in TFVs and the rise in sediment yield were significantly related to cyanobacterial biomass (as indicated by soil chlorophyll a). However, chlorophyll a amounts were very low compared to chlorophyll a amounts found at cooler desert sites, where chlorophyll a is often the most important factor in determining TFV and sediment yield. Multiple regression analyses showed that other factors at Fort Irwin were more important than cyanobacterial biomass in determining the overall site susceptibility to wind erosion. These factors included soil texture (especially the fine, medium and coarse sand fractions), rock cover, and the inherent stability of the soil (as indicated by subsurface soil stability tests). Thus, our results indicate that there is a threshold of biomass below which cyanobacterial crusts are not the dominant factor in soil vulnerability to wind erosion. Most undisturbed soil surfaces in the Mojave Desert region produce very little sediment, but even moderate disturbance increases soil loss from these sites. Because current weathering rates and dust inputs are very low, soil formation rates are low as well. Therefore, soil loss in this region is likely to have long-term effects.

Effect of prescribed fire for tick control in California chaparral.

PubMed

Padgett, K A; Casher, L E; Stephens, S L; Lane, R S

2009-09-01

Prescribed fire was investigated as a method for controlling ixodid and argasid ticks in chaparral habitats in northern California. Two experimental and two adjacent control plots within a wildlife preserve were monitored for 1 yr postburn. Ticks were collected by flagging vegetation, by CO2-baited pitfall trap, and by live-trapping rodents. Twice as many rodents were caught at control sites compared with burn sites and no dusky-footed woodrats, Neotoma fuscipes Baird, were found in the treatment sites postburn. This species is known to be a reservoir of the agents of Lyme disease, Borrelia burgdorferi sensu stricto Johnson, Schmid, Hyde, Steigerwalt & Brenner, and human granulocytic anaplasmosis, Anaplasma phagocytophilum Dumler, Barbet, Bekker, Dasch, Palmer, Ray, Rikihisa, Rurangirwa. Six ixodid tick species were removed from rodents (Ixodes pacificus Cooley & Kohls, Ixodes jellisoni Cooley & Kohls, Ixodes spinipalpis Hadwen & Nuttall, Ixodes woodi Bishopp, Dermacentor occidentalis Marx, and Dermacentor parumapertus Neumann), two of which transmit bacterial zoonotic agents to people in the far-western United States. There was no decrease in number of ticks per animal trapped at either burn site compared with controls; in fact, the mean number of immature I. pacificus per rodent was significantly higher at one burn site than its control site. Soil refugia may protect ticks from fire-induced mortality; the argasid tick Ornithodoros coriaceus Koch, which lives in soil, was unaffected by the prescribed fire as were I. pacificus and D. occidentalis buried in packets 2.5 cm below ground. We conclude that although prescribed fires in chaparral habitats may diminish local rodent abundance, it does not decrease tick loads on rodents. Furthermore, burning chaparral does not result in a decreased abundance of adult ixodid ticks on vegetation and apparently does not affect argasid or ixodid ticks that are sheltered within soil refugia.

The effect of top-level domains and advertisements on health web-site credibility.

PubMed

Walther, Joseph B; Wang, Zuoming; Loh, Tracy

2004-09-03

Concerns over health information on the Internet have generated efforts to enhance credibility markers; yet how users actually assess the credibility of online health information is largely unknown. This study set out to (1) establish a parsimonious and valid questionnaire instrument to measure credibility of Internet health information by drawing on various previous measures of source, news, and other credibility scales; and (2) to identify the effects of Web-site domains and advertising on credibility perceptions. Respondents (N = 156) examined one of 12 Web-site mock-ups and completed credibility scales in a 3 x 2 x 2 between-subjects experimental design. Factor analysis and validity checks were used for item reduction, and analysis of variance was employed for hypothesis testing of Web-site features' effects. In an attempt to construct a credibility instrument, three dimensions of credibility (safety, trustworthiness, and dynamism) were retained, reflecting traditional credibility sub-themes, but composed of items from disparate sources. When testing the effect of the presence or absence of advertising on a Web site on credibility, we found that this depends on the site's domain, with a trend for advertisements having deleterious effects on the credibility of sites with .org domain, but positive effects on sites with .com or .edu domains. Health-information Web-site providers should select domains purposefully when they can, especially if they must accept on-site advertising. Credibility perceptions may not be invariant or stable, but rather are sensitive to topic and context. Future research may employ these findings in order to compare other forms of health-information delivery to optimal Web-site features.

Image enhancement for on-site X-ray nondestructive inspection of reinforced concrete structures.

PubMed

Pei, Cuixiang; Wu, Wenjing; Ueaska, Mitsuru

2016-11-22

The use of portable and high-energy X-ray system can provide a very promising approach for on-site nondestructive inspection of inner steel reinforcement of concrete structures. However, the noise properties and contrast of the radiographic images for thick concrete structures do often not meet the demands. To enhance the images, we present a simple and effective method for noise reduction based on a combined curvelet-wavelet transform and local contrast enhancement based on neighborhood operation. To investigate the performance of this method for our X-ray system, we have performed several experiments with using simulated and experimental data. With comparing to other traditional methods, it shows that the proposed image enhancement method has a better performance and can significantly improve the inspection performance for reinforced concrete structures.

B 36N 36 fullerene-like nanocages: A novel material for drug delivery

NASA Astrophysics Data System (ADS)

Ganji, M. D.; Yazdani, H.; Mirnejad, A.

2010-07-01

We study interaction between B 36N 36 fullerene-like nanocage and glycine amino acid from the first- principles. Binding energy is calculated and glycine binding to the pure C 60 fullerene is compared. We also analyze the electronic structure and charge Mulliken population for the energetically most favorable complexes. Our results indicate that glycine can form stable bindings with B 36N 36 nanocage via their carbonyl oxygen (O) active site while, the C 60 fullerene might be unable to form stable bindings to glycine amino acid via their active sites, which is consistence with recent experimental and theoretical investigations. Thus, we arrive at the prediction that the B 36N 36 nanocage can be implemented as a novel material for drug delivery applications.

Predicting lysine glycation sites using bi-profile bayes feature extraction.

PubMed

Ju, Zhe; Sun, Juhe; Li, Yanjie; Wang, Li

2017-12-01

Glycation is a nonenzymatic post-translational modification which has been found to be involved in various biological processes and closely associated with many metabolic diseases. The accurate identification of glycation sites is important to understand the underlying molecular mechanisms of glycation. As the traditional experimental methods are often labor-intensive and time-consuming, it is desired to develop computational methods to predict glycation sites. In this study, a novel predictor named BPB_GlySite is proposed to predict lysine glycation sites by using bi-profile bayes feature extraction and support vector machine algorithm. As illustrated by 10-fold cross-validation, BPB_GlySite achieves a satisfactory performance with a Sensitivity of 63.68%, a Specificity of 72.60%, an Accuracy of 69.63% and a Matthew's correlation coefficient of 0.3499. Experimental results also indicate that BPB_GlySite significantly outperforms three existing glycation sites predictors: NetGlycate, PreGly and Gly-PseAAC. Therefore, BPB_GlySite can be a useful bioinformatics tool for the prediction of glycation sites. A user-friendly web-server for BPB_GlySite is established at 123.206.31.171/BPB_GlySite/. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Multivariate Approach for Comparing and Classifying Streamwater Quality

NASA Astrophysics Data System (ADS)

Hooper, R. P.; McGlynn, B. L.; Hjerdt, K. N.; McDonnell, J. J.

2001-05-01

Few measures exist for objectively comparing the chemistry of streams. We develop a multivariate technique, based on an eigenvalue analysis of streamwater concentrations, to facilitate comparison of water quality among sites across basin scales. A correlation matrix is constructed to include only solutes that mix conservatively. An eigenvalue analysis of this matrix is performed at each site to determine the approximate rank of the data set. If the ranks of all sites are roughly equal, one site is chosen as the reference site. The reduced set of eigenvectors from this site is chosen as the basis for a new, lower dimensional coordinate system and the data from the other sites are projected into this coordinate system. To assess the relative orientation of data from the reference site to all of the other sites, the relative bias (RB) and relative root mean square error (RRMSE) are calculated between the original and the projected points. The new technique was applied to multiple sites within three experimental watersheds to assess the consistency of water quality across the basin scale. The three watersheds were: Panola Mountain, Georgia, USA (6 solutes, 8 sites, 3 to 1000 ha); Sleepers River, Vermont, USA (5 solutes, 7 sites, 3 to 840 ha); and Maimai, South Island, New Zealand (4 solutes, 4 sites, 3 to 300 ha). Data from all sites were roughly planar with the first two eigenvectors explaining more than 90% of the variation. The RRMSEs for the reference site were generally between 5 and 10% with <0.1% RB. At Maimai, the RRMSE was roughly equivalent between the test sites and the 17-ha reference site, 5-8%; the RB was less than 4% at all sites. At Sleepers River, Ca and Mg had larger RRMSE at smaller basins relative to the 41 ha reference site; there was no consistent pattern to the RB for these solutes. Mg, Na, and SiO2 exhibited larger RRMSE (10-20%) and had substantial bias (10%, -20%, and 10%, respectively) at the 840-ha site compared with the 41-ha site. At Panola, only the 17-ha site was similar to the 41-ha reference site in RRMSE and had an RB<10%. The 8-ha site had an RRMSE about twice that of the reference site; Ca exhibited a 20% RB and Mg, -16% RB. All other sites had RRMSEs and RBs greater than 50% for at least one solute. These results indicate that the same set of processes control stream chemistry across a broad range of basin scales at Maimai, but that different processes are expressed at different scales to some extent at Sleepers River and more strongly at Panola Mountain. We hypothesize that this gradient reflects the relatively short residence time in the wetter Maimai basins and the progressively longer residence time in the drier Sleepers River and Panola basins. This new multivariate approach may be a way to objectively sort and classify stream chemistry characteristics from diverse watersheds and across basin scales.

Site productivity and diversity of the Middle Mountain long-term soil productivity study, West Virginia: Pre-experimental site characterization

Treesearch

Mary Beth Adams

2018-01-01

To better understand the impacts of a changing environment and interactions with forest management options for forest resources, including soil, large long-term experiments are required. Such experiments require careful documentation of reference or pre-experimental conditions. This publication describes the Middle Mountain Long-term Soil Productivity (LTSP) Study,...

Robustness of high-fidelity Rydberg gates with single-site addressability

NASA Astrophysics Data System (ADS)

Goerz, Michael H.; Halperin, Eli J.; Aytac, Jon M.; Koch, Christiane P.; Whaley, K. Birgitta

2014-09-01

Controlled-phase (cphase) gates can be realized with trapped neutral atoms by making use of the Rydberg blockade. Achieving the ultrahigh fidelities required for quantum computation with such Rydberg gates, however, is compromised by experimental inaccuracies in pulse amplitudes and timings, as well as by stray fields that cause fluctuations of the Rydberg levels. We report here a comparative study of analytic and numerical pulse sequences for the Rydberg cphase gate that specifically examines the robustness of the gate fidelity with respect to such experimental perturbations. Analytical pulse sequences of both simultaneous and stimulated Raman adiabatic passage (STIRAP) are found to be at best moderately robust under these perturbations. In contrast, optimal control theory is seen to allow generation of numerical pulses that are inherently robust within a predefined tolerance window. The resulting numerical pulse shapes display simple modulation patterns and can be rationalized in terms of an interference between distinct two-photon Rydberg excitation pathways. Pulses of such low complexity should be experimentally feasible, allowing gate fidelities of order 99.90-99.99% to be achievable under realistic experimental conditions.

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

Picón, A.; Lehmann, C. S.; Bostedt, C.

New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Specifically, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. In this paper, we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ionsmore » during the fragmentation of XeF 2 molecules following X-ray absorption at the Xe site.« less

[REACTIVE CHANGES IN SPINAL CORD MOTONEURONS AFTER SCIATIC NERVE INJURY AFTER HIGH-FREQUENCY ELECTROSURGICAL INSTRUMENT APPLICATION].

PubMed

Korsak, A; Chaikovsky, Yu; Sokurenko, L; Likhodiievskyi, V; Neverovskyi, A

2016-02-01

A new experimental model for tissues connection at peripheral nerve injury site in form of tissues welding was designed. In current study we investigated motoneuron state 1, 3, 6 and 12 weeks after peripheral nerve injury and surgical repair with high-frequency electrosurgical technology. Spinal cord sections was stained by Nissl method and observed with light microscopy. We found that postoperative period in animals from experimental groups characterized by qualitative changes in neurons from spinal motor centers that can be interpreted as compensatory processes as response to alteration. In animals from group with high-frequency electrosurgical technology usage stabilization processes passes more quickly comparatively to animals with epineural sutures. High-frequency electrosurgical technology usage provides less harmful effects on motoneurons than epineural suturing.

Use of digital land-cover data from the Landsat satellite in estimating streamflow characteristics in the Cumberland Plateau of Tennessee

USGS Publications Warehouse

Hollyday, E.F.; Hansen, G.R.

1983-01-01

Streamflow may be estimated with regression equations that relate streamflow characteristics to characteristics of the drainage basin. A statistical experiment was performed to compare the accuracy of equations using basin characteristics derived from maps and climatological records (control group equations) with the accuracy of equations using basin characteristics derived from Landsat data as well as maps and climatological records (experimental group equations). Results show that when the equations in both groups are arranged into six flow categories, there is no substantial difference in accuracy between control group equations and experimental group equations for this particular site where drainage area accounts for more than 90 percent of the variance in all streamflow characteristics (except low flows and most annual peak logarithms). (USGS)

Evaluating Daily Load Stimulus Formulas in Relating Bone Response to Exercise

NASA Technical Reports Server (NTRS)

Pennline, James A.; Mulugeta, Lealem

2014-01-01

Six formulas representing what is commonly referred to as "daily load stimulus" are identified, compared and tested in their ability to relate skeletal mechanical loading to bone maintenance and osteogenic response. Particular emphasis is placed on exercise- induced skeletal loading and whether or not the formulas can adequately capture the known experimental observations of saturation of continuous cyclic loading, rest insertion between repetitions (cycles), recovery of osteogenic potential following saturation, and multiple shorter bouts versus a single long bout of exercise. To evaluate the ability of the formulas to capture these characteristics, a set of exercise scenarios with type of exercise bout, specific duration, number of repetitions, and rest insertion between repetitions is defined. The daily load values obtained from the formulas for the loading conditions of the set of scenarios is illustrated. Not all of the formulas form estimates of daily load in units of stress or in terms of strain at a skeletal site due to the loading force from a specific exercise prescription. The comparative results show that none of the formulas are able to capture all of the experimentally observed characteristics of cyclic loading. However, the enhanced formula presented by Genc et al. does capture several characteristics of cyclic loading that the others do not, namely recovery of osteogenic potential and saturation. This could be a basis for further development of mathematical formulas that more adequately approximates the amount of daily stress at a skeletal site that contributes to bone adaptation.

On-site Rapid Diagnosis of Intracranial Hematoma using Portable Multi-slice Microwave Imaging System.

PubMed

Mobashsher, Ahmed Toaha; Abbosh, A M

2016-11-29

Rapid, on-the-spot diagnostic and monitoring systems are vital for the survival of patients with intracranial hematoma, as their conditions drastically deteriorate with time. To address the limited accessibility, high costs and static structure of currently used MRI and CT scanners, a portable non-invasive multi-slice microwave imaging system is presented for accurate 3D localization of hematoma inside human head. This diagnostic system provides fast data acquisition and imaging compared to the existing systems by means of a compact array of low-profile, unidirectional antennas with wideband operation. The 3D printed low-cost and portable system can be installed in an ambulance for rapid on-site diagnosis by paramedics. In this paper, the multi-slice head imaging system's operating principle is numerically analysed and experimentally validated on realistic head phantoms. Quantitative analyses demonstrate that the multi-slice head imaging system is able to generate better quality reconstructed images providing 70% higher average signal to clutter ratio, 25% enhanced maximum signal to clutter ratio and with around 60% hematoma target localization compared to the previous head imaging systems. Nevertheless, numerical and experimental results demonstrate that previous reported 2D imaging systems are vulnerable to localization error, which is overcome in the presented multi-slice 3D imaging system. The non-ionizing system, which uses safe levels of very low microwave power, is also tested on human subjects. Results of realistic phantom and subjects demonstrate the feasibility of the system in future preclinical trials.

Effects of initial climatic conditions on growth and accumulation of fluoride and nitrogen in leaves of two tropical tree species exposed to industrial air pollution.

PubMed

Furlan, Cláudia Maria; Domingos, Marisa; Salatino, Antonio

2007-03-15

Saplings of Tibouchina pulchra and Psidium guajava, cultivated under standardized soil conditions, were placed in two sites at Cubatão (state of São Paulo, southeast Brazil) to study the effects of air pollution on growth, biomass allocation and foliar nitrogen and fluoride concentrations. Thirty-six potted plants were maintained over two periods of one year (Jul/00 to Jun/01; Dec/00 to Nov/01) at each of two experimental sites with distinct levels of air pollution: Pilões River Valley (PV) with vegetation virtually unaffected by air pollution; and Mogi River Valley (MV) severely affected by pollutants released mainly by chemical, fertilizer, iron and steel industries. For both species, saplings growing at MV showed alterations of growth and biomass allocation, as well as increased leaf concentrations of nitrogen and fluoride. Comparing both experimental periods, the one starting in winter (the driest season in Southeastern Brazil) seemed to affect the saplings more severely, the differences of the measured parameters between MV and PV being higher than in the second period. Multivariate analysis revealed two groups of data: one representing the MV and the other the PV saplings. For both species, saplings growing at MV showed differences in chemical composition, growth and biomass allocation, compared with the PV saplings. The results suggested that seasonal conditions of the first months of sapling exposure (summer or winter) modulate the intensity of responses to pollution stress.

Elastic-plastic models for multi-site damage

NASA Technical Reports Server (NTRS)

Actis, Ricardo L.; Szabo, Barna A.

1994-01-01

This paper presents recent developments in advanced analysis methods for the computation of stress site damage. The method of solution is based on the p-version of the finite element method. Its implementation was designed to permit extraction of linear stress intensity factors using a superconvergent extraction method (known as the contour integral method) and evaluation of the J-integral following an elastic-plastic analysis. Coarse meshes are adequate for obtaining accurate results supported by p-convergence data. The elastic-plastic analysis is based on the deformation theory of plasticity and the von Mises yield criterion. The model problem consists of an aluminum plate with six equally spaced holes and a crack emanating from each hole. The cracks are of different sizes. The panel is subjected to a remote tensile load. Experimental results are available for the panel. The plasticity analysis provided the same limit load as the experimentally determined load. The results of elastic-plastic analysis were compared with the results of linear elastic analysis in an effort to evaluate how plastic zone sizes influence the crack growth rates. The onset of net-section yielding was determined also. The results show that crack growth rate is accelerated by the presence of adjacent damage, and the critical crack size is shorter when the effects of plasticity are taken into consideration. This work also addresses the effects of alternative stress-strain laws: The elastic-ideally-plastic material model is compared against the Ramberg-Osgood model.

Ab initio calculation of the deprotonation constants of an atomistically defined nanometer-sized, aluminium hydroxide oligomer

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

Wander, Matthew C. F.; Shuford, Kevin L.; Rustad, James R.

Aluminium possesses significant and diverse chemistry. Numerous compounds have been defined, and the elucidation of their chemistry is of significant geochemical interest. In this paper, a brucite-like, eight-aluminium aqueous cluster is modelled with density functional theory to identify its primary site of deprotonation and the associated pK(a) constant using both explicit (a full first solvent shell) and implicit solvent. Two methods for calculating the pK(a) are compared. We found that a bond density approach is better than a direct energy calculation for ions with large charge and high symmetry. The terminal aluminium atoms have equatorial ligated waters that in solventmore » have one long O-H bond. This site is more reactive than any of the other protons on the particle. Insights into the experimental crystal structure and Bader's Atoms in Molecules density analysis are presented as routes to reduce the computational time required for the identification of protonation sites.« less

Multiple sup 3 H-oxytocin binding sites in rat myometrial plasma membranes

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

Crankshaw, D.; Gaspar, V.; Pliska, V.

1990-01-01

The affinity spectrum method has been used to analyse binding isotherms for {sup 3}H-oxytocin to rat myometrial plasma membranes. Three populations of binding sites with dissociation constants (Kd) of 0.6-1.5 x 10(-9), 0.4-1.0 x 10(-7) and 7 x 10(-6) mol/l were identified and their existence verified by cluster analysis based on similarities between Kd, binding capacity and Hill coefficient. When experimental values were compared to theoretical curves constructed using the estimated binding parameters, good fits were obtained. Binding parameters obtained by this method were not influenced by the presence of GTP gamma S (guanosine-5'-O-3-thiotriphosphate) in the incubation medium. The bindingmore » parameters agree reasonably well with those found in uterine cells, they support the existence of a medium affinity site and may allow for an explanation of some of the discrepancies between binding and response in this system.« less

Lysine acetylation sites prediction using an ensemble of support vector machine classifiers.

PubMed

Xu, Yan; Wang, Xiao-Bo; Ding, Jun; Wu, Ling-Yun; Deng, Nai-Yang

2010-05-07

Lysine acetylation is an essentially reversible and high regulated post-translational modification which regulates diverse protein properties. Experimental identification of acetylation sites is laborious and expensive. Hence, there is significant interest in the development of computational methods for reliable prediction of acetylation sites from amino acid sequences. In this paper we use an ensemble of support vector machine classifiers to perform this work. The experimentally determined acetylation lysine sites are extracted from Swiss-Prot database and scientific literatures. Experiment results show that an ensemble of support vector machine classifiers outperforms single support vector machine classifier and other computational methods such as PAIL and LysAcet on the problem of predicting acetylation lysine sites. The resulting method has been implemented in EnsemblePail, a web server for lysine acetylation sites prediction available at http://www.aporc.org/EnsemblePail/. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

DOE PAGES

Picón, A.; Lehmann, C. S.; Bostedt, C.; ...

2016-05-23

New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Specifically, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. In this paper, we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ionsmore » during the fragmentation of XeF 2 molecules following X-ray absorption at the Xe site.« less

Evaluation of Site Effects Using Numerical and Experimental Analyses In Cittas Di Castello (italy)

NASA Astrophysics Data System (ADS)

Pergalani, F.; de Franco, R.; Compagnoni, M.; Caielli, G.

In the paper the results of the numerical and experimental analyses, in a site of the Umbria Region (Città di Castello - PG), finalized to the evaluations of site effects are shown. The aim of the work was to compare the two type of analyses, to give some methodologies that may be used at the level of urban planning, to consider these as- pects. Therefore a series of geologic, geomorphologic (1:5.000 scale), geotechnic and seismic analyses have been carried out, to identify the areas affected to local effects and to characterize the lithotechnic units. The expected seismic inputs are been indi- viduated and 2D (Quad4M, Hudson et al., 1993) numerical analyses have been done. An experimental analysis, using the registrations of small events, has been done. The results, for the two approaches, were performed in terms of elastic pseudo-acceleration spectra and amplification factors, as a ratio between spectral intensity (Housner, 1952), calculated using the pseudo-velocity spectra, in the periods of 0.1-0.5 s and 0.1-2.5 s of output and input. The results have been analyzed and compared, to give a method- ology that may be exhaustive and precise. The conclusions can be summarized in the following points: u° the results of the two approaches are coherent; u° the differences between the two approaches are: the use of the numerical analysis is easy and quick but, in this case, the use of 2D analysis produces a simplification of real geometry; the use of experimental analysis allows to consider the 3D conditions, but, in this case, the registrations of events characterized by low energy, do not allow to consider the non linear behavior of materials, moreover it is necessary to perform the registrations for a period depending from the seismicity of the region (1 month - two years); u° the possi- bility of integration of the two methodologies allows to perform a complete analysis, using the advantages of the two methods. Housner G.W., Spectrum Intensities of strong motion earthquakes. Proc. of the Symp. on Earth. and Blast Effects on Structures. Earth. Eng. Res. Inst., 1952. Hudson M.B., Idriss I.M., Beikae M. QUAD4M, A computer program for evaluating the seismic response of soil structure by variable damping finite element procedures. Report of Dip. of Civil & Env. Eng., University of California, Davis, 1993.

A Hierarchical Mechanism of RIG-I Ubiquitination Provides Sensitivity, Robustness and Synergy in Antiviral Immune Responses.

PubMed

Sun, Xiaoqiang; Xian, Huifang; Tian, Shuo; Sun, Tingzhe; Qin, Yunfei; Zhang, Shoutao; Cui, Jun

2016-07-08

RIG-I is an essential receptor in the initiation of the type I interferon (IFN) signaling pathway upon viral infection. Although K63-linked ubiquitination plays an important role in RIG-I activation, the optimal modulation of conjugated and unanchored ubiquitination of RIG-I as well as its functional implications remains unclear. In this study, we determined that, in contrast to the RIG-I CARD domain, full-length RIG-I must undergo K63-linked ubiquitination at multiple sites to reach full activity. A systems biology approach was designed based on experiments using full-length RIG-I. Model selection for 7 candidate mechanisms of RIG-I ubiquitination inferred a hierarchical architecture of the RIG-I ubiquitination mode, which was then experimentally validated. Compared with other mechanisms, the selected hierarchical mechanism exhibited superior sensitivity and robustness in RIG-I-induced type I IFN activation. Furthermore, our model analysis and experimental data revealed that TRIM4 and TRIM25 exhibited dose-dependent synergism. These results demonstrated that the hierarchical mechanism of multi-site/type ubiquitination of RIG-I provides an efficient, robust and optimal synergistic regulatory module in antiviral immune responses.

A Hierarchical Mechanism of RIG-I Ubiquitination Provides Sensitivity, Robustness and Synergy in Antiviral Immune Responses

PubMed Central

Sun, Xiaoqiang; Xian, Huifang; Tian, Shuo; Sun, Tingzhe; Qin, Yunfei; Zhang, Shoutao; Cui, Jun

2016-01-01

RIG-I is an essential receptor in the initiation of the type I interferon (IFN) signaling pathway upon viral infection. Although K63-linked ubiquitination plays an important role in RIG-I activation, the optimal modulation of conjugated and unanchored ubiquitination of RIG-I as well as its functional implications remains unclear. In this study, we determined that, in contrast to the RIG-I CARD domain, full-length RIG-I must undergo K63-linked ubiquitination at multiple sites to reach full activity. A systems biology approach was designed based on experiments using full-length RIG-I. Model selection for 7 candidate mechanisms of RIG-I ubiquitination inferred a hierarchical architecture of the RIG-I ubiquitination mode, which was then experimentally validated. Compared with other mechanisms, the selected hierarchical mechanism exhibited superior sensitivity and robustness in RIG-I-induced type I IFN activation. Furthermore, our model analysis and experimental data revealed that TRIM4 and TRIM25 exhibited dose-dependent synergism. These results demonstrated that the hierarchical mechanism of multi-site/type ubiquitination of RIG-I provides an efficient, robust and optimal synergistic regulatory module in antiviral immune responses. PMID:27387525

A Hierarchical Mechanism of RIG-I Ubiquitination Provides Sensitivity, Robustness and Synergy in Antiviral Immune Responses

NASA Astrophysics Data System (ADS)

Sun, Xiaoqiang; Xian, Huifang; Tian, Shuo; Sun, Tingzhe; Qin, Yunfei; Zhang, Shoutao; Cui, Jun

2016-07-01

RIG-I is an essential receptor in the initiation of the type I interferon (IFN) signaling pathway upon viral infection. Although K63-linked ubiquitination plays an important role in RIG-I activation, the optimal modulation of conjugated and unanchored ubiquitination of RIG-I as well as its functional implications remains unclear. In this study, we determined that, in contrast to the RIG-I CARD domain, full-length RIG-I must undergo K63-linked ubiquitination at multiple sites to reach full activity. A systems biology approach was designed based on experiments using full-length RIG-I. Model selection for 7 candidate mechanisms of RIG-I ubiquitination inferred a hierarchical architecture of the RIG-I ubiquitination mode, which was then experimentally validated. Compared with other mechanisms, the selected hierarchical mechanism exhibited superior sensitivity and robustness in RIG-I-induced type I IFN activation. Furthermore, our model analysis and experimental data revealed that TRIM4 and TRIM25 exhibited dose-dependent synergism. These results demonstrated that the hierarchical mechanism of multi-site/type ubiquitination of RIG-I provides an efficient, robust and optimal synergistic regulatory module in antiviral immune responses.

Uniform Sampling Table Method and its Applications II--Evaluating the Uniform Sampling by Experiment.

PubMed

Chen, Yibin; Chen, Jiaxi; Chen, Xuan; Wang, Min; Wang, Wei

2015-01-01

A new method of uniform sampling is evaluated in this paper. The items and indexes were adopted to evaluate the rationality of the uniform sampling. The evaluation items included convenience of operation, uniformity of sampling site distribution, and accuracy and precision of measured results. The evaluation indexes included operational complexity, occupation rate of sampling site in a row and column, relative accuracy of pill weight, and relative deviation of pill weight. They were obtained from three kinds of drugs with different shape and size by four kinds of sampling methods. Gray correlation analysis was adopted to make the comprehensive evaluation by comparing it with the standard method. The experimental results showed that the convenience of uniform sampling method was 1 (100%), odds ratio of occupation rate in a row and column was infinity, relative accuracy was 99.50-99.89%, reproducibility RSD was 0.45-0.89%, and weighted incidence degree exceeded the standard method. Hence, the uniform sampling method was easy to operate, and the selected samples were distributed uniformly. The experimental results demonstrated that the uniform sampling method has good accuracy and reproducibility, which can be put into use in drugs analysis.

Prediction of distal residue participation in enzyme catalysis.

PubMed

Brodkin, Heather R; DeLateur, Nicholas A; Somarowthu, Srinivas; Mills, Caitlyn L; Novak, Walter R; Beuning, Penny J; Ringe, Dagmar; Ondrechen, Mary Jo

2015-05-01

A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues. 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Study of sorption-retarded U(VI) diffusion in Hanford silt/clay material.

PubMed

Bai, Jing; Liu, Chongxuan; Ball, William P

2009-10-15

A diffusion cell method was applied to measure the effective pore diffusion coefficient (Dp) for U(VI) under strictly controlled chemical conditions in a silt/clay sediment from the U.S. Department of Energy Hanford site, WA. "Inward-flux" diffusion studies were conducted in which [U(VI)] in both aqueous and solid phases was measured as a function of distance in the diffusion cell under conditions of constant concentration at the cell boundaries. A sequential extraction method was developed to measure sorbed contaminant U(VI) in the solid phase containing extractable background U(VI). The effect of sorption kinetics on U(VI) interparticle diffusion was evaluated by comparing sorption-retarded diffusion models with sorption described either as equilibrium or intraparticle diffusion-limited processes. Both experimental and modeling results indicated that (1) a single pore diffusion coefficient can simulate the diffusion of total aqueous U(VI), and (2) the local equilibrium assumption (LEA) is appropriate for modeling sorption-retarded diffusion under the given experimental conditions. Dp of 1.6-1.7 x 10(-6) cm2/s was estimated in aqueous solution at pH 8.0 and saturated with respect to calcite, as relevant to some subsurface regions of the Hanford site.

Interface Mediated Nucleation and Growth of Dislocations in fcc-bcc nanocomposite

NASA Astrophysics Data System (ADS)

Zhang, Ruifeng; Wang, Jian; Beyerlein, Irene J.; Germann, Timothy C.

2011-03-01

Heterophase interfaces play a crucial role in determining material strength for nanostructured materials because they can block, store, nucleate, and remove dislocations, the essential defects that enable plastic deformation. Much recent theoretical and experimental effort has been conducted on nanostructured Cu-Nb multilayer composites that exhibited extraordinarily high strength, ductility, and resistance to radiation and mechanical loading. In decreasing layer thicknesses to the order of a few tens of nanometers or less, the deformation behavior of such composites is mainly controlled by the Cu/Nb interface. In this work, we focus on the cooperative mechanisms of dislocation nucleation and growth from Cu/Nb interfaces, and their interaction with interface. Two types of experimentally observed Cu/Nb incoherent interfaces are comparatively studied. We found that the preferred dislocation nucleation sites are closely related to atomic interface structure, which in turn, depend on the orientation relationship. The activation stress and energies for an isolated Shockley dislocation loop of different sizes from specific interface sites depend strongly on dislocation size, atomic interface pattern, and loading conditions. Such findings provide important insight into the mechanical response of a wide range of fcc/bcc metallic nanocomposites via atomic interface design.

Insecticide ADME for support of early-phase discovery: combining classical and modern techniques.

PubMed

David, Michael D

2017-04-01

The two factors that determine an insecticide's potency are its binding to a target site (intrinsic activity) and the ability of its active form to reach the target site (bioavailability). Bioavailability is dictated by the compound's stability and transport kinetics, which are determined by both physical and biochemical characteristics. At BASF Global Insecticide Research, we characterize bioavailability in early research with an ADME (Absorption, Distribution, Metabolism and Excretion) approach, combining classical and modern techniques. For biochemical assessment of metabolism, we purify native insect enzymes using classical techniques, and recombinantly express individual insect enzymes that are known to be relevant in insecticide metabolism and resistance. For analytical characterization of an experimental insecticide and its metabolites, we conduct classical radiotracer translocation studies when a radiolabel is available. In discovery, where typically no radiolabel has been synthesized, we utilize modern high-resolution mass spectrometry to probe complex systems for the test compounds and its metabolites. By using these combined approaches, we can rapidly compare the ADME properties of sets of new experimental insecticides and aid in the design of structures with an improved potential to advance in the research pipeline. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Intra-uterine experimental infection by Ureaplasma diversum induces TNF-α mediated womb inflammation in mice.

PubMed

Silva, Jamile R; Ferreira, Lício F A A; Oliveira, Percíllia V S; Nunes, Ivanéia V; Pereira, Ítalo S; Timenetsky, Jorge; Marques, Lucas M; Figueiredo, Tiana B; Silva, Robson A A

2016-01-01

Ureaplasma diversum is an opportunistic pathogen associated with uterine inflammation, impaired embryo implantation, infertility, abortions, premature birth of calves and neonatal pneumonia in cattle. It has been suggested that the intra-uterine infection by Ureaplasma diversum can cause vascular changes that hinder the success of pregnancy. Thus, the aim of this study was to evaluate the changes of intrauterine site of A/J mice in estrus or proestrus phase inoculated with Ureaplasma diversum. The infection was monitored at 24, 48 and 72 hours by the PCR methodology to detect the Ureaplasma in the inoculation site and the profile of circulating blood cells. Morphological changes, intensity of inflammation and the production of cytokines were compared. The infected mice showed local inflammation through the production of IFN-γ and TNF-α. Ureaplasma diversum infections in the reproductive tract of studied mice seemed to be associated with the production of pro-inflammatory cytokines in uterine parenchyma. The levels of TNF-α of infected mice were dependent on the bacterial load of inoculated Ureaplasma. Uterine experimental infections by Ureaplasma diversum have not been mentioned yet and herein we presented the first report of an intrauterine infection model in mice.

Gastric fundus submucosa as a site for islets transplantation: An experimental study.

PubMed

de Mesquita, Gustavo Heluani Antunes; Jardim, Yuri Justi; Iuamoto, Leandro Ryuchi; Suguita, Fabio Yuji; Essu, Felipe Futema; Oliveira, Lucas Torres; Meyer, Alberto; Crescenzi, Alessandra; Rocha-Santos, Vinícius; Galvão, Flavio H F; Andraus, Wellington; Chaib, Eleazar; D'Albuquerque, Luiz Augusto Carneiro

2018-04-01

Islets of Langerhans transplantation is a promising alternative for glycemic control in patients with type 1 diabetes. The graft site is a factor that has large impact on the functioning of this transplant, and the stomach appears to be a promising location. Our objective is to describe a new experimental model for the grafting of Islets of Langerhans in rat stomachs. Islets of Langerhans were extracted from 45 isogenic male rats of the Lewis lineage and transplanted into 9 isogenic rats of the Wistar lineage; 5 in the gastric body submucosa, and 4 in the gastric fundus submucosa. Normoglycemia was defined as two successive measurements of <250 mg/dL. No immunosuppression was used. The two groups glycemia control improvement were compared with t -student test. The results obtained following the transplantation of the islets in 9 rats showed between 995 and 2310 islets transplanted (mean of 1367). The rats from the gastric submucosa group had a better glycemic level improvement, with a confidence equal to 83.94%. Islets graft into the gastric fundus submucosa is a viable model with potential for adequate glycemic control. This model gives potential for new perspectives and future studies in this area.

Comparative analysis of different sensor data (Landsat-TM and MOMS) for earth observation and impact on future sensor development

NASA Technical Reports Server (NTRS)

Bodechtel, J.; Zilger, J.; Salomonson, V. V.

1986-01-01

The missions of the German Modular Optoelectronic Multispectral Scanner (MOMS) aboard two STS flights demonstrated the feasibility of a novel concept with regard to both technical and scientific objectives. On account of the successful missions, a cooperation was agreed between the German Federal Minister for Research nad Technology and NASA for comparing MOMS observations with the more familiar operational Landsat-TM data over selected test sites, as a means of obtaining some relative measure of performance. This paper summarizes the results obtained and presents the MOMS-02, a further experimental representative of the MOMS program aiming at the realization of an operational system for the mid-nineties.

Comparison and analysis on the serum-binding characteristics of aspirin-zinc complex and aspirin.

PubMed

Zhang, Hua-Xin; Zhang, Qun; Wang, Hong-Lin; Li, Li-Wei

2017-09-01

This study was designed to compare the protein-binding characteristics of aspirin-zinc complex (AZN) with those of aspirin itself. AZN was synthesized and interacted with a model transport protein, human serum albumin (HSA). Three-dimensional fluorescence, ultraviolet-visible and circular dichroism (CD) spectra were used to characterize the interaction of AZN with HSA under physiological conditions. The interaction mechanism was explored using a fluorescence quenching method and thermodynamic calculation. The binding site and binding locality of AZN on HSA were demonstrated using a fluorescence probe technique and Förster non-radiation energy transfer theory. Synchronous fluorescence and CD spectra were employed to reveal the effect of AZN on the native conformation of the protein. The HSA-binding results for AZN were compared with those for aspirin under consistent experimental conditions, and indicated that aspirin acts as a guide in AZN when binding to Sudlow's site I, in subdomain IIA of the HSA molecule. Moreover, compared with aspirin, AZN showed greater observed binding constants with, but smaller changes in the α-helicity of, HSA, which proved that AZN might be easier to transport and have less toxicity in vivo. Copyright © 2017 John Wiley & Sons, Ltd.

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.

PubMed

Chaudhuri, Rima; Sadrieh, Arash; Hoffman, Nolan J; Parker, Benjamin L; Humphrey, Sean J; Stöckli, Jacqueline; Hill, Adam P; James, David E; Yang, Jean Yee Hwa

2015-08-19

Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog ( www.phosphortholog.com ) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community. Here we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites in all our example data sets by more than double when compared to those recovered using existing resources such as PhosphoSitePlus. PhosphOrtholog is the first tool that enables mapping of thousands of novel and known protein phosphorylation sites across species, accessible through an easy-to-use web interface. Identification of conserved PTMs across species from large-scale experimental data increases our knowledgebase of functional PTM sites. Moreover, PhosphOrtholog is generic being applicable to other PTM datasets such as acetylation, ubiquitination and methylation.

Sixty Minutes of Physical Activity per Day Included Within Preschool Academic Lessons Improves Early Literacy.

PubMed

Kirk, Stacie M; Kirk, Erik P

2016-03-01

The effects of increases in physical activity (PA) on early literacy skills in preschool children are not known. Fifty-four African-American preschool children from a low socioeconomic urban Head Start participated over 8 months. A 2-group, quasi-experimental design was used with one preschool site participating in the PA intervention and a second site participating as the control site. The PA program was designed to promote 300 minutes/week of moderate to vigorous PA academic lessons. Academic achievement related to early literacy and phonological awareness in the areas of rhyming and alliteration were assessed at baseline, 4 and 8 months. Over 8 months, rhyming significantly (p < .01) improved in the PA group (173 ± 12%) compared with the controls (28 ± 8%) resulting in between group differences at 8 months (p < .01). Alliteration significantly (p < .01) improved in the PA group (52 ± 16%) compared with controls (13 ± 5%), resulting in between group differences at 8 months (p < .01). As minutes of exposure to moderate to vigorous PA increased, the change in picture naming (R(2) = .35, p < .05), alliteration (R(2) = .38, p < .05), and rhyming (R(2) = .42, p < .05), increased. A teacher-directed PA program is effective at increasing PA and improving early literacy. © 2016, American School Health Association.

Overpressure and consolidation near the seafloor of Brazos-Trinity Basin IV, northwest deepwater Gulf of Mexico

NASA Astrophysics Data System (ADS)

Schneider, Julia; Flemings, Peter B.; Dugan, Brandon; Long, Hui; Germaine, John T.

2009-05-01

Pore water overpressures (u*) within mudstones beneath Brazos-Trinity Basin IV (deepwater Gulf of Mexico, offshore Texas) are greater than 70% of the hydrostatic vertical effective stress (σ'vh) [λ* = 0.7 = (u*/σ'vh)]. These results are compatible with recent observations that suggest sedimentation rates in this region are rapid (6 mm/a). We compare the petrophysical properties and pore pressures within a 127-m-thick package of mudstone penetrated at two locations: Integrated Ocean Drilling Program (IODP) sites U1319 and U1320. Site U1319 is at the margin of Brazos-Trinity Basin IV, whereas Site U1320 lies at its center, beneath 180 m of turbidite fill. Experimentally derived preconsolidation stresses and an in situ pore pressure measurement record overpressure at Site U1319 and Site U1320 (λ* ˜ 0.2 to 0.8 and λ* ˜ 0.8, respectively). We use these data to define an average vertical effective stress gradient. Assuming that void ratio (e) is proportional to the log of vertical effective stress (σ'v), we predict pore pressures (u) throughout the mudstone at both sites using bulk density data. Overpressures are greater at Site U1320 due to rapid deposition of the overlying turbidites. However, a large fraction of the overpressure induced by the turbidite load applied at Site U1320 has dissipated by drainage into the overlying basin fill. High overpressures near the seafloor drive shallow fluid flow, reduce slope stability, and may explain large submarine landslides.

Alveolar process preservation at implants installed immediately into extraction sockets using deproteinized bovine bone mineral - an experimental study in dogs.

PubMed

Caneva, Marco; Botticelli, Daniele; Morelli, Fabrizio; Cesaretti, Gianfranco; Beolchini, Marco; Lang, Niklaus P

2012-07-01

To evaluate the soft tissue and the dimensional changes of the alveolar bony crest at sites where deproteinized bovine bone mineral (DBBM) particles, concomitantly with the placement of a collagen membrane, were used at implants installed into sockets immediately after tooth extraction. The pulp tissue of the mesial roots of (3) P(3) was removed in six Labrador dogs, and the root canals were filled. Flaps were elevated bilaterally, the premolars hemi-sectioned, and the distal roots removed. Recipient sites were prepared in the distal alveolus, and implants were placed. At the test sites, DBBM particles were placed in the residual marginal defects concomitantly with the placement of a collagen membrane. No treatment augmentation was performed at the control sites. A non-submerged healing was allowed. Impressions were obtained at baseline and at the time of sacrifice performed 4 months after surgery. The cast models obtained were analyzed using an optical system to evaluate dimensional variations. Block sections of the implant sites were obtained for histological processing and soft tissue assessments. After 4 months of healing, no differences in soft tissue dimensions were found between the test and control sites based on the histological assessments. The location of the soft tissue at the buccal aspect was, however, more coronal at the test compared with the control sites (1.8 ± 0.8 and 0.9 ± 0.8 mm, respectively). At the three-dimensional evaluation, the margin of the soft tissues at the buccal aspect appeared to be located more apically and lingually. The vertical dislocation was 1 ± 0.6 and 2.7 ± 0.5 mm at the test and control sites, respectively. The area of the buccal shrinkage of the alveolar crest was significantly smaller at the test sites (5.9 ± 2.4 mm(2) ) compared with the control sites (11.5 ± 1.7 mm(2) ). The use of DBBM particles concomitantly with the application of a collagen membrane used at implants placed into sockets immediately after tooth extraction contributed to the preservation of the alveolar process. © 2011 John Wiley & Sons A/S.

Effects of borrow site preparation and fertilization on natural revegetation

DOT National Transportation Integrated Search

1987-01-01

This study report describes the effects of experimental fertilization and surface conditioning of a gravel borrow site which lacked a topsoil covering. In summary, borrow site revegetation by fireweed may be greatly enhanced by scarifying and fertili...

A histopathologic evaluation of the Plasma Skin Regeneration System (PSR) versus a standard carbon dioxide resurfacing laser in an animal model.

PubMed

Fitzpatrick, R; Bernstein, E; Iyer, S; Brown, D; Andrews, P; Penny, K

2008-02-01

A variety of high energy, pulsed, and scanned carbon dioxide lasers are available to perform cutaneous resurfacing. Rhytec has developed a device for skin regeneration that utilizes energy delivered via a burst of nitrogen plasma. This study was undertaken to benchmark the energy outputs of the plasma skin regeneration device as compared to an ultra-short pulsed carbon dioxide laser (the control device). The two systems were compared for time to complete healing, and the healing response post-treatment. Three Yucatan mini-pigs were utilized for this study. Following anesthesia, five experimental sites were marked along the skin atop the psoas muscle on each side of the spine. Treatment was applied using either the plasma skin regeneration system or the carbon dioxide laser, with one site remaining untreated as a control. Biopsies were taken from all treatment sites 0, 2, 7, 14, 30, and 60 days following treatment and processed to hematoxylin-eosin staining. Histopathologic examination was performed by observers blinded as to the treatment conditions. Skin treated with the plasma skin regeneration device showed a wider range of tissue effects across the energy settings used as compared to the laser treatment. All treatment sites had clinically regenerated epidermis by 7 days after treatment, with active cellular response below the D/E junction noted at the day 30 time-point at energies ranging from 2 to 4 J. The Rhytec PSR system provides an attractive alternative to standard CO2 laser with good remodeling of tissue architecture. Epidermis regenerated after PSR treatment shows a smoother surface profile than adjacent untreated tissue.

Structural, spectral, NLO and MEP analysis of the [MgO2Ti2(OPri)6], [MgO2Ti2(OPri)2(acac)4] and [MgO2Ti2(OPri)2(bzac)4] by DFT method

NASA Astrophysics Data System (ADS)

Sayin, Koray; Karakaş, Duran

2015-06-01

Quantum chemical calculations are performed on [MgO2Ti2(OPri)6] and [MgO2Ti2(OPri)2(L)4] complexes. L is acetylacetonate (acac) and benzoylacetonate (bzac) anion. The crystal structures of these complexes have not been obtained as experimentally but optimized structures of these complexes are obtained as theoretically in this study. Universal force field (UFF) and DFT/B3LYP method are used to obtain optimized structures. Theoretical spectral analysis (IR, 1H and 13C NMR) is compared with their experimental values. A good agreement is found between experimental and theoretical spectral analysis. These results mean that the optimized structures of mentioned complexes are appropriate. Additionally, the active sites of mentioned complexes are determined by molecular electrostatic potential (MEP) diagrams and non-linear optical (NLO) properties are investigated.

Experimental and DFT studies of (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline: electronic and vibrational properties.

PubMed

Sun, Wenqi; Yuan, Guozan; Liu, Jingxin; Ma, Li; Liu, Chengbu

2013-04-01

The title molecule (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline (DPEQ) was synthesized and characterized by FT-IR, UV-vis, NMR spectroscopy. The molecular geometry, vibrational frequencies and gauge independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the compound in the ground state have been calculated by using the density functional theory (DFT) method. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. The calculated results indicate that the theoretical vibrational frequencies, 1H and 13C NMR chemical shift values show good agreement with experimental data. The electronic properties like UV-vis spectral analysis and HOMO-LUMO analysis of DPEQ have been reported and compared with experimental data. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP). Copyright © 2013 Elsevier B.V. All rights reserved.

Experimental and DFT studies of (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline: Electronic and vibrational properties

NASA Astrophysics Data System (ADS)

Sun, Wenqi; Yuan, Guozan; Liu, Jingxin; Ma, Li; Liu, Chengbu

2013-04-01

The title molecule (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline (DPEQ) was synthesized and characterized by FT-IR, UV-vis, NMR spectroscopy. The molecular geometry, vibrational frequencies and gauge independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the compound in the ground state have been calculated by using the density functional theory (DFT) method. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. The calculated results indicate that the theoretical vibrational frequencies, 1H and 13C NMR chemical shift values show good agreement with experimental data. The electronic properties like UV-vis spectral analysis and HOMO-LUMO analysis of DPEQ have been reported and compared with experimental data. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP).

Incongruence Between Observers’ and Observed Facial Muscle Activation Reduces Recognition of Emotional Facial Expressions From Video Stimuli

PubMed Central

Wingenbach, Tanja S. H.; Brosnan, Mark; Pfaltz, Monique C.; Plichta, Michael M.; Ashwin, Chris

2018-01-01

According to embodied cognition accounts, viewing others’ facial emotion can elicit the respective emotion representation in observers which entails simulations of sensory, motor, and contextual experiences. In line with that, published research found viewing others’ facial emotion to elicit automatic matched facial muscle activation, which was further found to facilitate emotion recognition. Perhaps making congruent facial muscle activity explicit produces an even greater recognition advantage. If there is conflicting sensory information, i.e., incongruent facial muscle activity, this might impede recognition. The effects of actively manipulating facial muscle activity on facial emotion recognition from videos were investigated across three experimental conditions: (a) explicit imitation of viewed facial emotional expressions (stimulus-congruent condition), (b) pen-holding with the lips (stimulus-incongruent condition), and (c) passive viewing (control condition). It was hypothesised that (1) experimental condition (a) and (b) result in greater facial muscle activity than (c), (2) experimental condition (a) increases emotion recognition accuracy from others’ faces compared to (c), (3) experimental condition (b) lowers recognition accuracy for expressions with a salient facial feature in the lower, but not the upper face area, compared to (c). Participants (42 males, 42 females) underwent a facial emotion recognition experiment (ADFES-BIV) while electromyography (EMG) was recorded from five facial muscle sites. The experimental conditions’ order was counter-balanced. Pen-holding caused stimulus-incongruent facial muscle activity for expressions with facial feature saliency in the lower face region, which reduced recognition of lower face region emotions. Explicit imitation caused stimulus-congruent facial muscle activity without modulating recognition. Methodological implications are discussed. PMID:29928240

Incongruence Between Observers' and Observed Facial Muscle Activation Reduces Recognition of Emotional Facial Expressions From Video Stimuli.

PubMed

Wingenbach, Tanja S H; Brosnan, Mark; Pfaltz, Monique C; Plichta, Michael M; Ashwin, Chris

2018-01-01

According to embodied cognition accounts, viewing others' facial emotion can elicit the respective emotion representation in observers which entails simulations of sensory, motor, and contextual experiences. In line with that, published research found viewing others' facial emotion to elicit automatic matched facial muscle activation, which was further found to facilitate emotion recognition. Perhaps making congruent facial muscle activity explicit produces an even greater recognition advantage. If there is conflicting sensory information, i.e., incongruent facial muscle activity, this might impede recognition. The effects of actively manipulating facial muscle activity on facial emotion recognition from videos were investigated across three experimental conditions: (a) explicit imitation of viewed facial emotional expressions (stimulus-congruent condition), (b) pen-holding with the lips (stimulus-incongruent condition), and (c) passive viewing (control condition). It was hypothesised that (1) experimental condition (a) and (b) result in greater facial muscle activity than (c), (2) experimental condition (a) increases emotion recognition accuracy from others' faces compared to (c), (3) experimental condition (b) lowers recognition accuracy for expressions with a salient facial feature in the lower, but not the upper face area, compared to (c). Participants (42 males, 42 females) underwent a facial emotion recognition experiment (ADFES-BIV) while electromyography (EMG) was recorded from five facial muscle sites. The experimental conditions' order was counter-balanced. Pen-holding caused stimulus-incongruent facial muscle activity for expressions with facial feature saliency in the lower face region, which reduced recognition of lower face region emotions. Explicit imitation caused stimulus-congruent facial muscle activity without modulating recognition. Methodological implications are discussed.

The alpha-fetoprotein (AFP) third domain: a search for AFP interaction sites of cell cycle proteins.

PubMed

Mizejewski, G J

2016-09-01

The carboxy-terminal third domain of alpha-fetoprotein (AFP-3D) is known to harbor binding and/or interaction sites for hydrophobic ligands, receptors, and binding proteins. Such reports have established that AFP-3D consists of amino acid (AA) sequence stretches on the AFP polypeptide that engages in protein-to-protein interactions with various ligands and receptors. Using a computer software program specifically designed for such interactions, the present report identified AA sequence fragments on AFP-3D that could potentially interact with a variety of cell cycle proteins. The cell cycle proteins identified were (1) cyclins, (2) cyclin-dependent kinases, (3) cell cycle-associated proteins (inhibitors, checkpoints, initiators), and (4) ubiquitin ligases. Following detection of the AFP-3D to cell cycle protein interaction sites, the computer-derived AFP localization AA sequences were compared and aligned with previously reported hydrophobic ligand and receptor interaction sites on AFP-3D. A literature survey of the association of cell cycle proteins with AFP showed both positive relationships and correlations. Previous reports of experimental AFP-derived peptides effects on various cell cycle proteins served to confirm and verify the present computer cell cycle protein identifications. Cell cycle protein interactions with AFP-CD peptides have been reported in cultured MCF-7 breast cancer cells subjected to mRNA microarray analysis. After 7 days in culture with MCF-7 cells, the AFP-derived peptides were shown to downregulate cyclin E, SKP2, checkpoint suppressors, cyclin-dependent kinases, and ubiquitin ligases that modulate cyclin E/CdK2 transition from the G1 to the S-phase of the cell cycle. Thus, the experimental data on AFP-CD interaction with cell cycle proteins were consistent with the "in silico" findings.

Comparative studies on the human serum albumin binding of the clinically approved EGFR inhibitors gefitinib, erlotinib, afatinib, osimertinib and the investigational inhibitor KP2187.

PubMed

Dömötör, Orsolya; Pelivan, Karla; Borics, Attila; Keppler, Bernhard K; Kowol, Christian R; Enyedy, Éva A

2018-05-30

Binding interactions between human serum albumin (HSA) and four approved epidermal growth factor receptor (EGFR) inhibitors gefitinib (GEF), erlotinib (ERL), afatinib (AFA), osimertinib (OSI), as well as the experimental drug KP2187, were investigated by means of spectrofluorometric and molecular modelling methods. Steady-state and time resolved spectrofluorometric techniques were carried out, including direct quenching of protein fluorescence and site marker displacement measurements. Proton dissociation processes and solvent dependent fluorescence properties were investigated as well. The EGFR inhibitors were predominantly presented in their single protonated form (HL + ) at physiological pH except ERL, which is charge-neutral. Significant solvent dependent fluorescence properties were found for GEF, ERL and KP2187, namely their emission spectra show strong dependence on the polarity and the hydrogen bonding ability of the solvents. The inhibitors proved to be bound at site I of HSA (in subdomain IIA) in a weak-to-moderate fashion (logK' 3.9-4.9) using spectrofluorometry. OSI (logK' 4.3) and KP2187 can additionally bind in site II (in subdomain IIIA), while GEF, ERL and AFA clearly show no interaction here. Docking methods qualitatively confirmed binding site preferences of compounds GEF and KP2187, and indicated that they probably bind to HSA in their neutral forms. Binding constants calculated on the basis of the various experimental data indicate a weak-to-moderate binding on HSA, only OSI exhibits somewhat higher affinity towards this protein. However, model calculations performed at physiological blood concentrations of HSA resulted in high (ca. 90%) bound fractions for the inhibitors, highlighting the importance of plasma protein binding. Copyright © 2018 Elsevier B.V. All rights reserved.

Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks.

PubMed

Pan, Xiaoyong; Shen, Hong-Bin

2018-05-02

RNA-binding proteins (RBPs) take over 5∼10% of the eukaryotic proteome and play key roles in many biological processes, e.g. gene regulation. Experimental detection of RBP binding sites is still time-intensive and high-costly. Instead, computational prediction of the RBP binding sites using pattern learned from existing annotation knowledge is a fast approach. From the biological point of view, the local structure context derived from local sequences will be recognized by specific RBPs. However, in computational modeling using deep learning, to our best knowledge, only global representations of entire RNA sequences are employed. So far, the local sequence information is ignored in the deep model construction process. In this study, we present a computational method iDeepE to predict RNA-protein binding sites from RNA sequences by combining global and local convolutional neural networks (CNNs). For the global CNN, we pad the RNA sequences into the same length. For the local CNN, we split a RNA sequence into multiple overlapping fixed-length subsequences, where each subsequence is a signal channel of the whole sequence. Next, we train deep CNNs for multiple subsequences and the padded sequences to learn high-level features, respectively. Finally, the outputs from local and global CNNs are combined to improve the prediction. iDeepE demonstrates a better performance over state-of-the-art methods on two large-scale datasets derived from CLIP-seq. We also find that the local CNN run 1.8 times faster than the global CNN with comparable performance when using GPUs. Our results show that iDeepE has captured experimentally verified binding motifs. https://github.com/xypan1232/iDeepE. xypan172436@gmail.com or hbshen@sjtu.edu.cn. Supplementary data are available at Bioinformatics online.

An experimental assessment of vehicle disturbance effects on migratory shorebirds

USGS Publications Warehouse

Tarr, Nathan M.; Simons, T.R.; Pollock, K.H.

2010-01-01

Off-road vehicle (ORV) traffic is one of several forms of disturbance thought to affect shorebirds at migration stopover sites. Attempts to measure disturbance effects on shorebird habitat use and behavior at stopover sites are difficult because ORV disturbance is frequently confounded with habitat and environmental factors. We used a before-after-control-impact experimental design to isolate effects of vehicle disturbance from shorebird responses to environmental and habitat factors. We manipulated disturbance levels within beach closures along South Core Banks, North Carolina, USA, and measured changes in shorebird abundance and location, as well as the activity of one focal species, the sanderling (Calidris alba), within paired control and impact plots. We applied a discrete treatment level of one flee-response-inducing event every 10 minutes on impact plots. We found that disturbance reduced total shorebird and black-bellied plover (Pluvialis squatarola) abundance and reduced relative use of microhabitat zones above the swash zone (wet sand and dry sand) by sanderlings, black-bellied plovers, willets (Tringa semipalmata), and total shorebirds. Sanderlings and total shorebirds increased use of the swash zone in response to vehicle disturbance. Disturbance reduced use of study plots by sanderlings for resting and increased sanderling activity, but we did not detect an effect of vehicle disturbance on sanderling foraging activity. We provide the first estimates of how a discrete level of disturbance affects shorebird distributions among ocean beach microhabitats. Our findings provide a standard to which managers can compare frequency and intensity of disturbance events at other shorebird stopover and roosting sites and indicate that limiting disturbance will contribute to use of a site by migratory shorebirds. ?? 2010 The Wildlife Society.

Tissue oxygen saturation and finger perfusion index in central hypovolemia: influence of pain.

PubMed

Høiseth, Lars Ø; Hisdal, Jonny; Hoff, Ingrid E; Hagen, Ove A; Landsverk, Svein A; Kirkebøen, Knut A

2015-04-01

Tissue oxygen saturation and peripheral perfusion index are proposed as early indirect markers of hypovolemia in trauma patients. Hypovolemia is associated with increased sympathetic nervous activity. However, many other stimuli, such as pain, also increase sympathetic activity. Since pain is often present in trauma patients, its effect on the indirect measures of hypovolemia needs to be clarified. The aim of this study was, therefore, to explore the effects of hypovolemia and pain on tissue oxygen saturation (measurement sites: cerebral, deltoid, forearm, and thenar) and finger photoplethysmographic perfusion index. Experimental study. University hospital clinical circulation and research laboratory. Twenty healthy volunteers. Central hypovolemia was induced with lower body negative pressure (-60 mm Hg) and pain by the cold pressor test (ice water exposure). Interventions were performed in a 2×2 fashion with the combination of lower body negative pressure or not (normovolemia), and ice water or not (sham). Each subject was thus exposed to four experimental sequences, each lasting for 8 minutes. Measurements were averaged over 30 seconds. For each person and sequence, the minimal value was analyzed. Tissue oxygenation in all measurement sites and finger perfusion index were reduced during hypovolemia/sham compared with normovolemia/sham. Tissue oxygen saturation (except cerebral) and perfusion index were reduced by pain during normovolemia. There was a larger reduction in tissue oxygenation (all measurement sites) and perfusion index during hypovolemia and pain than during normovolemia and pain. Pain (cold pressor test) reduces tissue oxygen saturation in all measurement sites (except cerebral) and perfusion index. In the presence of pain, tissue oxygen saturation and perfusion index are further reduced by hypovolemia (lower body negative pressure, -60 mm Hg). Thus, pain must be considered when evaluating tissue oxygen saturation and perfusion index as markers of hypovolemia in trauma patients.

Exploration of enzyme-ligand interactions in CYP2D6 & 3A4 homology models and crystal structures using a novel computational approach.

PubMed

Kjellander, Britta; Masimirembwa, Collen M; Zamora, Ismael

2007-01-01

New crystal structures of human CYP2D6 and CYP3A4 have recently been reported, and in this study, we wanted to compare them with previously used homology models with respect to predictions of site of metabolism and ligand-enzyme interactions. The data set consisted of a family of synthetic opioid analgesics with the aim to cover both CYP2D6 and CYP3A4, as most of these compounds are metabolized by both isoforms. The program MetaSite was used for the site of metabolism predictions, and the results were validated by experimental assessment of the major metabolites formed with recombinant CYP450s. This was made on a selection of 14 compounds in the data set. The prediction rates for MetaSite were 79-100% except for the CYP3A4 homology model, which picked the correct site in half of the cases. Despite differences in orientation of some important amino acids in the active sites, the MetaSite-predicted sites were the same for the different structures, with the exception of the CYP3A4 homology model. Further exploration of interactions with ligands was done by docking substrates/inhibitors in the different structures with the docking program GLUE. To address the challenge in interpreting patterns of enzyme-ligand interactions for the large number of different docking poses, a new computational tool to handle the results from the dockings was developed, in which the output highlights the relative importance of amino acids in CYP450-substrate/inhibitor interactions. The method is based on calculations of the interaction energies for each pose with the surrounding amino acids. For the CYP3A4 structures, this method was compared with consensus principal component analysis (CPCA), a commonly used method for structural comparison to evaluate the usefulness of the new method. The results from the two methods were comparable with each other, and the highlighted amino acids resemble those that were identified to have a different orientation in the compared structures. The new method has clear advantages over CPCA in that it is far simpler to interpret and there is no need for protein alignment. The methodology enables structural comparison but also gives insights on important amino acid substrate/inhibitor interactions and can therefore be very useful when suggesting modifications of new chemical entities to improve their metabolic profiles.

Spontaneous progression of experimentally induced periimplantitis.

PubMed

Zitzmann, N U; Berglundh, T; Ericsson, I; Lindhe, J

2004-10-01

Periimplantitis represents an inflammatory condition that is associated with the presence of a submarginal biofilm and with advanced breakdown of soft and mineralized tissues surrounding endosseous implants. Animal models have been used to describe mechanisms involved in the pathogenesis and treatment of the soft and hard tissue lesions of periimplantitis. The aim of the present experiment was to study the presence and progression of inflammatory lesions in tissues surrounding implants exposed to "experimental periimplantitis". Five Labrador dogs were used. In each dog, 2 or 3 implants were placed in both the left and right edentulous premolar regions of the mandible. Abutment connection was performed 4 months later and a plaque control regimen was initiated and maintained for 5 months. "Experimental periimplantitis" was subsequently induced by ligature placement and plaque accumulation was allowed to progress until about 40% of the height of the supporting bone had been lost. The ligatures were removed, but plaque formation was allowed to continue for an additional 12 months. Radiographs of all implant sites were obtained before and after active "experimental periimplantitis" as well as at the end of the experiment. Biopsies were harvested from the implant sites in 3 of the dogs. The tissue samples were prepared for light microscopy and the sections were used for histometric and morphometric examinations. One implant was lost during the first 2 months of "experimental periimplantitis" and two implants were lost during the 12 months that followed ligature removal. The radiographic examination indicated that varying amounts of additional bone loss occurred in the majority of the implant sites also following ligature removal. The mucosa of all implant sites harbored inflammatory lesions that extended apically of the pocket epithelium. The lesions were separated from the marginal bone by a zone of apparently normal connective tissue. A remission of the destructive inflammatory lesion in the periimplant tissues was seen in some sites following ligature removal, but in the majority of sites additional loss of supporting bone occurred. Copyright Blackwell Munksgaard, 2004

Physically disturbed deep-sea macrofauna in the Peru Basin, southeast Pacific, revisited 7 years after the experimental impact

NASA Astrophysics Data System (ADS)

Borowski, Christian

Long-term disturbance effects of a physical disturbance experiment on the benthic macrofauna (>500 μm), with particular emphasis on the dominant Polychaeta, were investigated in connection with the German ATESEPP joint programme in 4150 m depth in the Peru Basin of the tropical southeast (SE) Pacific. The study site was the 10.8 km 2 experimental field of the disturbance and re colonization experiment (DISCOL) conducted in early 1989. This programme had the objective to simulate some of the potential disturbance effects of manganese nodule mining on the bottom-dwelling biota with a towed "plough-harrow" disturber, and subsequently to investigate the resultant community responses with three post-impact samplings during a period of 3 years. Seven years after disturbance, in early 1996, the DISCOL site was revisited, and this study focuses on temporal development of the macrofauna over that extended period. Box core samples obtained during all post-impact expeditions from the disturber tracks ( disturbed treatment) were compared with unploughed sediments from the experimental field ( undisturbed treatment) and with samples from unimpacted sites of the surrounding ( reference treatment). The experiment did not cause the disastrous long-term community changes in the sediment dwelling macrofauna that previously were predicted to follow large-scale disturbances. Abundance recoveries of the macrofaunal taxa were largely terminated after 7 years. Major differences in the faunal compositions at the selected taxonomic levels of higher macrofauna taxa, polychaete families and polychaete species between disturbed and control sites were not observed, but certain disturbance effects remained present over the entire 7-year period: Within-treatment data heterogeneity for the higher macrofauna taxa and the polychaete families was greater in the disturber track samples than in undisturbed and reference treatments. Enhanced heterogeneity was expressed by significantly steeper regression slopes of variance-to-mean ratios of faunal abundances ( p<0.05) and enhanced spatial aggregation at the levels of higher macrofauna taxa and polychaete families. Hurlbert rarefaction E( Sn) and Shannon's diversity index H' calculated in non-standard ways for polychaete species revealed that patterns of diminished "diversity" in the disturbed treatments, which were observed during the later DISCOL period, were still present after 7 years, although the intensity of this signal became weaker. Recent abundance differences between treatments for the Bivalvia, Cumacea and the sigalionid polychaete species Leanira sp. A suggested that unploughed areas from the experimental field possibly were also affected by subtle long-term influences of particle plume settlement caused by the disturber action. A brief comparison with macrofauna abundance data from other ATESEPP sample locations in the Peru Basin revealed highest similarity between the sites located in the manganese nodule province, suggesting that similar disturbance effects can be expected for these areas. Nevertheless, the experimental impact by far did not reach industrial mining impact dimensions and interpretation of the results with regard to commercial mining requires caution.

Effects of environmental change on plant species density: Comparing predictions with experiments

USGS Publications Warehouse

Gough, L.; Grace, J.B.

1999-01-01

Ideally, general ecological relationships may be used to predict responses of natural communities to environmental change, but few attempts have been made to determine the reliability of predictions based on descriptive data. Using a previously published structural equation model (SEM) of descriptive data from a coastal marsh landscape, we compared these predictions against observed changes in plant species density resulting from field experiments (manipulations of soil fertility, flooding, salinity, and mammalian herbivory) in two areas within the same marsh. In general, observed experimental responses were fairly consistent with predictions. The largest discrepancy occurred when sods were transplanted from high- to low-salinity sites and herbivores selectively consumed a particularly palatable plant species in the transplanted sods. Individual plot responses to some treatments were predicted more accurately than others. Individual fertilized plot responses were not consistent with predictions (P > 0.05), nor were fenced plots (herbivore exclosures; R2 = 0.15) compared to unfenced plots (R2 = 0.53). For the remaining treatments, predictions reasonably matched responses (R2 = 0.63). We constructed an SEM for the experimental data; it explained 60% of the variance in species density and showed that fencing and fertilization led to decreases in species density that were not predicted from treatment effects on community biomass or observed disturbance levels. These treatments may have affected the ratio of live to dead biomass, and competitive exclusion likely decreased species density in fenced and fertilized plots. We conclude that experimental validation is required to determine the predictive value of comparative relationships derived from descriptive data.

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.

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

Lee, Xuhui

This is the AmeriFlux version of the carbon flux data for the site US-GMF Great Mountain Forest. Site Description - The experimental site is in the Great Mountain Forest on moderately hilly terrain in Norfolk, Connecticut. The site is a naturally regenerating forest impacted by fires, logging, hurricanes, and cultivation over the past century. The site switched from a continuous measurement mode to a campaign mode on DOY 125, 2004.

Tree swallows (Tachycineta bicolor) nesting on wetlands impacted by oil sands mining are highly parasitized by the bird blow fly Protocalliphora spp.

PubMed

Gentes, Marie-Line; Whitworth, Terry L; Waldner, Cheryl; Fenton, Heather; Smits, Judit E

2007-04-01

Oil sands mining is steadily expanding in Alberta, Canada. Major companies are planning reclamation strategies for mine tailings, in which wetlands will be used for the bioremediation of water and sediments contaminated with polycyclic aromatic hydrocarbons and naphthenic acids during the extraction process. A series of experimental wetlands were built on companies' leases to assess the feasibility of this approach, and tree swallows (Tachycineta bicolor) were designated as upper trophic biological sentinels. From May to July 2004, prevalence and intensity of infestation with bird blow flies Protocalliphora spp. (Diptera: Calliphoridae) were measured in nests on oil sands reclaimed wetlands and compared with those on a reference site. Nestling growth and survival also were monitored. Prevalence of infestation was surprisingly high for a small cavity nester; 100% of the 38 nests examined were infested. Nests on wetlands containing oil sands waste materials harbored on average from 60% to 72% more blow fly larvae than those on the reference site. Nestlings on reclaimed sites suffered mean parasitic burdens about twice that of those on the reference site; and for comparable parasitic load, they exhibited greater pathologic effects (e.g., decreased body mass) than control nestlings. The heavy blow fly infestation on oil sands-impacted wetlands suggests that oil sands mining disturbs several components of the local ecosystem, including habitat characteristics, blow fly predators, and host resistance to parasites.

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

Housing First Improves Adherence to Antipsychotic Medication Among Formerly Homeless Adults With Schizophrenia: Results of a Randomized Controlled Trial

PubMed Central

Moniruzzaman, Akm; Fazel, Seena; McCandless, Lawrence; Procyshyn, Ric; Somers, Julian M.

2017-01-01

Abstract Adherence to antipsychotic medication is a significant challenge among homeless patients. No experimental trials have investigated the impact of Housing First on adherence among patients with schizophrenia. We investigated whether Housing First in congregate and scattered-site configurations resulted in superior adherence compared to usual care. Adult participants (n = 165) met criteria for homelessness, schizophrenia, and initiation of antipsychotic pharmacotherapy prior to recruitment to an unblinded, 3-arm randomized controlled trial in Vancouver, Canada. Randomization arms were: congregate Housing First (CHF) with on-site supports (including physician and pharmacy services); scattered-site Housing First (SHF) with Assertive Community Treatment; or treatment as usual (TAU) consisting of existing services. Participants were followed for an average of 2.6 years. Adherence to antipsychotic medication was measured using the medication possession ratio (MPR), and 1-way ANOVA was used to compare outcomes between the 3 conditions. Data were drawn from comprehensive pharmacy records. Prior to randomization, mean MPR among participants was very low (0.44–0.48). Mean MPR in the follow-up period was significantly different between study arms (P < .001) and approached the guideline threshold of 0.80 in SHF. Compared to TAU, antipsychotic adherence was significantly higher in SHF but not in CHF. The results demonstrate that further implementation of SHF is indicated among homeless people with schizophrenia, and that urgent action is needed to address very low levels of antipsychotic adherence in this population (trial registration: ISRCTN57595077). PMID:27665002

Comparative safety, immunogenicity, and efficacy of several anti-H5N1 influenza experimental vaccines in a mouse and chicken models (Testing of killed and live H5 vaccine).

PubMed

Gambaryan, Alexandra S; Lomakina, Natalia F; Boravleva, Elizaveta Y; Kropotkina, Ekaterina A; Mashin, Vadim V; Krasilnikov, Igor V; Klimov, Alexander I; Rudenko, Larisa G

2012-05-01

Parallel testing of inactivated (split and whole virion) and live vaccine was conducted to compare the immunogenicity and protective efficacy against homologous and heterosubtypic challenge by H5N1 highly pathogenic avian influenza virus. Four experimental live vaccines based on two H5N1 influenza virus strains were tested; two of them had hemagglutinin (HA) of A/Vietnam/1203/04 strain lacking the polybasic HA cleavage site, and two others had hemagglutinins from attenuated H5N1 virus A/Chicken/Kurgan/3/05, with amino acid substitutions of Asp54/Asn and Lys222/Thr in HA1 and Val48/Ile and Lys131/Thr in HA2 while maintaining the polybasic HA cleavage site. The neuraminidase and non-glycoprotein genes of the experimental live vaccines were from H2N2 cold-adapted master strain A/Leningrad/134/17/57 (VN-Len and Ku-Len) or from the apathogenic H6N2 virus A/Gull/Moscow/3100/2006 (VN-Gull and Ku-Gull). Inactivated H5N1 and H1N1 and live H1N1 vaccine were used for comparison. All vaccines were applied in a single dose. Safety, immunogenicity, and protectivity against the challenge with HPAI H5N1 virus A/Chicken/Kurgan/3/05 were estimated. All experimental live H5 vaccines tested were apathogenic as determined by weight loss and conferred more than 90% protection against lethal challenge with A/Chicken/Kurgan/3/05 infection. Inactivated H1N1 vaccine in mice offered no protection against challenge with H5N1 virus, while live cold-adapted H1N1 vaccine reduced the mortality near to zero level. The high yield, safety, and protectivity of VN-Len and Ku-Len made them promising strains for the production of inactivated and live vaccines against H5N1 viruses. © 2011 Blackwell Publishing Ltd.

An efficient method to transcription factor binding sites imputation via simultaneous completion of multiple matrices with positional consistency.

PubMed

Guo, Wei-Li; Huang, De-Shuang

2017-08-22

Transcription factors (TFs) are DNA-binding proteins that have a central role in regulating gene expression. Identification of DNA-binding sites of TFs is a key task in understanding transcriptional regulation, cellular processes and disease. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) enables genome-wide identification of in vivo TF binding sites. However, it is still difficult to map every TF in every cell line owing to cost and biological material availability, which poses an enormous obstacle for integrated analysis of gene regulation. To address this problem, we propose a novel computational approach, TFBSImpute, for predicting additional TF binding profiles by leveraging information from available ChIP-seq TF binding data. TFBSImpute fuses the dataset to a 3-mode tensor and imputes missing TF binding signals via simultaneous completion of multiple TF binding matrices with positional consistency. We show that signals predicted by our method achieve overall similarity with experimental data and that TFBSImpute significantly outperforms baseline approaches, by assessing the performance of imputation methods against observed ChIP-seq TF binding profiles. Besides, motif analysis shows that TFBSImpute preforms better in capturing binding motifs enriched in observed data compared with baselines, indicating that the higher performance of TFBSImpute is not simply due to averaging related samples. We anticipate that our approach will constitute a useful complement to experimental mapping of TF binding, which is beneficial for further study of regulation mechanisms and disease.

Botulinum toxin A, brain and pain.

PubMed

Matak, Ivica; Lacković, Zdravko

2014-01-01

Botulinum neurotoxin type A (BoNT/A) is one of the most potent toxins known and a potential biological threat. At the same time, it is among the most widely used therapeutic proteins used yearly by millions of people, especially for cosmetic purposes. Currently, its clinical use in certain types of pain is increasing, and its long-term duration of effects represents a special clinical value. Efficacy of BoNT/A in different types of pain has been found in numerous clinical trials and case reports, as well as in animal pain models. However, sites and mechanisms of BoNT/A actions involved in nociception are a matter of controversy. In analogy with well known neuroparalytic effects in peripheral cholinergic synapses, presently dominant opinion is that BoNT/A exerts pain reduction by inhibiting peripheral neurotransmitter/inflammatory mediator release from sensory nerves. On the other hand, growing number of behavioral and immunohistochemical studies demonstrated the requirement of axonal transport for BoNT/A's antinociceptive action. In addition, toxin's enzymatic activity in central sensory regions was clearly identified after its peripheral application. Apart from general pharmacology, this review summarizes the clinical and experimental evidence for BoNT/A antinociceptive activity and compares the data in favor of peripheral vs. central site and mechanism of action. Based on literature review and published results from our laboratory we propose that the hypothesis of peripheral site of BoNT/A action is not sufficient to explain the experimental data collected up to now. Copyright © 2014 Elsevier Ltd. All rights reserved.

Correlation studies on nitrogen for sunflower crop across the agroclimatic variability.

PubMed

Nasim, Wajid; Belhouchette, Hatem; Tariq, Muhammad; Fahad, Shah; Hammad, Hafiz Mohkum; Mubeen, Muhammad; Munis, Muhammad Farooq Hussain; Chaudhary, Hassan Javed; Khan, Imran; Mahmood, Faisal; Abbas, Tauqeer; Rasul, Fahd; Nadeem, Muhammad; Bajwa, Ali Ahsan; Ullah, Najeeb; Alghabari, Fahad; Saud, Shah; Mubarak, Hussani; Ahmad, Rafiq

2016-02-01

Nitrogen (N) fertilizer is an important yield limiting factor for sunflower production. The correlation between yield components and growth parameters of three sunflower hybrids (Hysun-33, Hysun-38, Pioneer-64A93) were studied with five N rates (0, 60, 120, 180, 240 kg ha(-1)) at three different experimental sites during the two consecutive growing seasons 2008 and 2009. The results revealed that total dry matter (TDM) production and grain yield were positively and linearly associated with leaf area index (LAI), leaf area duration (LAD), and crop growth rate (CGR) at all three sites of the experiments. The significant association of yield with growth components indicated that the humid climate was most suitable for sunflower production. Furthermore, the association of these components can be successfully used to predict the grain yield under diverse climatic conditions. The application of N at increased rate of 180 kg ha(-1) resulted in maximum yield as compared to standard rate (120 kg ha(-1)) at all the experimental sites. In this way, N application rate was significantly correlated with growth and development of sunflower under a variety of climatic conditions. Keeping in view such relationship, the N dose can be optimized for sunflower crop in a particular region to maximize the productivity. Multilocation trails help to predict the input rates precisely while taking climatic variations into account also. In the long run, results of this study provides basis for sustainable sunflower production under changing climate.

AmeriFlux US-SRC Santa Rita Creosote

DOE Data Explorer

Kurc, Shirley [University of Arizona

2016-01-01

This is the AmeriFlux version of the carbon flux data for the site US-SRC Santa Rita Creosote. Site Description - Part of the Santa Rita Experimental Range since 1901; Site vegetation has been dominated by Creosote bush since at least 1934

Biogeochemical and metabolic responses to the flood pulse in a semiarid floodplain

USGS Publications Warehouse

Valett, H.M.; Baker, M.A.; Morrice, J.A.; Crawford, C.S.; Molles, M.C.; Dahm, Clifford N.; Moyer, D.L.; Thibault, J.R.; Ellis, L.M.

2005-01-01

Flood pulse inundation of riparian forests alters rates of nutrient retention and organic matter processing in the aquatic ecosystems formed in the forest interior. Along the Middle Rio Grande (New Mexico, USA), impoundment and levee construction have created riparian forests that differ in their inter-flood intervals (IFIs) because some floodplains are still regularly inundated by the flood pulse (i.e., connected), while other floodplains remain isolated from flooding (i.e., disconnected). This research investigates how ecosystem responses to the flood pulse relate to forest IFI by quantifying nutrient and organic matter dynamics in the Rio Grande floodplain during three years of experimental flooding of the disconnected floodplain and during a single year of natural flooding of the connected floodplain. Surface and subsurface conditions in paired sites (control, flood) established in the two floodplain types were monitored to address metabolic and biogeochemical responses. Compared to dry controls, rates of respiration in the flooded sites increased by up to three orders of magnitude during the flood pulse. In the disconnected forest, month-long experimental floods produced widespread anoxia of four-week duration during each of the three years of flooding. In contrast, water in the connected floodplain remained well oxygenated (3-8 ppm). Material budgets for experimental floods showed the disconnected floodplain to be a sink for inorganic nitrogen and suspended solids, but a potential source of dissolved organic carbon (DOC). Compared to the main stem of the Rio Grande, flood-water on the connected floodplain contained less nitrate, but comparable concentrations of DOC, phosphate-phosphorus, and ammonium-nitrogen. Results suggest that floodplain IFI drives metabolic and biogeochemical responses during the flood pulse. Impoundment and fragmentation have altered floodplains from a mosaic of patches with variable IFI to a bimodal distribution. Relatively predictable flooding occurs in the connected forest, while inundation of the disconnected forest occurs only as the result of managed application of water. In semiarid floodplains, water is scarce except during the flood pulse. Ecosystem responses to the flood pulse are related to the IFI and other measures of flooding history that help describe spatial variation in ecosystem function.

Peste des Petits Ruminants Virus Tissue Tropism and Pathogenesis in Sheep and Goats following Experimental Infection

PubMed Central

Truong, Thang; Boshra, Hani; Embury-Hyatt, Carissa; Nfon, Charles; Gerdts, Volker; Tikoo, Suresh; Babiuk, Lorne A.; Kara, Pravesh; Chetty, Thireshni; Mather, Arshad; Wallace, David B.; Babiuk, Shawn

2014-01-01

Peste des petits ruminants (PPR) is a viral disease which primarily affects small ruminants, causing significant economic losses for the livestock industry in developing countries. It is endemic in Saharan and sub-Saharan Africa, the Middle East and the Indian sub-continent. The primary hosts for peste des petits ruminants virus (PPRV) are goats and sheep; however recent models studying the pathology, disease progression and viremia of PPRV have focused primarily on goat models. This study evaluates the tissue tropism and pathogenesis of PPR following experimental infection of sheep and goats using a quantitative time-course study. Upon infection with a virulent strain of PPRV, both sheep and goats developed clinical signs and lesions typical of PPR, although sheep displayed milder clinical disease compared to goats. Tissue tropism of PPRV was evaluated by real-time RT-PCR and immunohistochemistry. Lymph nodes, lymphoid tissue and digestive tract organs were the predominant sites of virus replication. The results presented in this study provide models for the comparative evaluation of PPRV pathogenesis and tissue tropism in both sheep and goats. These models are suitable for the establishment of experimental parameters necessary for the evaluation of vaccines, as well as further studies into PPRV-host interactions. PMID:24498032

Peste des petits ruminants virus tissue tropism and pathogenesis in sheep and goats following experimental infection.

PubMed

Truong, Thang; Boshra, Hani; Embury-Hyatt, Carissa; Nfon, Charles; Gerdts, Volker; Tikoo, Suresh; Babiuk, Lorne A; Kara, Pravesh; Chetty, Thireshni; Mather, Arshad; Wallace, David B; Babiuk, Shawn

2014-01-01

Peste des petits ruminants (PPR) is a viral disease which primarily affects small ruminants, causing significant economic losses for the livestock industry in developing countries. It is endemic in Saharan and sub-Saharan Africa, the Middle East and the Indian sub-continent. The primary hosts for peste des petits ruminants virus (PPRV) are goats and sheep; however recent models studying the pathology, disease progression and viremia of PPRV have focused primarily on goat models. This study evaluates the tissue tropism and pathogenesis of PPR following experimental infection of sheep and goats using a quantitative time-course study. Upon infection with a virulent strain of PPRV, both sheep and goats developed clinical signs and lesions typical of PPR, although sheep displayed milder clinical disease compared to goats. Tissue tropism of PPRV was evaluated by real-time RT-PCR and immunohistochemistry. Lymph nodes, lymphoid tissue and digestive tract organs were the predominant sites of virus replication. The results presented in this study provide models for the comparative evaluation of PPRV pathogenesis and tissue tropism in both sheep and goats. These models are suitable for the establishment of experimental parameters necessary for the evaluation of vaccines, as well as further studies into PPRV-host interactions.

How far in-silico computing meets real experiments. A study on the structure and dynamics of spin labeled vinculin tail protein by molecular dynamics simulations and EPR spectroscopy

PubMed Central

2013-01-01

Background Investigation of conformational changes in a protein is a prerequisite to understand its biological function. To explore these conformational changes in proteins we developed a strategy with the combination of molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy. The major goal of this work is to investigate how far computer simulations can meet the experiments. Methods Vinculin tail protein is chosen as a model system as conformational changes within the vinculin protein are believed to be important for its biological function at the sites of cell adhesion. MD simulations were performed on vinculin tail protein both in water and in vacuo environments. EPR experimental data is compared with those of the simulated data for corresponding spin label positions. Results The calculated EPR spectra from MD simulations trajectories of selected spin labelled positions are comparable to experimental EPR spectra. The results show that the information contained in the spin label mobility provides a powerful means of mapping protein folds and their conformational changes. Conclusions The results suggest the localization of dynamic and flexible regions of the vinculin tail protein. This study shows MD simulations can be used as a complementary tool to interpret experimental EPR data. PMID:23445506

AHR-related activities in a creosote-adapted population of adult atlantic killifish, Fundulus heteroclitus, two decades post-EPA superfund status at the Atlantic Wood Site, Portsmouth, VA USA.

PubMed

Wojdylo, Josephine V; Vogelbein, Wolfgang; Bain, Lisa J; Rice, Charles D

2016-08-01

Atlantic killifish, Fundulus heteroclitus, are adapted to creosote-based PAHs at the US EPA Superfund site known as Atlantic Wood (AW) on the southern branch of the Elizabeth River, VA USA. Subsequent to the discovery of the AW population in the early 1990s, these fish were shown to be recalcitrant to CYP1A induction by PAHs under experimental conditions, and even to the time of this study, killifish embryos collected from the AW site are resistant to developmental deformities typically associated with exposure to PAHs in reference fish. Historically, however, 90 +% of the adult killifish at this site have proliferative hepatic lesions including cancer of varying severity. Several PAHs at this site are known to be ligands for the aryl hydrocarbon receptor (AHR). In this study, AHR-related activities in AW fish collected between 2011 and 2013 were re-examined nearly 2 decades after first discovery. This study shows that CYP1A mRNA expression is three-fold higher in intestines of AW killifish compared to a reference population. Using immunohistochemistry, CYP1A staining in intestines was uniformly positive compared to negative staining in reference fish. Livers of AW killifish were examined by IHC to show that CYP1A and AHR2 protein expression reflect lesions-specific patterns, probably representing differences in intrinsic cellular physiology of the spectrum of proliferative lesions comprising the hepatocarcinogenic process. We also found that COX2 mRNA expression levels were higher in AW fish livers compared to those in the reference population, suggesting a state of chronic inflammation. Overall, these findings suggest that adult AW fish are responsive to AHR signaling, and do express CYP1A and AHR2 proteins in intestines at a level above what was observed in the reference population. Copyright © 2016 Elsevier B.V. All rights reserved.

AHR-related Activities in a Creosote-Adapted Population of Adult Atlantic Killifish, Fundulus heteroclitus, Two Decades Post-EPA Superfund Status at the Atlantic Wood Site, Portsmouth, VA USA

PubMed Central

Wojdylo, Josephine V.; Vogelbein, Wolfgang; Bain, Lisa J.; Rice, Charles D.

2016-01-01

Atlantic killifish, Fundulus heteroclitus, are adapted to creosote-based PAHs at the US EPA Superfund site known as Atlantic Wood (AW) on the southern branch of the Elizabeth River, VA USA. Subsequent to the discovery of the AW population in the early 1990s, these fish were shown to be recalcitrant to CYP1A induction by PAHs under experimental conditions, and even to the time of this study, killifish embryos collected from the AW site are resistant to developmental deformities typically associated with exposure to PAHs in reference fish. Historically, however, 90+% of the adult killifish at this site have proliferative hepatic lesions including cancer of varying severity. Several PAHs at this site are known to be ligands for the aryl hydrocarbon receptor (AHR). In this study, AHR-related activities in AW fish collected between 2011–2013 were re-examined nearly 2 decades after first discovery. This study shows that CYP1A mRNA expression is three-fold higher in intestines of AW killifish compared to a reference population. Using immunohistochemistry, CYP1A staining in intestines was uniformly positive compared to negative staining in reference fish. Livers of AW killifish were examined by IHC to show that CYP1A and AHR2 protein expression reflect lesions-specific patterns, probably representing differences in intrinsic cellular physiology of the spectrum of proliferative lesions comprising the hepatocarcinogenic process. We also found that COX2 mRNA expression levels were higher in AW fish livers compared to those in the reference population, suggesting a state of chronic inflammation. Overall, these findings suggest that adult AW fish are responsive to AHR signaling, and do express CYP1A and AHR2 proteins in intestines at a level above what was observed in the reference population. PMID:27262937

Insights into molecular interactions between CaM and its inhibitors from molecular dynamics simulations and experimental data.

PubMed

González-Andrade, Martin; Rodríguez-Sotres, Rogelio; Madariaga-Mazón, Abraham; Rivera-Chávez, José; Mata, Rachel; Sosa-Peinado, Alejandro; Del Pozo-Yauner, Luis; Arias-Olguín, Imilla I

2016-01-01

In order to contribute to the structural basis for rational design of calmodulin (CaM) inhibitors, we analyzed the interaction of CaM with 14 classic antagonists and two compounds that do not affect CaM, using docking and molecular dynamics (MD) simulations, and the data were compared to available experimental data. The Ca(2+)-CaM-Ligands complexes were simulated 20 ns, with CaM starting in the "open" and "closed" conformations. The analysis of the MD simulations provided insight into the conformational changes undergone by CaM during its interaction with these ligands. These simulations were used to predict the binding free energies (ΔG) from contributions ΔH and ΔS, giving useful information about CaM ligand binding thermodynamics. The ΔG predicted for the CaM's inhibitors correlated well with available experimental data as the r(2) obtained was 0.76 and 0.82 for the group of xanthones. Additionally, valuable information is presented here: I) CaM has two preferred ligand binding sites in the open conformation known as site 1 and 4, II) CaM can bind ligands of diverse structural nature, III) the flexibility of CaM is reduced by the union of its ligands, leading to a reduction in the Ca(2+)-CaM entropy, IV) enthalpy dominates the molecular recognition process in the system Ca(2+)-CaM-Ligand, and V) the ligands making more extensive contact with the protein have higher affinity for Ca(2+)-CaM. Despite their limitations, docking and MD simulations in combination with experimental data continue to be excellent tools for research in pharmacology, toward a rational design of new drugs.

PhosphoBase: a database of phosphorylation sites.

PubMed Central

Blom, N; Kreegipuu, A; Brunak, S

1998-01-01

PhosphoBase is a database of experimentally verified phosphorylation sites. Version 1.0 contains 156 entries and 398 experimentally determined phosphorylation sites. Entries are compiled and revised from the literature and from major protein sequence databases such as SwissProt and PIR. The entries provide information about the phosphoprotein and the exact position of its phosphorylation sites. Furthermore, part of the entries contain information about kinetic data obtained from enzyme assays on specific peptides. To illustrate the use of data extracted from PhosphoBase we present a sequence logo displaying the overall conservation of positions around serines phosphorylated by protein kinase A (PKA). PhosphoBase is available on the WWW at http://www.cbs.dtu.dk/databases/PhosphoBase/ PMID:9399879

EPR and optical studies of Cu2+ ions doped in magnesium potassium phosphate hexahydrate single crystals

NASA Astrophysics Data System (ADS)

Kripal, Ram; Shukla, Santwana

2011-03-01

An electron paramagnetic resonance (EPR) study of Cu2+-doped magnesium potassium phosphate is performed at liquid nitrogen temperature (LNT; 77 K). Two magnetically non-equivalent sites for Cu2+ are observed. The spin Hamiltonian parameters are determined with the fitting of spectra to a rhombic symmetry crystalline field. The ground state wavefunction is also determined. The g-anisotropy is evaluated and compared with the experimental value. With the help of an optical study, the nature of the bonding in the complex is discussed.

Atomistic insight into the adsorption site selectivity of stepped Au(111) surfaces

NASA Astrophysics Data System (ADS)

Gaspari, Roberto; Pignedoli, Carlo A.; Fasel, Roman; Treier, Matthias; Passerone, Daniele

2010-07-01

Using classical and ab initio simulations, we study the interplay between the Au(111) surface reconstruction and monoatomic steps on a vicinal face. The experimentally observed discommensuration line patterns on a specific vicinal are reproduced and explained, and a complete description of the structure is given. An unusual atomic arrangement is shown to be responsible for the lower reactivity of hcp segments of step edges compared to the one of fcc segments. Our results provide an unprecedented understanding of the electronic and geometric properties of the complex Au(111) surface.

Early supra- and subgingival plaque formation in experimental gingivitis in smokers and never-smokers.

PubMed

Branco, Paula; Weidlich, Patricia; Oppermann, Rui Vicente; Rösing, Cassiano Kuchenbecker

2015-01-01

To evaluate supragingival and subgingival plaque formation on the dentogingival area in smokers and never smokers using the experimental gingivitis model and a plaque scoring system that considers the presence of an area free of plaque between plaque and the gingival sulcus called the plaque free zone (PFZ). Male volunteers, 9 current smokers and 10 never-smokers, refrained from oral hygiene procedures in the maxillary incisors and canines (test teeth) for 25 days. Under conditions of clinically healthy gingiva (phase 1) and gingival inflammation (phase 2), the supragingival plaque formation pattern was observed for 4 days in the dentogingival area. Gingival crevicular fluid was also measured. Plaque was dyed with fucsine and its presence was recorded by a calibrated examiner based on a 3-criteria scoring system: 0 - absence of stained plaque; 1 - presence of stained plaque and supragingival PFZ; 2 - presence of stained plaque and absence of PFZ, indicating that subgingival plaque formation has taken place. In both phases, smokers presented a significantly lower relative frequency of sites with subgingival plaque compared to never-smokers (P < 0.001). Mean gingival crevicular fluid was significantly higher in the presence of gingival inflammation for both groups (P = 0.001), whereas smokers demonstrated a significantly lower frequency of gingival bleeding than did non-smokers (23.6% vs 66.1%; P < 0.001). Smokers presented significantly lower percentages of sites with subgingival plaque in all experimental periods and presented less gingival inflammation as shown by GBI and gingival crevicular fluid quantification.

Use of spectroscopic techniques for uranium(VI)/montmorillonite interaction modeling.

PubMed

Kowal-Fouchard, A; Drot, R; Simoni, E; Ehrhardt, J J

2004-03-01

To experimentally identify both clay sorption sites and sorption equilibria and to understand the retention mechanisms at a molecular level, we have characterized the structure of hexavalent uranium surface complexes resulting from the interaction between the uranyl ions and the surface retention groups of a montmorillonite clay. We have performed laser-induced fluorescence spectroscopy (LIFS) and X-ray photoelectron spectroscopy (XPS) on uranyl ion loaded montmorillonite. These structural results were then compared to those obtained from the study of uranyl ions sorbed onto an alumina and also from U(VI) sorbed on an amorphous silica. This experimental approach allowed for a clear determination of the reactive surface sites of montmorillonite for U(VI) sorption. The lifetime values and the U4f XPS spectra of uranium(VI) sorbed on montmorillonite have shown that this ion is sorbed on both exchange and edge sites. The comparison of U(VI)/clay and U(VI)/oxide systems has determined that the interaction between uranyl ions and montmorillonite edge sites occurs via both [triple bond]AlOH and [triple bond]SiOH surface groups and involves three distinct surface complexes. The surface complexation modeling of the U(VI)/montmorillonite sorption edges was determined using the constant capacitance model and the above experimental constraints. The following equilibria were found to account for the uranyl sorption mechanisms onto montmorillonite for metal concentrations ranged from 10(-6) to 10(-3) M and two ionic strengths (0.1 and 0.5 M): 2[triple bond]XNa + UO2(2+) <==> ([triple bond]X)2UO2 + 2Na+, log K0(exch) = 3.0; [triple bond]Al(OH)2 + UO2(2+) <==> [triple bond]Al(OH)2UO2(2+), log K0(Al) = 14.9; [triple bond]Si(OH)2 + UO2(2+) <==> [triple bond]SiO2UO2 + 2H+, log K0(Si1) = -3.8; and [triple bond]Si(OH)2 + 3UO2(2+) + 5H2O <==> [triple bond]SiO2(UO2)3(OH)5- + 7H+, log K0(Si2) = -20.0.

Mesophotic bioerosion: Variability and structural impact on U.S. Virgin Island deep reefs

NASA Astrophysics Data System (ADS)

Weinstein, David K.; Smith, Tyler B.; Klaus, James S.

2014-10-01

Mesophotic reef corals, found 30-150 m below sea level, build complex structures that provide habitats for diverse ecosystems. Whereas bioerosion is known to impact the development and persistence of shallow reef structures, little is known regarding the extent of mesophotic bioerosion or how it might affect deeper reef geomorphology and carbonate accretion. Originally pristine experimental coral substrates and collected coral rubble were both used to investigate the variation and significance of mesophotic coral reef bioerosion south of St. Thomas, U.S. Virgin Islands. Bioerosion rates were calculated from experimental coral substrates exposed as framework for 1 and 2 years at four structurally distinct mesophotic coral reef habitats (between 30 and 45 m) as well as at a mid-shelf patch reef (21 m) and a shallow fringing patch reef (9 m). The long-term effects of macroboring were assessed by examining coral rubble collected at all sites. Overall, differences in bioerosional processes were found between shallow and mesophotic reefs. Increases in bioerosion on experimental substrates (amount of weight lost) were related to both decreasing seawater depth and increasing biomass of bioeroding parrotfish. Significant differences in coral skeleton bioerosion rates were also found between the transitional mesophotic reef zone (30-35 m) and the upper mesophotic reef zone (35-50 m) after 2 years of exposure, ranging from - 19.6 to 3.7 g/year. Total coral rubble macroboring was greater at most deep sites compared to shallower sites. Bioerosional grazing was found to dominate initial substrate modification in reefs 30.7 m and shallower, but sponges are believed to act as the main time-averaged long-term substrate bioeroders in reefs between 35 and 50 m. Although initial substrate bioerosion rates of a uniform substrate were relatively homogeneous in the 35-50 m depth zone, comparison of site composition suggests that mesophotic bioerosion will vary depending on the amount, location, and type of available substrate, and the duration both coral rubble and in situ coral framework are exposed on the seafloor. These variations may exaggerate pronounced structural differences in mesophotic reef habitats that experience few other methods of erosion.

Structure, Process, and Culture Differences of Pediatric Trauma Centers Participating in an International Comparative Effectiveness Study of Children with Severe Traumatic Brain Injury.

PubMed

Larsen, Gitte Y; Schober, Michelle; Fabio, Anthony; Wisniewski, Stephen R; Grant, Mary Jo C; Shafi, Nadeem; Bennett, Tellen D; Hirtz, Deborah; Bell, Michael J

2016-06-01

Traumatic brain injury (TBI) is an important worldwide cause of death and disability for children. The Approaches and Decisions for Acute Pediatric TBI (ADAPT) Trial is an observational, cohort study to compare the effectiveness of six aspects of TBI care. Understanding the differences between clinical sites-including their structure, clinical processes, and culture differences-will be necessary to assess differences in outcome from the study and can inform the overall community regarding differences across academic centers. We developed a survey and queried ADAPT site principal investigators with a focus on six domains: (i) hospital, (ii) pediatric intensive care unit (PICU), (iii) medical staff characteristics, (iv) quality of care, (v) medication safety, and (vi) safety culture. Summary statistics were used to describe differences between centers. ADAPT clinical sites that enrolled a subject within the first year (32 US-based, 11 international) were studied. A wide variation in site characteristics was observed in hospital and ICU characteristics, including an almost sevenfold range in ICU size (8-55 beds) and more than fivefold range of overall ICU admissions (537-2623). Nursing staffing (predominantly 1:1 or 1:2) and the presence of pharmacists within the ICU (79 %) were less variable, and most sites "strongly agreed" or "agreed" that Neurosurgery and Critical Care teams worked well together (81.4 %). However, a minority of sites (46 %) used an explicit protocol for treatment of children with severe TBI care. We found a variety of inter-center structure, process, and culture differences. These intrinsic differences between sites may begin to explain why interventional studies have failed to prove efficacy of experimental therapies. Understanding these differences may be an important factor in analyzing future ADAPT trial results and in determining best practices for pediatric severe TBI.

The Effect of Top-Level Domains and Advertisements on Health Web Site Credibility

PubMed Central

Wang, Zuoming; Loh, Tracy

2004-01-01

Background Concerns over health information on the Internet have generated efforts to enhance credibility markers; yet how users actually assess the credibility of online health information is largely unknown. Objective This study set out to (1) establish a parsimonious and valid questionnaire instrument to measure credibility of Internet health information by drawing on various previous measures of source, news, and other credibility scales; and (2) to identify the effects of Web-site domains and advertising on credibility perceptions. Methods Respondents (N = 156) examined one of 12 Web-site mock-ups and completed credibility scales in a 3 x 2 x 2 between-subjects experimental design. Factor analysis and validity checks were used for item reduction, and analysis of variance was employed for hypothesis testing of Web-site features' effects. Results In an attempt to construct a credibility instrument, three dimensions of credibility (safety, trustworthiness, and dynamism) were retained, reflecting traditional credibility sub-themes, but composed of items from disparate sources. When testing the effect of the presence or absence of advertising on a Web site on credibility, we found that this depends on the site's domain, with a trend for advertisements having deleterious effects on the credibility of sites with .org domain, but positive effects on sites with .com or .edu domains. Conclusions Health-information Web-site providers should select domains purposefully when they can, especially if they must accept on-site advertising. Credibility perceptions may not be invariant or stable, but rather are sensitive to topic and context. Future research may employ these findings in order to compare other forms of health-information delivery to optimal Web-site features. PMID:15471750

Bird assemblage response to restoration of fire-suppressed longleaf pine sandhills.

PubMed

Steen, David A; Conner, L M; Smith, Lora L; Provencher, Louis; Hiers, J Kevin; Pokswinski, Scott; Helms, Brian S; Guyer, Craig

2013-01-01

The ecological restoration of fire-suppressed habitats may require a multifaceted approach. Removal of hardwood trees together with reintroduction of fire has been suggested as a method of restoring fire-suppressed longleaf pine (Pinus palustris) forests; however, this strategy, although widespread, has not been evaluated on large spatial and temporal scales. We used a landscape-scale experimental design to examine how bird assemblages in fire-suppressed longleaf pine sandhills responded to fire alone or fire following mechanical removal or herbicide application to reduce hardwood levels. Individual treatments were compared to fire-suppressed controls and reference sites. After initial treatment, all sites were managed with prescribed fire, on an approximately two- to three-year interval, for over a decade. Nonmetric multidimensional scaling ordinations suggested that avian assemblages on sites that experienced any form of hardwood removal differed from assemblages on both fire-suppressed sites and reference sites 3-4 years after treatment (i.e., early posttreatment). After >10 years of prescribed burning on all sites (i.e., late posttreatment), only assemblages at sites treated with herbicide were indistinguishable from assemblages at reference sites. By the end of the study, individual species that were once indicators of reference sites no longer contributed to making reference sites unique. Occupancy modeling of these indicator species also demonstrated increasing similarity across treatments over time. Overall, although we documented long-term and variable assemblage-level change, our results indicate occupancy for birds considered longleaf pine specialists was similar at treatment and reference sites after over a decade of prescribed burning, regardless of initial method of hardwood removal. In other words, based on the response of species highly associated with the habitat, we found no justification for the added cost and effort of fire surrogates; fire alone was sufficient to restore these species.

Validity of Torque-Data Collection at Multiple Sites: A Framework for Collaboration on Clinical-Outcomes Research in Sports Medicine.

PubMed

Kuenze, Christopher; Eltouhky, Moataz; Thomas, Abbey; Sutherlin, Mark; Hart, Joseph

2016-05-01

Collecting torque data using a multimode dynamometer is common in sports-medicine research. The error in torque measurements across multiple sites and dynamometers has not been established. To assess the validity of 2 calibration protocols across 3 dynamometers and the error associated with torque measurement for each system. Observational study. 3 university laboratories at separate institutions. 2 Biodex System 3 dynamometers and 1 Biodex System 4 dynamometer. System calibration was completed using the manufacturer-recommended single-weight method and an experimental calibration method using a series of progressive weights. Both calibration methods were compared with a manually calculated theoretical torque across a range of applied weights. Relative error, absolute error, and percent error were calculated at each weight. Each outcome variable was compared between systems using 95% confidence intervals across low (0-65 Nm), moderate (66-110 Nm), and high (111-165 Nm) torque categorizations. Calibration coefficients were established for each system using both calibration protocols. However, within each system the calibration coefficients generated using the single-weight (System 4 = 2.42 [0.90], System 3a = 1.37 [1.11], System 3b = -0.96 [1.45]) and experimental calibration protocols (System 4 = 3.95 [1.08], System 3a = -0.79 [1.23], System 3b = 2.31 [1.66]) were similar and displayed acceptable mean relative error compared with calculated theoretical torque values. Overall, percent error was greatest for all 3 systems in low-torque conditions (System 4 = 11.66% [6.39], System 3a = 6.82% [11.98], System 3b = 4.35% [9.49]). The System 4 significantly overestimated torque across all 3 weight increments, and the System 3b overestimated torque over the moderate-torque increment. Conversion of raw voltage to torque values using the single-calibration-weight method is valid and comparable to a more complex multiweight calibration process; however, it is clear that calibration must be done for each individual system to ensure accurate data collection.

Effects of organic matter removal, soil compaction, and vegetation control on 5-year seedling performance: a regional comparison of long-term soil productivity sites

Treesearch

Robert L. Fleming; Robert F. Powers; Neil W. Foster; J. Marty Kranabetter; D. Andrew Scott; Felix Jr. Ponder; Shannon Berch; William K. Chapman; Richard D. Kabzems; Kim H. Ludovici; David M. Morris; Deborah S. Page-Dumroese; Paul T. Sanborn; Felipe G. Sanchez; Douglas M. Stone; Allan E. Tiarks

2006-01-01

We examined fifth-year seedling response to soil disturbance and vegetation control at 42 experimental locations representing 25 replicated studies within the North American Long-Term Soil Productivity (LTSP) program. These studies share a common experimental design while encompassing a wide range of climate, site conditions, and forest types. Whole-tree harvest had...

Woody vegetation following even-aged, uneven-aged, and no-harvest treatments on the Missouri Ozark Forest Ecosystem Project Sites

Treesearch

John M. Kabrick; Randy G. Jensen; Stephen R. Shifley; David R. Larsen

2002-01-01

The Missouri Ozark Forest Ecosystem Project (MOFEP) experimentally tests forest ecosystem response to (a) even-aged management with clearcutting, (b) uneven-aged management with single-tree and group selection, and (c) no-harvesting. The nine MOFEP experimental sites in the southeast Missouri Ozarks are small landscapes ranging from 772 ac (312 ha) to 1,271 ac (514 ha...

Experimental and model-based analysis of differences in perception of cutaneous electrical stimulation across the sole of the foot.

PubMed

Frahm, Ken Steffen; Mørch, Carsten Dahl; Grill, Warren M; Andersen, Ole Kæseler

2013-09-01

During electrocutaneous stimulations, variation in skin properties across locations can lead to differences in neural activation. However, little focus has been given to the effect of different skin thicknesses on neural activation. Electrical stimulation was applied to six sites across the sole of the foot. The intensities used were two and four times perception threshold. The subjects (n = 8) rated the perception quality and intensity using the McGill Pain Questionnaire and a visual analog scale (VAS). A finite element model was developed and combined with the activation function (AF) to estimate neural activation. Electrical stimulation was perceived as significantly less sharp at the heel compared to all other sites, except one site in the forefoot (logistic regression, p < 0.05). The VAS scores were significantly higher in the arch than at the heel (RM ANOVA, p < 0.05). The model showed that the AF was between 91 and 231 % higher at the five other sites than at the heel. The differences in perception across the sole of the foot indicated that the CNS received different inputs depending on the stimulus site. The lower AF at the heel indicated that the skin thicknesses could contribute to the perceived differences.

Electrets used in measuring rocket exhaust effluents from the space shuttle's solid rocket booster during static test firing, DM-3

NASA Technical Reports Server (NTRS)

Susko, M.

1979-01-01

The purpose of this experimental research was to compare Marshall Space Flight Center's electrets with Thiokol's fixed flow air samplers during the Space Shuttle Solid Rocket Booster Demonstration Model-3 static test firing on October 19, 1978. The measurement of rocket exhaust effluents by Thiokol's samplers and MSFC's electrets indicated that the firing of the Solid Rocket Booster had no significant effect on the quality of the air sampled. The highest measurement by Thiokol's samplers was obtained at Plant 3 (site 11) approximately 8 km at a 113 degree heading from the static test stand. At sites 11, 12, and 5, Thiokol's fixed flow air samplers measured 0.0048, 0.00016, and 0.00012 mg/m3 of CI. Alongside the fixed flow measurements, the electret counts from X-ray spectroscopy were 685, 894, and 719 counts. After background corrections, the counts were 334, 543, and 368, or an average of 415 counts. An additional electred, E20, which was the only measurement device at a site approximately 20 km northeast from the test site where no power was available, obtained 901 counts. After background correction, the count was 550. Again this data indicate there was no measurement of significant rocket exhaust effluents at the test site.

Treating pain on skin graft donor sites: Review and clinical recommendations.

PubMed

Sinha, Sarthak; Schreiner, Amanda J; Biernaskie, Jeff; Nickerson, Duncan; Gabriel, Vincent A

2017-11-01

Split-thickness skin grafting is the most common reconstructive procedure in managing burn injuries. Harvesting split-thickness skin creates a new partial thickness wound referred to as the donor site. Pain at the donor site is reported to be one of the most distressing symptoms during the early postoperative period. Here, we (a) identify strategies for managing donor site pain, (b) assess the quality of individual studies, and (c) formulate evidence-based recommendations based on the amount and consistency of evidence. Our analysis revealed five distinct approaches to minimize donor site pain. These include: continuous subcutaneous local anesthetic infusion (three studies), subcutaneous anesthetic injection (five studies), topical agents (six studies), nonpharmacological interventions (three studies), and wound dressings (18 studies). Available randomized control trials typically evaluated pain on standardized scales (i.e. Visual Analog Scale, Numerical Rating Scale), and compared the experimental group with standard care. Recommended treatments include: (a) subcutaneous anesthetic injection of adrenaline-lidocaine; (b) ice application; (c) topical agents, such as lidocaine and bupivacaine; and (d) hydrocolloid- and polyurethane-based wound dressings accompanied with fibrin sealant. Methodologically sound randomized control trials examining the efficacy of modified tumescent solution, ropivacaine, plasma therapy, noncontact ultrasound, and morphine gels are lacking and should be a priority for future research.

Evaluation of relocation of unionid mussels to in situ refugia

USGS Publications Warehouse

Cope, W.G.; Hove, M.C.; Waller, D.L.; Hornbach, D.J.; Bartsch, M.R.; Cunningham, L.A.; Dunn, H.L.; Kapuscinski, A.R.

2003-01-01

The aim of this study was to evaluate the recovery and survival of four species of unionid mussles [pimpleback, Quadrula pustulosa pustulosa (I. Lea, 1831); spike, Elliptio dilatata (Rafinesque, 1820); Higgins eye, Lampsilis higginsii (I. Lea, 1857); and pocketbook, Lampsilis cardium (Rafinesque, 1820)] that were experimentally relocated to in situ refugia in the St Croix River of Minnesota and Wisconsin, USA. In 1996, 150 mussels of each of the first three species (450 total) were relocated to three 5 x 5 m study grids (Site A), one near Lakeland, Minnesota, which served as a source-site control, and two in the experimental refuge 48 km upstream, near Franconia, Minnesota. In a second relocation in 1997, L. Cardium was substituted for L. Higginsii and 150 mussels of this and each of the other two species (450 total), were relocated to two study grids (Site B). The source site control was near Sunrise, Minnesota and the experimental refuge was 14 km downstream near Almelund, Minnesota. Mussel recovery, survival and substratum characteristics were evaluated annually at Site A for 2 years and for 3 years at Site B. Mean annual recovery of all three species ranged from 90 to 100% at Site A, and from 34 to 70% at site B. The mean annual survival of recaptured mussels ranged from 85 to 100% at Site A, and from 88 to 100% at Site B. The textural characteristics of the substratum differed significantly between the control and the two refuge locations at the beginning of the study, but did not differ from this initial status among subsequent years at Site A. At Site B, there was a significant shift in textural characteristics from large to smaller fractions over the four years. The relatively high survival of mussels during this study demonstrates the importance of proper handling and transport protocols when relocating mussels and the selection of suitable relocation habitat with stable substratum. When established correctly, in situ refugia may be a viable tool for preserving unionid mussels.

Evaluation of relocation of unionid mussels to in situ refugia

USGS Publications Warehouse

Cope, W.G.; Hove, M.C.; Waller, D.L.; Hornbach, D.J.; Bartsch, M.R.; Cunningham, L.A.; Dunn, H.L.; Kapuscinski, A.R.

2003-01-01

The aim of this study was to evaluate the recovery and survival of four species of unionid mussles [pimpleback, Quadrula pustulosa pustulosa (I. Lea, 1831); spike, Elliptio dilatata (Rafinesque, 1820); Higgins eye, Lampsilis higginsii (I. Lea, 1857); and pocketbook, Lampsilis cardium (Rafinesque, 1820)] that were experimentally relocated to in situ refugia in the St Croix River of Minnesota and Wisconsin, USA. In 1996, 150 mussels of each of the first three species (450 total) were relocated to three 5 ?? 5 m study grids (Site A), one near Lakeland, Minnesota, which served as a source-site control, and two in the experimental refuge 48 km upstream, near Franconia, Minnesota. In a second relocation in 1997, L. cardium was substituted for L. higginsii and 150 mussels of this and each of the other two species (450 total), were relocated to two study grids (Site B). The source site control was near Sunrise, Minnesota and the experimental refuge was 14 km downstream near Almelund, Minnesota. Mussel recovery, survival and substratum characteristics were evaluated annually at Site A for 2 years and for 3 years at Site B. Mean annual recovery of all three species ranged from 90 to 100% at Site A, and from 34 to 70% at site B. The mean annual survival of recaptured mussels ranged from 85 to 100% at Site A, and from 88 to 100% at Site B. The textural characteristics of the substratum differed significantly between the control and the two refuge locations at the beginning of the study, but did not differ from this initial status among subsequent years at Site A. At Site B, there was a significant shift in textural characteristics from large to smaller fractions over the four years. The relatively high survival of mussels during this study demonstrates the importance of proper handling and transport protocols when relocating mussels and the selection of suitable relocation habitat with stable substratum. When established correctly, in situ refugia may be a viable tool for preserving unionid mussels.

A simple method for comparing immunogold distributions in two or more experimental groups illustrated using GLUT1 labelling of isolated trophoblast cells.

PubMed

Mayhew, T M; Desoye, G

2004-07-01

Colloidal gold-labelling, combined with transmission electron microscopy, is a valuable technique for high-resolution immunolocalization of identified antigens in different subcellular compartments. Whilst the technique has been applied to placental tissues, few quantitative studies have been made. Subcellular compartments exist in three main categories (viz. organelles, membranes, filaments/tubules) and this affects the possibilities for quantification. Generally, gold particles are counted in order to compare either (a) compartments within an experimental group or (b) compartmental labelling distributions between groups. For the former, recent developments make it possible to test whether or not there is differential (nonrandom) labelling of compartments. The methods (relative labelling index and labelling density) are ideally suited to analysing label in one category of compartment (organelle or membrane or filament) but may be adapted to deal with a mixture of categories. They also require information about compartment size (e.g. profile area or trace length). Here, a simple and efficient method for drawing between-group comparisons of labelling distributions is presented. The method does not require information about compartment size or specimen magnification. It relies on multistage random sampling of specimens and unbiased counting of gold particles associated with different compartments. Distributions of observed gold counts in different experimental groups are compared by contingency table analysis with degrees of freedom for chi-squared (chi(2)) values being determined by the numbers of compartments and experimental groups. Compartmental values of chi(2)which contribute substantially to total chi(2)identify the principal subcellular sites of between-group differences. The method is illustrated using datasets from immunolabelling studies on the localization of GLUT1 glucose transporters in cultured human trophoblast cells exposed to different treatments.

Site-preference and valency for rare-earth sites in (R-Ce)(2)Fe14B magnets

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

Alam, A; Khan, M; McCallum, RW

2013-01-28

Rare-earth (R) permanent magnets of R2Fe14B have technological importance due to their high energy products, and they have two R-sites (Wyckoff 4f and 4g, with four-fold multiplicity) that affect chemistry and valence. Designing magnetic behavior and stability via alloying is technologically relevant to reduce critical (expensive) R-content while retaining key properties; cerium, an abundant (cheap) R-element, offers this potential. We calculate magnetic properties and Ce site preference in (R1-xCex)(2)Fe14B [R = La, Nd] using density functional theory (DFT) methods-including a DFT+U scheme to treat localized 4f-electrons. Fe moments compare well with neutron data-almost unaffected by Hubbard U, and weakly affectedmore » by spin-orbit coupling. In La2Fe14B, Ce alloys for 0 <= x <= 1 and prefers smaller R(4f) sites, as observed, a trend we find unaffected by valence. Whereas, in Nd2Fe14B, Ce is predicted to have limited alloying (x <= 0.3) with a preference for larger R(4g) sites, resulting in weak partial ordering and segregation. The Curie temperatures versus x for (Nd, Ce) were predicted for a typical sample processing and verified experimentally. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4789527]« less

Does sex-ratio selection influence nest-site choice in a reptile with temperature-dependent sex determination?

PubMed

Mitchell, Timothy S; Maciel, Jessica A; Janzen, Fredric J

2013-12-07

Evolutionary theory predicts that dioecious species should produce a balanced primary sex ratio maintained by frequency-dependent selection. Organisms with environmental sex determination, however, are vulnerable to maladaptive sex ratios, because environmental conditions vary spatio-temporally. For reptiles with temperature-dependent sex determination, nest-site choice is a behavioural maternal effect that could respond to sex-ratio selection, as mothers could adjust offspring sex ratios by choosing nest sites that will have particular thermal properties. This theoretical prediction has generated decades of empirical research, yet convincing evidence that sex-ratio selection is influencing nesting behaviours remains absent. Here, we provide the first experimental evidence from nature that sex-ratio selection, rather than only viability selection, is probably an important component of nest-site choice in a reptile with temperature-dependent sex determination. We compare painted turtle (Chrysemys picta) neonates from maternally selected nest sites with those from randomly selected nest sites, observing no substantive difference in hatching success or survival, but finding a profound difference in offspring sex ratio in the direction expected based on historical records. Additionally, we leverage long-term data to reconstruct our sex ratio results had the experiment been repeated in multiple years. As predicted by theory, our results suggest that sex-ratio selection has shaped nesting behaviour in ways likely to enhance maternal fitness.

Does sex-ratio selection influence nest-site choice in a reptile with temperature-dependent sex determination?

PubMed Central

Mitchell, Timothy S.; Maciel, Jessica A.; Janzen, Fredric J.

2013-01-01

Evolutionary theory predicts that dioecious species should produce a balanced primary sex ratio maintained by frequency-dependent selection. Organisms with environmental sex determination, however, are vulnerable to maladaptive sex ratios, because environmental conditions vary spatio-temporally. For reptiles with temperature-dependent sex determination, nest-site choice is a behavioural maternal effect that could respond to sex-ratio selection, as mothers could adjust offspring sex ratios by choosing nest sites that will have particular thermal properties. This theoretical prediction has generated decades of empirical research, yet convincing evidence that sex-ratio selection is influencing nesting behaviours remains absent. Here, we provide the first experimental evidence from nature that sex-ratio selection, rather than only viability selection, is probably an important component of nest-site choice in a reptile with temperature-dependent sex determination. We compare painted turtle (Chrysemys picta) neonates from maternally selected nest sites with those from randomly selected nest sites, observing no substantive difference in hatching success or survival, but finding a profound difference in offspring sex ratio in the direction expected based on historical records. Additionally, we leverage long-term data to reconstruct our sex ratio results had the experiment been repeated in multiple years. As predicted by theory, our results suggest that sex-ratio selection has shaped nesting behaviour in ways likely to enhance maternal fitness. PMID:24266033

Experimental Models of C. albicans-Streptococcal Co-infection.

PubMed

Sobue, Takanori; Diaz, Patricia; Xu, Hongbin; Bertolini, Martinna; Dongari-Bagtzoglou, Anna

2016-01-01

Interactions of C. albicans with co-colonizing bacteria at mucosal sites can be synergistic or antagonistic in disease development, depending on the bacterial species and mucosal site. Mitis group streptococci and C. albicans colonize the oral mucosa of the majority of healthy individuals. These streptococci have been termed "accessory pathogens," defined by their ability to initiate multispecies biofilm assembly and promote the virulence of the mixed bacterial biofilm community in which they participate. To demonstrate whether interactions with Mitis group streptococci limit or promote the potential of C. albicans to become an opportunistic pathogen, in vitro and in vivo co-infection models are needed. Here, we describe two C. albicans-streptococcal co-infection models: an organotypic oral mucosal tissue model that incorporates salivary flow and a mouse model of oral co-infection that requires reduced levels of immunosuppression compared to single fungal infection.

Impulse propagation over a complex site: a comparison of experimental results and numerical predictions.

PubMed

Dragna, Didier; Blanc-Benon, Philippe; Poisson, Franck

2014-03-01

Results from outdoor acoustic measurements performed in a railway site near Reims in France in May 2010 are compared to those obtained from a finite-difference time-domain solver of the linearized Euler equations. During the experiments, the ground profile and the different ground surface impedances were determined. Meteorological measurements were also performed to deduce mean vertical profiles of wind and temperature. An alarm pistol was used as a source of impulse signals and three microphones were located along a propagation path. The various measured parameters are introduced as input data into the numerical solver. In the frequency domain, the numerical results are in good accordance with the measurements up to a frequency of 2 kHz. In the time domain, except a time shift, the predicted waveforms match the measured waveforms with a close agreement.

LLNL 10(a)(1)(A) Annual Report (TE-053672-2)--2005

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

Woollett, J

2006-01-26

This report summarizes research related to Lawrence Livermore National Laboratory's (LLNL) Experimental Test Site, Site 300 (S300), located within Alameda and San Joaquin Counties (Figure 1) and conducted under the 10(a)(1)(A) (Recovery) permit TE-053672-2. This property is held in ownership by the U.S. Department of Energy/National Nuclear Security Administration (NNSA). The 2005 Recovery research at S300 involved fieldwork associated with only two species: Alameda whipsnake (Masticophis lateralis euryxanthus) and the California red-legged frog (Rana aurora draytonii) (RLF). Note: the whipsnake subspecies existing at S300 shows taxonomic variation (generally 50% chaparral whipsnake [Masticophis lateralis] traits) when compared to the Alameda whipsnakemore » (Riemer 1954) and therefore it will be referred to as ''California whipsnake (Masticophis lateralis)'' (CWS) for classification purposes in this report (Swaim 2004).« less

Synthesis, characterization and antistructure modeling of Ni nano ferrite

NASA Astrophysics Data System (ADS)

Kane, S. N.; Raghuvanshi, S.; Satalkar, M.; Reddy, V. R.; Deshpande, U. P.; Tatarchuk, T. R.; Mazaleyrat, F.

2018-05-01

We report the role played by cation distribution in determining magnetic properties by comparing dry gel, thermally annealed Ni ferrite prepared by sol-gel auto-combustion technique. X-ray diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM) and Mössbauer spectroscopy were used to characterize the samples. Both XRD and Mössbauer measurements validate the formation of spinel phase with grain diameter 39.13-45.53 nm. First time antistructural modeling for Ni ferrite is reported to get information on active surface centers. Decrease of Debye temperature θD in annealed sample shows enhancement of lattice vibrations. With thermal annealing experimental and Néel magnetic moment (nBe, nBN) increases, suggesting migration of Ni2+ from B to A site with concurrent migration of Fe3+ from A to B site (non-equilibrium cationic distribution), affecting magnetic properties.

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing.

PubMed

Guo, Hongshan; Zhu, Ping; Guo, Fan; Li, Xianlong; Wu, Xinglong; Fan, Xiaoying; Wen, Lu; Tang, Fuchou

2015-05-01

The heterogeneity of DNA methylation within a population of cells necessitates DNA methylome profiling at single-cell resolution. Recently, we developed a single-cell reduced-representation bisulfite sequencing (scRRBS) technique in which we modified the original RRBS method by integrating all the experimental steps before PCR amplification into a single-tube reaction. These modifications enable scRRBS to provide digitized methylation information on ∼1 million CpG sites within an individual diploid mouse or human cell at single-base resolution. Compared with the single-cell bisulfite sequencing (scBS) technique, scRRBS covers fewer CpG sites, but it provides better coverage for CpG islands (CGIs), which are likely to be the most informative elements for DNA methylation. The entire procedure takes ∼3 weeks, and it requires strong molecular biology skills.

Socket preservation using bovine bone mineral and collagen membrane: a randomized controlled clinical trial with histologic analysis.

PubMed

Cardaropoli, Daniele; Tamagnone, Lorenzo; Roffredo, Alessandro; Gaveglio, Lorena; Cardaropoli, Giuseppe

2012-08-01

After tooth extraction, varying amounts of bone resorption occur because of qualitative and quantitative changes at the edentulous site of the alveolar process. The aims of this randomized controlled clinical trial were (1) to compare the postextraction changes in residual ridge dimensions during spontaneous healing with those during socket preservation, (2) to analyze the histologic and histomorphometric aspects of the grafted sockets, and (3) to compare probing procket depth (PPD) and clinical attachment level (CAL) changes at teeth adjacent to extraction sites. Forty-eight teeth were extracted from 41 patients referred for extraction of 1 or more maxillary or mandibular premolars or molars. The edentulous sites were randomly assigned to the control (EXT, extraction alone) or experimental groups (SP, extraction and socket preservation). In the SP group, the sockets were filled with bovine bone mineral and covered with porcine collagen membrane. At baseline and after 4 months, PPD, gingival recession (REC), and CAL were measured at teeth adjacent to the edentulous sites. The changes in ridge dimensions from baseline to 4 months were assessed on dental casts. At 4 months, bone was harvested from the grafted areas in the SP group and the edentulous areas in the EXT group. PPD, REC, and CAL were comparable between groups. However, from baseline to 4 months, the SP group showed significantly less reduction in ridge width (1.04 ± 1.08 mm vs 4.48 ± 0.65 mm, P < .001) and height (0.46 ± 0.46 mm vs 1.54 ± 0.33 mm, P < .001). Histologically, the grafted sockets exhibited various stages of bone maturation and formation without inflammatory responses. No significant difference in the mineralized and nonmineralized fractions was noted between the groups. Socket preservation using bovine bone mineral and porcine collagen membrane considerably limits the amount of horizontal and vertical bone resorption when compared with extraction alone.

Dietary fish oil supplementation inhibits formation of endometriosis-associated adhesions in a chimeric mouse model.

PubMed

Herington, Jennifer L; Glore, Dana R; Lucas, John A; Osteen, Kevin G; Bruner-Tran, Kaylon L

2013-02-01

To examine whether dietary fish oil supplementation reduces development of spontaneous endometriosis-associated adhesions using an established model. Laboratory-based study. Medical center research laboratory. PATIENT(S)/ANIMAL(S): Disease-free women of reproductive age and nude mice. Women were not provided any intervention. Mice were randomized to receive fish oil supplementation or control diet. Experimental endometriosis was established in mice via injection of human endometrial tissue within 16 hours of ovariectomy. Mice were provided standard or menhaden fish oil-supplemented diets for ≥ 2 weeks before initiation of experimental endometriosis and until killing them 1 week later. At necropsy, mice were examined for the presence and extent of adhesions and endometriotic-like lesions. Tissues were excised and morphologically characterized. Adhesions/lesions were reduced in mice provided with dietary fish oil compared with control animals. Leukocytes were more numerous within the adhesions/lesions of the mice maintained on the standard diet compared with animals provided with fish oil. As indicated by staining intensity, collagen deposition was greater at adhesion sites within control mice compared with fish oil-supplemented animals. Wound-healing associated with surgery created an inflammatory peritoneal microenvironment that promoted the development of both experimental endometriosis and adhesions in a murine model. Targeting excessive inflammation with fish oil may be an effective adjuvant therapy to reduce the development of postsurgical adhesions related to endometriosis. Copyright © 2013 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Geotechnical Site Investigation Using S-waves with Implications for Ground Motion Analysis

NASA Astrophysics Data System (ADS)

Hassan, Bilal; Butt, Stephen D.; Hurich, Charles A.

2017-12-01

Evaluation results of shear wave attenuation-based ground motion restricted by fracture orientation and rheology, from among those of an extended experimental study, are presented herein. The issues of competence of fractured bedrock dynamically disturbed multilaterally are assessed. Disturbance is primarily modelled by Sh and Sv stimulation, given fracture orientation, while subjected to direct fracture stress regime conditions varying in time. Hence, directionalities of polarisation and stress are taken into consideration simultaneously following simple site-specific non-erodetic approach. Comparison of spectral curves and spectral ratio curves of attenuation with respect to variations of direction and stress emphasise the amplification of the `seismic response' in one direction compared to the other, i.e. vertical vs. horizontal, in terms of weighing possibilities of or predicting structural integrity against failure. The composite analyses of multiple spectral curves not only enable determination of the orientation of the fracture set/s in space but also allow inferring the nature of more amplified response perpendicular to the crack surface compared to that of a response parallel to the crack surface.

Site-selective local fluorination of graphene induced by focused ion beam irradiation.

PubMed

Li, Hu; Daukiya, Lakshya; Haldar, Soumyajyoti; Lindblad, Andreas; Sanyal, Biplab; Eriksson, Olle; Aubel, Dominique; Hajjar-Garreau, Samar; Simon, Laurent; Leifer, Klaus

2016-01-29

The functionalization of graphene remains an important challenge for numerous applications expected by this fascinating material. To keep advantageous properties of graphene after modification or functionalization of its structure, local approaches are a promising road. A novel technique is reported here that allows precise site-selective fluorination of graphene. The basic idea of this approach consists in the local radicalization of graphene by focused ion beam (FIB) irradiation and simultaneous introduction of XeF2 gas. A systematic series of experiments were carried out to outline the relation between inserted defect creation and the fluorination process. Based on a subsequent X-ray photoelectron spectroscopy (XPS) analysis, a 6-fold increase of the fluorine concentration on graphene under simultaneous irradiation was observed when compared to fluorination under normal conditions. The fluorine atoms are predominately localized at the defects as indicated from scanning tunneling microscopy (STM). The experimental findings are confirmed by density functional theory which predicts a strong increase of the binding energy of fluorine atoms when bound to the defect sites. The developed technique allows for local fluorination of graphene without using resists and has potential to be a general enabler of site-selective functionalization of graphene using a wide range of gases.

Site-selective local fluorination of graphene induced by focused ion beam irradiation

NASA Astrophysics Data System (ADS)

Li, Hu; Daukiya, Lakshya; Haldar, Soumyajyoti; Lindblad, Andreas; Sanyal, Biplab; Eriksson, Olle; Aubel, Dominique; Hajjar-Garreau, Samar; Simon, Laurent; Leifer, Klaus

2016-01-01

The functionalization of graphene remains an important challenge for numerous applications expected by this fascinating material. To keep advantageous properties of graphene after modification or functionalization of its structure, local approaches are a promising road. A novel technique is reported here that allows precise site-selective fluorination of graphene. The basic idea of this approach consists in the local radicalization of graphene by focused ion beam (FIB) irradiation and simultaneous introduction of XeF2 gas. A systematic series of experiments were carried out to outline the relation between inserted defect creation and the fluorination process. Based on a subsequent X-ray photoelectron spectroscopy (XPS) analysis, a 6-fold increase of the fluorine concentration on graphene under simultaneous irradiation was observed when compared to fluorination under normal conditions. The fluorine atoms are predominately localized at the defects as indicated from scanning tunneling microscopy (STM). The experimental findings are confirmed by density functional theory which predicts a strong increase of the binding energy of fluorine atoms when bound to the defect sites. The developed technique allows for local fluorination of graphene without using resists and has potential to be a general enabler of site-selective functionalization of graphene using a wide range of gases.

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

Evaluation of neutron flux parameters in irradiation sites of research reactor using the Westcott-formalism for the k0 neutron activation analysis method

NASA Astrophysics Data System (ADS)

Kasban, H.; Hamid, Ashraf

2015-12-01

Instrumental Neutron Activation Analysis using k0 (k0-INAA) method has been used to determine a number of elements in sediment samples collected from El-Manzala Lake in Egypt. k0-INAA according to Westcott's formalism has been implemented using the complete irradiation kit of the fast pneumatic rabbit and some selected manually loaded irradiation sites for short and long irradiation at Egypt Second Research Reactor (ETRR-2). Zr-Au and Co sets as neutron flux monitors are used to determine the neutron flux parameters (f and α) in each irradiation sites. Two reference materials IAEA Soil-7 samples have been inserted and implemented for data validation and an internal monostandard multi monitor used (k0 based IM-NAA). It was given a good agreement between the experimental analyzed values and that obtained of the certified values. The major and trace elements in the sediment samples have been evaluated with the use of Co as an internal and Au as an external monostandard comparators. The concentrations of the elements (Cr, Mn and Zn) in the sediment samples of the present work are discussed regarding to those obtained from other sites.

Construction and Deciphering of Human Phosphorylation-Mediated Signaling Transduction Networks.

PubMed

Zhang, Menghuan; Li, Hong; He, Ying; Sun, Han; Xia, Li; Wang, Lishun; Sun, Bo; Ma, Liangxiao; Zhang, Guoqing; Li, Jing; Li, Yixue; Xie, Lu

2015-07-02

Protein phosphorylation is the most abundant reversible covalent modification. Human protein kinases participate in almost all biological pathways, and approximately half of the kinases are associated with disease. PhoSigNet was designed to store and display human phosphorylation-mediated signal transduction networks, with additional information related to cancer. It contains 11 976 experimentally validated directed edges and 216 871 phosphorylation sites. Moreover, 3491 differentially expressed proteins in human cancer from dbDEPC, 18 907 human cancer variation sites from CanProVar, and 388 hyperphosphorylation sites from PhosphoSitePlus were collected as annotation information. Compared with other phosphorylation-related databases, PhoSigNet not only takes the kinase-substrate regulatory relationship pairs into account, but also extends regulatory relationships up- and downstream (e.g., from ligand to receptor, from G protein to kinase, and from transcription factor to targets). Furthermore, PhoSigNet allows the user to investigate the impact of phosphorylation modifications on cancer. By using one set of in-house time series phosphoproteomics data, the reconstruction of a conditional and dynamic phosphorylation-mediated signaling network was exemplified. We expect PhoSigNet to be a useful database and analysis platform benefiting both proteomics and cancer studies.

Integrating a suicide prevention program into the primary health care network: a field trial study in Iran.

PubMed

Malakouti, Seyed Kazem; Nojomi, Marzieh; Poshtmashadi, Marjan; Hakim Shooshtari, Mitra; Mansouri Moghadam, Fariba; Rahimi-Movaghar, Afarin; Afghah, Susan; Bolhari, Jafar; Bazargan-Hejazi, Shahrzad

2015-01-01

To describe and evaluate the feasibility of integrating a suicide prevention program with Primary Health Care services and evaluate if such system can improve screening and identification of depressive disorder, reduce number of suicide attempters, and lower rate of suicide completion. This was a quasi-experimental trial in which one community was exposed to the intervention versus the control community with no such exposure. The study sites were two counties in Western Iran. The intervention protocol called for primary care and suicide prevention collaboration at different levels of care. The outcome variables were the number of suicides committed, the number of documented suicide attempts, and the number of identified depressed cases. We identified a higher prevalence of depressive disorders in the intervention site versus the control site (χ (2) = 14.8, P < 0.001). We also found a reduction in the rate of suicide completion in the intervention region compared to the control, but a higher prevalence of suicide attempts in both the intervention and the control sites. Integrating a suicide prevention program with the Primary Health Care network enhanced depression and suicide surveillance capacity and subsequently reduced the number of suicides, especially in rural areas.

Adsorption of O2, SO2, and SO3, on nickel oxide - Mechanism for sulfate formation

NASA Technical Reports Server (NTRS)

Mehandru, S. P.; Anderson, A. B.

1986-01-01

Calculations based on the atom superposition and electron delocalization molecular orbital technique suggest that O2 will adsorb preferentially end-on at an angle 45 deg from normal on a nickel cation site on the (100) surface of NiO. SO2 adsorption is also stronger on the nickel site; SO2 bonds through the sulfur atom in a plane perpendicular to the surface. Adsorption energies for SO3 on the nickel and oxygen sites are comparable in the preferred orientation in which the SO3 plane is parallel to the surface. The calculations suggest that the strength of adsorption varies as O2 greater than SO2 greater than SO3. On activation, SO3 adsorbed to an O(2-) site forms a trigonal pyramidal SO4 species which yields, with a low barrier, a tetrahedral sulfate anion. Subsequently the anion reorients on the surface. Alternative mechanisms which require the formation of Ni(3+) or O(-) are discussed. NiSO4 thus formed may play a passivating role for the corrosion of Ni at low temperatures in the SO2 + O2 + SO3 atmospheres and an active role at high temperatures, as discussed in the experimental literature.

May Dietary Supplementation Augment Respiratory Burst in Wound-Site Inflammatory Cells?

PubMed

Das, Amitava; Dickerson, Ryan; Ghatak, Piya Das; Gordillo, Gayle M; Chaffee, Scott; Saha, Abhijoy; Khanna, Savita; Roy, Sashwati

2018-02-10

Persistent infection contributes to wound chronicity. At the wound site, NADPH oxidase (NOX) activity in immune cells fights infection to enable the healing process. Fermented papaya preparation (FPP) is a carbohydrate-rich nutritional supplement that has demonstrated ability to bolster respiratory burst in experimental rodent systems. In FPP, glucose coexists with fructose and maltose in addition to multiple other sugar alcohols such as inositol. We have previously reported that FPP supplementation augments wound healing in diabetic mice via improvement of respiratory burst activity of wound innate immune cells. In this clinical study ( clinicaltrials.gov : NCT02332993), chronic wound patients were orally supplemented with FPP daily. Inducible production of reactive oxygen species was significantly higher in wound-site immune cells from patients supplemented with FPP and on standard of care (SoC) for wound management compared with those patients receiving SoC alone. Wound closure in FPP-supplemented patients showed improvement. Importantly, the consumption of this mixture of carbohydrates, including significant amounts of glucose, did not increase HbA1c. These observations warrant a full-length clinical trial testing the hypothesis that FPP improves wound closure by augmenting NOX activity in immune cells at the wound site. Antioxid. Redox Signal. 28, 401-405.

Plant communities in harsh sites are less invaded: a summary of observations and proposed explanations

PubMed Central

Zefferman, Emily; Stevens, Jens T.; Charles, Grace K.; Dunbar-Irwin, Mila; Emam, Taraneh; Fick, Stephen; Morales, Laura V.; Wolf, Kristina M.; Young, Derek J. N.; Young, Truman P.

2015-01-01

Plant communities in abiotically stressful, or ‘harsh’, habitats have been reported to be less invaded by non-native species than those in more moderate habitats. Here, we synthesize descriptive and experimental evidence for low levels of invasion in habitats characterized by a variety of environmental stressors: low nitrogen; low phosphorus; saline, sodic or alkaline soils; serpentine soils; low soil moisture; shallow/rocky soils; temporary inundation; high shade; high elevation; and high latitude. We then discuss major categories of hypotheses to explain this pattern: the propagule limitation mechanism suggests invasion of harsh sites is limited by relatively low arrival rates of propagules compared with more moderate habitats, while invasion resistance mechanisms suggest that harsh habitats are inherently less invasible due to stressful abiotic conditions and/or increased effects of biotic resistance from resident organisms. Both propagule limitation and invasion resistance may simultaneously contribute to low invadedness of harsh sites, but the management implications of these mechanisms differ. If propagule limitation is more important, managers should focus on reducing the likelihood of propagule introductions. If invasion resistance mechanisms are in play, managers should focus on restoring or maintaining harsh conditions at a site to reduce invasibility. PMID:26002746

The binuclear nickel center in the A-cluster of acetyl-CoA synthase (ACS) and two biomimetic dinickel complexes studied by X-ray absorption and emission spectroscopy

NASA Astrophysics Data System (ADS)

Schrapers, P.; Mebs, S.; Ilina, Y.; Warner, D. S.; Wörmann, C.; Schuth, N.; Kositzki, R.; Dau, H.; Limberg, C.; Dobbek, H.; Haumann, M.

2016-05-01

Acetyl-CoA synthase (ACS) is involved in the bacterial carbon oxide conversion pathway. The binuclear nickel sites in ACS enzyme and two biomimetic synthetic compounds containing a Ni(II)Ni(II) unit (1 and 2) were compared using XAS/XES. EXAFS analysis of ACS proteins revealed similar Ni-N/O/S bond lengths and Ni-Ni/Fe distances as in the crystal structure in oxidized ACS, but elongated Ni-ligand bonds in reduced ACS, suggesting more reduced nickel species. The XANES spectra of ACS and the dinickel complexes showed overall similar shapes, but less resolved pre-edge and edge features in ACS, attributed to more distorted square-planar nickel sites in particular in reduced ACS. DFT calculation of pre-edge absorption and Kβ2,5 emission features reproduced the experimental spectra of the synthetic complexes, was sensitive even to the small geometry differences in 1 and 2, and indicated low-spin Ni(II) sites. Comparison of nickel sites in proteins and biomimetic compounds is valuable for deducing structural and electronic differences in response to ligation and redox changes.

Potential influence of birds on soil testate amoebae in the Arctic

NASA Astrophysics Data System (ADS)

Mazei, Yuri A.; Lebedeva, Natalia V.; Taskaeva, Anastasia A.; Ivanovsky, Alexander A.; Chernyshov, Viktor A.; Tsyganov, Andrey N.; Payne, Richard J.

2018-06-01

Birds can be an important agent of environmental change in High Arctic ecosystems, particularly due to the role of seabirds as a vector transferring nutrients from the marine to terrestrial realms. The soils of bird nesting sites are known to host distinct plant communities but the consequences of bird modification for microorganisms are much less clear. Our focus here is testate amoebae: a widely-distributed group of protists with significant roles in many aspects of ecosystem functioning. We compared the testate amoeba assemblages of a site on Spitsbergen (Svalbard archipelago) affected by nesting birds, with nearby control sites. We found differences in assemblage between sites, typified by reduced relative abundance of Phryganella acropodia and Centropyxis aerophila in bird-modified soils. These changes may reflect a reduced availability of fungal food sources. We found no evidence for differences in assemblage diversity or test concentration between bird-modified and control soils. Our dataset is small but results provide the first evidence for the potential effect of bird modification of soils on testate amoebae in the Arctic. Results show only limited similarity to experimental studies of nutrient addition, implying that response mechanisms may be more complicated than simply additional nutrient supply.

AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis.

PubMed

Greener, Joe G; Sternberg, Michael J E

2015-10-23

Despite being hugely important in biological processes, allostery is poorly understood and no universal mechanism has been discovered. Allosteric drugs are a largely unexplored prospect with many potential advantages over orthosteric drugs. Computational methods to predict allosteric sites on proteins are needed to aid the discovery of allosteric drugs, as well as to advance our fundamental understanding of allostery. AlloPred, a novel method to predict allosteric pockets on proteins, was developed. AlloPred uses perturbation of normal modes alongside pocket descriptors in a machine learning approach that ranks the pockets on a protein. AlloPred ranked an allosteric pocket top for 23 out of 40 known allosteric proteins, showing comparable and complementary performance to two existing methods. In 28 of 40 cases an allosteric pocket was ranked first or second. The AlloPred web server, freely available at http://www.sbg.bio.ic.ac.uk/allopred/home, allows visualisation and analysis of predictions. The source code and dataset information are also available from this site. Perturbation of normal modes can enhance our ability to predict allosteric sites on proteins. Computational methods such as AlloPred assist drug discovery efforts by suggesting sites on proteins for further experimental study.

Predicting the Spatial Variability of Fuel Moisture Content in Mountainous Eucalyptus Forests

NASA Astrophysics Data System (ADS)

Sheridan, G. J.; Nyman, P.; Lane, P. N. J.; Metzen, D.

2014-12-01

In steep mountainous landscapes, topographic aspect can play a significant role in small-scale (ie. scales in the order of 10's ha) variability in surface fuel moisture. Experimental sites for monitoring microclimate variables and moisture content in litter and in near-surface soils were established at a control site and on four contrasting aspects (north, south, east and west) in southeast Australia. At each of the four microclimate sites sensors are arranged to measure the soil moisture (2 replicates), surface fuel moisture at 2.5cm depth (12 replicates), precipitation throughfall (3 replicates), radiation (3 replicates), and screen level relative humidity, air temperature, leaf wetness, and wind speed (1 replicate of each). Temperature and relative humidity are also measured within the dead fine surface fuel using Ibutton's (4 replicates). All measurements are logged continuously at 15 min intervals. The moisture content of the surface fuel is estimated using a novel method involving high-replication of low-cost continuous soil moisture sensors placed at the centre of a 5cm deep sample of fine dead surface fuel, referred to here as "litter-packs". The litter-packs were constructed from fuels collected from the area surrounding the microclimate site. The initial results show the moisture regime on the forest floor was highly sensitive to the incoming shortwave radiation, which was up to 6 times higher in the north-facing (equatorial) slopes due to slope orientation and the sparse vegetation compared to vegetation on the south-facing (polar facing) slopes. Differences in shortwave radiation resulted in peak temperatures within the litter that were up to 2 times higher on the equatorial-facing site than those on the polar-facing site. For instance, on a day in November 2013 with maximum open air temperature of 35o C, the temperatures within the litter layer at the north-facing and south-facing sites were 54o C and 32o C, respectively, despite air temperature at the two sites differing by less than 2o C. The minimum gravimetric water content in the litter layer on the same day was 21% on the equatorial-facing slope and 85% on the polar-facing slope. The experimental data has been used to calibrate a topographic downscaling algorithm, yielding estimates of surface fuel moisture at 20m resolution.

Gold leaching by organic base polythionates: new non-toxic and secure technology.

PubMed

Smolyaninov, Vladislav; Shekhvatova, Galina; Vainshtein, Mikhail

2014-01-01

The article present a review on own experimental and some published data which are related with the gold leaching. It is well-known that the most common and usual process of the leaching with cyanide can be dangerous, needs a great water consumption, and additional costs for remediation of the poisoned and toxic sites. The experimental data described production of poythionates which are not toxic but perspective for the prosperous gold leaching. The paper dedicated to the safe gold leaching with thiosulfates and organic salts of polythionic acids (organic base polythionates). The method of production of these polythionates based on the Smolyaninov reaction is described in stages and in details for the first time. Possible application of the polythionates application in the gold leaching is discussed and its advantages are compared with the gold leaching by cyanation.

Behavioural evidence of magnetoreception in dolphins: detection of experimental magnetic fields

NASA Astrophysics Data System (ADS)

Kremers, Dorothee; López Marulanda, Juliana; Hausberger, Martine; Lemasson, Alban

2014-11-01

Magnetoreception, meaning the perception of magnetic fields, is supposed to play an important role for orientation/navigation in some terrestrial and aquatic species. Although some spatial observations of free-ranging cetaceans' migration routes and stranding sites led to the assumption that cetaceans may be sensitive to the geomagnetic field, experimental evidence is lacking. Here, we tested the spontaneous response of six captive bottlenose dolphins to the presentation of two magnetized and demagnetized controlled devices while they were swimming freely. Dolphins approached the device with shorter latency when it contained a strongly magnetized neodymium block compared to a control demagnetized block that was identical in form and density and therefore undistinguishable with echolocation. We conclude that dolphins are able to discriminate the two stimuli on the basis of their magnetic properties, a prerequisite for magnetoreception-based navigation.

Behavioural evidence of magnetoreception in dolphins: detection of experimental magnetic fields.

PubMed

Kremers, Dorothee; López Marulanda, Juliana; Hausberger, Martine; Lemasson, Alban

2014-11-01

Magnetoreception, meaning the perception of magnetic fields, is supposed to play an important role for orientation/navigation in some terrestrial and aquatic species. Although some spatial observations of free-ranging cetaceans' migration routes and stranding sites led to the assumption that cetaceans may be sensitive to the geomagnetic field, experimental evidence is lacking. Here, we tested the spontaneous response of six captive bottlenose dolphins to the presentation of two magnetized and demagnetized controlled devices while they were swimming freely. Dolphins approached the device with shorter latency when it contained a strongly magnetized neodymium block compared to a control demagnetized block that was identical in form and density and therefore undistinguishable with echolocation. We conclude that dolphins are able to discriminate the two stimuli on the basis of their magnetic properties, a prerequisite for magnetoreception-based navigation.

Variability in goethite surface site density: evidence from proton and carbonate sorption.

PubMed

Villalobos, Mario; Trotz, Maya A; Leckie, James O

2003-12-15

Goethite is a representative iron oxide in natural environments due to its abundance and thermodynamic stability and may be responsible for many surface-mediated processes, including ion retention and mobility in aqueous settings. A large variability in morphologies and specific surface areas of goethite crystals exists but little work has been done to compare surface reactivity between them. The present work offers experimental evidence for the existence of an inverse relationship between sorption capacity for protons and carbonate ions and specific surface area of goethite for three synthetic goethite preparations spanning surface area differences by a factor of 2. An explanation for this was found by assuming a variable reactive site density between preparations in direct relationship to their sorption capacity based on congruency of carbonate sorption computed on a per-site basis. Previous evidence of maximum sorption capacities supports this explanation, and site density ratios between the goethites studied here were obtained. Triple layer surface complexation modeling was successful in describing adsorption data for all goethite preparations using equal stoichiometries. A new formulation of standard state for activities of surface species based on a 1.0 mole fraction of sites on the solid allowed transformation of the conventional molar concentration-based affinity constants to values based on site occupancy. In this fashion, by applying the appropriate site density ratios, a single set of affinity constant values was found that described accurately the adsorption data for all preparations.

Dynamics of aspen root biomass and sucker production following fire

Treesearch

Roy A. Renkin; Don G. Despain

2001-01-01

Changes in preburn aspen root biomass 8 years following prescribed fire were analyzed for five experimental sites distributed across a moisture gradient. Total root biomass decreased across all sites but was proportionately greater in xeric than mesic sites. Response of post-burn aspen suckers to ungulate browsing varied according to site and treatment. Browsing...

A pilot study on remediation of sediments enriched by oyster farming wastes using granulated coal ash.

PubMed

Yamamoto, T; Kim, K H; Shirono, K

2015-01-15

In order to evaluate the ability of granulated coal ash (GCA), a byproduct of coal thermal electric power stations, to remove hydrogen sulfide from organically enriched sediments, a pilot study was carried out at oyster farming sites, where sediments were enriched with oyster feces and dead oysters. Concentration of hydrogen sulfide in the interstitial water of the sediment decreased to nearly zero in both experimental sites, whereas it remained over 0.2mg/l in the control site. Concentration of acid volatile sulfide (AVS) in the sediment also decreased significantly in both experimental sites, while remained over 0.4 mg/g in the control site. Increases were observed in both the number of benthic microalgae species and the individual number of benthic animals in the surface sediments. This may have been due to the decrease in hydrogen sulfide. Copyright © 2014 Elsevier Ltd. All rights reserved.

Survey of existing underground openings for in-situ experimental facilities

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

Wollenberg, H.; Graf, A.; Strisower, B.

1981-07-01

In an earlier project, a literature search identified 60 underground openings in crystalline rock capable of providing access for an in-situ experimental facility to develop geochemical and hydrological techniques for evaluating sites for radioactive waste isolation. As part of the current project, discussions with state geologists, owners, and operators narrowed the original group to 14. Three additional sites in volcanic rock and one site in granite were also identified. Site visits and application of technical criteria, including the geologic and hydrologic settings and depth, extent of the rock unit, condition, and accessibility of underground workings, determined four primary candidate sites:more » the Helms Pumped Storage Project in grandiodorite of the Sierra Nevada, California; the Tungsten Queen Mine in Precambrian granodiorite of the North Carolina Piedmont; the Mount Hope Mine in Precambrian granite and gneiss of northern New Jersey; and the Minnamax Project in the Duluth gabbro complex of northern Minnesota.« less

The Use of Tooth Particles as a Biomaterial in Post-Extraction Sockets. Experimental Study in Dogs.

PubMed

Calvo-Guirado, José Luis; Maté-Sánchez de Val, José Eduardo; Ramos-Oltra, María Luisa; Pérez-Albacete Martínez, Carlos; Ramírez-Fernández, María Piedad; Maiquez-Gosálvez, Manuel; Gehrke, Sergio A; Fernández-Domínguez, Manuel; Romanos, Georgios E; Delgado-Ruiz, Rafael Arcesio

2018-05-06

Objectives : The objective of this study was to evaluate new bone formation derived from freshly crushed extracted teeth, grafted immediately in post-extraction sites in an animal model, compared with sites without graft filling, evaluated at 30 and 90 days. Material and Methods : The bilateral premolars P2, P3, P4 and the first mandibular molar were extracted atraumatically from six Beagle dogs. The clean, dry teeth were ground immediately using the Smart Dentin Grinder. The tooth particles obtained were subsequently sieved through a special sorting filter into two compartments; the upper container isolating particles over 1200 μm, the lower container isolated particles over 300 μm. The crushed teeth were grafted into the post-extraction sockets at P3, P4 and M1 (test group) (larger and smaller post-extraction alveoli), while P2 sites were left unfilled and acted as a control group. Tissue healing and bone formation were evaluated by histological and histomorphometric analysis after 30 and 90 days. Results : At 30 days, test site bone formation was greater in the test group than the control group ( p < 0.05); less immature bone was observed in the test group (25.71%) than the control group (55.98%). At 90 days, significant differences in bone formation were found with more in the test group than the control group. No significant differences were found in new bone formation when comparing the small and large alveoli post-extraction sites. Conclusions : Tooth particles extracted from dog’s teeth, grafted immediately after extractions can be considered a suitable biomaterial for socket preservation.

Follow-up and timeliness after an abnormal cancer screening among underserved, urban women in a patient navigation program

PubMed Central

Markossian, Talar W.; Darnell, Julie S.; Calhoun, Elizabeth A.

2012-01-01

Background We evaluated the efficacy of a Chicago-based cancer patient navigation program developed to increase the proportion of patients reaching diagnostic resolution and reduce the time from abnormal screening test to definitive diagnostic resolution. Methods Women with an abnormal breast (n=352) or cervical (n=545) cancer screening test were recruited for the quasi-experimental study. Navigation subjects originated from five federally qualified health center sites and one safety net hospital. Records-based concurrent control subjects were selected from 20 sites. Control sites had similar characteristics to the navigated sites in terms of patient volume, racial/ethnic composition, and payor mix. Mixed-effects logistic regression and Cox proportional hazard regression analyses were conducted to compare navigation and control patients reaching diagnostic resolution by 60 days and time to resolution, adjusting for demographic covariates and site. Results Compared to controls, the breast navigation group had shorter time to diagnostic resolution (aHR=1.65, CI=1.20–2.28) and the cervical navigation group had shorter time to diagnostic resolution for those who resolved after 30 days (aHR= 2.31, CI=1.75–3.06), with no difference before 30 days (aHR= 1.42, CI=0.83–2.43). Variables significantly associated with longer time to resolution for breast cancer screening abnormalities were being older, never partnered, abnormal mammogram and BI-RADS 3, and being younger and Black for cervical abnormalities. Conclusions Patient navigation reduces time from abnormal cancer finding to definitive diagnosis in underserved women. Impact Results support efforts to use patient navigation as a strategy to reduce cancer disparities among socioeconomically disadvantaged women. PMID:23045544

Follow-up and timeliness after an abnormal cancer screening among underserved, urban women in a patient navigation program.

PubMed

Markossian, Talar W; Darnell, Julie S; Calhoun, Elizabeth A

2012-10-01

We evaluated the efficacy of a Chicago-based cancer patient navigation program developed to increase the proportion of patients reaching diagnostic resolution and reduce the time from abnormal screening test to definitive diagnostic resolution. Women with an abnormal breast (n = 352) or cervical (n = 545) cancer screening test were recruited for the quasi-experimental study. Navigation subjects originated from five federally qualified health center sites and one safety net hospital. Records-based concurrent control subjects were selected from 20 sites. Control sites had similar characteristics to the navigated sites in terms of patient volume, racial/ethnic composition, and payor mix. Mixed-effects logistic regression and Cox proportional hazard regression analyses were conducted to compare navigation and control patients reaching diagnostic resolution by 60 days and time to resolution, adjusting for demographic covariates and site. Compared with controls, the breast navigation group had shorter time to diagnostic resolution (aHR = 1.65, CI = 1.20-2.28) and the cervical navigation group had shorter time to diagnostic resolution for those who resolved after 30 days (aHR = 2.31, CI = 1.75-3.06), with no difference before 30 days (aHR = 1.42, CI = 0.83-2.43). Variables significantly associated with longer time to resolution for breast cancer screening abnormalities were being older, never partnered, abnormal mammogram and BI-RADS 3, and being younger and Black for cervical abnormalities. Patient navigation reduces time from abnormal cancer finding to definitive diagnosis in underserved women. Results support efforts to use patient navigation as a strategy to reduce cancer disparities among socioeconomically disadvantaged women. 2012 AACR

Soybean yield in relation to distance from the Itaipu reservoir

NASA Astrophysics Data System (ADS)

de Faria, Rogério Teixeira; Junior, Ruy Casão; Werner, Simone Silmara; Junior, Luiz Antônio Zanão; Hoogenboom, Gerrit

2016-07-01

Crops close to small water bodies may exhibit changes in yield if the water mass causes significant changes in the microclimate of areas near the reservoir shoreline. The scientific literature describes this effect as occurring gradually, with higher intensity in the sites near the shoreline and decreasing intensity with distance from the reservoir. Experiments with two soybean cultivars were conducted during four crop seasons to evaluate soybean yield in relation to distance from the Itaipu reservoir and determine the effect of air temperature and water availability on soybean crop yield. Fifteen experimental sites were distributed in three transects perpendicular to the Itaipu reservoir, covering an area at approximately 10 km from the shoreline. The yield gradient between the site closest to the reservoir and the sites farther away in each transect did not show a consistent trend, but varied as a function of distance, crop season, and cultivar. This finding indicates that the Itaipu reservoir does not affect the yield of soybean plants grown within approximately 10 km from the shoreline. In addition, the variation in yield among the experimental sites was not attributed to thermal conditions because the temperature was similar within transects. However, the crop water availability was responsible for higher differences in yield among the neighboring experimental sites related to water stress caused by spatial variability in rainfall, especially during the soybean reproductive period in January and February.

SPRUCE S1 Bog and SPRUCE Experiment Location Survey Results, 2015

DOE Data Explorer

Griffiths, Natalie A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hook, L. A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hanson, P. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.

2016-01-01

This data set provides a record of the horizontal and vertical survey results of SPRUCE experimental infrastructure and measurement locations on the S1-Bog on the Marcell Experimental Forest and the SPRUCE experimental site within the S1-Bog.

Bayesian inversions of a dynamic vegetation model in four European grassland sites

NASA Astrophysics Data System (ADS)

Minet, J.; Laloy, E.; Tychon, B.; François, L.

2015-01-01

Eddy covariance data from four European grassland sites are used to probabilistically invert the CARAIB dynamic vegetation model (DVM) with ten unknown parameters, using the DREAM(ZS) Markov chain Monte Carlo (MCMC) sampler. We compare model inversions considering both homoscedastic and heteroscedastic eddy covariance residual errors, with variances either fixed a~priori or jointly inferred with the model parameters. Agreements between measured and simulated data during calibration are comparable with previous studies, with root-mean-square error (RMSE) of simulated daily gross primary productivity (GPP), ecosystem respiration (RECO) and evapotranspiration (ET) ranging from 1.73 to 2.19 g C m-2 day-1, 1.04 to 1.56 g C m-2 day-1, and 0.50 to 1.28 mm day-1, respectively. In validation, mismatches between measured and simulated data are larger, but still with Nash-Sutcliffe efficiency scores above 0.5 for three out of the four sites. Although measurement errors associated with eddy covariance data are known to be heteroscedastic, we showed that assuming a classical linear heteroscedastic model of the residual errors in the inversion do not fully remove heteroscedasticity. Since the employed heteroscedastic error model allows for larger deviations between simulated and measured data as the magnitude of the measured data increases, this error model expectedly lead to poorer data fitting compared to inversions considering a constant variance of the residual errors. Furthermore, sampling the residual error variances along with model parameters results in overall similar model parameter posterior distributions as those obtained by fixing these variances beforehand, while slightly improving model performance. Despite the fact that the calibrated model is generally capable of fitting the data within measurement errors, systematic bias in the model simulations are observed. These are likely due to model inadequacies such as shortcomings in the photosynthesis modelling. Besides model behaviour, difference between model parameter posterior distributions among the four grassland sites are also investigated. It is shown that the marginal distributions of the specific leaf area and characteristic mortality time parameters can be explained by site-specific ecophysiological characteristics. Lastly, the possibility of finding a common set of parameters among the four experimental sites is discussed.

Effects of long-term (10 years) exposure to elevated CO2 and O3 on trembling Aspen carbon and nitrogen metabolism at the aspen FACE (Free-Air Carbon Dioxide Enrichment) study site

Treesearch

Rakesh Minocha; Stephanie Long; Subhash Minocha; Paula Marquardt; Neil Nelson; Mark. Kubiske

2010-01-01

This study was conducted at the Aspen Free-Air Carbon Dioxide Enrichment (FACE) experimental site, Rhinelander, WI, (USA). Since 1998, 12 experimental rings planted in 1997 underwent four different treatments: control; elevated CO2 (560 ppm); elevated O3 (1.5X ambient) and elevated CO2 (560 ppm) + O...

The chemical characteristics of soil in control and experimentally thinned plots in mesic oak forests along a historical deposition gradient

Treesearch

Ralph E. J. Boerner; Elaine Kennedy Sutherland

1997-01-01

This study examined the variations in the chemical parameters of soils of seven forests located along a historical deposition gradient spanning 8.5° longitude from southern Illinois to central West Virginia. Four to six mature control plots were sampled on two of the sites, and two experimentally thinned and two control plots were sampled on the remaining five sites....

A refined electrofishing technique for collecting Silver Carp: Implications for management

USGS Publications Warehouse

Bouska, Wesley W.; Glover, David C.; Bouska, Kristen; Garvey, James E.

2017-01-01

Detecting nuisance species at low abundance or in newly established areas is critical to developing pest management strategies. Due to their sensitivity to disturbance and erratic jumping behavior, Silver Carp Hypophthalmichthys molitrix can be difficult to collect with traditional sampling methods. We compared catch per unit effort (CPUE) of all species from a Long Term Resource Monitoring (LTRM) electrofishing protocol to an experimental electrofishing technique designed to minimize Silver Carp evasion through tactical boat maneuvering and selective application of power. Differences in CPUE between electrofishing methods were detected for 2 of 41 species collected across 2 years of sampling at 20 sites along the Illinois River. The mean catch rate of Silver Carp using the experimental technique was 2.2 times the mean catch rate of the LTRM electrofishing technique; the increased capture efficiency at low relative abundance emphasizes the utility of this method for early detection. The experimental electrofishing also collected slightly larger Silver Carp (mean: 510.7 mm TL versus 495.2 mm TL), and nearly four times as many Silver Carp independently jumped into the boat during experimental transects. Novel sampling approaches, such as the experimental electrofishing technique used in this study, should be considered to increase probability of detection for aquatic nuisance species.

A solid-state [sup 13]C NMR study of the molecular motion of ethylene adsorbed on a silver surface

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

Jianxin Wang; Ellis, P.D.

1993-01-13

The reorientation of ethylene on a silver catalyst surface has been studied by solid-state [sup 13]C NMR. The static cross-polarization spectra at different temperatures have been measured. Different jump site models are proposed to simulate the experimental results. It was found that the models involving a low number of jump sites are more sensitive to the experimental details. By comparison of the simulated and experimental results, the 6- and 4-site jump models are chosen as the most satisfactory model to fit the experimental spectra. On the basis of this representation, the activation energy derived for the jump process is 4.3more » kJ/mol. From the simulated results, it was concluded that the symmetry axis for the motion of the ethylene at low temperatures ([minus]173 to ca. [minus]45[degrees]C) is perpendicular to the plane of the ethylene molecule. At higher temperatures motion about other axes is initiated such that at room temperature a nearly isotropically averaged [sup 13]C shielding tensor is observed. 20 refs., 9 figs.« less

Hartree-Fock investigation of muon trapping in the chemical ferromagnet 4-(/p-chlorobenzylideneamino)-TEMPO

NASA Astrophysics Data System (ADS)

Jeong, Junho; Briere, Tina M.; Sahoo, N.; Das, T. P.; Ohira, Seiko; Nishiyama, K.; Nagamine, K.

2000-08-01

First-principles unrestricted Hartree-Fock theory is used to obtain the trapping sites for muon and muonium in ferromagnetic p-Cl-Ph-CHN-TEMPO (4-( p-chlorobenzylideneamino)- 2,2,6,6-tetramethylpiperidin-1-yloxyl) and the hyperfine interaction tensors for these sites. Using the calculated hyperfine interactions to fit the two experimentally observed muon spin rotation frequencies, it has been concluded that the two most likely candidates for explaining the experimental data are a muon trapped at the chlorine site and a singlet muonium state at the radical oxygen. The direction of the easy axis is also determined.

Site alteration effects from rocket exhaust impingment during a simulated Viking Mars landing. Part 1: Nozzle development and physical site alternation

NASA Technical Reports Server (NTRS)

Romine, G. L.; Reisert, T. D.; Gliozzi, J.

1973-01-01

A potential interference problem for the Viking '75 scientific investigation of the Martian surface resulting from retrorocket exhaust plume impingement of the surface was investigated experimentally and analytically. It was discovered that the conventional bell nozzle originally planned for the Viking Lander retrorockets would produce an unacceptably large amount of physical disturbance to the landing site. An experimental program was subsequently undertaken to find and/or develop a nozzle configuration which would significantly reduce the site alteration. A multiple nozzle configuration, consisting of 18 small bell nozzles, was shown to produce a level of disturbance that was considered by the Viking Lander Science Teams to be acceptable on the basis of results from full-scale tests on simulated Martian soils.

Investigating and Modeling Ecosystem Response to an Experimental and a Natural Ice Storm

NASA Astrophysics Data System (ADS)

Fakhraei, H.; Driscoll, C. T.; Rustad, L.; Campbell, J. L.; Groffman, P.; Fahey, T.; Likens, G.; Swaminathan, R.

2017-12-01

Our understanding of ecosystem response to the extreme events is generally limited to rare observations from the natural historical events. However, investigating extreme events under controlled conditions can improve our understanding of these natural phenomena. A novel field experiment was conducted in a northern hardwood forest at the Hubbard Brook Experimental Forest in New Hampshire in the northeastern United States to quantify the influence of ice storms on the ecological processes. During subfreezing conditions in the winters of 2016 and 2017, water from a nearby stream was pumped and sprayed on the canopy of eight experimental plots to accrete ice to a targeted thickness on the canopy. The experiment was conducted at three levels of icing thickness (0.25, 0.5, 0.75 in.) in 2016 comparable to the naturally occurring 1998 ice storm and a second 0.5 in. treatment 2017 which were compared with reference plots. The most notable response of the icing treatments was a marked increase in fine and course litter fall which increased exponentially with increases in the icing thickness. Post-treatment openings in the canopy caused short-term increases in soil temperature in the ice-treatment plots compared to the reference plots. No response from the ice storm treatments were detected for soil moisture, net N mineralization, net nitrification, or denitrification after both natural and experimental ice storm. In contrast to the marked increase in the stream water nitrate after the natural occurring 1998 ice storm, we have not observed any significant change in soil solution N concentrations in the experimental ice storm treatments. Inconsistency in the response between the natural and experimental ice storm is likely due to differences in geophysical characteristics of the study sites including slope and lateral uptake of nutrient by the trees outside the experimental plots. In order to evaluate the long-term impacts of ice storms on northern hardwood forests, we used the biogeochemical model, PnET-BGC. The model was calibrated to the study watersheds using observations from the natural and experimental ice storms. Future projections for ice storm events were estimated from an advanced climate model and applied to the calibrated PnET-BGC model to simulate future impacts of ice storms on the northern hardwood forests.

40 CFR 172.1 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... grants permission to a permittee or a permittee's designated participant for the use of an experimental use pesticide at an application site owned or controlled by the cooperator. Experimental animals means... supervising the use or evaluation of, an experimental use pesticide to be applied at a specific application...

AmeriFlux US-Rls RCEW Low Sagebrush

DOE Data Explorer

Flerchinger, Gerald [USDA Agricultural Research Service

2018-01-01

This is the AmeriFlux version of the carbon flux data for the site US-Rls RCEW Low Sagebrush. Site Description - The site is located on the USDA-ARS's Reynolds Creek Experimental Watershed. It is dominated by low sagebrush on land managed by USDI Bureau of Land Management.

Comparisons of the skeletal locations of putative plutonium-induced osteosarcomas in humans with those in beagle dogs and with naturally occurring tumors in both species.

PubMed

Miller, Scott C; Lloyd, Ray D; Bruenger, Fred W; Krahenbuhl, Melinda P; Polig, Erich; Romanov, Sergey A

2003-11-01

Osteosarcomas occur from exposures to bone-seeking, alpha-particle-emitting isotopes, particularly plutonium. The skeletal distribution of putative 239Pu-induced osteosarcomas reported in Mayak Metallurgical and Radiochemical Plutonium Plant workers is compared with those observed in canine studies, and these are compared with distributions of naturally occurring osteosarcomas in both species. In the Mayak workers, 29% and 71% of the osteosarcomas were in the peripheral and central skeleton, respectively, with the spine having the most tumors (36%). An almost identical distribution of plutonium-induced osteosarcomas was reported for dogs injected with 239Pu as young adults. This distribution of osteosarcomas is quite different from the distributions of naturally occurring osteosarcomas for both species. In the Cooperative Osteosarcoma Study Group in humans (1,736 osteosarcomas from all ages), over 91% of the tumors occurred in the peripheral skeleton. In the Mayo Clinic group of older individuals (>40 years old), over 60% of the osteosarcomas appeared in the peripheral skeleton. The distribution of naturally occurring osteosarcomas in the canine is similar to that in the adult human. The similarities of the distributions of plutonium-associated osteosarcomas in the Mayak workers with those found in experimental studies suggest that many of the reported osteosarcomas may have been associated with plutonium exposures. These results also support the experimental paradigm that plutonium osteosarcomas have a preference for well vascularized cancellous bone sites. These sites have a greater initial deposition of plutonium, but also greater turnover due to elevated bone remodeling rates.

Electronic structures of C u 2 O , C u 4 O 3 , and CuO: A joint experimental and theoretical study

DOE PAGES

Wang, Y.; Lany, S.; Ghanbaja, J.; ...

2016-12-14

We present a joint experimental and theoretical study for the electronic structures of copper oxides including Cu 2O, CuO, and the metastable mixed-valence oxide Cu 4O 3. The optical band gap is determined by experimental optical absorption coefficient, and the electronic structure in valence and conduction bands is probed by photoemission and electron energy loss spectroscopies, respectively. Furthermore, we compare our experimental results with many-body GW calculations utilizing an additional on-site potential for d-orbital energies that facilitates tractable and predictive computations. The side-by-side comparison between the three oxides, including a band insulator (Cu2O) and two Mott/charge-transfer insulators (CuO, Cu 4Omore » 3) leads to a consistent picture for the optical and band-structure properties of the Cu oxides, strongly supporting indirect band gaps of about 1.2 and 0.8 eV in CuO and Cu 4O 3, respectively. This comparison also points towards surface oxidation and reduction effects that can complicate the interpretation of the photoemission spectra.« less

An Eco-hydrologic Assessment of Small Experimental Catchments with Various Land Uses within the Panama Canal Watershed: Agua Salud Project

NASA Astrophysics Data System (ADS)

Crouch, T. D.; Ogden, F. L.; Stallard, R. F.; Smithsonian Tropical Research Institute, Panama Canal Watershed Experiment, Agua Salud Project

2010-12-01

Hydrological processes in the humid tropics are poorly understood and an important topic when it comes to water management in the seasonal tropics. The Smithsonian Tropical Research Institute, Panama Canal Watershed Experiment, Agua Salud Project, seeks to understand these processes and quantify the long-term effects of different land cover and uses across the Panama Canal Watershed. One of the project’s main objectives is to understand how reforestation effects seasonal stream flows. To meet this objective, a baseline characterization of hydrology on the small catchment scale is being assessed across different land uses typical in rural Panama. The small experimental catchments are found within Panama’s protected Soberania National Park and the adjacent headwaters of the Agua Salud and Mendoza Rivers, all of which are part of the greater Panama Canal Watershed. The land uses being monitored include a variety of control catchments as well as treated pasture sites. The catchments used for this study include a mature old regrowth forest, a 50% deforested or mosaic regrowth site, an active pasture and a monoculture invasive grass site (saccharum spontaneum) as experimental controls and two treated catchments that were recently abandoned pastures converted to teak and native species timber plantations. Installed instrumentation includes a network of rain gauges, v-notched weirs, atmometers, an eddy covariance system and an assortment of meteorological and automated geochemical sampling systems. Spatial, rainfall, runoff and ET data across these six geologically and topographically similar catchments are available from 2009 and 2010. Classic water balance and paired catchment techniques were used to compare the catchments on an annual, seasonal, and event basis. This study sets the stage for hydrologic modeling and for better understanding the effects of vegetation and land-use history on rainfall-runoff processes for the Agua Salud Project and Panama Canal Watershed Experiment.

Ridge augmentation using recombinant human fibroblast growth factor-2 with biodegradable gelatin sponges incorporating β-tricalcium phosphate: a preclinical study in dogs.

PubMed

Hoshi, S; Akizuki, T; Matsuura, T; Ikawa, T; Kinoshita, A; Oda, S; Tabata, Y; Matsui, M; Izumi, Y

2016-02-01

Fibroblast growth factor-2 (FGF-2) regulates the proliferation and differentiation of osteogenic cells, resulting in the promotion of bone formation. Biodegradable gelatin sponges incorporating β-tricalcium phosphate (β-TCP) have been reported as a scaffold, which has the ability to control growth factor release, offering sufficient mechanical strength and efficient migration of mesenchymal cells. In this study, we evaluated the effects of the combined use of recombinant human FGF-2 (rhFGF-2) and gelatin/β-TCP sponge on ridge augmentation in dogs. Six male beagle dogs were used in this study. Twelve wk after tooth extraction, bilateral 10 × 5 mm (width × depth) saddle-type defects were created 3 mm apart from the mesial side of the maxillary canine. At the experimental sites, the defects were filled with gelatin/β-TCP sponge infiltrated with 0.3% rhFGF-2, whereas gelatin/β-TCP sponge infiltrated with saline was applied to the control sites. Eight wk after surgery, qualitative and quantitative analyses were performed. There were no signs of clinical inflammation at 8 wk after surgery. Histometric measurements revealed that new bone height at the experimental sites (2.98 ± 0.65 mm) was significantly greater than that at the control sites (1.56 ± 0.66 mm; p = 0.004). The total tissue height was greater at the experimental sites (6.62 ± 0.66 mm) than that at the control sites (5.95 ± 0.74 mm), although there was no statistical significant difference (p = 0.051). Cast model measurements revealed that the residual defect height at the experimental sites (2.31 ± 0.50 mm) was significantly smaller than that at the control sites (3.51 ± 0.78 mm; p = 0.012). The combined use of rhFGF-2 and gelatin/β-TCP sponge promotes ridge augmentation in canine saddle-type bone defects. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

AmeriFlux US-SRG Santa Rita Grassland

DOE Data Explorer

Scott, Russell [United States Department of Agriculture

2016-01-01

This is the AmeriFlux version of the carbon flux data for the site US-SRG Santa Rita Grassland. Site Description - Semidesert C4 grassland, lies in Pasture 1 on the Santa Rita Experimental Range. This is the companion site for US-SRM, but has much less mesquite encroachment.

AmeriFlux US-Rms RCEW Mountain Big Sagebrush

DOE Data Explorer

Flerchinger, Gerald [USDA Agricultural Research Service

2017-01-01

This is the AmeriFlux version of the carbon flux data for the site US-Rms RCEW Mountain Big Sagebrush. Site Description - The site is located on the USDA-ARS's Reynolds Creek Experimental Watershed. It is dominated by mountain big sagebrush on land managed by USDI Bureau of Land Management.

ESTIMATING THE RATE OF NATURAL BIOATTENUATION OF GROUND WATER CONTAMINANTS BY A MASS CONSERVATION APPROACH

EPA Science Inventory

Recent field and experimental research has shown that certain classes of subsurface contaminants can biodegrade at many sites. A number of site specific factors influences the rate of biodegradation, which helps determine the ultimate extent of contamination at these sites. The...

National Centers for Environmental Prediction

Science.gov Websites

/ VISION | About EMC EMC > GEFS > OPERATIONAL PRODUCTS Home Operational Products Experimental Data Global Ensemble products posted by the GEFS model team are experimental analysis and forecast products , and you will find them listed under the "Experimental Data" section of our web site. The

Experimental study and modelling of selenite sorption onto illite and smectite clays.

PubMed

Missana, T; Alonso, U; García-Gutiérrez, M

2009-06-15

This study provides a large set of experimental selenite sorption data for pure smectite and illite. Similar sorption behavior existed in both clays: linear within a large range of the Se concentrations investigated (from 1x10(-10) to 1x10(-3) M); and independent of ionic strength. Selenite sorption was also analysed in the illite/smectite system with the clays mixed in two different proportions, as follows: (a) 30% illite-70% smectite and (b) 43% illite-57% smectite. The objective of the study was to provide the simplest model possible to fit the experimental data, a model also capable of describing selenite sorption in binary illite/smectite clay systems. Selenite sorption data, separately obtained in the single mineral systems, were modeled using both a one- and a two-site non-electrostatic model that took into account the formation of two complexes at the edge sites of the clay. Although the use of a two-site model slightly improved the fit of data at a pH below 4, the simpler one-site model reproduced satisfactorily all the sorption data from pH 3 to 8. The complexation constants obtained by fitting sorption data of the individual minerals were incorporated into a model to predict the adsorption of selenium in the illite/smectite mixtures; the model's predictions were consistent with the experimental adsorption data.

Pain referral and regional deep tissue hyperalgesia in experimental human hip pain models.

PubMed

Izumi, Masashi; Petersen, Kristian Kjær; Arendt-Nielsen, Lars; Graven-Nielsen, Thomas

2014-04-01

Hip disorder patients typically present with extensive pain referral and hyperalgesia. To better understand underlying mechanisms, an experimental hip pain model was established in which pain referrals and hyperalgesia could be studied under standardized conditions. In 16 healthy subjects, pain was induced by hypertonic saline injection into the gluteus medius tendon (GMT), adductor longus tendon (ALT), or gluteus medius muscle (GMM). Isotonic saline was injected contralaterally as control. Pain intensity was assessed on a visual analogue scale (VAS), and subjects mapped the pain distribution. Before, during, and after injections, passive hip joint pain provocation tests were completed, together with quantitative sensory testing as follows: pressure pain thresholds (PPTs), cuff algometry pain thresholds (cuff PPTs), cutaneous pin-prick sensitivity, and thermal pain thresholds. Hypertonic saline injected into the GMT resulted in higher VAS scores than hypertonic injections into the ALT and GMM (P<.05). Referred pain areas spread to larger parts of the leg after GMT and GMM injections compared with more regionalized pain pattern after ALT injections (P<.05). PPTs at the injection site were decreased after hypertonic saline injections into GMT and GMM compared with baseline, ALT injections, and isotonic saline. Cuff PPTs from the thigh were decreased after hypertonic saline injections into the ALT compared with baseline, GMT injections, and isotonic saline (P<.05). More subjects had positive joint pain provocation tests after hypertonic compared with isotonic saline injections (P<.05), indicating that this provocation test also assessed hyperalgesia in extra-articular soft tissues. The experimental models may open for better understanding of pain mechanisms associated with painful hip disorders. Copyright © 2014 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

10 CFR 960.3-2-2-3 - Comparative evaluation of all sites proposed for nomination.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Comparative evaluation of all sites proposed for...-3 Comparative evaluation of all sites proposed for nomination. Sixth, for those potentially... reasonable comparative evaluation of each such site with all other such sites shall be made. For each site...

10 CFR 960.3-2-2-3 - Comparative evaluation of all sites proposed for nomination.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Comparative evaluation of all sites proposed for...-3 Comparative evaluation of all sites proposed for nomination. Sixth, for those potentially... reasonable comparative evaluation of each such site with all other such sites shall be made. For each site...

10 CFR 960.3-2-2-3 - Comparative evaluation of all sites proposed for nomination.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Comparative evaluation of all sites proposed for...-3 Comparative evaluation of all sites proposed for nomination. Sixth, for those potentially... reasonable comparative evaluation of each such site with all other such sites shall be made. For each site...

10 CFR 960.3-2-2-3 - Comparative evaluation of all sites proposed for nomination.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Comparative evaluation of all sites proposed for...-3 Comparative evaluation of all sites proposed for nomination. Sixth, for those potentially... reasonable comparative evaluation of each such site with all other such sites shall be made. For each site...

10 CFR 960.3-2-2-3 - Comparative evaluation of all sites proposed for nomination.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Comparative evaluation of all sites proposed for...-3 Comparative evaluation of all sites proposed for nomination. Sixth, for those potentially... reasonable comparative evaluation of each such site with all other such sites shall be made. For each site...

Experimental warming differentially affects microbial structure and activity in two contrasted moisture sites in a Sphagnum-dominated peatland.

PubMed

Delarue, Frédéric; Buttler, Alexandre; Bragazza, Luca; Grasset, Laurent; Jassey, Vincent E J; Gogo, Sébastien; Laggoun-Défarge, Fatima

2015-04-01

Several studies on the impact of climate warming have indicated that peat decomposition/mineralization will be enhanced. Most of these studies deal with the impact of experimental warming during summer when prevalent abiotic conditions are favorable to decomposition. Here, we investigated the effect of experimental air warming by open-top chambers (OTCs) on water-extractable organic matter (WEOM), microbial biomasses and enzymatic activities in two contrasted moisture sites named Bog and Fen sites, the latter considered as the wetter ones. While no or few changes in peat temperature and water content appeared under the overall effect of OTCs, we observed that air warming smoothed water content differences and led to a decrease in mean peat temperature at the warmed Bog sites. This thermal discrepancy between the two sites led to contrasting changes in microbial structure and activities: a rise in hydrolytic activity at the warmed Bog sites and a relative enhancement of bacterial biomass at the warmed Fen sites. These features were not associated with any change in WEOM properties namely carbon and sugar contents and aromaticity, suggesting that air warming did not trigger any shift in OM decomposition. Using various tools, we show that the use of single indicators of OM decomposition can lead to fallacious conclusions. Lastly, these patterns may change seasonally as a consequence of complex interactions between groundwater level and air warming, suggesting the need to improve our knowledge using a high time-resolution approach. Copyright © 2015 Elsevier B.V. All rights reserved.

Prediction of TF target sites based on atomistic models of protein-DNA complexes

PubMed Central

Angarica, Vladimir Espinosa; Pérez, Abel González; Vasconcelos, Ana T; Collado-Vides, Julio; Contreras-Moreira, Bruno

2008-01-01

Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition. PMID:18922190

Energy profile, spectroscopic (FT-IR, FT-Raman and FT-NMR) and DFT studies of 4-bromoisophthalic acid

NASA Astrophysics Data System (ADS)

Arjunan, V.; Thirunarayanan, S.; Mohan, S.

2018-04-01

The stable conformer of 4-bromoisophthalic acid (BIPA) has been identified by potential energy profile analysis. All the structural parameters of 4-bromoisophthalic acid are determined by B3LYP method with 6-311++G**, 6-31G** and cc-pVTZ basis sets. The fundamental vibrations are analysed with the use of FT-IR (4000-400 cm-1) and FT-Raman (4000-100 cm-1) spectra. The harmonic vibrational frequencies are theoretically calculated and compared with experimental FTIR and FT-Raman frequencies. The 1H and 13C NMR spectra have been analysed and compared with theoretical 1H and 13C NMR chemical shifts calculated by gauge independent atomic orbital (GIAO) method. The electronic properties, such as HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) energies are determined by B3LYP/cc-pVTZ method. The electron density distribution and site of chemical reactivity of BIPA molecule have been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP). Stability of the molecules arising from hyperconjugative interactions, charge delocalizations have been analysed by using natural bond orbital (NBO) analysis. The thermodynamic properties and atomic natural charges of the compound are analysed and the reactive sites of the molecule are identified. The global and local reactivity descriptors are evaluated to analyse the chemical reactivity and site selectivity of molecule through Fukui functions.

Strontium and barium in aqueous solution and a potassium channel binding site

NASA Astrophysics Data System (ADS)

Chaudhari, Mangesh I.; Rempe, Susan B.

2018-06-01

Ion hydration structure and free energy establish criteria for understanding selective ion binding in potassium (K+) ion channels and may be significant to understanding blocking mechanisms as well. Recently, we investigated the hydration properties of Ba2+, the most potent blocker of K+ channels among the simple metal ions. Here, we use a similar method of combining ab initio molecular dynamics simulations, statistical mechanical theory, and electronic structure calculations to probe the fundamental hydration properties of Sr2+, which does not block bacterial K+ channels. The radial distribution of water around Sr2+ suggests a stable 8-fold geometry in the local hydration environment, similar to Ba2+. While the predicted hydration free energy of -331.8 kcal/mol is comparable with the experimental result of -334 kcal/mol, the value is significantly more favorable than the -305 kcal/mol hydration free energy of Ba2+. When placed in the innermost K+ channel blocking site, the solvation free energies and lowest energy structures of both Sr2+ and Ba2+ are nearly unchanged compared with their respective hydration properties. This result suggests that the block is not attributable to ion trapping due to +2 charge, and differences in blocking behavior arise due to free energies associated with the exchange of water ligands for channel ligands instead of free energies of transfer from water to the binding site.

Comparing Different Strategies in Directed Evolution of Enzyme Stereoselectivity: Single- versus Double-Code Saturation Mutagenesis.

PubMed

Sun, Zhoutong; Lonsdale, Richard; Li, Guangyue; Reetz, Manfred T

2016-10-04

Saturation mutagenesis at sites lining the binding pockets of enzymes constitutes a viable protein engineering technique for enhancing or inverting stereoselectivity. Statistical analysis shows that oversampling in the screening step (the bottleneck) increases astronomically as the number of residues in the randomization site increases, which is the reason why reduced amino acid alphabets have been employed, in addition to splitting large sites into smaller ones. Limonene epoxide hydrolase (LEH) has previously served as the experimental platform in these methodological efforts, enabling comparisons between single-code saturation mutagenesis (SCSM) and triple-code saturation mutagenesis (TCSM); these employ either only one or three amino acids, respectively, as building blocks. In this study the comparative platform is extended by exploring the efficacy of double-code saturation mutagenesis (DCSM), in which the reduced amino acid alphabet consists of two members, chosen according to the principles of rational design on the basis of structural information. The hydrolytic desymmetrization of cyclohexene oxide is used as the model reaction, with formation of either (R,R)- or (S,S)-cyclohexane-1,2-diol. DCSM proves to be clearly superior to the likewise tested SCSM, affording both R,R- and S,S-selective mutants. These variants are also good catalysts in reactions of further substrates. Docking computations reveal the basis of enantioselectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

LigandRNA: computational predictor of RNA–ligand interactions

PubMed Central

Philips, Anna; Milanowska, Kaja; Łach, Grzegorz; Bujnicki, Janusz M.

2013-01-01

RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA–small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA–ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a “meta-predictor” leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl. PMID:24145824

Medicine Sellers for Prevention and Control of Sexually Transmitted Infections: Effect of a Quasi-Experimental Training Intervention in Bangladesh.

PubMed

Alam, Nazmul; Alam, Anadil; Fournier, Pierre

2015-01-01

This study used a quasi-experimental pre-post design to test whether short training can improve medicine sellers' (MSs) practices and skills for prevention and control of sexually transmitted infections (STIs) in Bangladesh. The training included lectures, printed materials, and identification of referral sites. Difference-in-differences estimation was used to determine the effects of intervention on key primary and secondary outcomes. Advice given by the MSs in intervention group for partner treatment and condoms use increased significantly by 11% and 9%, respectively, after adjusting for baseline differences in education, religion, age, duration of training, and study site. Referral of clients to qualified service providers increased by 5% in the intervention group compared to the comparison group, but this change was not found to be statistically significant. Significantly higher proportion of MSs in the intervention group recognized the recommended medications as per the national syndromic management guidelines in Bangladesh for treatment of urethral discharge and genital ulcer symptoms. Short training intervention was found to be effective in improving MSs' practice of promoting condom use and partner treatment to the clients. We anticipate the need for broad based training programs of MSs to improve their skills for the prevention and control of STI/HIV in Bangladesh.

CPLA 1.0: an integrated database of protein lysine acetylation.

PubMed

Liu, Zexian; Cao, Jun; Gao, Xinjiao; Zhou, Yanhong; Wen, Longping; Yang, Xiangjiao; Yao, Xuebiao; Ren, Jian; Xue, Yu

2011-01-01

As a reversible post-translational modification (PTM) discovered decades ago, protein lysine acetylation was known for its regulation of transcription through the modification of histones. Recent studies discovered that lysine acetylation targets broad substrates and especially plays an essential role in cellular metabolic regulation. Although acetylation is comparable with other major PTMs such as phosphorylation, an integrated resource still remains to be developed. In this work, we presented the compendium of protein lysine acetylation (CPLA) database for lysine acetylated substrates with their sites. From the scientific literature, we manually collected 7151 experimentally identified acetylation sites in 3311 targets. We statistically studied the regulatory roles of lysine acetylation by analyzing the Gene Ontology (GO) and InterPro annotations. Combined with protein-protein interaction information, we systematically discovered a potential human lysine acetylation network (HLAN) among histone acetyltransferases (HATs), substrates and histone deacetylases (HDACs). In particular, there are 1862 triplet relationships of HAT-substrate-HDAC retrieved from the HLAN, at least 13 of which were previously experimentally verified. The online services of CPLA database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). The CPLA database is freely available for all users at: http://cpla.biocuckoo.org.

Solid-state NMR calculations for metal oxides and gallates: Shielding and quadrupolar parameters for perovskites and related phases

NASA Astrophysics Data System (ADS)

Middlemiss, Derek S.; Blanc, Frédéric; Pickard, Chris J.; Grey, Clare P.

2010-05-01

The NMR parameters obtained from solid-state DFT calculations within the GIPAW approach for 17O- and 69/71Ga-sites in a range of predominantly oxide-based (group II monoxides, SrTiO 3, BaZrO 3, BaSnO 3, BaTiO 3, LaAlO 3, LaGaO 3, SrZrO 3, MgSiO 3 and Ba 2In 2O 5), and gallate (α- and β-Ga 2O 3, LiGaO 2, NaGaO 2, GaPO 4 and LaGaO 3) materials are compared with experimental values, with a view to the future application of a similar approach to doped phases of interest as candidate intermediate temperature solid oxide fuel cell (ITSOFC) electrolytes. Isotropic and anisotropic chemical shift parameters, quadrupolar coupling constants, and associated asymmetries are presented and analyzed. The unusual GaO 5 site occurring in LaGaGe 2O 7 is also fully characterised. In general, it is found that the theoretical results closely track the experimental trends, though some deviations are identified and discussed, particularly in regard to quadrupolar ηQ-values. The high quality of the computed results suggests that this approach can be extended to study more complex and disordered phases.

Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A.

PubMed

Maurer, Manuela; de Beer, Stephanie B A; Oostenbrink, Chris

2016-04-15

The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data.

Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A

PubMed Central

Maurer, Manuela; de Beer, Stephanie B. A.; Oostenbrink, Chris

2018-01-01

The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data. PMID:27092480

CPLA 1.0: an integrated database of protein lysine acetylation

PubMed Central

Liu, Zexian; Cao, Jun; Gao, Xinjiao; Zhou, Yanhong; Wen, Longping; Yang, Xiangjiao; Yao, Xuebiao; Ren, Jian; Xue, Yu

2011-01-01

As a reversible post-translational modification (PTM) discovered decades ago, protein lysine acetylation was known for its regulation of transcription through the modification of histones. Recent studies discovered that lysine acetylation targets broad substrates and especially plays an essential role in cellular metabolic regulation. Although acetylation is comparable with other major PTMs such as phosphorylation, an integrated resource still remains to be developed. In this work, we presented the compendium of protein lysine acetylation (CPLA) database for lysine acetylated substrates with their sites. From the scientific literature, we manually collected 7151 experimentally identified acetylation sites in 3311 targets. We statistically studied the regulatory roles of lysine acetylation by analyzing the Gene Ontology (GO) and InterPro annotations. Combined with protein–protein interaction information, we systematically discovered a potential human lysine acetylation network (HLAN) among histone acetyltransferases (HATs), substrates and histone deacetylases (HDACs). In particular, there are 1862 triplet relationships of HAT-substrate-HDAC retrieved from the HLAN, at least 13 of which were previously experimentally verified. The online services of CPLA database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). The CPLA database is freely available for all users at: http://cpla.biocuckoo.org. PMID:21059677

Comparisons of sets of electron-neutral scattering cross sections and calculated swarm parameters in Kr and Xe

NASA Astrophysics Data System (ADS)

Bordage, M. C.; Hagelaar, G. J. M.; Pitchford, L. C.; Biagi, S. F.; Puech, V.

2011-10-01

Xenon is used in a number of application areas ranging from light sources to x-ray detectors for imaging in medicine, border security and high-energy particle physics. There is a correspondingly large body of data available for electron scattering cross sections and swarm parameters in Xe, whereas data for Kr are more limited. In this communication we show intercomparisons of the cross section sets in Xe and Kr presently available on the LXCat site. Swarm parameters calculated using these cross sections sets are compared with experimental data, also available on the LXCat site. As was found for Ar, diffusion coefficients calculated using these cross section data in a 2-term Boltzmann solver are higher than Monte Carlo results by about 30% over a range of E/N from 1 to 100 Td. We find otherwise good agreement in Xe between 2-term and Monte Carlo results and between measured and calculated values of electron mobility, ionization rates and light emission (dimer) at atmospheric pressure. The available cross section data in Kr yield swarm parameters in agreement with the limited experimental data. The cross section compilations and measured swarm parameters used in this work are available on-line at www.lxcat.laplace. univ-tlse.fr.

Central site monitoring: results from a test of accuracy in identifying trials and sites failing Food and Drug Administration inspection.

PubMed

Lindblad, Anne S; Manukyan, Zorayr; Purohit-Sheth, Tejashri; Gensler, Gary; Okwesili, Paul; Meeker-O'Connell, Ann; Ball, Leslie; Marler, John R

2014-04-01

Site monitoring and source document verification account for 15%-30% of clinical trial costs. An alternative is to streamline site monitoring to focus on correcting trial-specific risks identified by central data monitoring. This risk-based approach could preserve or even improve the quality of clinical trial data and human subject protection compared to site monitoring focused primarily on source document verification. To determine whether a central review by statisticians using data submitted to the Food and Drug Administration (FDA) by clinical trial sponsors can identify problem sites and trials that failed FDA site inspections. An independent Analysis Center (AC) analyzed data from four anonymous new drug applications (NDAs) where FDA had performed site inspections overseen by FDA's Office of Scientific Investigations (OSI). FDA team members in the OSI chose the four NDAs from among all NDAs with data in Study Data Tabulation Model (SDTM) format. Two of the NDAs had data that OSI had deemed unreliable in support of the application after FDA site inspections identified serious data integrity problems. The other two NDAs had clinical data that OSI deemed reliable after site inspections. At the outset, the AC knew only that the experimental design specified two NDAs with significant problems. FDA gave the AC no information about which NDAs had problems, how many sites were inspected, or how many were found to have problems until after the AC analysis was complete. The AC evaluated randomization balance, enrollment patterns, study visit scheduling, variability of reported data, and last digit reference. The AC classified sites as 'High Concern', 'Moderate Concern', 'Mild Concern', or 'No Concern'. The AC correctly identified the two NDAs with data deemed unreliable by OSI. In addition, central data analysis correctly identified 5 of 6 (83%) sites for which FDA recommended rejection of data and 13 of 15 sites (87%) for which any regulatory deviations were identified during inspection. Of the six sites for which OSI reviewed inspections and found no deviations, the central process flagged four at the lowest level of concern, one at a moderate level, and one was not flagged. Central data monitoring during the conduct of a trial while data checking was in progress was not evaluated. Systematic central monitoring of clinical trial data can identify problems at the same trials and sites identified during FDA site inspections. Central data monitoring in conjunction with an overall monitoring process that adapts to identify risks as a trial progresses has the potential to reduce the frequency of site visits while increasing data integrity and decreasing trial costs compared to processes that are dependent primarily on source documentation.

Water regime of mechanical-biological pretreated waste materials under fast-growing trees.

PubMed

Rüth, Björn; Lennartz, Bernd; Kahle, Petra

2007-10-01

In this study mechanical-biological pre-treated waste material (MBP) was tested for suitability to serve as an alternative surface layer in combination with fast-growing and water-consumptive trees for final covers at landfill sites. The aim was to quantify evapotranspiration and seepage losses by numerical model simulations for two sites in Germany. In addition, the leaf area index (LAI) of six tree species over the growing season as the driving parameter for transpiration calculations was determined experimentally. The maximum LAI varied between 3.8 and 6.1 m2 m(-2) for poplar and willow clones, respectively. The evapotranspiration calculations revealed that the use of MBP waste material for re-cultivation enhanced evapotranspiration by 40 mm year(-1) (10%) over an 11 year calculation period compared to a standard mineral soil. Between 82% (for LAI(max) = 3.8) and 87% (for LAI(max) = 6.1) of the average annual precipitation (506 mm) could be retained from the surface layer assuming eastern German climate conditions, compared with a retention efficiency between 79 and 82% for a mineral soil. Although a MBP layer in conjunction with water-consumptive trees can reduce vertical water losses as compared to mineral substrates, the effect is not sufficient to meet legal regulations.

Magnetic Compton scattering study of Laves phase ZrFe2 and Sc doped ZrFe2: Experiment and Green function based relativistic calculations

NASA Astrophysics Data System (ADS)

Bhatt, Samir; Mund, H. S.; Kumar, Kishor; Bapna, Komal; Dashora, Alpa; Itou, M.; Sakurai, Y.; Ahuja, B. L.

2018-05-01

Spin momentum densities of ferromagnetic ZrFe2 and Zr0.8Sc0.2Fe2 have been measured using magnetic Compton scattering with 182.65 keV circularly polarized synchrotron radiations. Site specific spin moments, which are responsible for the formation of total spin moment, have been deduced from Compton line shapes. At room temperature, the computed spin moment of ZrFe2 is found to be slightly higher than that of Sc doped ZrFe2 which is in consensus with the magnetization data. To compare the experimental data, we have also computed magnetic Compton profiles (MCPs), total and partial spin projected density of states (DOS) and the site specific spin moments using spin-polarized relativistic Korringa-Kohn-Rostoker method. It is observed that the spin moment at Fe site is aligned antiparallel to that of Zr site in both ZrFe2 and Zr0.8Sc0.2Fe2. The MCP results when compared with vibrating sample magnetometer based magnetization data, show a very small contribution of orbital moment in the formation of total magnetic moments in both the compounds. The DOS of ferromagnetic ground state of ZrFe2 and Zr0.8Sc0.2Fe2 are interpreted on the basis of a covalent magnetic model beyond the Stoner rigid band model. It appears that on alloying between a magnetic and a non-magnetic partner (with low valence), a polarization develops on the non-magnetic atom which is anti-parallel to that of the magnetic atom.

Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: Application to solvatochromic shift calculations

NASA Astrophysics Data System (ADS)

Minezawa, Noriyuki; Kato, Shigeki

2007-02-01

The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: application to solvatochromic shift calculations.

PubMed

Minezawa, Noriyuki; Kato, Shigeki

2007-02-07

The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

Illumina Amplicon Sequencing of 16S rRNA Tag Reveals Bacterial Community Development in the Rhizosphere of Apple Nurseries at a Replant Disease Site and a New Planting Site

PubMed Central

Sun, Jian; Zhang, Qiang; Zhou, Jia; Wei, Qinping

2014-01-01

We used a next-generation, Illumina-based sequencing approach to characterize the bacterial community development of apple rhizosphere soil in a replant site (RePlant) and a new planting site (NewPlant) in Beijing. Dwarfing apple nurseries of ‘Fuji’/SH6/Pingyitiancha trees were planted in the spring of 2013. Before planting, soil from the apple rhizosphere of the replant site (ReSoil) and from the new planting site (NewSoil) was sampled for analysis on the Illumina MiSeq platform. In late September, the rhizosphere soil from both sites was resampled (RePlant and NewPlant). More than 16,000 valid reads were obtained for each replicate, and the community was composed of five dominant groups (Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria). The bacterial diversity decreased after apple planting. Principal component analyses revealed that the rhizosphere samples were significantly different among treatments. Apple nursery planting showed a large impact on the soil bacterial community, and the community development was significantly different between the replanted and newly planted soils. Verrucomicrobia were less abundant in RePlant soil, while Pseudomonas and Lysobacter were increased in RePlant compared with ReSoil and NewPlant. Both RePlant and ReSoil showed relatively higher invertase and cellulase activities than NewPlant and NewSoil, but only NewPlant soil showed higher urease activity, and this soil also had the higher plant growth. Our experimental results suggest that planting apple nurseries has a significant impact on soil bacterial community development at both replant and new planting sites, and planting on new site resulted in significantly higher soil urease activity and a different bacterial community composition. PMID:25360786

Accurate in silico identification of protein succinylation sites using an iterative semi-supervised learning technique.

PubMed

Zhao, Xiaowei; Ning, Qiao; Chai, Haiting; Ma, Zhiqiang

2015-06-07

As a widespread type of protein post-translational modifications (PTMs), succinylation plays an important role in regulating protein conformation, function and physicochemical properties. Compared with the labor-intensive and time-consuming experimental approaches, computational predictions of succinylation sites are much desirable due to their convenient and fast speed. Currently, numerous computational models have been developed to identify PTMs sites through various types of two-class machine learning algorithms. These methods require both positive and negative samples for training. However, designation of the negative samples of PTMs was difficult and if it is not properly done can affect the performance of computational models dramatically. So that in this work, we implemented the first application of positive samples only learning (PSoL) algorithm to succinylation sites prediction problem, which was a special class of semi-supervised machine learning that used positive samples and unlabeled samples to train the model. Meanwhile, we proposed a novel succinylation sites computational predictor called SucPred (succinylation site predictor) by using multiple feature encoding schemes. Promising results were obtained by the SucPred predictor with an accuracy of 88.65% using 5-fold cross validation on the training dataset and an accuracy of 84.40% on the independent testing dataset, which demonstrated that the positive samples only learning algorithm presented here was particularly useful for identification of protein succinylation sites. Besides, the positive samples only learning algorithm can be applied to build predictors for other types of PTMs sites with ease. A web server for predicting succinylation sites was developed and was freely accessible at http://59.73.198.144:8088/SucPred/. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bimetallic Effect of Single Nanocatalysts Visualized by Super-Resolution Catalysis Imaging

DOE PAGES

Chen, Guanqun; Zou, Ningmu; Chen, Bo; ...

2017-11-01

Compared with their monometallic counterparts, bimetallic nanoparticles often show enhanced catalytic activity associated with the bimetallic interface. Direct quantitation of catalytic activity at the bimetallic interface is important for understanding the enhancement mechanism, but challenging experimentally. Here using single-molecule super-resolution catalysis imaging in correlation with electron microscopy, we report the first quantitative visualization of enhanced bimetallic activity within single bimetallic nanoparticles. We focus on heteronuclear bimetallic PdAu nanoparticles that present a well-defined Pd–Au bimetallic interface in catalyzing a photodriven fluorogenic disproportionation reaction. Our approach also enables a direct comparison between the bimetallic and monometallic regions within the same nanoparticle. Theoreticalmore » calculations further provide insights into the electronic nature of N–O bond activation of the reactant (resazurin) adsorbed on bimetallic sites. Subparticle activity correlation between bimetallic enhancement and monometallic activity suggests that the favorable locations to construct bimetallic sites are those monometallic sites with higher activity, leading to a strategy for making effective bimetallic nanocatalysts. Furthermore, the results highlight the power of super-resolution catalysis imaging in gaining insights that could help improve nanocatalysts.« less

The effectiveness of nutrition education: Applying the Health Belief Model in child-feeding practices to use pulses for complementary feeding in Southern Ethiopia.

PubMed

Mulualem, Demmelash; Henry, Carol J; Berhanu, Getenesh; Whiting, Susan J

2016-01-01

Complementary foods (CFs) in Ethiopia are cereal based and adding locally grown pulses (legumes) to CF would provide needed nutrients. To assess the effects of nutrition education (NEd) using Health Belief Model (HBM) in promoting pulses for CF, a 6-month quasi-experimental study was conducted in 160 mother-child pairs. Knowledge, attitude, and practice (KAP) questions were given to mothers at baseline, midline, and endline, along with anthropometric measurements of children. NEd involving discussions and recipe demonstrations was given twice monthly for 6 months to the intervention group (n = 80) while control mothers received usual education. At baseline, mothers' KAP scores were low at both sites; at 3 and 6 months of NEd, mean KAP scores of mothers increased (p < 0.05) compared to the control site. Significant improvements in children's mean weight, weight for height, and weight for age occurred in the intervention site only. Nutritional status of children improved after providing mothers with pulse-based NEd.

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

Chen, Guanqun; Zou, Ningmu; Chen, Bo

Compared with their monometallic counterparts, bimetallic nanoparticles often show enhanced catalytic activity associated with the bimetallic interface. Direct quantitation of catalytic activity at the bimetallic interface is important for understanding the enhancement mechanism, but challenging experimentally. Here using single-molecule super-resolution catalysis imaging in correlation with electron microscopy, we report the first quantitative visualization of enhanced bimetallic activity within single bimetallic nanoparticles. We focus on heteronuclear bimetallic PdAu nanoparticles that present a well-defined Pd–Au bimetallic interface in catalyzing a photodriven fluorogenic disproportionation reaction. Our approach also enables a direct comparison between the bimetallic and monometallic regions within the same nanoparticle. Theoreticalmore » calculations further provide insights into the electronic nature of N–O bond activation of the reactant (resazurin) adsorbed on bimetallic sites. Subparticle activity correlation between bimetallic enhancement and monometallic activity suggests that the favorable locations to construct bimetallic sites are those monometallic sites with higher activity, leading to a strategy for making effective bimetallic nanocatalysts. Furthermore, the results highlight the power of super-resolution catalysis imaging in gaining insights that could help improve nanocatalysts.« less

Evaluation of formalin-fixed paraffin-embedded tissues obtained from vaccine site-associated sarcomas of cats for DNA of feline immunodeficiency virus.

PubMed

Kidney, B A; Ellis, J A; Haines, D M; Jackson, M L

2000-09-01

To evaluate the use of a polymerase chain reaction (PCR) method for detection of feline immunodeficiency virus (FIV) DNA, using formalin-fixed paraffin-embedded (FFPE) tissues, and to use this method to evaluate tissues obtained from vaccine site-associated sarcomas (VSS) of cats for FIV DNA. 50 FFPE tissue blocks from VSS of cats and 50 FFPE tissue blocks from cutaneous non-vaccine site-associated fibrosarcomas (non-VSS) of cats. DNA was extracted from FFPE sections of each tumor and regions of the gag gene of FIV were amplified by a PCR, using 3 sets of primers. Sensitivity of the method was compared between frozen and FFPE tissues, using splenic tissue obtained from a cat that had been experimentally infected with FIV. We did not detect FIV DNA in VSS or non-VSS tissues. Sensitivity of the PCR method was identical for frozen or FFPE tissues. It is possible to detect FIV DNA in FFPE tissues by use of a PCR. We did not find evidence to support direct FIV involvement in the pathogenesis of VSS in cats.

Site-targeted complement inhibition by a complement receptor 2-conjugated inhibitor (mTT30) ameliorates post-injury neuropathology in mouse brains.

PubMed

Rich, Megan C; Keene, Chesleigh N; Neher, Miriam D; Johnson, Krista; Yu, Zhao-Xue; Ganivet, Antoine; Holers, V Michael; Stahel, Philip F

2016-03-23

Intracerebral complement activation after severe traumatic brain injury (TBI) leads to a cascade of neuroinflammatory pathological sequelae that propagate host-mediated secondary brain injury and adverse outcomes. There are currently no specific pharmacological agents on the market to prevent or mitigate the development of secondary cerebral insults after TBI. A novel chimeric CR2-fH compound (mTT30) provides targeted inhibition of the alternative complement pathway at the site of tissue injury. This experimental study was designed to test the neuroprotective effects of mTT30 in a mouse model of closed head injury. The administration of 500 μg mTT30 i.v. at 1 h, 4 h and 24 h after head injury attenuated complement C3 deposition in injured brains, reduced the extent of neuronal cell death, and decreased post-injury microglial activation, compared to vehicle-injected placebo controls. These data imply that site-targeted alternative pathway complement inhibition may represent a new promising therapeutic avenue for the future management of severe TBI. Copyright © 2016. Published by Elsevier Ireland Ltd.

A comparative study of the hydrogen-bonding patterns and prototropism in solid 2-thiocytosine (potential antileukemic agent) and cytosine, as studied by 1H-14N NQDR and QTAIM/ DFT.

PubMed

Latosińska, Jolanta N; Seliger, Janez; Zagar, Veselko; Burchardt, Dorota V

2012-01-01

A potential antileukemic and anticancer agent, 2-thiocytosine (2-TC), has been studied experimentally in the solid state by (1)H-(14)N NMR-NQR double resonance (NQDR) and theoretically by the quantum theory of atoms in molecules (QTAIM)/density functional theory (DFT). Eighteen resonance frequencies on (14)N were detected at 180 K and assigned to particular nitrogen sites (-NH(2), -N=, and -NH-) in 2-thiocytosine. Factors such as the nonequivalence of molecules (connected to the duplication of sites) and possible prototropic tautomerism (capable of modifying the type of site due to proton transfer) were taken into account during frequency assignment. The result of replacing oxygen with sulfur, which leads to changes in the intermolecular interaction pattern and molecular aggregation, is discussed. This study demonstrates the advantages of combining NQDR and DFT to extract detailed information on the H-bonding properties of crystals with complex H-bonding networks. Solid-state properties were found to have a profound impact on the stabilities and reactivities of both compounds.

Examination of Relationship Between Photonic Signatures and Fracture Strength of Fused Silica Used in Orbiter Windows

NASA Technical Reports Server (NTRS)

Yost, William T.; Cramer, K. Elliott; Estes, Linda R.; Salem, Jonathan A.; Lankford, James, Jr.; Lesniak, Jon

2011-01-01

A commercially available grey-field polariscope (GFP) instrument for photoelastic examination is used to assess impact damage inflicted upon the outermost pane of the orbiter windows. Four categories of damage: hyper-velocity impacts that occur during space-flight (HVI); hypervelocity impacts artificially made at the Hypervelocity Impact Technology Facility (HIT-F); impacts made by larger objects falling onto the pane surface to simulate dropped items on the window during service/storage of vehicle (Bruises); and light scratches from dull objects designed to mimic those that might occur by dragging a dull object across the glass surface (Chatter Checks) are examined. The damage sites are cored from fused silica window carcasses, examined with the GFP and other methodologies, and broken using the ASTM Standard C1499-09 to measure the fracture strength. A correlation is made between the fracture strength and damage-site measurements including geometrical measurements and GFP measurements of photoelastic retardation (stress patterns) surrounding the damage sites. An analytical damage model to predict fracture strength from photoelastic retardation measurements is presented and compared with experimental results.

Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model.

PubMed

Tsai, Min-Yeh; Yuan, Jian-Min; Teranishi, Yoshiaki; Lin, Sheng Hsien

2012-09-01

Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.

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

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.

PubMed

De Witte, Dieter; Van de Velde, Jan; Decap, Dries; Van Bel, Michiel; Audenaert, Pieter; Demeester, Piet; Dhoedt, Bart; Vandepoele, Klaas; Fostier, Jan

2015-12-01

The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected. We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays. BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Predictive and comparative analysis of Ebolavirus proteins

PubMed Central

Cong, Qian; Pei, Jimin; Grishin, Nick V

2015-01-01

Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus. PMID:26158395

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements

PubMed Central

De Witte, Dieter; Van de Velde, Jan; Decap, Dries; Van Bel, Michiel; Audenaert, Pieter; Demeester, Piet; Dhoedt, Bart; Vandepoele, Klaas; Fostier, Jan

2015-01-01

Motivation: The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected. Results: We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays. Availability and implementation: BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller Contact: Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26254488

Predictive and comparative analysis of Ebolavirus proteins.

PubMed

Cong, Qian; Pei, Jimin; Grishin, Nick V

2015-01-01

Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus.

Comparative Assessment of Conventional Composites and Coloured Compomers in Permanent Molars of Children with Mixed Dentition: A Pilot Study

PubMed Central

Kohli, Divyata; Badakar, Chandrashekhar M; Vyavahare, Supriya S; Shah, Parin P; Gokhale, Niraj S; Patel, Punit M; Mundada, Madhura V

2017-01-01

Introduction Early treatment of carious lesions in children is important for the maintenance of oral health. Multicoloured restorations could be the impetus for an extremely nervous or defiant child to take dental treatment. Aim The aim of this study was to assess and compare the clinical success of conventional composites and coloured compomer material in first permanent molars of children with mixed dentition. Materials and Methods A total of sixty sites, divided into two groups, with thirty subjects in each group using split mouth design were chosen amongst patients reporting to Department of Pedodontics and Preventive Dentistry. In control group conventional composites were placed, similarly coloured compomers were placed in experimental group under standard operating protocol. Patients were recalled for assessment of clinical success amongst control as well as experimental group at regular intervals of one; three and six months follow up based on Modified Ryge’s Criteria. Statistical analysis was done using Chi-square test using SPSS version 20.0 (Chicago, USA). Results Both conventional composites and coloured compomers had comparable retention rates in terms of anatomical form, marginal integrity, secondary caries and marginal discolouration. Conclusion The coloured compomer material showed promising results in this six month follow up study in permanent molars and had properties comparable to that of conventional composites. PMID:28764297

RNA editing in Drosophila melanogaster: new targets and functionalconsequences

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

Stapleton, Mark; Carlson, Joseph W.; Celniker, Susan E.

2006-09-05

Adenosine deaminases that act on RNA (ADARs) catalyze the site-specific conversion of adenosine to inosine in primary mRNA transcripts. These re-coding events affect coding potential, splice-sites, and stability of mature mRNAs. ADAR is an essential gene and studies in mouse, C. elegans, and Drosophila suggest its primary function is to modify adult behavior by altering signaling components in the nervous system. By comparing the sequence of isogenic cDNAs to genomic DNA, we have identified and experimentally verified 27 new targets of Drosophila ADAR. Our analyses lead us to identify new classes of genes whose transcripts are targets of ADAR includingmore » components of the actin cytoskeleton, and genes involved in ion homeostasis and signal transduction. Our results indicate that editing in Drosophila increases the diversity of the proteome, and does so in a manner that has direct functional consequences on protein function.« less

Multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) approach to the correlated exciton-vibrational dynamics in the FMO complex

NASA Astrophysics Data System (ADS)

Schulze, Jan; Shibl, Mohamed F.; Al-Marri, Mohammed J.; Kühn, Oliver

2016-05-01

The coupled quantum dynamics of excitonic and vibrational degrees of freedom is investigated for high-dimensional models of the Fenna-Matthews-Olson complex. This includes a seven- and an eight-site model with 518 and 592 harmonic vibrational modes, respectively. The coupling between local electronic transitions and vibrations is described within the Huang-Rhys model using parameters that are obtained by discretization of an experimental spectral density. Different pathways of excitation energy flow are analyzed in terms of the reduced one-exciton density matrix, focussing on the role of vibrational and vibronic excitations. Distinct features due to both competing time scales of vibrational and exciton motion and vibronically assisted transfer are observed. The question of the effect of initial state preparation is addressed by comparing the case of an instantaneous Franck-Condon excitation at a single site with that of a laser field excitation.

Do you "like" my photo? Facebook use maintains eating disorder risk.

PubMed

Mabe, Annalise G; Forney, K Jean; Keel, Pamela K

2014-07-01

Social media sites, such as Facebook, merge two factors that influence risk for eating disorders:media and peers. Previous work has identified cross-sectional and temporal associations between Facebook use and disordered eating. This study sought to replicate and extend these findings using an experimental design. In Study 1, 960 women completed self-report surveys regarding Facebook use and disordered eating. In Study 2, 84 women were randomly assigned to use Facebook or to use an alternate internet site for 20 min. More frequent Facebook use was associated with greater disordered eating in a cross-sectional survey. Facebook use was associated with the maintenance of weight/shape concerns and state anxiety compared to an alternate internet activity. Facebook use may contribute to disordered eating by maintaining risk for eating pathology. As such, targeting Facebook use may be helpful in intervention and prevention programs.

Phase stabilisation of hexagonal barium titanate doped with transition metals: A computational study

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

Dawson, J.A., E-mail: mtp09jd@sheffield.ac.uk; Freeman, C.L.; Harding, J.H.

Interatomic potentials recently developed for the modelling of BaTiO{sub 3} have been used to explore the stabilisation of the hexagonal polymorph of BaTiO{sub 3} by doping with transition metals (namely Mn, Co, Fe and Ni) at the Ti-site. Classical simulations have been completed on both the cubic and hexagonal polymorphs to investigate the energetic consequences of transition metal doping on each polymorph. Ti-site charge compensation mechanisms have been used for the multi-valent transition metal ions and cluster binding energies have been considered. Simulations show a significant energetic gain when doping occurs at Ti sites in the face sharing dimers (Ti{submore » 2} sites) of the hexagonal polymorph compared with the doping of the cubic polymorph. This energetic difference between the two polymorphs is true for all transition metals tested and all charge states and in the case of tri- and tetra-valent dopants negative solution energies are found for the hexagonal polymorph suggesting actual polymorph stabilisation occurs with the incorporation of these ions as observed experimentally. Oxidation during incorporation of Ni{sup 2+} and Fe{sup 3+} ions has also been considered. - Graphical abstract: The representation of the strongest binding energy clusters for tri-valent dopants—(a) Ti{sub 2}/O{sub 1} cluster and (b) Ti{sub 2}/O{sub 2} cluster. Highlights: ► Classical simulations show a significant energetic gain when doping occurs at Ti sites in the face sharing dimers (Ti2 sites) of the hexagonal polymorph compared with the doping of the cubic polymorph. ► This energetic difference between the two polymorphs is true for all transition metals tested and all charge states. ► In the case of tri- and tetra- valent dopants negative solution energies are found for the hexagonal polymorph suggesting actual polymorph stabilisation occurs with the incorporation of these ions.« less

Multichannel Analysis of Surface Waves and Down-Hole Tests in the Archeological "Palatine Hill" Area (Rome, Italy): Evaluation and Influence of 2D Effects on the Shear Wave Velocity

NASA Astrophysics Data System (ADS)

Di Fiore, V.; Cavuoto, G.; Tarallo, D.; Punzo, M.; Evangelista, L.

2016-05-01

A joint analysis of down-hole (DH) and multichannel analysis of surface waves (MASW) measurements offers a complete evaluation of shear wave velocity profiles, especially for sites where a strong lateral variability is expected, such as archeological sites. In this complex stratigraphic setting, the high "subsoil anisotropy" (i.e., sharp lithological changes due to the presence of anthropogenic backfill deposits and/or buried man-made structures) implies a different role for DH and MASW tests. This paper discusses some results of a broad experimental program conducted on the Palatine Hill, one of the most ancient areas of the city of Rome (Italy). The experiments were part of a project on seismic microzoning and consisted of 20 MASW and 11 DH tests. The main objective of this study was to examine the difficulties related to the interpretation of the DH and MASW tests and the reliability limits inherent in the application of the noninvasive method in complex stratigraphic settings. As is well known, DH tests provide good determinations of shear wave velocities (Vs) for different lithologies and man-made materials, whereas MASW tests provide average values for the subsoil volume investigated. The data obtained from each method with blind tests were compared and were correlated to site-specific subsurface conditions, including lateral variability. Differences between punctual (DH) and global (MASW) Vs measurements are discussed, quantifying the errors by synthetic comparison and by site response analyses. This study demonstrates that, for archeological sites, VS profiles obtained from the DH and MASW methods differ by more than 15 %. However, the local site effect showed comparable results in terms of natural frequencies, whereas the resolution of the inverted shear wave velocity was influenced by the fundamental mode of propagation.

Mixing soil samples across experimental units ignores uncertainty and generates falsely precise estimates of soil biota effects on plants

USDA-ARS?s Scientific Manuscript database

A number of recent soil biota studies have deviated from the standard experimental approach of generating a distinct data value for each experimental unit (e.g. Yang et al., 2013; Gundale et al., 2014). Instead, these studies have mixed together soils from multiple experimental units (i.e. sites wi...

Shell colour, temperature, (micro)habitat structure and predator pressure affect the behaviour of Cepaea nemoralis

NASA Astrophysics Data System (ADS)

Rosin, Zuzanna M.; Kwieciński, Zbigniew; Lesicki, Andrzej; Skórka, Piotr; Kobak, Jarosław; Szymańska, Anna; Osiejuk, Tomasz S.; Kałuski, Tomasz; Jaskulska, Monika; Tryjanowski, Piotr

2018-06-01

Although shell colour polymorphism of the land snail Cepaea nemoralis is a well-known phenomenon, proximate and ultimate factors driving its evolution remain uncertain. Polymorphic species show variation in behavioural responses to selective forces. Therefore, we estimated effects of various environmental factors (temperature, humidity, food availability, (micro)habitat structure and predatory pressure) on behavioural response (frequency of locomotion, climbing and hiding) of C. nemoralis morphs, in experimental and natural conditions. In the experimental part of study, the frequency of locomotion was negatively affected by temperature and the presence of food and positively influenced by the presence of light. Morphs significantly differed in behavioural responses to environmental variability. Pink mid-banded and yellow five-banded morphs climbed less often and hide in shelter more often than yellow and pink unbanded individuals when temperature was low and food was absent. Snails fed most often at moderate temperature compared to low and high temperatures. Field investigations partially confirmed differences among morphs in frequency of climbing, but not in terms of probability of hiding in sheltered sites. In natural colonies, temperature and (micro)habitat structure significantly affected frequency of climbing as well as hiding in shelter. Snails more often hid in sheltered sites where thrushes preyed on Cepaea. Tendency of unbanded morphs to climb trees may have evolved under avian predatory pressure as thrushes forage on a ground. Tendency of banded morphs to hide in sheltered sites may reflect prey preferences for cryptic background. The results implicate that differential behaviour of C. nemoralis morphs compensate for their morphological and physiological limitations of adaptation to habitat.

Slopewash, surface runoff and fine-litter transport in forest and landslide scars in humid-tropical steeplands, Luquillo Experimental Forest, Puerto Rico

USGS Publications Warehouse

Larsen, M.C.; Torres-Sanchez, A. J.; Concepcion, I.M.

1999-01-01

Rainfall, slopewash (the erosion of soil particles), surface runoff and fine-litter transport at humid-tropical steepland sites in the Luquillo Experimental Forest, Puerto Rico (18??20' N, 65??45' W) were measured from 1991 to 1995. Hillslopes underlain by (1) Cretaceous tuffaceous sandstone and siltstone in subtropical rain (tabonuco) forest with vegetation recovering from Hurricane Hugo (1989), and (2) Tertiary quartz diorite in subtropical lower montane wet (colorado and dwarf) forest with undisturbed forest canopy were compared to recent landslide scars. Monthly surface runoff on these very steep hillslopes (24??to 43??) was only 0.2 to 0.5 per cent of monthly rainfall. Slopewash was higher in sandy loam soils whose parent material is quartz diorite (averaging 46 g m-2 a-1) than in silty clay loam soils derived from tuffaceous sandstone and siltstone where the average was 9 g m-2 a-1. Annual slopewash of 100 to 349 g m-2 on the surfaces of two recent, small landslide scars was measured initially but slopewash decreased to only 3 to 4 g m-2 a-1 by the end of the study. The mean annual mass of fine litter (mainly leaves and twigs) transported downslope at the forested sites ranged from 5 to 8 g m-2 and was lower at the tabonuco forest site, where post-Hurricane Hugo recovery is still in progress. Mean annual fine-litter transport was 2.5 g m-2 on the two landslide scars.

How supportive supervision influences immunization session site practices: a quasi-experimental study in Odisha, India.

PubMed

Panda, Bhuputra; Pati, Sanghamitra; Nallala, Srinivas; Chauhan, Abhimanyu S; Anasuya, Anita; Som, Meena; Zodpey, Sanjay

2015-01-01

Routine immunization (RI) is a key child survival intervention. Ensuring acceptable standards of RI service delivery is critical for optimal outcomes. Accumulated evidences suggest that 'supportive supervision' improves the quality of health care services in general. During 2009-2010, the Government of Odisha and UNICEF jointly piloted this strategy in four districts to improve RI program outcomes. The present study aims to assess the effect of this strategy on improvement of skills and practices at immunization session sites. A quasi-experimental 'post-test only' study design was adopted to compare the opinion and practices of frontline health workers and their supervisors in four intervention districts (IDs) with two control districts (CDs). Altogether, we interviewed 111 supervisor-supervisee (health worker) pairs using semi-structured interview schedules and case vignettes. We also directly observed health workers' practices during immunization sessions at 111 sites. Data were analyzed with SPSS version 16.0. The mean knowledge score of supervisors in CDs was significantly higher than in intervention groups. Variegated responses were obtained on case vignettes. The control group performed better in solving certain hypothetically asked problems, whereas the intervention group scored better in others. Health workers in IDs gave a lower rating to their respective supervisors' knowledge, skill, and frequency of supervision. Logistics and vaccine availability were better in CDs. Notwithstanding other limitations, supportive supervision may not have independent effects on improving the quality of immunization services. Addressing systemic issues, such as the availability of essential logistics, supply chain management, timely indenting, and financial resources, could complement the supportive supervision strategy in improving immunization service delivery.

CisSERS: Customizable in silico sequence evaluation for restriction sites

DOE PAGES

Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus; ...

2016-04-12

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated tomore » enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.« less

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces

PubMed Central

Zerbe, Brandon S.; Hall, David R.

2013-01-01

In the context of protein-protein interactions, the term “hot spot” refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening. PMID:22770357

Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces.

PubMed

Zerbe, Brandon S; Hall, David R; Vajda, Sandor; Whitty, Adrian; Kozakov, Dima

2012-08-27

In the context of protein-protein interactions, the term "hot spot" refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research, a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening.

CisSERS: Customizable in silico sequence evaluation for restriction sites

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

Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated tomore » enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.« less

Shell colour, temperature, (micro)habitat structure and predator pressure affect the behaviour of Cepaea nemoralis.

PubMed

Rosin, Zuzanna M; Kwieciński, Zbigniew; Lesicki, Andrzej; Skórka, Piotr; Kobak, Jarosław; Szymańska, Anna; Osiejuk, Tomasz S; Kałuski, Tomasz; Jaskulska, Monika; Tryjanowski, Piotr

2018-05-09

Although shell colour polymorphism of the land snail Cepaea nemoralis is a well-known phenomenon, proximate and ultimate factors driving its evolution remain uncertain. Polymorphic species show variation in behavioural responses to selective forces. Therefore, we estimated effects of various environmental factors (temperature, humidity, food availability, (micro)habitat structure and predatory pressure) on behavioural response (frequency of locomotion, climbing and hiding) of C. nemoralis morphs, in experimental and natural conditions. In the experimental part of study, the frequency of locomotion was negatively affected by temperature and the presence of food and positively influenced by the presence of light. Morphs significantly differed in behavioural responses to environmental variability. Pink mid-banded and yellow five-banded morphs climbed less often and hide in shelter more often than yellow and pink unbanded individuals when temperature was low and food was absent. Snails fed most often at moderate temperature compared to low and high temperatures. Field investigations partially confirmed differences among morphs in frequency of climbing, but not in terms of probability of hiding in sheltered sites. In natural colonies, temperature and (micro)habitat structure significantly affected frequency of climbing as well as hiding in shelter. Snails more often hid in sheltered sites where thrushes preyed on Cepaea. Tendency of unbanded morphs to climb trees may have evolved under avian predatory pressure as thrushes forage on a ground. Tendency of banded morphs to hide in sheltered sites may reflect prey preferences for cryptic background. The results implicate that differential behaviour of C. nemoralis morphs compensate for their morphological and physiological limitations of adaptation to habitat.

Fitness consequences of northward dispersal as possible adaptation to climate change, using experimental translocation of a migratory passerine.

PubMed

Burger, Claudia; Nord, Andreas; Nilsson, Jan-Åke; Gilot-Fromont, Emmanuelle; Both, Christiaan

2013-01-01

Climate change leads to rapid, differential changes in phenology across trophic levels, often resulting in temporal mismatches between predators and their prey. If a species cannot easily adjust its timing, it can adapt by choosing a new breeding location with a later phenology of its prey. In this study, we experimentally investigated whether long-distance dispersal to northern breeding grounds with a later phenology could be a feasible process to restore the match between timing of breeding and peak food abundance and thus improve reproductive success. Here, we report the successful translocation of pied flycatchers (Ficedula hypoleuca) to natural breeding sites 560 km to the Northeast. We expected translocated birds to have a fitness advantage with respect to environmental phenology, but to potentially pay costs through the lack of other locally adapted traits. Translocated individuals started egg laying 11 days earlier than northern control birds, which were translocated only within the northern site. The number of fledglings produced was somewhat lower in translocated birds, compared to northern controls, and fledglings were in lower body condition. Translocated individuals were performing not significantly different to control birds that remained at the original southern site. The lack of advantage of the translocated individuals most likely resulted from the exceptionally cold spring in which the experiment was carried out. Our results, however, suggest that pied flycatchers can successfully introduce their early breeding phenotype after dispersing to more northern areas, and thus that adaptation through dispersal is a viable option for populations that get locally maladapted through climate change.

Evaluation of a Social Marketing Campaign Targeting Preschool Children

ERIC Educational Resources Information Center

Johnson, Susan L.; Bellows, Laura; Beckstrom, Leslie; Anderson, Jennifer

2007-01-01

Objectives: To determine the effectiveness of a pilot social marketing program to increase preschoolers' willingness to try new foods. Methods: Four Head Start centers participated (2 experimental, 2 control) in a study using a quasi-experimental design. Experimental sites received a 12-week intervention developed using social marketing…

Flowfield Comparisons from Three Navier-Stokes Solvers for an Axisymmetric Separate Flow Jet

NASA Technical Reports Server (NTRS)

Koch, L. Danielle; Bridges, James; Khavaran, Abbas

2002-01-01

To meet new noise reduction goals, many concepts to enhance mixing in the exhaust jets of turbofan engines are being studied. Accurate steady state flowfield predictions from state-of-the-art computational fluid dynamics (CFD) solvers are needed as input to the latest noise prediction codes. The main intent of this paper was to ascertain that similar Navier-Stokes solvers run at different sites would yield comparable results for an axisymmetric two-stream nozzle case. Predictions from the WIND and the NPARC codes are compared to previously reported experimental data and results from the CRAFT Navier-Stokes solver. Similar k-epsilon turbulence models were employed in each solver, and identical computational grids were used. Agreement between experimental data and predictions from each code was generally good for mean values. All three codes underpredict the maximum value of turbulent kinetic energy. The predicted locations of the maximum turbulent kinetic energy were farther downstream than seen in the data. A grid study was conducted using the WIND code, and comments about convergence criteria and grid requirements for CFD solutions to be used as input for noise prediction computations are given. Additionally, noise predictions from the MGBK code, using the CFD results from the CRAFT code, NPARC, and WIND as input are compared to data.

Comparison of protocols for measuring cosmetic ingredient distribution in human and pig skin.

PubMed

Gerstel, D; Jacques-Jamin, C; Schepky, A; Cubberley, R; Eilstein, J; Grégoire, S; Hewitt, N; Klaric, M; Rothe, H; Duplan, H

2016-08-01

The Cosmetics Europe Skin Bioavailability and Metabolism Task Force aims to improve the measurement and prediction of the bioavailability of topically-exposed compounds for risk assessment. Key parameters of the experimental design of the skin penetration studies were compared. Penetration studies with frozen human and pig skin were conducted in two laboratories, according to the SCCS and OECD 428 guidelines. The disposition in skin was measured 24h after finite topical doses of caffeine, resorcinol and 7-ethoxycoumarin. The bioavailability distribution in skin layers of cold and radiolabelled chemicals were comparable. Furthermore, the distribution of each chemical was comparable in human and pig skin. The protocol was reproducible across the two laboratories. There were small differences in the amount of chemical detected in the skin layers, which were attributed to differences in washing procedures and anatomical sites of the skin used. In conclusion, these studies support the use of pig skin as an alternative source of skin should the availability of human skin become a limiting factor. If radiolabelled chemicals are not available, cold chemicals can be used, provided that the influence of chemical stability, reactivity or metabolism on the experimental design and the relevance of the data obtained is considered. Copyright © 2016. Published by Elsevier Ltd.

[Experimental intervention study of safe injection in basic-level hospitals in Hunan by medical staff].

PubMed

Li, Li; Li, Yinglan; Long, Yanfang; Zhou, Yang; Lu, Jingmei; Wu, Ying

2013-07-01

To experimentally intervene safe injection by medical staff in basic-level hospitals and observe the recent and long-term effect after the intervention and to provide practical measures to improve safe injection. We used random sampling methods to set up groups in county hospitals and township hospitals of Hunan Province, and offered lectures, delivered safe injection guide, brochure and on-site guidance in the experimental group. We surveyed the 2 groups after the intervention at 1 month and 6 months to compare the effect of unsafe injection behaviors and safe injection behaviors. One month after the intervention, the unsafe injection rate in the experimental group decreased from 27.8% to 21.7%, while in the control group injection the unsafe injection rate rose from 26.0% to 27.9%, with significant difference (P<0.01). Six months after the intervention, the unsafe injection rate in the experimental group declined to 18.4% while the unsafe injection rate in the control group also dropped to 22.4%, with significant difference (P<0.01). Unsafe injection rate was decreased in the experimental group at different intervention points, with significant difference (P<0.01). The safe injection behavior scores in the experimental group were higher than those in the control group after the intervention of 1 month and 6 month intervention (P<0.01); the experimental group got higher scores after the intervention (P<0.01). Training of safe injection, distribution of safe injection guide, and comprehensive intervention model can significantly change the primary care practitioners' behaviors in unsafe injections and it is worth promoting.

Ozone concentrations at the Bulgarian Govedartsi ecosystem site in early summer of 1994 and 1995

Treesearch

Evgeny Donev; Karl Zeller; Christo Bojinov

1998-01-01

Ozone measurements are presented from the Bulgarian Govedartsi ecosystem study site, Ovnarsko No. 3. The site is located on the south slope of the Govedartsi Valley in the northwestern part of the Rila Mountain area. The Rila is the highest mountain in the Balkan peninsula and is representative of rural conditions in that part of Europe. The experimental site, Ovnarsko...

Nanomedicines for HIV therapy.

PubMed

Siccardi, Marco; Martin, Philip; McDonald, Tom O; Liptrott, Neill J; Giardiello, Marco; Rannard, Steve; Owen, Andrew

2013-02-01

Heterogeneity in response to HIV treatments has been attributed to several causes including variability in pharmacokinetic exposure. Nanomedicine applications have a variety of advantages compared with traditional formulations, such as the potential to increase bioavailability and specifically target the site of action. Our group is focusing on the development of nanoformulations using a closed-loop design process in which nanoparticle optimization (disposition, activity and safety) is a continuous process based on experimental pharmacological data from in vitro and in vivo models. Solid drug nanoparticles, polymer-based drug-delivery carriers as well as nanoemulsions are nanomedicine options with potential application to improve antiretroviral deployment.